Dr. Krezel’s Publications:
Robert Obermann, Bereket Yemane, Cassie Jarvis, Francisco M Franco, Yevhenii Kyriukha, William Nolan, Beth Gohara, Andrzej M Krezel, Scott A Wildman & James W Janetka (2024). “Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction” ChemMedChem. 2024 Apr 16;19(8):e202300648. doi: 10.1002/cmdc.202300648. Epub 2024 Mar 5. (Abstract)
Continue reading →Shixuan Liu, Shuang Li, Andrzej M. Krezel, & Weikai Li (2022). “Stabilization and structure determination of integral membrane proteins by termini restraining” Nat Protoc. 2022 Jan 17. doi: 10.1038/s41596-021-00656-5. Online ahead of print. (Abstract)
Continue reading →Shixuan Liu, Shuang Li, Guomin Shen, Narayanasami Sukumar, Andrzej M. Krezel, & Weikai Li (2021). “Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation” Science. 2021 Jan 1;371(6524):eabc5667. doi: 10.1126/science.abc5667. Epub 2020 Nov 5. (Abstract)
Continue reading →Chen J., Castelvecchi G.D., Li-Villarreal N., Raught B., Krezel A.M., McNeill H., & Solnica-Krezel L. (2018). “Atypical Cadherin Dachsous1b Interacts with Ttc28 and Aurora B to Control Microtubule Dynamics in Embryonic Cleavages.” Dev Cell. 2018 May 7;45(3):376-391.e5. doi: 10.1016/j.devcel.2018.04.009. (Abstract)
Continue reading →Rocha A.G., Franco A., Krezel A.M., Rumsey J.M., Alberti J.M., Knight W.C., Biris N., Zacharioudakis E., Janetka J.W., Baloh R.H., Kitsis R.N., Mochly-Rosen D., Townsend R.R., Gavathiotis E., & Dorn G.W. 2nd (2018). “MFN2 agonists reverse mitochondrial defects in preclinical models of Charcot-Marie-Tooth disease type 2A.” Science. 2018 Apr 20;360(6386):336-341. doi: 10.1126/science.aao1785. (Abstract)
Continue reading →McCune B.T., Tang W., Lu J., Eaglesham J.B., Thorne L., Mayer A.E., Condiff E., Nice T.J., Goodfellow I., Krezel A.M., & Virgin H.W. (2017). “Noroviruses Co-opt the Function of Host Proteins VAPA and VAPB for Replication via a Phenylalanine-Phenylalanine-Acidic-Tract-Motif Mimic in Nonstructural Viral Protein NS1/2.” MBio. 2017 Jul 11;8(4). pii: e00668-17. doi: 10.1128/mBio.00668-17. (Abstract)
Continue reading →Shu Q., Krezel A.M., Cusumano Z.T., Pinkner J.S., Klein R., Hultgren S.J., & Frieden C. (2016). “Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.” Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7130-5. doi: 10.1073/pnas.1607222113. Epub 2016 Jun 13. (Abstract)
Continue reading →Krishna U., Romero-Gallo J., Suarez G., Azah A., Krezel A.M., Varga M.G., Forsyth M.H., & Peek R.M. Jr. (2016). “Genetic Evolution of a Helicobacter pylori Acid-Sensing Histidine Kinase and Gastric Disease.” J Infect Dis. 2016 Aug 15;214(4):644-8. doi: 10.1093/infdis/jiw189. Epub 2016 May 10. (Abstract)
Continue reading →Borin B.N., Tang W., & Krezel A.M. (2014). “Helicobacter pylori RNA polymerase α-subunit C-terminal domain shows features unique to ɛ-proteobacteria and binds NikR/DNA complexes.” Protein Sci. 2014 Apr;23(4):454-63. doi: 10.1002/pro.2427. Epub 2014 Feb 4. (Abstract)
Continue reading →Borin B.N., Tang W., Nice T.J., McCune B.T., Virgin H.W., & Krezel A.M. (2013). “Murine norovirus protein NS1/2 aspartate to glutamate mutation, sufficient for persistence, reorients side chain of surface exposed tryptophan within a novel structured domain.” Proteins. 2014 Jul;82(7):1200-9. doi: 10.1002/prot.24484. Epub 2013 Dec 26. (Abstract)
Continue reading →Loh J.T., Gupta S.S., Friedman D.B., Krezel A.M., & Cover T.L. (2010). “Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system.” J Bacteriol. 2010 Apr;192(8):2034-43. doi: 10.1128/JB.01703-08. Epub 2010 Feb 12. (Abstract)
Continue reading →Gupta S.S., Borin B.N., Cover T.L., & Krezel A.M. (2009). “Structural analysis of the DNA-binding domain of the Helicobacter pylori response regulator ArsR.” J Biol Chem. 2009 Mar 6;284(10):6536-45. doi: 10.1074/jbc.M804592200. Epub 2008 Dec 30. (Abstract)
Continue reading →Borin B.N. & Krezel A.M. (2008). “Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator.” Proteins. 2008 Oct;73(1):265-8. doi: 10.1002/prot.22159. (Abstract)
Continue reading →Hu T., Krezel A.M., Li C., & Coffey R.J. (2006). “Structural studies of human Naked2: a biologically active intrinsically unstructured protein.” Biochem Biophys Res Commun. 2006 Dec 1;350(4):911-5. Epub 2006 Oct 2. (Abstract)
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Dr. Janetka’s Publications: (oldest on top)
Han, Z., Pinkner, J.S., Ford, B., Obermann, R., Nolan, W., Wildman, S.A., Hobbs, D., Ellenberger, T., Cusumano, C.K., Hultgren, S.J. and Janetka, J.W.
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Structure-based drug design and optimization of mannoside bacterial FimH antagonists.
J Med Chem. 53(12):4779-92. doi: 10.1021/jm100438s. (2010) (Abstract)Oza V., Ashwell S., Brassil P., Breed J., Deng C., Ezhuthachan J., Haye H., Horn C., Janetka J., Lyne P., Newcombe N., Otterbien L., Pass M., Read J., Roswell S., Su M., Toader D., Yu D., Yu Y., Valentine A., Webborn P., White A., Zabludoff S., and Zheng X.
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Discovery of a novel class of triazolones as checkpoint kinase inhibitors–hit to lead exploration.
Bioorg Med Chem Lett. 20(17):5133-8. doi: 10.1016/j.bmcl.2010.07.015. (2010) (Abstract)Ma C.X., Janetka J.W., and Piwnica-Worms H.
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Death by releasing the breaks: CHK1 inhibitors as cancer therapeutics.
Trends Mol Med. 17(2):88-96. doi: 10.1016/j.molmed.2010.10.009. (2011) (Abstract)Cusumano C.K., Pinkner J.S., Han Z., Greene S.E., Ford B.A., Crowley J.R., Henderson J.P., Janetka J.W., and Hultgren S.J.
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Treatment and prevention of urinary tract infection with orally active FimH inhibitors.
Sci Transl Med. 3(109):109ra115. doi: 10.1126/scitranslmed.3003021. (2011) (Abstract)Han Z., Pinkner J.S., Ford B., Chorell E., Crowley J.M., Cusumano C.K., Campbell S., Henderson J.P., Hultgren S.J., and Janetka J.W. (2012) “Lead optimization studies on FimH antagonists: discovery of potent and orally bioavailable ortho-substituted biphenyl mannosides.” J Med Chem. 2012 Apr 26;55(8):3945-59. doi: 10.1021/jm300165m. Epub 2012 Apr 13. (Abstract)
Continue reading →Kostakioti M., Hadjifrangiskou M., Cusumano C.K., Hannan T.J., Janetka J.W., & Hultgren S.J. (2012). “Distinguishing the contribution of type 1 pili from that of other QseB-misregulated factors when QseC is absent during urinary tract infection.” Infect Immun. 2012 Aug;80(8):2826-34. doi: 10.1128/IAI.00283-12. Epub 2012 Jun 4. (Abstract)
Continue reading →Oza V., Ashwell S., Almeida L., Brassil P., Breed J., Deng C., Gero T., Grondine M., Horn C., Ioannidis S., Liu D., Lyne P., Newcombe N., Pass M., Read J., Ready S., Rowsell S., Su M., Toader D., Vasbinder M., Yu D., Yu Y., Xue Y., Zabludoff S., and Janetka J. (2012) “Discovery of checkpoint kinase inhibitor (S)-5-(3-fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by structure-based design and optimization of thiophenecarboxamide ureas.” J Med Chem. 2012 Jun 14;55(11):5130-42. doi: 10.1021/jm300025r. Epub 2012 Jun 4. (Abstract)
Continue reading →Guiton P.S., Cusumano C.K., Kline K.A., Dodson K.W., Han Z., Janetka J.W., Henderson J.P., Caparon M.G., & Hultgren S.J. (2012). “Combinatorial small-molecule therapy prevents uropathogenic Escherichia coli catheter-associated urinary tract infections in mice.” Antimicrob Agents Chemother. 2012 Sep;56(9):4738-45. doi: 10.1128/AAC.00447-12. Epub 2012 Jun 25.
Continue reading →Yang B., Hird A.W., Russell D.J., Fauber B.P., Dakin L.A., Zheng X., Su Q., Godin R., Brassil P., Devereaux E., and Janetka J.W. (2012) “Discovery of novel hedgehog antagonists from cell-based screening: Isosteric modification of p38 bisamides as potent inhibitors of SMO.” Bioorg Med Chem Lett. 2012 Jul 15;22(14):4907-11. doi: 10.1016/j.bmcl.2012.04.104. Epub 2012 Apr 30. (Abstract)
Continue reading →Totsika M., Kostakioti M., Hannan T.J., Upton M., Beatson S.A., Janetka J.W., Hultgren S.J., & Schembri M.A. (2013). “A FimH inhibitor prevents acute bladder infection and treats chronic cystitis caused by multidrug-resistant uropathogenic Escherichia coli ST131.” J Infect Dis. 2013 Sep;208(6):921-8. doi: 10.1093/infdis/jit245. Epub 2013 Jun 3. (Abstract)
Continue reading →Han Z., Harris P.K., Jones D.E., Chugani R., Kim T., Agarwal M., Shen W., Wildman S.A., & Janetka J.W. (2014). “Inhibitors of HGFA, Matriptase, and Hepsin Serine Proteases: A Nonkinase Strategy to Block Cell Signaling in Cancer.” ACS Med Chem Lett. 2014 Oct 9;5(11):1219-24. doi: 10.1021/ml500254r. eCollection 2014 Nov 13. (Abstract)
Continue reading →Franco F.M., Jones D.E., Harris P.K., Han Z., Wildman S.A., Jarvis C.M., & Janetka J.W. (2015). “Structure-based discovery of small molecule hepsin and HGFA protease inhibitors: Evaluation of potency and selectivity derived from distinct binding pockets.” Bioorg Med Chem. 2015 May 15;23(10):2328-43. doi: 10.1016/j.bmc.2015.03.072. Epub 2015 Apr 4. (Abstract)
Continue reading →Greene S.E., Hibbing M.E., Janetka J., Chen S.L., & Hultgren S.J. (2015). “Human Urine Decreases Function and Expression of Type 1 Pili in Uropathogenic Escherichia coli.” MBio. 2015 Jun 30;6(4):e00820. doi: 10.1128/mBio.00820-15. (Abstract)
Continue reading →Mydock-McGrane L.K., Cusumano Z.T., & Janetka J.W. (2016). “Mannose-derived FimH antagonists: a promising anti-virulence therapeutic strategy for urinary tract infections and Crohn’s disease.” Expert Opin Ther Pat. 2016;26(2):175-97. doi: 10.1517/13543776.2016.1131266. Epub 2016 Jan 22. (Abstract)
Continue reading →Jarvis C., Han Z., Kalas V., Klein R., Pinkner J.S., Ford B., Binkley J., Cusumano C.K., Cusumano Z., Mydock-McGrane L., Hultren S.J., & Janetka J.W. (2016). “Antivirulence Isoquinolone Mannosides: Optimization of the Biaryl Aglycone for FimH Lectin Binding Affinity and Efficacy in the Treatment of Chronic UTI.” ChemMedChem. 2016 Feb 17;11(4):367-73. doi: 10.1002/cmdc.201600006. Epub 2016 Jan 26. (Abstract)
Continue reading →Simpson C., Jones N.G., Hull-Ryde E.A., Kireev D., Stashko M., Tang K., Janetka J., Wildman S.A., Zuercher W.J., Schapira M., Hui R., Janzen W., & Sibley L.D. (2016). “Identification of small molecule inhibitors that block the Toxoplasma gondii rhoptry kinase ROP18.” ACS Infect Dis. 2016 Mar 11;2(3):194-206. Epub 2015 Dec 28. (Abstract)
Continue reading →Han Z., Harris P.K.W., Karmakar P., Kim T., Owusu B.Y., Wildman S.A., Klampfer, L., & Janetka J.W. (2016). “α-Ketobenzothiazole Serine Protease Inhibitors of Aberrant HGF/c-MET and MSP/RON Kinase Pathway Signaling in Cancer.” ChemMedChem. 2016 Mar 17;11(6):585-99. doi: 10.1002/cmdc.201500600. Epub 2016 Feb 17. (Abstract)
Continue reading →Wang Q., Heizer E., Rosa B.A., Wildman S.A., Janetka J.W., & Mitreva, M. (2016). “Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.” Infect Genet Evol. 2016 Apr;39:201-211. doi: 10.1016/j.meegid.2016.01.025. Epub 2016 Jan 30. (Abstract)
Continue reading →Smith J.A., Xu G., Feng R., Janetka J.W., & Moeller, K.D. (2016). “C‐Glycosides, Array‐based Addressable Libraries, and the Versatility of Constant Current Electrochemistry” Electroanalysis. 2016, Volume 28, Issue 11, Pages: 2808-2817. DOI: 10.1002/elan.201600200 (Abstract)
Continue reading →Mydock-McGrane L., Cusumano Z., Han Z., Binkley J., Kostakioti M., Hannan T., Pinkner J.S., Klein R.D., Kalas V., Crowley J., Rath N.P., Hultgren S.J., & Janetka J.W. (2016). “Antivirulence C-Mannosides as Antibiotic-Sparing, Oral Therapeutics for Urinary Tract Infections.” J Med Chem. 2016 Oct 27;59(20):9390-9408. Epub 2016 Oct 14. (Abstract)
Continue reading →Kalas V., Pinkner J.S., Hannan T.J., Hibbing M.E., Dodson K.W., Holehouse A.S., Zhang H., Tolia N.H., Gross M.L., Pappu R.V., Janetka J., & Hultgren S.J. (2017). “Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions.” Sci Adv. 2017 Feb 10;3(2):e1601944. doi: 10.1126/sciadv.1601944. eCollection 2017 Feb. (Abstract)
Continue reading →Budelier M.M., Cheng W.W., Bergdoll L., Chen Z.W., Abramson J., Krishnan K., Qian M., Covey D.F., Janetka J.W., & Evers A.S. (2017). “Click Chemistry Reagent for Identification of Sites of Covalent Ligand Incorporation in Integral Membrane Proteins.” Anal Chem. 2017 Feb 21;89(4):2636-2644. doi: 10.1021/acs.analchem.6b05003. Epub 2017 Feb 9. (Abstract)
Continue reading →Budelier M.M., Cheng W.W.L., Bergdoll L., Chen Z.W., Janetka J.W., Abramson J., Krishnan K., Mydock-McGrane L., Covey D.F., Whitelegge J.P., & Evers A.S. (2017). “Photoaffinity labeling with cholesterol analogues precisely maps a cholesterol-binding site in voltage-dependent anion channel-1.” J Biol Chem. 2017 Jun 2;292(22):9294-9304. doi: 10.1074/jbc.M116.773069. Epub 2017 Apr 10. (Abstract)
Continue reading →Owusu B.Y., Galemmo R., Janetka J., & Klampfer L. (2017). “Hepatocyte Growth Factor, a Key Tumor-Promoting Factor in the Tumor Microenvironment.” Cancers (Basel). 2017 Apr 17;9(4). pii: E35. doi: 10.3390/cancers9040035. (Abstract)
Continue reading →Mydock-McGrane L.K., Hannan T.J., & Janetka J.W. (2017). “Rational design strategies for FimH antagonists: new drugs on the horizon for urinary tract infection and Crohn’s disease.” Expert Opin Drug Discov. 2017 Jul;12(7):711-731. doi: 10.1080/17460441.2017.1331216. Epub 2017 Jun 2. (Abstract)
Continue reading →Owusu B.Y., Thomas S., Venukadasula P., Han Z., Janetka J.W., Galemmo R.A. Jr., & Klampfer L. (2017). “Targeting the tumor-promoting microenvironment in MET-amplified NSCLC cells with a novel inhibitor of pro-HGF activation.” Oncotarget. 2017 May 29;8(38):63014-63025. doi: 10.18632/oncotarget.18260. eCollection 2017 Sep 8. (Abstract)
Continue reading →Spaulding C.N., Klein R.D., Ruer S., Kau A.L., Schreiber H.L., Cusumano Z.T., Dodson K.W., Pinkner J.S., Fremont D.H., Janetka J.W., Remaut H., Gordon J.I., & Hultgren S.J. (2017). “Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist.” Nature. 2017 Jun 22;546(7659):528-532. doi: 10.1038/nature22972. Epub 2017 Jun 14. (Abstract)
Continue reading →Rutaganira F.U., Barks J., Dhason M.S., Wang Q., Lopez M.S., Long S., Radke J.B., Jones N.G., Maddirala A.R., Janetka J.W., El Bakkouri M., Hui R., Shokat K.M., & Sibley L.D. (2017). “Inhibition of calcium dependent protein kinase 1 (CDPK1) by pyrazolopyrimidine analogs decreases establishment and reoccurrence of central nervous system disease by Toxoplasma gondii.” J Med Chem. 2017 Dec 28;60(24):9976-9989. doi: 10.1021/acs.jmedchem.7b01192. Epub 2017 Oct 9. (Abstract)
Continue reading →Yang B., Vasbinder M., Hird A.W., Su Q., Wang H., Yu Y., Toader D., Lyne P.D., Read J.A., Breed J., Ioannidis S., Deng C., Grondine M., DeGrace N., Whitston D., Brassil P., & Janetka J.W. (2018). “Adventures in Scaffold Morphing: Discovery of Fused Ring Heterocyclic Checkpoint Kinase 1 (CHK1) Inhibitors.” J Med Chem. doi: 10.1021/acs.jmedchem.7b01490. (Abstract)
Continue reading →Spaulding C.N., Klein R.D., Schreiber H.L. 4th, Janetka J.W., & Hultgren S.J. (2018). “Precision antimicrobial therapeutics: the path of least resistance?” NPJ Biofilms Microbiomes. 2018 Feb 27;4:4. doi: 10.1038/s41522-018-0048-3. eCollection 2018. (Abstract)
Continue reading →James W. Janetka & Roseann M. Benson (2018). “Extracellular Targeting of Cell Signaling in Cancer: Strategies Directed at MET and RON Receptor Tyrosine Kinase Pathways” ISBN-13: 978-1119300182, ISBN-10: 1119300185 (Publisher)
Continue reading →Kalas V., Hibbing M.E., Maddirala A.R., Chugani R., Pinkner J.S., Mydock-McGrane L.K., Conover M.S., Janetka J.W., & Hultgren S.J. (2018). “Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection.” Proc Natl Acad Sci U S A. 2018 Mar 5. pii: 201720140. doi: 10.1073/pnas.1720140115. (Abstract)
Continue reading →Rocha A.G., Franco A., Krezel A.M., Rumsey J.M., Alberti J.M., Knight W.C., Biris N., Zacharioudakis E., Janetka J.W., Baloh R.H., Kitsis R.N., Mochly-Rosen D., Townsend R.R., Gavathiotis E., & Dorn G.W. 2nd (2018). “MFN2 agonists reverse mitochondrial defects in preclinical models of Charcot-Marie-Tooth disease type 2A.” Science. 2018 Apr 20;360(6386):336-341. doi: 10.1126/science.aao1785. (Abstract)
Continue reading →Tyagi R., Maddirala A.R., Elfawal M., Fischer C., Bulman C.A., Rosa B.A., Gao X., Chugani R., Zhou M., Helander J., Brindley P.J., Tseng C.C., Greig I.R., Sakanari J., Wildman S.A., Aroian R., Janetka J.W., & Mitreva M. (2018). “Small Molecule Inhibitors of Metabolic Enzymes Repurposed as a New Class of Anthelmintics.” ACS Infect Dis. 2018 Jul 13;4(7):1130-1145. doi: 10.1021/acsinfecdis.8b00090. Epub 2018 May 14. (Abstract)
Continue reading →Kawaguchi M., Yamamoto K., Takeda N., Fukushima T., Yamashita F., Sato K., Kitamura K., Hippo Y., Janetka J.W., & Kataoka H. (2019). “Hepatocyte growth factor activator inhibitor-2 stabilizes Epcam and maintains epithelial organization in the mouse intestine.” Commun Biol. 2019 Jan 4;2:11. doi: 10.1038/s42003-018-0255-8. eCollection 2019. (Abstract)
Continue reading →Damalanka V.C., Han Z., Karmakar P., O’Donoghue A.J., La Greca F., Kim T., Pant S., Helander J., Klefström J., Craik C.S., & Janetka J.W. (2019). “Discovery of Selective Matriptase and Hepsin Serine Protease Inhibitors: Useful Chemical Tools for Cancer Cell Biology.” J Med Chem. 2019 Jan 24;62(2):480-490. doi: 10.1021/acs.jmedchem.8b01536. Epub 2019 Jan 4. (Abstract)
Continue reading →Maddirala A., Klein R.D., Pinkner J., Kalas V., Hultgren S.J., & Janetka J.W. (2019). “Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through iterative rational drug design.” J Med Chem. 2019 Jan 24;62(2):467-479. doi: 10.1021/acs.jmedchem.8b01561. Epub 2019 Jan 2. (Abstract)
Continue reading →Damalanka V.C. & Janetka J.W. (2019). “Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2.” Future Med Chem. 2019 Apr;11(7):743-769. doi: 10.4155/fmc-2018-0446. Epub 2019 Apr 4. (Abstract)
Continue reading →Tyagi R., Elfawal M.A., Wildman S.A., Helander J., Bulman C.A., Sakanari J., Rosa B.A., Brindley P.J., Janetka J.W., Aroian R.V., & Mitreva M. (2019). “Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics.” Sci Rep. 2019 Jun 24;9(1):9085. doi: 10.1038/s41598-019-45548-7. (Abstract)
Continue reading →Vishnu C. Damalanka, Scott A. Wildman, & James W. Janetka (2019). “Piperidine carbamate peptidomimetic inhibitors of the serine proteases HGFA, matriptase and hepsin” MedChemComm. 18 Jul 2019, doi: 10.1039/C9MD00234K (Abstract)
Continue reading →Yang B., Hird A.W., Bodnarchuk M.S., Zheng X., Dakin L., Su Q., Daly K., Godin R., Hattersley M.M., Brassil P., Redmond S., John Russell D., & Janetka J.W. (2020). “Heteroarylamide smoothened inhibitors: Discovery of N-[2,4-dimethyl-5-(1-methylimidazol-4-yl)phenyl]-4-(2-pyridylmethoxy)benzamide (AZD8542) and N-[5-(1H-imidazol-2-yl)-2,4-dimethyl-phenyl]-4-(2- pyridylmethoxy)benzamide (AZD7254).” Bioorg Med Chem. 2020 Jan 15;28(2):115227. doi: 10.1016/j.bmc.2019.115227. Epub 2019 Dec 11. (Abstract)
Continue reading →James W Janetka, Allen T Hopper, Ziping Yang, Jennifer Barks, Mary Savari Dhason, Qiuling Wang, & L David Sibley (2020). “Optimizing Pyrazolopyrimidine Inhibitors of Calcium Dependent Protein Kinase 1 for Treatment of Acute and Chronic Toxoplasmosis” J Med Chem. 2020 Jun 11;63(11):6144-6163. doi: 10.1021/acs.jmedchem.0c00419. Epub 2020 Jun 1. (Abstract)
Continue reading →Vishnu C. Damalanka, Amarendar Reddy Maddirala, & James W. Janetka (2020). “Novel approaches to glycomimetic design: Development of small molecular weight lectin antagonists” Expert Opin Drug Discov. 2020 Dec 18. doi: 10.1080/17460441.2021.1857721. Online ahead of print. (Abstract)
Continue reading →Rahul Tyagi, Christina A. Bulman, Fidelis Cho-Ngwa, Chelsea Fischer, Chris Marcellino, Michelle R. Arkin, James H. McKerrow, Case W. McNamara, Matthew Mahoney, Nancy Tricoche, Shabnam Jawahar, James W. Janetka, Sara Lustigman, Judy Sakanari, & Makedonka Mitreva (2021). “An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease” Pathogens. 2021 Jan 14;10(1):71. doi: 10.3390/pathogens10010071. (Abstract)
Continue reading →Lisa K. McLellan, Michael R. McAllaster, Arthur S. Kim, Ľubomíra Tóthová, Patrick D. Olson, Jerome S. Pinkner, Allyssa L. Daugherty, Teri N. Hreha, James W. Janetka, Daved H. Fremont, Scott J. Hultgren, Herbert W. Virgin, & David A Hunstad (2021). “A host receptor enables type 1 pilus-mediated pathogenesis of Escherichia coli pyelonephritis” PLoS Pathog. 2021 Jan 29;17(1):e1009314. doi: 10.1371/journal.ppat.1009314. eCollection 2021 Jan. (Abstract)
Continue reading →Matthew Mahoney, Vishnu C. Damalanka, Michael A. Tartell, Dong Hee Chung, André Luiz Lourenco, Dustin Pwee, Anne E. Mayer Bridwell, Markus Hoffmann, Jorine Voss, Partha Karmakar, Nurit Azouz, Andrea M. Klingler, Paul W. Rothlauf, Cassandra E. Thompson, Melody Lee, Lidija Klampfer, Christina Stallings, Marc E. Rothenberg, Stefan Pöhlmann, Sean P. Whelan, Anthony J. O’Donoghue, Charles S. Craik, & James W. Janetka (2021). “A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells” Proc Natl Acad Sci U S A. 2021 Oct 26;118(43):e2108728118. doi: 10.1073/pnas.2108728118. (Abstract)
Continue reading →Vishnu C. Damalanka, Jorine J. L. P. Voss, Matthew W. Mahoney, Tina Primeau, Shunqiang Li, Lidija Klampfer, & James W. Janetka (2021). “Macrocyclic Inhibitors of HGF-Activating Serine Proteases Overcome Resistance to Receptor Tyrosine Kinase Inhibitors and Block Lung Cancer Progression” J Med Chem. 2021 Dec 13. doi: 10.1021/acs.jmedchem.1c01671. Online ahead of print. (Abstract)
Continue reading →Liana Beld, Hyeim Jung, Christina A. Bulman, Bruce A. Rosa, Peter U. Fischer, James W. Janetka, Sara Lustigman, Judy A. Sakanari, and Makedonka Mitreva (2022). “Aspartyl Protease Inhibitors as Anti-Filarial Drugs” Pathogens. 2022 Jun 18;11(6):707. doi: 10.3390/pathogens11060707. (Abstract)
Continue reading →Vivian Truong Jones, Ramona Graves-Deal, Zheng Cao, Galina Bogatcheva, Marisol A Ramirez, Sarah J Harmych, James N Higginbotham, Vineeta Sharma, Vishnu C Damalanka, Claudia C Wahoski, Neeraj Joshi, Maria Johnson Irudayam, Joseph T Roland, Gregory D Ayers, Qi Liu, Robert J Coffey, James W Janetka & Bhuminder Singh (2024). “Inhibition of autocrine HGF maturation overcomes cetuximab resistance in colorectal cancer” Cell Mol Life Sci. 2024 Jan 12;81(1):28. doi: 10.1007/s00018-023-05071-5. (Abstract)
Continue reading →Denis Belitškin, Pauliina Munne, Shishir M Pant, Johanna M Anttila, Ilida Suleymanova, Kati Belitškina, Daniel Kirchhofer, James Janetka, Taivo Käsper, Sami Jalil, Jeroen Pouwels, Topi A Tervonen & Juha Klefström (2024). “Hepsin promotes breast tumor growth signaling via the TGFβ-EGFR axis” Mol Oncol. 2024 Mar;18(3):547-561. doi: 10.1002/1878-0261.13545. Epub 2023 Nov 13. (Abstract)
Continue reading →Alpha Raj Mekapogu, Zhihong Xu, Srinivasa Pothula, Chamini Perera, Tony Pang, S M Zahid Hosen, Vishnu Damalanka, James Janetka, David Goldstein, Romano Pirola, Jeremy Wilson & Minoti Apte (2023). “HGF/c-Met pathway inhibition combined with chemotherapy increases cytotoxic T-cell infiltration and inhibits pancreatic tumour growth and metastasis” Cancer Lett. 2023 Aug 1:568:216286. doi: 10.1016/j.canlet.2023.216286. Epub 2023 Jun 22. (Abstract)
Continue reading →Amarendar Reddy Maddirala, Kevin Tamadonfar, Jerome S Pinkner, Denise Sanick, Scott J Hultgren & James W Janetka (2024). “Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections” J Med Chem. 2024 Mar 14;67(5):3668-3678. doi: 10.1021/acs.jmedchem.3c02128. Epub 2024 Feb 3. (Abstract)
Continue reading →Adrianus C M Boon, Traci L Bricker, Ethan J Fritch, Sarah R Leist, Kendra Gully, Ralph S Baric, Rachel L Graham, Brigid V Troan, Matthew Mahoney & James W Janetka (2024). “Efficacy of Host Cell Serine Protease Inhibitor MM3122 against SARS-CoV-2 for Treatment and Prevention of COVID-19” J Virol.2024 May 14;98(5):e0190323. doi: 10.1128/jvi.01903-23. Epub 2024 Apr 9. (Abstract)
Continue reading →Robert Obermann, Bereket Yemane, Cassie Jarvis, Francisco M Franco, Yevhenii Kyriukha, William Nolan, Beth Gohara, Andrzej M Krezel, Scott A Wildman & James W Janetka (2024). “Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction” ChemMedChem. 2024 Apr 16;19(8):e202300648. doi: 10.1002/cmdc.202300648. Epub 2024 Mar 5. (Abstract)
Continue reading →Vishnu C Damalanka, Victoria Banas, Paolo De Bona, Maithri M Kashipathy, Kevin Battaile, Scott Lovell, James W Janetka (2024). “Mechanism-Based Macrocyclic Inhibitors of Serine Proteases” J Med Chem. 2024 Mar 28;67(6):4833-4854. doi: 10.1021/acs.jmedchem.3c02388. Epub 2024 Mar 13. (Abstract)
Continue reading →Matthew W Mahoney, Jonathan Helander, Anoopjit S Kooner, Mariah Norman, Vishnu C Damalanka, Paolo De Bona, Paulina Kasperkiewicz, Wioletta Rut, Marcin Poreba, Maithri M Kashipathy, Kevin P Battaile, Scott Lovell, Anthony J O’Donoghue, Charles S Craik, Marcin Drag & James W Janetka (2024). “Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin” Protein Sci. 2024 Aug;33(8):e5110. doi: 10.1002/pro.5110. (Abstract)
Continue reading →Victoria Banas, Mostafa A Elfawal, Bruce A Rosa, Matthew Mahoney, Jacquelyn Kauffman, Emily Goetz, Paulina Chen, Raffi V Aroian, Makedonka Mitreva, James W Janetka
ACS Infect Dis. 2025 Jan 19. doi: 10.1021/acsinfecdis.4c00864. Online ahead of print.
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All Publications: (newest on top, only the most recent 3)
Victoria Banas, Mostafa A Elfawal, Bruce A Rosa, Matthew Mahoney, Jacquelyn Kauffman, Emily Goetz, Paulina Chen, Raffi V Aroian, Makedonka Mitreva, James W Janetka
ACS Infect Dis. 2025 Jan 19. doi: 10.1021/acsinfecdis.4c00864. Online ahead of print.
Continue reading →Das M, Hile SE, Brewster J, Boer JL, Bezalel-Buch R, Guo Q, Yang W, Burgers PM, Eckert KA, Freudenreich CH. “DNA polymerase zeta can efficiently replicate structures formed by AT/TA repeat sequences and prevent their deletion. ” Nucleic Acids Res. 2024 Dec 27:gkae1254. doi: 10.1093/nar/gkae1254. Online ahead of print. PMID: 39727171(Abstract)
Continue reading →Henze E, Ehrlich JJ, Robertson JL, Gelsleichter E, Kawate T. “The C-terminal activating domain promotes pannexin 1 channel opening.” Proc Natl Acad Sci U S A. 2024 Dec 17;121(51):e2411898121. doi: 10.1073/pnas.2411898121. Epub 2024 Dec 13. PMID: 39671183. (Abstract)
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Publications From Just 2014
Lin, Y.C., Li, L., Makarova, A.V., Burgers, P.M., Stone, M.P. and Lloyd, R.S.
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Molecular basis of aflatoxin-induced mutagenesis-role of the aflatoxin B1-formamidopyrimidine adduct.
Carcinogenesis 35:1461-1468 (2014). (Abstract)Galburt E.A., Tomko E.J., Stump W.T., & Ruiz Manzano A. (2014). “Force-dependent melting of supercoiled DNA at thermophilic temperatures.” Biophys Chem. 2014 Mar-Apr;187-188:23-8. doi: 10.1016/j.bpc.2014.01.001. Epub 2014 Jan 17. (Abstract)
Continue reading →Kohlhoff, K.J., Shukla, D., Lawrenz, M., Bowman, G.R., Konerding, D.E., Belov, D., Altman, R.B. and Pande, V.S.
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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Nature Chemistry 6:15-21 (2014). (Abstract)Liu S., Cheng W., Fowle Grider R., Shen G., and Li W.
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Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer.
Nat Commun. 5:3110. doi: 10.1038/ncomms4110. (2014) (Abstract)Borin B.N., Tang W., & Krezel A.M. (2014). “Helicobacter pylori RNA polymerase α-subunit C-terminal domain shows features unique to ɛ-proteobacteria and binds NikR/DNA complexes.” Protein Sci. 2014 Apr;23(4):454-63. doi: 10.1002/pro.2427. Epub 2014 Feb 4. (Abstract)
Continue reading →Park E., Ménétret J.F., Gumbart J.C., Ludtke S.J., Li W., Whynot A., Rapoport T.A., and Akey C.W.
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Structure of the SecY channel during initiation of protein translocation.
Nature. 506(7486):102-6. doi: 10.1038/nature12720. (2014) (Abstract)Genin G.M. & Elson E.L. (2014). “Mechanically guided cell migration: less of a stretch than ever.” Biophys J. 2014 Feb 18;106(4):776-7. doi: 10.1016/j.bpj.2014.01.016. (Abstract)
Continue reading →Shuman H., Greenberg M.J., Zwolak A., Lin T., Sindelar C.V., Dominguez R., & Ostap E.M. (2014). “A vertebrate myosin-I structure reveals unique insights into myosin mechanochemical tuning.” Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2116-21. doi: 10.1073/pnas.1321022111. Epub 2014 Jan 27. (Abstract)
Continue reading →Hall K.B. (2014). “Molecular biology: Protein binding cannot subdue a lively RNA.” Nature. 2014 Feb 20;506(7488):303-4. doi: 10.1038/nature13055. Epub 2014 Feb 12. (Abstract)
Continue reading →Cheng W. and Li W.
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Structural insights into ubiquinone biosynthesis in membranes.
Science. 343(6173):878-81. doi: 10.1126/science.1246774. (2014) (Abstract)Bowman, G.R. and Geissler, P.L.
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Extensive Conformational Heterogeneity within Protein Cores
J Phys Chem B 118:6417-6423.(2014). (Abstract)Borgo B. and Havranek J.J. (2014) “Motif-directed redesign of enzyme specificity.” Protein Sci. 2014 Mar;23(3):312-20. doi: 10.1002/pro.2417. Epub 2014 Feb 4. (Abstract)
Continue reading →Makarova, A.V., McElhinny, S.A., Watts, B.E., Kunkel, T.A. and Burgers, P.M.
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Ribonucleotide incorporation by yeast DNA polymerase ζ.
DNA Repair 18:63-67 (2014). (Abstract)Lin, Y.C., Li, L., Makarova, A.V., Burgers, P.M. and Lloyd, R.S.
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Error-prone replication bypass of the primary aflatoxin B1 DNA adduct, AFB1-N7-Gua.
J Biol Chem 289:18497-18506 (2014). (Abstract)Delaney K.J., Williams S.G., Lawler M., & Hall K.B. (2014). “Climbing the vertebrate branch of U1A/U2B″ protein evolution.” RNA. 2014 Jul;20(7):1035-45. doi: 10.1261/rna.044255.114. Epub 2014 May 19. (Abstract)
Continue reading →Williams S.G. & Hall K.B. (2014). “Linkage and allostery in snRNP protein/RNA complexes.” Biochemistry. 2014 Jun 10;53(22):3529-39. doi: 10.1021/bi500192a. Epub 2014 May 29. (Abstract)
Continue reading →Williams S.G. & Hall K.B. (2014). “Binding affinity and cooperativity control U2B″/snRNA/U2A’ RNP formation.” Biochemistry. 2014 Jun 17;53(23):3727-37. doi: 10.1021/bi500438e. Epub 2014 Jun 5. (Abstract)
Continue reading →Ilagan M.X. and Kopan R. (2014) “Monitoring Notch activation in cultured mammalian cells: luciferase complementation imaging assays.” Methods Mol Biol. 2014;1187:155-68. doi: 10.1007/978-1-4939-1139-4_12. (Abstract)
Continue reading →Lee K.S., Marciel A.B., Kozlov A.G., Schroeder C.M., Lohman T.M., & Ha T. (2014). “Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer.” J Mol Biol. 2014 Jun 26;426(13):2413-21. doi: 10.1016/j.jmb.2014.04.023. Epub 2014 May 2. (Abstract)
Continue reading →DeKoster G.T., Delaney K.J., & Hall K.B. (2014). “A compare-and-contrast NMR dynamics study of two related RRMs: U1A and SNF.” Biophys J. 2014 Jul 1;107(1):208-19. doi: 10.1016/j.bpj.2014.05.026. (Abstract)
Continue reading →Garner A.L., Weiss L., Manzano A.R., Galburt E.A., & Stallings C.L. (2014). “CarD integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria.” Mol Microbiol. 2014 Aug;93(4):682-97. doi: 10.1111/mmi.12681. Epub 2014 Jul 16. (Abstract)
Continue reading →Kunkel, T.A. and Burgers, P.M.
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Delivering nonidentical twins.
Nat Struct Mol Biol 21:649-651 (2014). (Abstract)Lin Y., Manning P.T., Jia J., Gaut J.P., Xiao Z., Capoccia B.J., Chen C.C., Hiebsch R.R., Upadhya G., Mohanakumar T., Frazier W.A., & Chapman W.C. (2014). “CD47 blockade reduces ischemia-reperfusion injury and improves outcomes in a rat kidney transplant model.” Transplantation. 2014 Aug 27;98(4):394-401. doi: 10.1097/TP.0000000000000252. (Abstract)
Continue reading →Hammes G. & Frieden C. (2014). “Robert A. Alberty” National Academy of Sciences. Biographical Memoirs. (Article)
Continue reading →Dovrat, D., Stodola, J.L., Burgers, P.M. and Aharoni, A.
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Sequential switching of binding partners on PCNA during in vitro Okazaki fragment maturation.
PNAS 111:14118-14123 (2014). (Abstract)Macdonald-Obermann J.L. & Pike L.J. (2014). “Different epidermal growth factor (EGF) receptor ligands show distinct kinetics and biased or partial agonism for homodimer and heterodimer formation.” J Biol Chem. 2014 Sep 19;289(38):26178-88. doi: 10.1074/jbc.M114.586826. Epub 2014 Aug 1. (Abstract)
Continue reading →Nguyen B., Sokoloski J.E., Galletto R., Elson E.L., Wold M.S., & Lohman T.M. (2014). “Diffusion of human replication protein A along single-stranded DNA.” J Mol Biol. 2014 Sep 23;426(19):3246-3261. doi: 10.1016/j.jmb.2014.07.014. Epub 2014 Jul 22. (Abstract)
Continue reading →Garai K., Verghese P.B., Baban B., Holtzman D.M., & Frieden C. (2014). “The binding of apolipoprotein E to oligomers and fibrils of amyloid-β alters the kinetics of amyloid aggregation.” Biochemistry. 2014 Oct 14;53(40):6323-31. doi: 10.1021/bi5008172. Epub 2014 Sep 25. (Abstract)
Continue reading →Galburt E.A. (2014). “Magnetic Tweezers Force Spectroscopy” Handbook of Imaging in Biological Mechanics. Chapter 38. DOI: 10.1201/b17566-51. ISBN: 9781466588134. (Abstract)
Continue reading →Han Z., Harris P.K., Jones D.E., Chugani R., Kim T., Agarwal M., Shen W., Wildman S.A., & Janetka J.W. (2014). “Inhibitors of HGFA, Matriptase, and Hepsin Serine Proteases: A Nonkinase Strategy to Block Cell Signaling in Cancer.” ACS Med Chem Lett. 2014 Oct 9;5(11):1219-24. doi: 10.1021/ml500254r. eCollection 2014 Nov 13. (Abstract)
Continue reading →Liu C., Ponder J.W., and Marshall G.R. (2014) “Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence.” Proteins. 2014 Nov;82(11):3043-61. doi: 10.1002/prot.24665. Epub 2014 Sep 20. (Abstract)
Continue reading →Frieden C. (2015). “ApoE: the role of conserved residues in defining function.” Protein Sci. 2015 Jan;24(1):138-44. doi: 10.1002/pro.2597. Epub 2014 Dec 9. (Abstract)
Continue reading →Feldmann, E.A. and Galletto, R.
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The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes.
Biochemistry 33:7471-7483 (2014). (Abstract)Greenberg M.J., Shuman H., & Ostap E.M. (2014). “Inherent force-dependent properties of β-cardiac myosin contribute to the force-velocity relationship of cardiac muscle.” Biophys J. 2014 Dec 16;107(12):L41-4. doi: 10.1016/j.bpj.2014.11.005. (Abstract)
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All Publications: (newest on top)
Victoria Banas, Mostafa A Elfawal, Bruce A Rosa, Matthew Mahoney, Jacquelyn Kauffman, Emily Goetz, Paulina Chen, Raffi V Aroian, Makedonka Mitreva, James W Janetka
ACS Infect Dis. 2025 Jan 19. doi: 10.1021/acsinfecdis.4c00864. Online ahead of print.
Continue reading →Das M, Hile SE, Brewster J, Boer JL, Bezalel-Buch R, Guo Q, Yang W, Burgers PM, Eckert KA, Freudenreich CH. “DNA polymerase zeta can efficiently replicate structures formed by AT/TA repeat sequences and prevent their deletion. ” Nucleic Acids Res. 2024 Dec 27:gkae1254. doi: 10.1093/nar/gkae1254. Online ahead of print. PMID: 39727171(Abstract)
Continue reading →Henze E, Ehrlich JJ, Robertson JL, Gelsleichter E, Kawate T. “The C-terminal activating domain promotes pannexin 1 channel opening.” Proc Natl Acad Sci U S A. 2024 Dec 17;121(51):e2411898121. doi: 10.1073/pnas.2411898121. Epub 2024 Dec 13. PMID: 39671183. (Abstract)
Continue reading →Walker EC, Javati S, Todd EM, Matlam JP, Lin X, Bryant M, Krone E, Ramani R, Chandra P, Green TP, Anaya EP, Zhou JY, Alexander KA, Tong RS, Yuasi L, Boluarte S, Yang F, Greenberg L, Nerbonne JM, Greenberg MJ, Clemens RA, Philips JA, Wilson LD, Halabi CM, DeBosch BJ, Blyth CC, Druley TE, Kazura JW, Pomat WS, Morley SC. “Novel coenzyme Q6 genetic variant increases susceptibility to pneumococcal disease.” Nat Immunol. 2024 Dec;25(12):2247-2258. doi: 10.1038/s41590-024-01998-4. Epub 2024 Nov 4. PMID: 39496954 (Abstract)
Continue reading →Ernst M, Mahoney-Kruszka R, Zelt NB, Robertson JL. “A roadmap to cysteine specific labeling of membrane proteins for single-molecule photobleaching studies.” Methods. 2024 Nov 23;234:21-35. doi: 10.1016/j.ymeth.2024.10.013. Epub ahead of print. PMID: 39586432.(Abstract)
Continue reading →Gao M, Chen L, Yang J, Dong S, Cao Q, Cui Z, Dong Y, Liu H, Shen Y, Yang H, Hao Z, Zhang L, Li W, Tie JK, Shen G. “Multimodal mechanisms of pathogenic variants in the signal peptide of FIX leading to hemophilia B”. Blood Adv. 2024 Aug 13;8(15):3893-3905. doi: 10.1182/bloodadvances.2023012432. PMID: 38820490
Continue reading →Matthew W Mahoney, Jonathan Helander, Anoopjit S Kooner, Mariah Norman, Vishnu C Damalanka, Paolo De Bona, Paulina Kasperkiewicz, Wioletta Rut, Marcin Poreba, Maithri M Kashipathy, Kevin P Battaile, Scott Lovell, Anthony J O’Donoghue, Charles S Craik, Marcin Drag & James W Janetka (2024). “Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin” Protein Sci. 2024 Aug;33(8):e5110. doi: 10.1002/pro.5110. (Abstract)
Continue reading →Michael J Greenberg (2024). “Super Relaxed or Super Stressed: Modeling Length-Dependent Activation in Cardiac Muscle” Biophys J.2024 Jul 26:S0006-3495(24)00492-2. doi: 10.1016/j.bpj.2024.07.033. (Abstract)
Continue reading →Meng Gao, Long Chen, Jinlong Yang, Shixia Dong, Qing Cao, Zihan Cui, Yanyan Dong, Hongli Liu, Yan Shen, Haiping Yang, Zhenyu Hao, Lei Zhang, Weikai Li, Jian-Ke Tie & Guomin Shen (2024). “Multimodal mechanisms of pathogenic variants in the signal peptide of FIX leading to hemophilia B” Blood Adv.2024 Aug 13;8(15):3893-3905. doi: 10.1182/bloodadvances.2023012432. (Abstract)
Continue reading →Jiyeon Lee, Julie M Dimitry, Jong Hee Song, Minsoo Son, Patrick W Sheehan, Melvin W King, G Travis Tabor, Young Ah Goo, Mitchell A Lazar, Leonard Petrucelli, Erik S Musiek (2023). “Microglial REV-ERBα regulates inflammation and lipid droplet formation to drive tauopathy in male mice” Nat Commun. 2023 Aug 25;14(1):5197. doi: 10.1038/s41467-023-40927-1. (Abstract)
Continue reading →Abhay K Singh, Calvin D Lewis, Cristian A W V Boas, Philipp Diebolder, Prashant N Jethva, Aaron Rhee, Jong Hee Song, Young Ah Goo, Shunqian Li, Michael L Nickels, Yongjian Liu, Buck E Rogers, Vaishali Kapoor & Dennis E Hallahan (2024). “Development of a [89Zr]Zr-labeled Human Antibody using a Novel Phage-displayed Human scFv Library” Clin Cancer Res. 2024 Apr 1;30(7):1293-1306. doi: 10.1158/1078-0432.CCR-23-3647. (Abstract)
Continue reading →Tusar Giri, Susan E Maloney, Saswat Giri, Young Ah Goo, Jong Hee Song, Minsoo Son, Eric Tycksen, Sara B Conyers, Annie Bice, Xia Ge, Joel R Garbow, James D Quirk, Adam Q Bauer & Arvind Palanisamy (2024). “Oxytocin-induced birth causes sex-specific behavioral and brain connectivity changes in developing rat offspring” iScience. 2024 Jan 22;27(2):108960. doi: 10.1016/j.isci.2024.108960. eCollection 2024 Feb 16. (Abstract)
Continue reading →Meaghan S Jankowski, Daniel Griffith, Divya G Shastry, Jacqueline F Pelham, Garrett M Ginell, Joshua Thomas, Pankaj Karande, Alex S Holehouse & Jennifer M Hurley (2024). “Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator” Nat Communn. 2024 Apr 25;15(1):3523. doi: 10.1038/s41467-024-47761-z. (Abstract)
Continue reading →Zongru Li, Qionghua Shen, Emery T Usher, Andrew P Anderson, Manuel Iburg, Richard Lin, Brandon Zimmer, Matthew D Meyer, Alex S Holehouse, Lingchong You, Ashutosh Chilkoti, Yifan Dai & George J Lu (2024). “Phase transition of GvpU regulates gas vesicle clustering in bacteria” Nat Microbiol. 2024 Apr;9(4):1021-1035. doi: 10.1038/s41564-024-01648-3. Epub 2024 Mar 29. (Abstract)
Continue reading →S Sanchez-Martinez, K Nguyen, S Biswas, V Nicholson, A V Romanyuk, J Ramirez, S Kc, A Akter, C Childs, E K Meese, E T Usher, G M Ginell, F Yu, E Gollub, M Malferrari, F Francia, G Venturoli, E W Martin, F Caporaletti, G Giubertoni, S Woutersen, S Sukenik, D N Woolfson, A S Holehouse & T C Boothby (2024). “Labile assembly of a tardigrade protein induces biostasis” Protein Sci.2024 Apr;33(4):e4941. doi: 10.1002/pro.4941. (Abstract)
Continue reading →Jeffrey M Lotthammer, Garrett M Ginell, Daniel Griffith, Ryan J Emenecker & Alex S Holehouse (2024). “Direct prediction of intrinsically disordered protein conformational properties from sequence” Nat Methods. 2024 Mar;21(3):465-476. doi: 10.1038/s41592-023-02159-5. Epub 2024 Jan 31. (Abstract)
Continue reading →Sourav Biswas, Edith Gollub, Feng Yu, Garrett Ginell, Alex Holehouse, Shahar Sukenik & Thomas C Boothby 1 (2024). “Helicity of a tardigrade disordered protein contributes to its protective function during desiccation” Protein Sci. 2024 Feb;33(2):e4872. doi: 10.1002/pro.4872. (Abstract)
Continue reading →David Moses, Karina Guadalupe, Feng Yu, Eduardo Flores, Anthony R Perez, Ralph McAnelly, Nora M Shamoon, Gagandeep Kaur, Estefania Cuevas-Zepeda, Andrea D Merg, Erik W Martin, Alex S Holehouse & Shahar Sukenik (2024). “Structural biases in disordered proteins are prevalent in the cell” Nat Struct Mol Biol. 2024 Feb;31(2):283-292. doi: 10.1038/s41594-023-01148-8. Epub 2024 Jan 4. (Abstract)
Continue reading →Alex S Holehouse & Birthe B Kragelund (2024). “The molecular basis for cellular function of intrinsically disordered protein regions” Nat Rev Mol Cell Biol. 2024 Mar;25(3):187-211. doi: 10.1038/s41580-023-00673-0. Epub 2023 Nov 13. (Abstract)
Continue reading →Priya R Banerjee, Alex S Holehouse, Richard Kriwacki, Paul Robustelli, Hao Jiang, Alexander I Sobolevsky, Jennifer M Hurley & Joshua T Mendell (2024). “Dissecting the biophysics and biology of intrinsically disordered proteins” Trends Biochem Sci. 2024 Feb;49(2):101-104. doi: 10.1016/j.tibs.2023.10.002. Epub 2023 Nov 8. (Abstract)
Continue reading →David Moses, Garrett M Ginell, Alex S Holehouse & Shahar Sukenik (2023). “Intrinsically disordered regions are poised to act as sensors of cellular chemistry” Trends Biochem Sci. 2023 Dec;48(12):1019-1034. doi: 10.1016/j.tibs.2023.08.001. Epub 2023 Aug 31. (Abstract)
Continue reading →Karol Buda, Katerina Cermakova, H Courtney Hodges, Eugenio F Fornasiero, Shahar Sukenik & Alex S Holehouse (2023). “Using graphs and charts in scientific figures” Trends Biochem Sci. 2023 Nov;48(11):913-916. doi: 10.1016/j.tibs.2023.08.011. (Abstract)
Continue reading →Gretchen A Meyer, Jeremie L A Ferey, James A Sanford, Liam S Fitzgerald, Akiva E Greenberg, Kristoffer Svensson, Michael J Greenberg & Simon Schenk (2024). “Insights into posttranslational regulation of skeletal muscle contractile function by the acetyltransferases, p300 and CBP” J Appl Physiol (1985). 2024 Jun 1;136(6):1559-1567. doi: 10.1152/japplphysiol.00156.2024. Epub 2024 May 9. (Abstract)
Continue reading →Venecia Valdez, Meisheng Ma, Bernardo Gouveia, Rui Zhang & Sabine Petry (2024). “HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2” bioRxiv. [Preprint]. 2023 Dec 18:2023.12.18.571906. doi: 10.1101/2023.12.18.571906. (Abstract)
Continue reading →Kiarash Jamali, Lukas Käll, Rui Zhang, Alan Brown, Dari Kimanius & Sjors H W Scheres (2024). “Automated model building and protein identification in cryo-EM maps” Nature. 2024 Apr;628(8007):450-457. doi: 10.1038/s41586-024-07215-4. Epub 2024 Feb 26. (Abstract)
Continue reading →Ankit Garg, Silvia Jansen, Rui Zhang, Kory J Lavine & Michael J Greenberg (2024). “Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility” bioRxiv. [Preprint]. 2024 Mar 12:2024.03.10.583979. doi: 10.1101/2024.03.10.583979. (Abstract)
Continue reading →Steven L Brody, Jiehong Pan, Tao Huang, Jian Xu, Huihui Xu, Jeffrey Koenitizer, Steven K Brennan, Rashmi Nanjundappa, Thomas G Saba, Andrew Berical, Finn J Hawkins, Xiangli Wang, Rui Zhang, Moe R Mahjoub, Amjad Horani & Susan K Dutcher (2024). “Loss of an extensive ciliary connectome induces proteostasis and cell fate switching in a severe motile ciliopathy” bioRxiv. [Preprint]. 2024 Mar 21:2024.03.20.585965. doi: 10.1101/2024.03.20.585965. (Abstract)
Continue reading →Jin Dai, Meisheng Ma, Qingwei Niu, Robyn J Eisert, Xiangli Wang, Poulomi Das, Karl F Lechtreck, Susan K Dutcher, Rui Zhang & Alan Brown (2024). “Mastigoneme structure reveals insights into the O-linked glycosylation code of native hydroxyproline-rich helices” Cell. 2024 Apr 11;187(8):1907-1921.e16. doi: 10.1016/j.cell.2024.03.005. Epub 2024 Mar 28. (Abstract)
Continue reading →Gabor Egervari, Desi C. Alexander, Greg Donahue, Hua Huang, Connor Hogan, Mariel Mendoza, Benjamin A. Garcia, Nancy M. Bonini, Shelley L. Berger (2024). “ACSS2 contributes to transcriptional regulation in Cajal-Retzius cells in a mouse model of Alzheimer’s disease” bioRxiv. [Preprint] (Abstract)
Continue reading →Jasmine Cubuk, Lina Greenberg, Akiva E Greenberg, Ryan J Emenecker, Melissa D Stuchell-Brereton, Alex S Holehouse, Andrea Soranno & Michael J Greenberg (2024). “Structural dynamics of the intrinsically disordered linker region of cardiac troponin T” bioRxiv. [Preprint]. 2024 May 31:2024.05.30.596451. doi: 10.1101/2024.05.30.596451. (Abstract)
Continue reading →Eva Fortea, Sangyun Lee, Rahul Chadda, Yiorgos Argyros, Priyanka Sandal, Robyn Mahoney-Kruszka, Hatice Didar Ciftci, Maria E Falzone, Gerard Huysmans, Janice L Robertson, Olga Boudker & Alessio Accardi (2024). “Structural basis of pH-dependent activation in a CLC transporter” Nat Struct Mol Biol. 2024 Apr;31(4):644-656. doi: 10.1038/s41594-023-01210-5. Epub 2024 Jan 26. (Abstract)
Continue reading →Melanie Ernst, Esam A Orabi, Randy B Stockbridge, José D Faraldo-Gómez & Janice L Robertson (2023). “Dimerization mechanism of an inverted-topology ion channel in membranes” Proc Natl Acad Sci U S A. 2023 Nov 21;120(47):e2308454120. doi: 10.1073/pnas.2308454120. Epub 2023 Nov 13. (Abstract)
Continue reading →Jasmine Cubuk, Jhullian J Alston, J Jeremías Incicco, Alex S Holehouse, Kathleen B Hall, Melissa D Stuchell-Brereton & Andrea Soranno (2024). “The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA” Nucleic Acids Res. 2024 Mar 21;52(5):2609-2624. doi: 10.1093/nar/gkad1215. (Abstract)
Continue reading →Melanie Ernst, Tugba N Ozturk, Janice L Robertson (2023). “A single-molecule method for measuring fluorophore labeling yields for the study of membrane protein oligomerization in membranes” PLoS One. 2023 Jan 20;18(1):e0280693. doi: 10.1371/journal.pone.0280693. eCollection 2023. (Abstract)
Continue reading →Rahul Chadda, Taeho Lee, Robyn Mahoney-Kruszka, Elizabeth G Kelley, Nathan Bernhardt, Priyanka Sandal & Janice L Robertson (2023). “A thermodynamic analysis of CLC transporter dimerization in lipid bilayers” Proc Natl Acad Sci U S A. 2023 Oct 10;120(41):e2305100120. doi: 10.1073/pnas.2305100120. Epub 2023 Oct 3. (Abstract)
Continue reading →Jennifer L Macdonald-Obermann & Linda J Pike (2024). “Extracellular domain mutations of the EGF receptor differentially modulate high-affinity and low-affinity responses to EGF receptor ligands” J Biol Chem. 2024 Mar;300(3):105763. doi: 10.1016/j.jbc.2024.105763. Epub 2024 Feb 16. (Abstract)
Continue reading →Nicole Fazio, Kacey N Mersch, Linxuan Hao, Timothy M Lohman (2023). “E. coli RecBCD Nuclease Domain Regulates Helicase Activity but not Single Stranded DNA Translocase Activity” bioRxiv. [Preprint]. 2023 Oct 17:2023.10.13.561901. doi: 10.1101/2023.10.13.561901. (Abstract)
Continue reading →Evelyn Ploetz, Benjamin Ambrose, Anders Barth, Richard Börner, Felix Erichson, Achillefs N Kapanidis, Harold D Kim, Marcia Levitus, Timothy M Lohman, Abhishek Mazumder, David S Rueda, Fabio D Steffen, Thorben Cordes, Steven W Magennis & Eitan Lerner (2023). “A new twist on PIFE: photoisomerisation-related fluorescence enhancement” Methods Appl Fluoresc. 2023 Oct 12;12(1):012001. doi: 10.1088/2050-6120/acfb58. (Abstract)
Continue reading →Chunyang Guo, Ming Cheng, Weikai Li& Michael L Gross (2023). “Precursor Reagent Hydrophobicity Affects Membrane Protein Footprinting” J Am Soc Mass Spectrom. 2023 Dec 6;34(12):2700-2710. doi: 10.1021/jasms.3c00272. Epub 2023 Nov 15. (Abstract)
Continue reading →Qing Cao, Zhenyu Hao, Cheng Li, Xuejie Chen, Meng Gao, Nan Jiang, Hongli Liu, Yan Shen, Haiping Yang, Shujuan Zhang, Aiying Yang, Weikai Li, Jian-Ke Tie & Guomin Shen (2023). “Molecular basis of inherited protein C deficiency results from genetic variations in the signal peptide and propeptide regions” J Thromb Haemost. 2023 Nov;21(11):3124-3137. doi: 10.1016/j.jtha.2023.06.021. Epub 2023 Jun 29. (Abstract)
Continue reading →Vishnu C Damalanka, Victoria Banas, Paolo De Bona, Maithri M Kashipathy, Kevin Battaile, Scott Lovell, James W Janetka (2024). “Mechanism-Based Macrocyclic Inhibitors of Serine Proteases” J Med Chem. 2024 Mar 28;67(6):4833-4854. doi: 10.1021/acs.jmedchem.3c02388. Epub 2024 Mar 13. (Abstract)
Continue reading →Robert Obermann, Bereket Yemane, Cassie Jarvis, Francisco M Franco, Yevhenii Kyriukha, William Nolan, Beth Gohara, Andrzej M Krezel, Scott A Wildman & James W Janetka (2024). “Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction” ChemMedChem. 2024 Apr 16;19(8):e202300648. doi: 10.1002/cmdc.202300648. Epub 2024 Mar 5. (Abstract)
Continue reading →Adrianus C M Boon, Traci L Bricker, Ethan J Fritch, Sarah R Leist, Kendra Gully, Ralph S Baric, Rachel L Graham, Brigid V Troan, Matthew Mahoney & James W Janetka (2024). “Efficacy of Host Cell Serine Protease Inhibitor MM3122 against SARS-CoV-2 for Treatment and Prevention of COVID-19” J Virol.2024 May 14;98(5):e0190323. doi: 10.1128/jvi.01903-23. Epub 2024 Apr 9. (Abstract)
Continue reading →Amarendar Reddy Maddirala, Kevin Tamadonfar, Jerome S Pinkner, Denise Sanick, Scott J Hultgren & James W Janetka (2024). “Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections” J Med Chem. 2024 Mar 14;67(5):3668-3678. doi: 10.1021/acs.jmedchem.3c02128. Epub 2024 Feb 3. (Abstract)
Continue reading →Alpha Raj Mekapogu, Zhihong Xu, Srinivasa Pothula, Chamini Perera, Tony Pang, S M Zahid Hosen, Vishnu Damalanka, James Janetka, David Goldstein, Romano Pirola, Jeremy Wilson & Minoti Apte (2023). “HGF/c-Met pathway inhibition combined with chemotherapy increases cytotoxic T-cell infiltration and inhibits pancreatic tumour growth and metastasis” Cancer Lett. 2023 Aug 1:568:216286. doi: 10.1016/j.canlet.2023.216286. Epub 2023 Jun 22. (Abstract)
Continue reading →Denis Belitškin, Pauliina Munne, Shishir M Pant, Johanna M Anttila, Ilida Suleymanova, Kati Belitškina, Daniel Kirchhofer, James Janetka, Taivo Käsper, Sami Jalil, Jeroen Pouwels, Topi A Tervonen & Juha Klefström (2024). “Hepsin promotes breast tumor growth signaling via the TGFβ-EGFR axis” Mol Oncol. 2024 Mar;18(3):547-561. doi: 10.1002/1878-0261.13545. Epub 2023 Nov 13. (Abstract)
Continue reading →Vivian Truong Jones, Ramona Graves-Deal, Zheng Cao, Galina Bogatcheva, Marisol A Ramirez, Sarah J Harmych, James N Higginbotham, Vineeta Sharma, Vishnu C Damalanka, Claudia C Wahoski, Neeraj Joshi, Maria Johnson Irudayam, Joseph T Roland, Gregory D Ayers, Qi Liu, Robert J Coffey, James W Janetka & Bhuminder Singh (2024). “Inhibition of autocrine HGF maturation overcomes cetuximab resistance in colorectal cancer” Cell Mol Life Sci. 2024 Jan 12;81(1):28. doi: 10.1007/s00018-023-05071-5. (Abstract)
Continue reading →Whitney R Grither, Breanna Baker, Vasilios A Morikis, Ma Xenia G Ilagan, Katherine C Fuh, & Gregory D Longmore (2024). “ROR2/Wnt5a Signaling Regulates Directional Cell Migration and Early Tumor Cell Invasion in Ovarian Cancer” Mol Cancer Res. 2024 May 2;22(5):495-507. doi: 10.1158/1541-7786.MCR-23-0616. (Abstract)
Continue reading →Sofia V Salvatore, Ma Xenia G Ilagan, Hongjin Shu, Peter M Lambert, Ann Benz, Mingxing Qian, Douglas F Covey, Charles F Zorumski, & Steven Mennerick (2024). “Neuroactive steroid effects on autophagy in a human embryonic kidney 293 (HEK) cell model” Sci Rep. 2024 Jan 10;14(1):1042. doi: 10.1038/s41598-024-51582-x. (Abstract)
Continue reading →Ankit Garg, Silvia Jansen, Rui Zhang, Kory J Lavine, & Michael J Greenberg (2024). “Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility” bioRxiv [Preprint]. 2024 Mar 12:2024.03.10.583979. doi: 10.1101/2024.03.10.583979 (Abstract)
Continue reading →Ankit Garg, Kory J Lavine, & Michael J Greenberg (2024). “Assessing Cardiac Contractility From Single Molecules to Whole Hearts” JACC Basic Transl Sci. 2023 Oct 11;9(3):414-439. doi: 10.1016/j.jacbts.2023.07.013. eCollection 2024 Mar. (Abstract)
Continue reading →Gretchen A Meyer, Jeremie L A Ferey, James A Sanford, Liam S Fitzgerald, Akiva E Greenberg, Kristoffer Svensson, Michael J Greenberg, & Simon Schenk (2024). “Insights into post-translational regulation of skeletal muscle contractile function by the acetyltransferases, p300 and CBP” bioRxiv [Preprint]. 2024 Feb 29:2024.02.27.582179. doi: 10.1101/2024.02.27.582179. (Abstract)
Continue reading →Shahnaz Ghahremani, Aditya Kanwal, Anthony Pettinato, Feria Ladha, Nicholas Legere, Ketan Thakar, Yanfen Zhu, Harianto Tjong, Andrea Wilderman, W Tom Stump, Lina Greenberg, Michael J Greenberg, Justin Cotney, Chia-Lin Wei, & J Travis Hinson (2024). “CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants” Circulation. 2024 Apr 16;149(16):1285-1297. doi: 10.1161/CIRCULATIONAHA.123.063972. Epub 2024 Jan 18. (Abstract)
Continue reading →Brent Scott & Michael J Greenberg (2023). “Multiscale biophysical models of cardiomyopathies reveal complexities challenging existing dogmas” Biophys J. 2023 Dec 19;122(24):4632-4634. doi: 10.1016/j.bpj.2023.11.014. Epub 2023 Nov 25. (Abstract)
Continue reading →Mor Varon, Daniel Dovrat, Jonathan Heuzé, Ioannis Tsirkas, Saurabh P Singh, Philippe Pasero, Roberto Galletto, & Amir Aharoni (2024). “Rrm3 and Pif1 division of labor during replication through leading and lagging strand G-quadruplex” Nucleic Acids Res. 2024 Feb 28;52(4):1753-1762. doi: 10.1093/nar/gkad1205. (Abstract)
Continue reading →Ankita Chadda, Alexander G Kozlov, Binh Nguyen, Timothy M Lohman, & Eric A Galburt (2024). “Mycobacterium tuberculosis Ku Stimulates Multi-round DNA Unwinding by UvrD1 Monomers” J Mol Biol. 2024 Jan 15;436(2):168367. doi: 10.1016/j.jmb.2023.168367. Epub 2023 Nov 14. (Abstract)
Continue reading →Drake Jensen, Ana Ruiz Manzano, Maxwell Rector, Eric J Tomko, M Thomas Record, & Eric A Galburt (2023). “High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase” J Cell Biol. 2024 Jan 1;223(1):e202312031. doi: 10.1083/jcb.202312031. Epub 2023 Dec 12. (Abstract)
Continue reading →John A Cooper (2024). “Capping protein regulators of actin assembly in budding yeast” J Cell Biol. 2024 Jan 1;223(1):e202312031. doi: 10.1083/jcb.202312031. Epub 2023 Dec 12. (Abstract)
Continue reading →Olivia L Mooren, Melissa D Stuchell-Brereton, Patrick McConnell, Chenbo Yan, Emily M Wilkerson, Dennis Goldfarb, John A Cooper, David Sept, & Andrea Soranno (2023). “Biophysical Mechanism of Allosteric Regulation of Actin Capping Protein” J Mol Biol. 2023 Dec 15;435(24):168342. doi: 10.1016/j.jmb.2023.168342. Epub 2023 Nov 2. (Abstract)
Continue reading →Richard Lauman, Hee Jong Kim, Lindsay K Pino, Alessandro Scacchetti, Yixuan Xie, Faith Robison, Simone Sidoli, Roberto Bonasio & Benjamin A Garcia (2023). “Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography” Anal Chem. 2023 Mar 28;95(12):5187-5195. doi: 10.1021/acs.analchem.2c04114. Epub 2023 Mar 14. (Abstract)
Continue reading →Josue Baeza, Barbara E. Coons, Zongtao Lin, John Riley, Mariel Mendoza, William H. Peranteau & Benjamin A Garcia (2024). “In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development” Cell Rep Methods. 2024 Feb 26;4(2):100713. doi: 10.1016/j.crmeth.2024.100713. (Abstract)
Continue reading →Richard M Searfoss, Rashmi Karki, Zongtao Lin, Faith Robison & Benjamin A Garcia (2023). “An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications” J Am Soc Mass Spectrom. 2023 Nov 1;34(11):2508-2517. doi: 10.1021/jasms.3c00223. Epub 2023 Oct 18. (Abstract)
Continue reading →Yixuan Xie, Francisca N. De Luna Vitorino, Ye Chen, Joanna K. Lempiäinen, Chenfeng Zhao, Robert T. Steinbock, Zongtao Lin, Xingyu Liu, Emily Zahn, Arabella L. Garcia, Matthew D. Weitzmancd & Benjamin A Garcia (2023). “SWAMNA: a comprehensive platform for analysis of nucleic acid modifications” Chem Commun. 2023, 59(83):12499-12502. (Abstract)
Continue reading →Evelyn Ploetz, Benjamin Ambrose, Anders Barth, Richard Börner, Felix Erichson, Achillefs N. Kapanidis, Harold D. Kim, Marcia Levitus, Timothy M. Lohman, Abhishek Mazumder, David S. Rueda, Fabio D. Steffen, Thorben Cordes, Steven W. Magennis, & Eitan Lerner (2023). “A new twist on PIFE: photoisomerisation-related fluorescence enhancement” ArXiv. 2023 Jul 10;arXiv:2302.12455v2. (Abstract)
Continue reading →Min Kyung Shinn, Sumit K. Chaturvedi, Alexander G. Kozlov, & Timothy M. Lohman (2023). “Allosteric effects of E. coli SSB and RecR proteins on RecO protein binding to DNA” Nucleic Acids Res. 2023 Mar 21;51(5):2284-2297. doi: 10.1093/nar/gkad084. (Abstract)
Continue reading →Zev J. Greenberg, Darlene Monlish, Luana Chiquetto Paracatu, Qian Dong, Michael P. Rettig, Nate Dee Roundy, Rofaida Gaballa, Weikai Li, Wei Yang, Cliff J. Luke, & Laura Schuettpelz (2022). “The tetraspanin CD53 protects stressed hematopoietic stem cells via promotion of DREAM complex- mediated quiescence” Blood. 2022 Dec 21;blood.2022016929. doi: 10.1182/blood.2022016929. Online ahead of print. (Abstract)
Continue reading →Peder J Lund, Leah A Gates, Marylene Leboeuf, Sarah A Smith, Lillian Chau, Mariana Lopes, Elliot S Friedman, Yedidya Saiman, Min Soo Kim, Clarissa A Shoffler, Christopher Petucci, C David Allis, Gary D Wu & Benjamin A Garcia (2022). “Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation” Cell Rep. 2022 Dec 13;41(11):111809. doi: 10.1016/j.celrep.2022.111809. (Abstract)
Continue reading →Garrett M. Ginell & Alex S. Holehouse (2022). “An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates” Methods Mol Biol. 2023;2563:95-116. doi: 10.1007/978-1-0716-2663-4_4. (Abstract)
Continue reading →Nicolás S. González-Foutel, Juliana Glavina, Wade M. Borcherds, Matías Safranchik, Susana Barrera-Vilarmau, Amin Sagar, Alejandro Estaña, Amelie Barozet, Nicolás A. Garrone, Gregorio Fernandez-Ballester, Clara Blanes-Mira, Ignacio E. Sánchez, Gonzalo de Prat-Gay, Juan Cortés, Pau Bernadó, Rohit V. Pappu, Alex S. Holehouse, Gary W. Daughdrill, & Lucía B. Chemes (2022). “Conformational buffering underlies functional selection in intrinsically disordered protein regions” Nat Struct Mol Biol. 2022 Aug;29(8):781-790. doi: 10.1038/s41594-022-00811-w. Epub 2022 Aug 10. (Abstract)
Continue reading →Liana Beld, Hyeim Jung, Christina A. Bulman, Bruce A. Rosa, Peter U. Fischer, James W. Janetka, Sara Lustigman, Judy A. Sakanari, and Makedonka Mitreva (2022). “Aspartyl Protease Inhibitors as Anti-Filarial Drugs” Pathogens. 2022 Jun 18;11(6):707. doi: 10.3390/pathogens11060707. (Abstract)
Continue reading →Yixuan Xie, Kevin A Janssen, Alessandro Scacchetti, Elizabeth G Porter, Zongtao Lin, Roberto Bonasio & Benjamin A Garcia (2022). “Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications” Anal Chem. 2022 May 24;94(20):7246-7254. doi: 10.1021/acs.analchem.2c00471. Epub 2022 May 12. (Abstract)
Continue reading →Alexander G. Kozlov, Xian Cheng, Hongshan Zhang, Min Kyung Shinn, Elizabeth Weiland, Binh Nguyen, Irina A. Shkel, Emily Zytkiewicz, Ilya J. Finkelstein, M. Thomas Record Jr., & Timothy M. Lohman (2022). “How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein” J Mol Biol. 2022 Mar 26;434(9):167562. doi: 10.1016/j.jmb.2022.167562. Online ahead of print.
Continue reading →Jie Sun, Weikai Li, & Michael L. Gross (2022). “Advances in mass spectrometry-based footprinting of membrane proteins” Proteomics. 2022 Apr;22(8):e2100222. doi: 10.1002/pmic.202100222. (Abstract)
Continue reading →Upasana L. Mallimadugula & Eric A. Galburt (2022). “Parallel path mechanisms lead to nonmonotonic force-velocity curves and an optimum load for molecular motor function” Phys Rev E. 2022 Mar;105(3-1):034405. doi: 10.1103/PhysRevE.105.034405. (Abstract)
Continue reading →Shixuan Liu, Shuang Li, Andrzej M. Krezel, & Weikai Li (2022). “Stabilization and structure determination of integral membrane proteins by termini restraining” Nat Protoc. 2022 Jan 17. doi: 10.1038/s41596-021-00656-5. Online ahead of print. (Abstract)
Continue reading →Jie Sun, Xiaoran Roger Liu, Shuang Li, Peng He, Weikai Li, & Michael L. Gross (2021). “Nanoparticles and photochemistry for native-like transmembrane protein footprinting” Nat Commun. 2021 Dec 14;12(1):7270. doi: 10.1038/s41467-021-27588-8. (Abstract)
Continue reading →Vishnu C. Damalanka, Jorine J. L. P. Voss, Matthew W. Mahoney, Tina Primeau, Shunqiang Li, Lidija Klampfer, & James W. Janetka (2021). “Macrocyclic Inhibitors of HGF-Activating Serine Proteases Overcome Resistance to Receptor Tyrosine Kinase Inhibitors and Block Lung Cancer Progression” J Med Chem. 2021 Dec 13. doi: 10.1021/acs.jmedchem.1c01671. Online ahead of print. (Abstract)
Continue reading →Maya Topf, Edina Rosta, Gregory R. Bowman, & Massimiliano Bonomi (2021). “Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function” Front Mol Biosci. 2021 Nov 29;8:799406. doi: 10.3389/fmolb.2021.799406. eCollection 2021. (Abstract)
Continue reading →Matthew Mahoney, Vishnu C. Damalanka, Michael A. Tartell, Dong Hee Chung, André Luiz Lourenco, Dustin Pwee, Anne E. Mayer Bridwell, Markus Hoffmann, Jorine Voss, Partha Karmakar, Nurit Azouz, Andrea M. Klingler, Paul W. Rothlauf, Cassandra E. Thompson, Melody Lee, Lidija Klampfer, Christina Stallings, Marc E. Rothenberg, Stefan Pöhlmann, Sean P. Whelan, Anthony J. O’Donoghue, Charles S. Craik, & James W. Janetka (2021). “A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells” Proc Natl Acad Sci U S A. 2021 Oct 26;118(43):e2108728118. doi: 10.1073/pnas.2108728118. (Abstract)
Continue reading →Samantha K. Barrick & Michael J. Greenberg (2021). “Cardiac myosin contraction and mechanotransduction in health and disease” J Biol Chem. 2021 Nov;297(5):101297. doi: 10.1016/j.jbc.2021.101297. Epub 2021 Oct 9. (Abstract)
Continue reading →Benjamin C. Stark, Yuanyuan Gao, Diane S. Sepich, Lakyn Belk, Matthew A. Culver, Bo Hu, Marlene Mekel, Wyndham Ferris, Jimann Shin, Lilianna Solnica-Krezel, Fang Lin, & John A. Cooper (2021). “CARMIL3 is important for cell migration and morphogenesis during early development in zebrafish” Dev Biol. 2022 Jan;481:148-159. doi: 10.1016/j.ydbio.2021.09.008. Epub 2021 Sep 30. (Abstract)
Continue reading →Chia-Chen Liu, Melissa E. Murray, Xia Li, Na Zhao, Na Wang, Michael G. Heckman, Francis Shue, Yuka Martens, Yonghe Li, Ana-Caroline Raulin, Cassandra L. Rosenberg, Sydney V. Doss, Jing Zhao, Melissa C. Wren, Lin Jia, Yingxue Ren, Tadafumi C. Ikezu, Wenyan Lu, Yuan Fu, Thomas Caulfield, Zachary A. Trottier, Joshua Knight, Yixing Chen, Cynthia Linares, Xue Wang, Aishe Kurti, Yan W. Asmann, Zbigniew K. Wszolek, Glenn E. Smith, Prashanthi Vemuri, Kejal Kantarci, David S. Knopman, Val J. Lowe, Clifford R. Jack Jr., Joseph E. Parisi, Tanis J. Ferman, Bradley F. Boeve, Neill R. Graff-Radford, Ronald C. Petersen, Steven G. Younkin, John D. Fryer, Hu Wang, Xianlin Han, Carl Frieden, Dennis W. Dickson, Owen A. Ross, & Guojun Bu (2021). “APOE3-Jacksonville (V236E) variant reduces self-aggregation and risk of dementia” Sci Transl Med. 2021 Sep 29;13(613):eabc9375. doi: 10.1126/scitranslmed.abc9375. Epub 2021 Sep 29. (Abstract)
Continue reading →Daniel Griffith & Alex S. Holehouse (2021). “PARROT is a flexible recurrent neural network framework for analysis of large protein datasets” Elife. 2021 Sep 17;10:e70576. doi: 10.7554/eLife.70576. (Abstract)
Continue reading →Nicole R. Wong, Jay Mohan, Benjamin J. Kopecky, Shuchi Guo, Lixia Du, Jamison Leid, Guoshuai Feng, Inessa Lokshina, Oleksandr Dmytrenko, Hannah Luehmann, Geetika Bajpai, Laura Ewald, Lauren Bell, Nikhil Patel, Andrea Bredemeyer, Carla J. Weinheimer, Jessica M. Nigro, Attila Kovacs, Sachio Morimoto, Peter O. Bayguinov, Max R. Fisher, W. Tom Stump, Michael Greenberg, James A. J. Fitzpatrick, Slava Epelman, Daniel Kreisel, Rajan Sah, Yongjian Liu, Hongzhen Hu, & Kory J. Lavine (2021). “Resident cardiac macrophages mediate adaptive myocardial remodeling” Immunity. 2021 Sep 14;54(9):2072-2088.e7. doi: 10.1016/j.immuni.2021.07.003. Epub 2021 Jul 27. (Abstract)
Continue reading →Hema Adhikari, Walaa E. Kattan, Shivesh Kumar, Pei Zhou, John F. Hancock, & Christopher M. Counter (2021). “Oncogenic KRAS is dependent upon an EFR3A-PI4KA signaling axis for potent tumorigenic activity” Nat Commun. 2021 Sep 9;12(1):5248. doi: 10.1038/s41467-021-25523-5. (Abstract)
Continue reading →Ishan Taneja & Alex S. Holehouse (2021). “Folded domain charge properties influence the conformational behavior of disordered tails” Curr Res Struct Biol. 2021 Sep 7;3:216-228. doi: 10.1016/j.crstbi.2021.08.002. eCollection 2021. (Abstract)
Continue reading →Linxuan Hao, Rui Zhang, & Timothy M. Lohman (2021). “Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting” J Mol Biol. 2021 Sep 3;433(18):167147. doi: 10.1016/j.jmb.2021.167147. Epub 2021 Jul 9. (Abstract)
Continue reading →Maria Papadaki, Theerachat Kampaengsri, Samantha K. Barrick, Stuart G. Campbell, Dirk von Lewinski, Peter P. Rainer, Samantha P. Harris, Michael J. Greenberg, & Jonathan A. Kirk (2021). “Myofilament glycation in diabetes reduces contractility by inhibiting tropomyosin movement, is rescued by cMyBPC domains” J Mol Cell Cardiol. 2021 Sep 3;162:1-9. doi: 10.1016/j.yjmcc.2021.08.012. Online ahead of print. (Abstract)
Continue reading →Ryan J. Emenecker, Daniel Griffith, & Alex S. Holehouse (2021). “Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure” Biophys J. 2021 Sep 2;S0006-3495(21)00725-6. doi: 10.1016/j.bpj.2021.08.039. Online ahead of print. (Abstract)
Continue reading →Fengbo Zhou, Yihu Yang, Saketh Chemuru, Weidong Cui, Shixuan Liu, Michael Gross, & Weikai Li (2021). “Footprinting Mass Spectrometry of Membrane Proteins: Ferroportin Reconstituted in Saposin A Picodiscs” Anal Chem. 2021 Aug 24;93(33):11370-11378. doi: 10.1021/acs.analchem.1c02325. Epub 2021 Aug 12. (Abstract)
Continue reading →Yanniv Dorone, Steven Boeynaems, Eduardo Flores, Benjamin Jin, Shannon Hateley, Flavia Bossi, Elena Lazarus, Janice G. Pennington, Emiel Michiels, Mathias De Decker, Katlijn Vints, Pieter Baatsen, George W. Bassel, Marisa S. Otegui, Alex S. Holehouse, Moises Exposito-Alonso, Shahar Sukenik, Aaron D. Gitler, Seung Y. Rhee (2021). “A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation” Cell. 2021 Aug 5;184(16):4284-4298.e27. doi: 10.1016/j.cell.2021.06.009. Epub 2021 Jul 6. (Abstract)
Continue reading →Neha Vithani, Michael D. Ward, Maxwell I. Zimmerman, Borna Novak, Jonathan H. Borowsky, Sukrit Singh, & Gregory R. Bowman (2021). “SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential” Biophys J. 2021 Jul 20;120(14):2880-2889. doi: 10.1016/j.bpj.2021.03.024. Epub 2021 Mar 29. (Abstract)
Continue reading →Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, & Gregory R. Bowman (2021). “SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome” Nat Chem. 2021 Jul;13(7):651-659. doi: 10.1038/s41557-021-00707-0. Epub 2021 May 24. (Abstract)
Continue reading →Shubhanjali Minhas & Alex S. Holehouse (2021). “Step on the cGAS! Viral inhibition of cGAS phase separation with cytosolic DNA” Mol Cell. 2021 Jul 1;81(13):2688-2689. doi: 10.1016/j.molcel.2021.06.007. (Abstract)
Continue reading →Samantha K. Barrick, Lina Greenberg, & Michael J. Greenberg (2021). “A Troponin T Variant Linked with Pediatric Dilated Cardiomyopathy Reduces the Coupling of Thin Filament Activation to Myosin and Calcium Binding” Mol Biol Cell. 2021 Jun 23;mbcE21020082. doi: 10.1091/mbc.E21-02-0082. Online ahead of print. (Abstract)
Continue reading →Elias A. Tannous & Peter M. Burgers (2021). “Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)” Crit Rev Biochem Mol Biol. 2021 Jun 20;1-14. doi: 10.1080/10409238.2021.1925218. Online ahead of print. (Abstract)
Continue reading →George R. Heath, Ekaterina Kots, Janice L. Robertson, Shifra Lansky, George Khelashvili, Harel Weinstein, & Simon Scheuring (2021). “Localization atomic force microscopy” Nature. 2021 Jun;594(7863):385-390. doi: 10.1038/s41586-021-03551-x. Epub 2021 Jun 16. (Abstract)
Continue reading →Melanie Ernst & Janice L. Robertson (2021). “The Role of the Membrane in Transporter Folding and Activity” J Mol Biol. 2021 Jun 15;167103. doi: 10.1016/j.jmb.2021.167103. Online ahead of print.
Continue reading →Mattia Bernetti, Kathleen B. Hall, & Giovanni Bussi (2021). “Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles” Nucleic Acids Res. 2021 Jun 9;gkab459. doi: 10.1093/nar/gkab459. Online ahead of print. (Abstract)
Continue reading →Ryan J. Emenecker, Alex S. Holehouse, & Lucia C. Strader (2021). “Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis” Cell Commun Signal. 2021 Jun 5;19(1):65. doi: 10.1186/s12964-021-00744-9. (Abstract)
Continue reading →Denis A. Kiktev, Margaret Dominska, Tony Zhang, Joseph Dahl, Elena I. Stepchenkova, Piotr Mieczkowski, Peter M. Burgers, Scott Lujan, Adam Burkholder, Thomas A. Kunkel, & Thomas D. Petes (2021). “The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ” Nucleic Acids Res. 2021 Jun 4;49(10):5623-5636. doi: 10.1093/nar/gkab371. (Abstract)
Continue reading →Binh Nguyen, Min Kyung Shinn, Elizabeth Weiland, & Timothy M. Lohman (2021). “Regulation of E. coli Rep helicase activity by PriC” J Mol Biol. 2021 Jun 1;433(15):167072. doi: 10.1016/j.jmb.2021.167072. Online ahead of print. (Abstract)
Continue reading →E. Sethe Burgie, Zachary T. K. Gannam, Katrice E. McLoughlin, Christopher D. Sherman, Alex S. Holehouse, Robert J. Stankey, & Richard D. Vierstra (2021). “Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families” Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2105649118. doi: 10.1073/pnas.2105649118. (Abstract)
Continue reading →Xiangli Wang, Yong Fu, Wandy L. Beatty, Meisheng Ma, Alan Brown, L. David Sibley, & Rui Zhang (2021). “Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins” Nat Commun. 2021 May 24;12(1):3065. doi: 10.1038/s41467-021-23351-1. (Abstract)
Continue reading →Michael D. Ward, Maxwell I. Zimmerman, Artur Meller, Moses Chung, S. J. Swamidass, & Gregory R. Bowman (2021). “Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets” Nat Commun. 2021 May 21;12(1):3023. doi: 10.1038/s41467-021-23246-1. (Abstract)
Continue reading →Sarah R. Clippinger, Paige E. Cloonan, Wei Wang, Lina Greenberg, W. Tom Stump, Paweorn Angsutararux, Jeanne M. Nerbonne, & Michael J. Greenberg (2021). “Mechanical dysfunction of the sarcomere induced by a pathogenic mutation in troponin T drives cellular adaptation” J Gen Physiol. 2021 May 3;153(5):e202012787. doi: 10.1085/jgp.202012787. (Abstract)
Continue reading →Alexander G. Kozlov & Timothy M. Lohman (2021). “Probing E. coli SSB Protein-DNA topology by reversing DNA backbone polarity” Biophys J. 2021 Apr 20;120(8):1522-1533. doi: 10.1016/j.bpj.2021.02.025. Epub 2021 Feb 23. (Abstract)
Continue reading →Rahul Chadda, Nathan Bernhardt, Elizabeth G. Kelley, Susana Cm. Teixeira, Kacie Griffith, Alejandro Gil-Ley, Tuğba N. Öztürk, Lauren E. Hughes, Ana Forsythe, Venkatramanan Krishnamani, José D. Faraldo-Gómez, & Janice L. Robertson (2021). “Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states” Elife. 2021 Apr 7;10:e63288. doi: 10.7554/eLife.63288. (Abstract)
Continue reading →Jasmine Cubuk, Jhullian J. Alston, J. Jeremías Incicco, Sukrit Singh, Melissa D. Stuchell-Brereton, Michael D. Ward, Maxwell I. Zimmerman, Neha Vithani, Daniel Griffith, Jason A. Wagoner, Gregory R. Bowman, Kathleen B. Hall, Andrea Soranno, & Alex S. Holehouse. (2021). “The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA” Nat Commun. 2021 Mar 29;12(1):1936. doi: 10.1038/s41467-021-21953-3. (Abstract)
Continue reading →Drake Jensen & Eric A. Galburt (2021). “The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation” J Bacteriol. 2021 Mar 23;203(8):e00512-20. doi: 10.1128/JB.00512-20. Print 2021 Mar 23. (Abstract)
Continue reading →Ming Cheng, Chunyang Guo, Weikai Li, & Michael L. Gross (2021). “Free-Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication” Angew Chem Int Ed Engl. 2021 Mar 10. doi: 10.1002/anie.202014096. Online ahead of print. (Abstract)
Continue reading →Weikai Li (2021). “Targeting multiple enzymes in vitamin K metabolism for anticoagulation” J Thromb Haemost. 2021 Mar;19(3):633-636. doi: 10.1111/jth.15212. (Abstract)
Continue reading →Michael J. Greenberg & Jil C. Tardiff (2021). “Complexity in genetic cardiomyopathies and new approaches for mechanism-based precision medicine” J Gen Physiol. 2021 Mar 1;153(3):e202012662. doi: 10.1085/jgp.202012662. (Abstract)
Continue reading →Adam L. Bailey, Oleksandr Dmytrenko, Lina Greenberg, Andrea L. Bredemeyer, Pan Ma, Jing Liu, Vinay Penna, Lulu Lai, Emma S. Winkler, Sanja Sviben, Erin Brooks, Ajith P. Nair, Kent A. Heck, Aniket S. Rali, Leo Simpson, Mehrdad Saririan, Dan Hobohm, W. Tom Stump, James A. Fitzpatrick, Xuping Xie, Pei-Yong Shi, J. Travis Hinson, Weng-Tein Gi, Constanze Schmidt, Florian Leuschner, Chieh-Yu Lin, Michael S. Diamond, Michael J. Greenberg, & Kory J. Lavine (2021). “SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis” JACC Basic Transl Sci. 2021 Feb 26. doi: 10.1016/j.jacbts.2021.01.002. Online ahead of print. (Abstract)
Continue reading →Min Kyung Shinn, Alexander G. Kozlov, & Timothy M. Lohman (2021). “Allosteric effects of SSB C-terminal tail on assembly of E. coli RecOR proteins” Nucleic Acids Res. 2021 Feb 26;49(4):1987-2004. doi: 10.1093/nar/gkaa1291. (Abstract)
Continue reading →Kacey Mersch, Tugba N. Ozturk, Kunwoong Park, Hyun-Ho Lim, & Janice L. Robertson (2021). “Altering CLC stoichiometry by reducing non-polar side-chains at the dimerization interface” J Mol Biol. 2021 Feb 20;433(8):166886. doi: 10.1016/j.jmb.2021.166886. Online ahead of print. (Abstract)
Continue reading →Michael D. Onken, Carol M. Makepeace, Kevin M. Kaltenbronn, Joelle Choi, Leonel Hernandez-Aya, Katherine N. Weilbaecher, Kisha D. Piggott, P. Kumar Rao, Carla M. Yuede, Alethia J. Dixon, Patrick Osei-Owusu, John A. Cooper, & Kendall J. Blumer (2021). “Targeting primary and metastatic uveal melanoma with a G protein inhibitor” J Biol Chem. 2021 Feb 9;100403. doi: 10.1016/j.jbc.2021.100403. Online ahead of print. (Abstract)
Continue reading →Lisa K. McLellan, Michael R. McAllaster, Arthur S. Kim, Ľubomíra Tóthová, Patrick D. Olson, Jerome S. Pinkner, Allyssa L. Daugherty, Teri N. Hreha, James W. Janetka, Daved H. Fremont, Scott J. Hultgren, Herbert W. Virgin, & David A Hunstad (2021). “A host receptor enables type 1 pilus-mediated pathogenesis of Escherichia coli pyelonephritis” PLoS Pathog. 2021 Jan 29;17(1):e1009314. doi: 10.1371/journal.ppat.1009314. eCollection 2021 Jan. (Abstract)
Continue reading →Elias A. Tannous, Luke A. Yates, Xiaodong Zhang, & Peter M. Burgers (2021). “Mechanism of auto-inhibition and activation of Mec1 ATR checkpoint kinase” Nat Struct Mol Biol. 2021 Jan;28(1):50-61. doi: 10.1038/s41594-020-00522-0. Epub 2020 Nov 9. (Abstract)
Continue reading →Jessica B. Behring, Sjoerd van der Post, Arshag D. Mooradian, Matthew J. Egan, Maxwell I. Zimmerman, Jenna L. Clements, Gregory R. Bowman, & Jason M. Held (2021). “Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation” Sci Signal. 2020 Jan 21;13(615):eaay7315. doi: 10.1126/scisignal.aay7315. (Abstract)
Continue reading →Wayne M. Barnes, Zhian Zhang, & Milko B. Kermekchiev (2021). “A Single Amino Acid Change to Taq DNA Polymerase Enables Faster PCR, Reverse Transcription and Strand-Displacement” Front. Bioeng. Biotechnol., 14 January 2021, doi: 10.3389/fbioe.2020.553474 (Abstract)
Continue reading →Rahul Tyagi, Christina A. Bulman, Fidelis Cho-Ngwa, Chelsea Fischer, Chris Marcellino, Michelle R. Arkin, James H. McKerrow, Case W. McNamara, Matthew Mahoney, Nancy Tricoche, Shabnam Jawahar, James W. Janetka, Sara Lustigman, Judy Sakanari, & Makedonka Mitreva (2021). “An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease” Pathogens. 2021 Jan 14;10(1):71. doi: 10.3390/pathogens10010071. (Abstract)
Continue reading →Michael D. Onken, Kendall J. Blumer, & John A. Cooper (2021). “Uveal melanoma cells use ameboid and mesenchymal mechanisms of cell motility crossing the endothelium” Mol Biol Cell. 2021 Jan 6;mbcE20040241. doi: 10.1091/mbc.E20-04-0241. Online ahead of print. (Abstract)
Continue reading →Thomas Blackwell, W. Tom Stump, Sarah R. Clippinger, & Michael J. Greenberg (2021). “Computational Tool for Ensemble Averaging of Single-Molecule Data” Biophys J. 2021 Jan 5;120(1):10-20. doi: 10.1016/j.bpj.2020.10.047. Epub 2020 Nov 26. (Abstract)
Continue reading →Shixuan Liu, Shuang Li, Guomin Shen, Narayanasami Sukumar, Andrzej M. Krezel, & Weikai Li (2021). “Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation” Science. 2021 Jan 1;371(6524):eabc5667. doi: 10.1126/science.abc5667. Epub 2020 Nov 5. (Abstract)
Continue reading →Vishnu C. Damalanka, Amarendar Reddy Maddirala, & James W. Janetka (2020). “Novel approaches to glycomimetic design: Development of small molecular weight lectin antagonists” Expert Opin Drug Discov. 2020 Dec 18. doi: 10.1080/17460441.2021.1857721. Online ahead of print. (Abstract)
Continue reading →Jesse G. Meyer, Natalie M. Niemi, David J. Pagliarini, & Joshua J. Coon (2020). “Quantitative shotgun proteome analysis by direct infusion” Nat Methods. 2020 Dec;17(12):1222-1228. doi: 10.1038/s41592-020-00999-z. Epub 2020 Nov 23. (Abstract)
Continue reading →Miao Gui, Meisheng Ma, Erica Sze-Tu, Xiangli Wang, Fujiet Koh, Ellen D. Zhong, Bonnie Berger, Joseph H. Davis, Susan K. Dutcher, Rui Zhang, & Alan Brown (2020). “Structures of radial spokes and associated complexes important for ciliary motility” Nat Struct Mol Biol. 2021 Jan;28(1):29-37. doi: 10.1038/s41594-020-00530-0. Epub 2020 Dec 14. (Abstract)
Continue reading →Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman, & Judith Klein-Seetharaman (2020). “Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 -human interactome” Pac Symp Biocomput. 2021;26:154-165. (Abstract)
Continue reading →Melanie A. Sparks, Peter M. Burgers, & Roberto Galletto (2020). “Pif1, RPA and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis” J Biol Chem. 2020 Nov 20;295(47):15883-15891. doi: 10.1074/jbc.RA120.015699. Epub 2020 Sep 10. (Abstract)
Continue reading →Joanna Kim & John A. Cooper (2020). “Junctional Localization of Septin 2 Is Required for Organization of Junctional Proteins in Static Endothelial Monolayers” Arterioscler Thromb Vasc Biol. 2020 Nov 5;ATVBAHA120315472. doi: 10.1161/ATVBAHA.120.315472. Online ahead of print. (Abstract)
Continue reading →Michael S. Kinch, Zachary Kraft, & Tyler Schwartz (2020). “Sources of innovation for new medicines: questions of sustainability” Drug Discov Today. 2020 Nov 2;S1359-6446(20)30443-8. doi: 10.1016/j.drudis.2020.10.026. Online ahead of print. (Abstract)
Continue reading →Daniel L. Kober, Melissa D. Stuchell-Brereton, Colin E. Kluender, Hunter B. Dean, Michael R. Strickland, Deborah F. Steinberg, Samantha S. Nelson, Berevan Baban, David M. Holtzman, Carl Frieden, Jennifer Alexander-Brett, Erik D. Roberson, Yuhua Song, & Tom J. Brett (2020). “Functional insights from biophysical study of TREM2 interactions with apoE and Aβ 1-42” Alzheimers Dement. 2020 Oct 8. doi: 10.1002/alz.12194. Online ahead of print. (Abstract)
Continue reading →James R. Riehl, Maxwell I. Zimmerman, Matthew F. Singh, Gregory R. Bowman, & ShiNung Ching (2020). “Computing and Optimizing Over All Fixed-Points of Discrete Systems on Large Networks” J R Soc Interface. 2020 Sep;17(170):20200126. doi: 10.1098/rsif.2020.0126. Epub 2020 Sep 9. (Abstract)
Continue reading →Kory J. Lavine & Michael J. Greenberg. (2020). “Beyond genomics-technological advances improving the molecular characterization and precision treatment of heart failure” Heart Fail Rev. 2020 Sep 3. doi: 10.1007/s10741-020-10021-5. Online ahead of print. (Abstract)
Continue reading →Mathivanan Chinnaraj, David A. Barrios, Carl Frieden, Tomasz Heyduk, Robert Flaumenhaft, & Nicola Pozzi. (2020). “Bioorthogonal Chemistry Enables Single-Molecule FRET Measurements of Catalytically Active Protein Disulfide Isomerase” Chembiochem. 2020 Aug 28. doi: 10.1002/cbic.202000537. Online ahead of print. (Abstract)
Continue reading →Weikai Li, Russell E. Bishop, & Filippo Mancia. (2020). “Integral Membrane Enzymes (2020)” J Mol Biol. 2020 Aug 21;432(18):4943-4945. doi: 10.1016/j.jmb.2020.07.022. Epub 2020 Jul 30. (Abstract)
Continue reading →Yihu Yang, Xiaoran Roger Liu, Zev J. Greenberg, Fengbo Zhou, Peng He, Lingling Fan, Shixuan Liu, Guomin Shen, Takeshi Egawa, Michael L. Gross, Laura G. Schuettpelz, & Weikai Li (2020). “Open conformation of tetraspanins shapes interaction partner networks on cell membranes” EMBO J (2020) e105246. 2020-08-16. doi: 10.15252/embj.2020105246. (Abstract)
Continue reading →Wenwen Gao, Yaqi Xu, Hongli Liu, Meng Gao, Qing Cao, Yiyi Wang, Longteng Cui, Rong Huang, Yan Shen, Sanqiang Li, Haiping Yang, Yixiang Chen, Chaokun Li, Haichuan Yu, Weikai Li, & Guomin Shen. (2020). “Characterization of missense mutations in the signal peptide and propeptide of FIX in hemophilia B by a cell-based assay” Blood Adv. 2020 Aug 11;4(15):3659-3667. doi: 10.1182/bloodadvances.2020002520. (Abstract)
Continue reading →Rachel Bezalel-Buch, Young K. Cheun, Upasana Roy, Orlando D. Schärer, & Peter M. Burgers (2020). “Bypass of DNA interstrand crosslinks by a Rev1-DNA polymerase ζ complex” Nucleic Acids Res. 2020 Jul 7;gkaa580. doi: 10.1093/nar/gkaa580. Online ahead of print. (Abstract)
Continue reading →Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, & Gregory R. Bowman (2020). “Citizen Scientists Create an Exascale Computer to Combat COVID-19” bioRxiv. 2020 Jun 28;2020.06.27.175430. doi: 10.1101/2020.06.27.175430. Preprint (Abstract)
Continue reading →Katarzyna Dubiel, Camille Henry, Lisanne M. Spenkelink, Alexander G. Kozlov, Elizabeth A. Wood, Slobodan Jergic, Nicholas E. Dixon, Antoine M. van Oijen, Michael M. Cox, Timothy M. Lohman, Steven J. Sandler, & James L. Keck (2020). “Development of a Single-Stranded DNA-binding Protein Fluorescent Fusion Toolbox” Nucleic Acids Res. 2020 Jun 19;48(11):6053-6067. doi: 10.1093/nar/gkaa320. (Abstract)
Continue reading →Shuang Li, Shixuan Liu, Xiaoran Roger Liu, Mengru Mira Zhang, and Weikai Li. (2020). “Competitive tight-binding inhibition of VKORC1 underlies warfarin dosage variation and antidotal efficacy” Blood Adv. 2020 May 26; 4(10): 2202–2212. Published online 2020 May 20. doi: 10.1182/bloodadvances.2020001750 (Abstract)
Continue reading →Jason D Fernandes, Sarvenaz Sarabipour, Christopher T Smith, Natalie M Niemi, Nafisa M Jadavji, Ariangela J Kozik, Alex S Holehouse, Vikas Pejaver, Orsolya Symmons, Alexandre W Bisson Filho, & Amanda Haage (2020). “A survey-based analysis of the academic job market” Elife. 2020 Jun 12;9:e54097. doi: 10.7554/eLife.54097. Online ahead of print. (Abstract)
Continue reading →Eliza A. Ruben, Prafull S. Gandhi, Zhiwei Chen, Sarah K. Koester, Gregory T. DeKoster, Carl Frieden, & Enrico Di Cera. (2020). “19 F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2” J Biol Chem. 2020 Jun 12;295(24):8227-8235. doi: 10.1074/jbc.RA120.013419. Epub 2020 May 1. (Abstract)
Continue reading →James W Janetka, Allen T Hopper, Ziping Yang, Jennifer Barks, Mary Savari Dhason, Qiuling Wang, & L David Sibley (2020). “Optimizing Pyrazolopyrimidine Inhibitors of Calcium Dependent Protein Kinase 1 for Treatment of Acute and Chronic Toxoplasmosis” J Med Chem. 2020 Jun 11;63(11):6144-6163. doi: 10.1021/acs.jmedchem.0c00419. Epub 2020 Jun 1. (Abstract)
Continue reading →Justin R. Porter, Artur Meller, Maxwell I. Zimmerman, Michael J. Greenberg, & Gregory R. Bowman (2020). “Conformational Distributions of Isolated Myosin Motor Domains Encode Their Mechanochemical Properties” Elife. 2020 May 29;9:e55132. doi: 10.7554/eLife.55132. (Abstract)
Continue reading →Shuang Li, Shixuan Liu, Yihu Yang, & Weikai Li (2020). “Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases” J Mol Biol. 2020 May 20;S0022-2836(20)30350-8. doi: 10.1016/j.jmb.2020.05.009. Online ahead of print. (Abstract)
Continue reading →James Brett Case, Paul W Rothlauf, Rita E Chen, Zhuoming Liu, Haiyan Zhao, Arthur S Kim, Louis-Marie Bloyet, Qiru Zeng, Stephen Tahan, Lindsay Droit, Ma Xenia G Ilagan, Michael A Tartell, Gaya Amarasinghe, Jeffrey P Henderson, Shane Miersch, Mart Ustav, Sachdev Sidhu, Herbert W Virgin, David Wang, Siyuan Ding, Davide Corti, Elitza S Theel, Daved H Fremont, Michael S Diamond, & Sean P J Whelan (2020). “Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2” bioRxiv. 2020 May 18;2020.05.18.102038. doi: 10.1101/2020.05.18.102038. Preprint (Abstract)
Continue reading →John T. Petroff 2nd, Ailing Tong, Lawrence J. Chen, Gregory T. Dekoster, Farha Khan, Jeff Abramson, Carl Frieden, & Wayland W. L. Cheng (2020). “Charge Reduction of Membrane Proteins in Native Mass Spectrometry Using Alkali Metal Acetate Salts” Anal Chem. 2020 May 5;92(9):6622-6630. doi: 10.1021/acs.analchem.0c00454. Epub 2020 Apr 14. (Abstract)
Continue reading →Brown C.A., Hu L., Sun Z., Patel M.P., Singh S., Porter J.R., Sankaran B., Prasad B.V.V., Bowman G.R., & Palzkill T. (2020). “Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance.” J Biol Chem. 2020 Apr 16. pii: jbc.RA119.012489. doi: 10.1074/jbc.RA119.012489. [Epub ahead of print] (Abstract)
Continue reading →Patrick McConnell, Marlene Mekel, Alex G. Kozlov, Olivia L. Mooren, Timothy M. Lohman, & John A. Cooper (2020). “Comparative Analysis of CPI-Motif Regulation of Biochemical Functions of Actin Capping Protein” Biochemistry. 2020 Mar 24;59(11):1202-1215. doi: 10.1021/acs.biochem.0c00092. Epub 2020 Mar 10. (Abstract)
Continue reading →Holehouse A.S. & Sukenik S. (2020). “Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning.” J Chem Theory Comput. 2020 Mar 10;16(3):1794-1805. doi: 10.1021/acs.jctc.9b00604. Epub 2020 Feb 17. (Abstract)
Continue reading →Hohl M., Mojumdar A., Hailemariam S., Kuryavyi V., Ghisays F., Sorenson K., Chang M., Taylor B.S., Patel D.J., Burgers P.M., Cobb J.A., & Petrini J.H.J. (2020). “Modeling cancer genomic data in yeast reveals selection against ATM function during tumorigenesis.” PLoS Genet. 2020 Mar 18;16(3):e1008422. doi: 10.1371/journal.pgen.1008422. [Epub ahead of print] (Abstract)
Continue reading →Antonija Kuzmanic, Gregory R. Bowman, Jordi Juarez-Jimenez, Julien Michel, & Francesco L. Gervasio (2020). “Investigating Cryptic Binding Sites by Molecular Dynamics Simulations” Acc Chem Res. 2020 Mar 17;53(3):654-661. doi: 10.1021/acs.accounts.9b00613. Epub 2020 Mar 5. (Abstract)
Continue reading →Joanna Kim & John A. Cooper (2020). “Septin Roles and Mechanisms in Organization of Endothelial Cell Junctions” bioRxiv. doi: https://doi.org/10.1101/2020.03.04.977199 (Abstract)
Continue reading →Jordan E. Ezekian, Sarah R. Clippinger, Jaquelin M. Garcia, Qixin Yang, Susan Denfield, Aamir Jeewa, William J. Dreyer, Wenxin Zou, Yuxin Fan, Hugh D. Allen, Jeffrey J. Kim, Michael J. Greenberg, & Andrew P. Landstrom (2020). “Variant R94C in TNNT2-Encoded Troponin T Predisposes to Pediatric Restrictive Cardiomyopathy and Sudden Death Through Impaired Thin Filament Relaxation Resulting in Myocardial Diastolic Dysfunction” J Am Heart Assoc. 2020 Mar 3;9(5):e015111. doi: 10.1161/JAHA.119.015111. Epub 2020 Feb 26. (Abstract)
Continue reading →Rawlings A.E., Liravi P., Corbett S., Holehouse A.S., & Staniland S.S. (2020). “Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6.” PLoS One. 2020 Feb 25;15(2):e0228708. doi: 10.1371/journal.pone.0228708. eCollection 2020. (Abstract)
Continue reading →Matthew A. Cruz, Thomas E. Frederick, Sukrit Singh, Neha Vithani, Maxwell I. Zimmerman, Justin R. Porter, Katelyn E. Moeder, Gaya K. Amarasinghe, & Gregory R. Bowman (2020). “Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments” bioRxiv. doi: https://doi.org/10.1101/2020.02.09.940510 (Abstract)
Continue reading →Martin E.W., Holehouse A.S., Peran I., Farag M., Incicco J.J., Bremer A., Grace C.R., Soranno A., Pappu R.V., & Mittag T. (2020). “Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.” Science. 2020 Feb 7;367(6478):694-699. doi: 10.1126/science.aaw8653. (Abstract)
Continue reading →Greig J.A., Nguyen T.A., Lee M., Holehouse A.S., Posey A.E., Pappu R.V., & Jedd G. (2020). “Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation.” Mol Cell. 2020 Feb 6. pii: S1097-2765(20)30046-0. doi: 10.1016/j.molcel.2020.01.025. [Epub ahead of print] (Abstract)
Continue reading →Choi J.M., Holehouse A.S., & Pappu R.V. (2020). “Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions.” Annu Rev Biophys. 2020 Jan 31. doi: 10.1146/annurev-biophys-121219-081629. [Epub ahead of print] (Abstract)
Continue reading →Yang B., Hird A.W., Bodnarchuk M.S., Zheng X., Dakin L., Su Q., Daly K., Godin R., Hattersley M.M., Brassil P., Redmond S., John Russell D., & Janetka J.W. (2020). “Heteroarylamide smoothened inhibitors: Discovery of N-[2,4-dimethyl-5-(1-methylimidazol-4-yl)phenyl]-4-(2-pyridylmethoxy)benzamide (AZD8542) and N-[5-(1H-imidazol-2-yl)-2,4-dimethyl-phenyl]-4-(2- pyridylmethoxy)benzamide (AZD7254).” Bioorg Med Chem. 2020 Jan 15;28(2):115227. doi: 10.1016/j.bmc.2019.115227. Epub 2019 Dec 11. (Abstract)
Continue reading →Zev J. Greenberg, Darlene A. Monlish, Rachel L. Bartnett, Yihu Yang, Guomin Shen, Weikai Li, Jeffrey J. Bednarski, & Laura G. Schuettpelz. (2020). “The Tetraspanin CD53 Regulates Early B Cell Development by Promoting IL-7R Signaling.” J Immunol. 2020 Jan 1;204(1):58-67. doi: 10.4049/jimmunol.1900539. Epub 2019 Nov 20. (Abstract)
Continue reading →Welty R., Rau M., Pabit S., Dunstan M.S., Conn G.L., Pollack L., & Hall K.B. (2019). “Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain.” J Mol Biol. 2019 Dec 24. pii: S0022-2836(19)30710-7. doi: 10.1016/j.jmb.2019.12.010. [Epub ahead of print] (Abstract)
Continue reading →Maybruck B.T., Lam W.C., Specht C.A., Ilagan M.X.G., Donlin M.J., & Lodge J.K. (2019). “The Aminoalkylindole BML-190 Negatively Regulates Chitosan Synthesis via the Cyclic AMP/Protein Kinase A1 Pathway in Cryptococcus neoformans.” mBio. 2019 Dec 17;10(6). pii: e02264-19. doi: 10.1128/mBio.02264-19. (Abstract)
Continue reading →Singh S.P., Soranno A., Sparks M.A., & Galletto R. (2019). “Branched unwinding mechanism of the Pif1 family of DNA helicases.” Proc Natl Acad Sci U S A. 2019 Nov 19. pii: 201915654. doi: 10.1073/pnas.1915654116. [Epub ahead of print] (Abstract)
Continue reading →Jordan E Ezekian, Sarah R Clippinger, Jackie Garcia, Susan W Denfield, Aamir Jeewa, William Dreyer, Wenxin Zou, Yuxin Fan, Hugh D Allen, Jeffrey Kim, Michael Greenberg, & Andrew P Landstrom (2019). “The Mutation R94C InTNNT2-encoded Troponin T Predisposes to Restrictive Cardiomyopathy and Pediatric Sudden Death Through Impaired Thin Filament Relaxation Resulting in Myocardial Diastolic Dysfunction” American Heart Association, Inc. 11 Nov 2019, Circulation. 2019;140:A12139 (Abstract)
Continue reading →Yates L.A., Williams R.M., Hailemariam S., Ayala R., Burgers P., & Zhang X. (2019). “Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations.” Structure. 2019 Nov 4. pii: S0969-2126(19)30353-3. doi: 10.1016/j.str.2019.10.012. [Epub ahead of print] (Abstract)
Continue reading →Sparks J.L., Gerik K.J., Stith C.M., Yoder B.L., & Burgers P.M. (2019). “The roles of fission yeast exonuclease 5 in nuclear and mitochondrial genome stability.” DNA Repair (Amst). 2019 Nov;83:102720. doi: 10.1016/j.dnarep.2019.102720. Epub 2019 Sep 21. (Abstract)
Continue reading →Alexander G. Kozlov, Min Kyung Shinn, & Timothy M. Lohman (2019). “Regulation of Nearest-neighbor cooperative binding of E. coli SSB protein to DNA” Biophysical Journal. 28 October 2019. doi.org/10.1016/j.bpj.2019.09.047 (Abstract)
Continue reading →Meisheng Ma, Mihaela Stoyanova, Griffin Rademacher, Susan K. Dutcher, Alan Brown, & Rui Zhang (2019). “Structure of the Decorated Ciliary Doublet Microtubule” Cell. Volume 179, Issue 4, 31 October 2019, Pages 909-922.e12. doi: 10.1016/j.cell.2019.09.030 (Abstract)
Continue reading →Weisz D.A., Johnson V.M., Niedzwiedzki D.M., Shinn M.K., Liu H., Klitzke C.F., Gross M.L., Blankenship R.E., Lohman T.M., & Pakrasi H.B. (2019). “A novel chlorophyll protein complex in the repair cycle of photosystem II.” Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21907-21913. doi: 10.1073/pnas.1909644116. Epub 2019 Oct 8. (Abstract)
Continue reading →Hailemariam S., De Bona P., Galletto R., Hohl M., Petrini J.H., & Burgers P.M. (2019). “The telomere-binding protein Rif2 and ATP-bound Rad50 have opposing roles in the activation of yeast Tel1ATM kinase.” J Biol Chem. 2019 Oct 22. pii: jbc.RA119.011077. doi: 10.1074/jbc.RA119.011077. [Epub ahead of print] (Abstract)
Continue reading →John B Wojcik, Dylan M Marchione, Simone Sidoli, Anissa Djedid, Amanda Lisby, Jacek Majewski & Benjamin A Garcia (2019). “Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors” Cancer Res. 2019 Jul 1;79(13):3205-3219. doi: 10.1158/0008-5472.CAN-18-3704. Epub 2019 Mar 21. (Abstract)
Continue reading →Clippinger S.R., Cloonan P.E., Greenberg L., Ernst M., Stump W.T., & Greenberg M.J. (2019). “Disrupted mechanobiology links the molecular and cellular phenotypes in familial dilated cardiomyopathy” Proc Natl Acad Sci U S A. 2019 Aug 19. pii: 201910962. doi: 10.1073/pnas.1910962116. [Epub ahead of print] (Abstract)
Continue reading →Ordabayev Y.A., Nguyen B., Kozlov A.G., Jia H., & Lohman T.M. (2019). “UvrD helicase activation by MutL involves rotation of its 2B subdomain.” Proc Natl Acad Sci U S A. 2019 Jul 30. pii: 201905513. doi: 10.1073/pnas.1905513116. [Epub ahead of print] (Abstract)
Continue reading →Sparks M.A., Singh S.P, Burgers P.M., & Galletto R. (2019). “Complementary roles of Pif1 helicase and single stranded DNA binding proteins in stimulating DNA replication through G-quadruplexes.” Nucleic Acids Res. 2019 Jul 24. pii: gkz608. doi: 10.1093/nar/gkz608. [Epub ahead of print] (Abstract)
Continue reading →Shinn M.K., Kozlov A.G., Nguyen B., Bujalowski W.M., & Lohman T.M. (2019). “Are the intrinsically disordered linkers involved in SSB binding to accessory proteins?” Nucleic Acids Res. 2019 Jul 22. pii: gkz606. doi: 10.1093/nar/gkz606. [Epub ahead of print] (Abstract)
Continue reading →Vishnu C. Damalanka, Scott A. Wildman, & James W. Janetka (2019). “Piperidine carbamate peptidomimetic inhibitors of the serine proteases HGFA, matriptase and hepsin” MedChemComm. 18 Jul 2019, doi: 10.1039/C9MD00234K (Abstract)
Continue reading →Boyle, S., D’Eustachio, P., Egan, S.E., Haw, R., Ilagan, M.X.G., Jassal, B., Joutel, A., & Orlic-Milacic, M. (2019). “Signaling by NOTCH” Reactome. R-HSA-157118 (Abstract)
Continue reading →Anumita Saha-Shah, Melody Esmaeili, Simone Sidoli, Hyojeong Hwang, Jing Yang, Peter S Klein & Benjamin A Garcia (2019). “Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis” Anal Chem. 2019 Jul 16;91(14):8891-8899. doi: 10.1021/acs.analchem.9b00327. Epub 2019 Jun 27. (Abstract)
Continue reading →Tyagi R., Elfawal M.A., Wildman S.A., Helander J., Bulman C.A., Sakanari J., Rosa B.A., Brindley P.J., Janetka J.W., Aroian R.V., & Mitreva M. (2019). “Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics.” Sci Rep. 2019 Jun 24;9(1):9085. doi: 10.1038/s41598-019-45548-7. (Abstract)
Continue reading →Zhu D.X., Garner A.L., Galburt E.A., & Stallings C.L. (2019). “CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis” Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13573-13581. doi: 10.1073/pnas.1900176116. Epub 2019 Jun 19. (Abstract)
Continue reading →Nguyen B., Ciuba M.A., Kozlov A.G., Levitus M., & Lohman T.M. (2019). “Protein Environment and DNA Orientation Affect Protein-Induced Cy3 Fluorescence Enhancement.” Biophys J. 2019 Jun 7. pii: S0006-3495(19)30448-5. doi: 10.1016/j.bpj.2019.05.026. [Epub ahead of print] (Abstract)
Continue reading →Jensen D., Ruiz Manzano A., Rammohan J., Stallings C.L., & Galburt E.A. (2019). “CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase.” Nucleic Acids Res. 2019 May 25. pii: gkz449. doi: 10.1093/nar/gkz449. [Epub ahead of print] (Abstract)
Continue reading →Simone Sidoli, Yekaterina Kori, Mariana Lopes, Zuo-Fei Yuan, Hee Jong Kim, Katarzyna Kulej, Kevin A Janssen, Laura M Agosto, Julia Pinheiro Chagas da Cunha, Andrew J Andrews & Benjamin A Garcia (2019). “One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry” Genome Res. 2019 Jun;29(6):978-987. doi: 10.1101/gr.247353.118. Epub 2019 May 23. (Abstract)
Continue reading →Dyson H.J., Hall K.B., & Piston D.W. (2019). “Economics and Politics of Publishing in Our Mission-Driven Society.” Biophys J. 2019 May 21;116(10):E1-E2. doi: 10.1016/j.bpj.2019.04.019. Epub 2019 May 1. (Abstract)
Continue reading →Sarem Hailemariam, Sandeep Kumar, & Peter M. Burgers (2019). “Activation of Tel1ATM kinase requires Rad50 ATPase and long nucleosome-free DNA, but no DNA ends.” J Biol Chem. 2019 Jun 28;294(26):10120-10130. doi: 10.1074/jbc.RA119.008410. Epub 2019 May 9. (Abstract)
Continue reading →Heitmeier M.R., Hresko R.C., Edwards R.L., Prinsen M.J., Ilagan M.X.G., Odom John A.R, & Hruz P.W. (2019). “Identification of druggable small molecule antagonists of the Plasmodium falciparum hexose transporter PfHT and assessment of ligand access to the glucose permeation pathway via FLAG-mediated protein engineering.” PLoS One. 2019 May 9;14(5):e0216457. doi: 10.1371/journal.pone.0216457. eCollection 2019. (Abstract)
Continue reading →Barrick S.K., Clippinger S.R., Greenberg L., & Greenberg M.J. (2019). “Computational Tool to Study Perturbations in Muscle Regulation and Its Application to Heart Disease.” Biophys J. 2019 May 7. pii: S0006-3495(19)30379-0. doi: 10.1016/j.bpj.2019.05.002. [Epub ahead of print] (Abstract)
Continue reading →Harding R.J., Loppnau P., Ackloo S., Lemak A., Hutchinson A., Hunt B., Holehouse A.S., Ho J.C., Fan L., Toledo-Sherman L., Seitova A., & Arrowsmith C.H. (2019). “Design and characterization of mutant and wildtype huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems.” J Biol Chem. 2019 Apr 26;294(17):6986-7001. doi: 10.1074/jbc.RA118.007204. Epub 2019 Mar 6. (Abstract)
Continue reading →Yang Z., Yan H., Dai W., Jing J., Yang Y., Mahajan S., Zhou Y., Li W., Macaubas C., Mellins E.D., Shih C.C., Fitzpatrick J.A.J., & Faccio R. (2019). “Tmem178 negatively regulates store-operated calcium entry in myeloid cells via association with STIM1.” J Autoimmun. 2019 Jul;101:94-108. doi: 10.1016/j.jaut.2019.04.015. Epub 2019 Apr 22. (Abstract)
Continue reading →Damalanka V.C. & Janetka J.W. (2019). “Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2.” Future Med Chem. 2019 Apr;11(7):743-769. doi: 10.4155/fmc-2018-0446. Epub 2019 Apr 4. (Abstract)
Continue reading →Heffern E.F., Ramani R., Marshall G., Kyei G.B. (2019). “Identification of isoform-selective hydroxamic acid derivatives that potently reactivate HIV from latency.” J Virus Erad. 2019 Apr 1;5(2):84-91. (Abstract)
Continue reading →Michael Kinch (2019). “The End of the Beginning: Cancer, Immunity, and the Future of a Cure” ISBN-13: 978-1643130255, ISBN-10: 1643130250
Continue reading →Wang H., Eschweiler J., Cui W., Zhang H., Frieden C., Ruotolo B.T., & Gross M.L. (2019) “Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers.” J Am Soc Mass Spectrom. 2019 Mar 18. doi: 10.1007/s13361-019-02148-z. [Epub ahead of print] (Abstract)
Continue reading →Tomko E.J. & Galburt E.A. (2019). “Single-molecule approach for studying RNAP II transcription initiation using magnetic tweezers.” Methods. 2019 Mar 18. pii: S1046-2023(18)30297-4. doi: 10.1016/j.ymeth.2019.03.010. [Epub ahead of print] (Abstract)
Continue reading →Singh S.P., Kukshal V., & Galletto R. (2019). “A stable tetramer is not the only oligomeric state that mitochondrial single-stranded DNA binding proteins can adopt.” J Biol Chem. 2019 Mar 15;294(11):4137-4144. doi: 10.1074/jbc.RA118.007048. Epub 2019 Jan 7. (Abstract)
Continue reading →Porter J.R., Moeder K.E., Sibbald C.A., Zimmerman M.I., Hart K.M., Greenberg M.J., & Bowman G.R. (2019). “Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.” Biophys J. 2019 Mar 5;116(5):818-830. doi: 10.1016/j.bpj.2018.11.3144. Epub 2019 Jan 25. (Abstract)
Continue reading →Natarajan V Bhanu, Simone Sidoli, Zuo-Fei Yuan, Rosalynn C Molden & Benjamin A Garcia (2019). “Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis” J Biol Chem. 2019 May 17;294(20):8296-8308. doi: 10.1074/jbc.RA118.004977. Epub 2019 Mar 14. (Abstract)
Continue reading →Mondol T., Stodola J.L., Galletto R., & Burgers P.M. (2019). “PCNA accelerates the nucleotide incorporation rate by DNA polymerase δ.” Nucleic Acids Res. 2019 Feb 28;47(4):1977-1986. doi: 10.1093/nar/gky1321. (Abstract)
Continue reading →Burgers, P.M. (2019). “Solution to the 50-year-old Okazaki-fragment problem.” Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3358-3360. doi: 10.1073/pnas.1900372116. Epub 2019 Feb 15. (Abstract)
Continue reading →Frieden, C. (2019). “Protein oligomerization as a metabolic control mechanism: Application to apoE.” Protein Sci. 2019 Apr;28(4):837-842. doi: 10.1002/pro.3583. Epub 2019 Feb 18. (Abstract)
Continue reading →Min Kyung Shinn, Alexander G. Kozlov, & Timothy M. Lohman. (2019). “Binding Specificity of E. coli SSB C-Terminal Tails to SIPs” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 77a. (Abstract)
Continue reading →Drake Jensen, Ana Ruiz Manzano, Christina L. Stallings, & Eric A. Galburt. (2019). “Regulation of Mycobacterial RNA Polymerase Promoter Escape Kinetics by Transcription Factors Card and RbpA” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 210a. (Abstract)
Continue reading →Eric A. Galburt, Eric J. Tomko, James Fishburn, & Steven Hahn. (2019). “Tfiih Generates a Six-Base-Pair Open Complex during Eukaryotic Transcription Initiation” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Pages 209a-210a. (Abstract)
Continue reading →Sarah R. Clippinger, Paige E. Cloonan, Lina Greenberg, William Stump, & Michael J. Greenberg. (2019). “A Familial Dilated Cardiomyopathy Mutation Decreases Myosin Generated Tension at the Molecular Level and Alters Mechanosensing at the Cellular Level” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 30a. (Abstract)
Continue reading →Samantha K. Barrick & Michael J. Greenberg. (2019). “Molecular Mechanism of a Mutation Implicated in Pediatric-Onset Heart Disesase” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 115a. (Abstract)
Continue reading →Felicia Gibson, Andrea Soranno, Wenwei Zheng, & Sara M. Vaiana. (2019). “Extracting Sequence-Dependent Intra-Protein Interaction Parameters from Photo-Induced Electron Transfer Measurements of IDPs” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 202a. (Abstract)
Continue reading →Andrea Soranno, Jeremias Incicco, Paolo De Bona, Eric Tomko, Eric Galburt, & Roberto Galletto. (2019). “Shelterin Components Modulate the Phase-Separation Propensity of Telomeres” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Pages 467a-468a. (Abstract)
Continue reading →Melissa D. Stuchell-Brereton, Berevan Baban, Greg DeKoster, Carl Frieden, & Andrea Soranno. (2019). “Single-Molecule Conformational Analysis of Apolipoprotein E” Biophysical Journal. Volume 116, Issue 3, Supplement 1, 15 February 2019, Page 167a. (Abstract)
Continue reading →Porter J.R., Zimmerman M.I., & Bowman G.R. (2019). “Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.” J Chem Phys. 2019 Jan 28;150(4):044108. doi: 10.1063/1.5063794. (Abstract)
Continue reading →Griesenauer R.H., Schillebeeckx C., & Kinch M.S. (2019). “Assessing the public landscape of clinical-stage pharmaceuticals through freely available online databases.” Drug Discov Today. 2019 Jan 25. pii: S1359-6446(18)30258-7. doi: 10.1016/j.drudis.2019.01.010. [Epub ahead of print] (Abstract)
Continue reading →Maddirala A., Klein R.D., Pinkner J., Kalas V., Hultgren S.J., & Janetka J.W. (2019). “Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through iterative rational drug design.” J Med Chem. 2019 Jan 24;62(2):467-479. doi: 10.1021/acs.jmedchem.8b01561. Epub 2019 Jan 2. (Abstract)
Continue reading →Damalanka V.C., Han Z., Karmakar P., O’Donoghue A.J., La Greca F., Kim T., Pant S., Helander J., Klefström J., Craik C.S., & Janetka J.W. (2019). “Discovery of Selective Matriptase and Hepsin Serine Protease Inhibitors: Useful Chemical Tools for Cancer Cell Biology.” J Med Chem. 2019 Jan 24;62(2):480-490. doi: 10.1021/acs.jmedchem.8b01536. Epub 2019 Jan 4. (Abstract)
Continue reading →Makurath M.A., Whitley K.D., Nguyen B., Lohman T.M., & Chemla Y.R. (2019). “Regulation of Rep helicase unwinding by an auto-inhibitory subdomain.” Nucleic Acids Res. 2019 Mar 18;47(5):2523-2532. doi: 10.1093/nar/gkz023. (Abstract)
Continue reading →Katarzyna Dubiel, Angela R. Myers, Alexander G. Kozlov, Olivia Yang, Jichuan Zhang, Taekjip Ha, Timothy M. Lohman, & James L. Keck (2019). “Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins” J Mol Biol. 2019 Jan 18;431(2):178-195. doi: 10.1016/j.jmb.2018.11.019. Epub 2018 Nov 22. (Abstract)
Continue reading →Lisa Eshun-Wilson, Rui Zhang, Didier Portran, Maxence Nachury, Daniel Toso, Thomas Lohr, Michelle Vendruscolo, Massimiliano Bonomi, James Fraser, & Eva Nogales (2019). “Effects of α-tubulin acetylation on microtubule structure and stability” bioRxiv. January 09, 2019. doi.org/10.1101/516591. (Abstract)
Continue reading →Kawaguchi M., Yamamoto K., Takeda N., Fukushima T., Yamashita F., Sato K., Kitamura K., Hippo Y., Janetka J.W., & Kataoka H. (2019). “Hepatocyte growth factor activator inhibitor-2 stabilizes Epcam and maintains epithelial organization in the mouse intestine.” Commun Biol. 2019 Jan 4;2:11. doi: 10.1038/s42003-018-0255-8. eCollection 2019. (Abstract)
Continue reading →Knoverek C.R., Amarasinghe G.K., & Bowman G.R. (2018). “Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.” Trends Biochem Sci. 2019 Apr;44(4):351-364. doi: 10.1016/j.tibs.2018.11.007. Epub 2018 Dec 14. (Abstract)
Continue reading →Dahan D., Tsirkas I., Dovrat D., Sparks M.A., Singh S.P., Galletto R., & Aharoni A. (2018). “Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures.” Nucleic Acids Res. 2018 Dec 14;46(22):11847-11857. doi: 10.1093/nar/gky1065. (Abstract)
Continue reading →Galburt E.A. (2018). “The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression.” Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11604-E11613. doi: 10.1073/pnas.1809454115. Epub 2018 Nov 21. (Abstract)
Continue reading →Zimmerman M.I., Porter J.R., Sun X., Silva R.R., & Bowman G.R. (2018). “Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.” J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500. Epub 2018 Oct 23. (Abstract)
Continue reading →Kiehart D.P. & Cooper J.A. (2018). “Contractile protein biochemistry in the Pollard Lab in Baltimore.” Biophys Rev. 2018 Nov 8. doi: 10.1007/s12551-018-0477-5. [Epub ahead of print] (Abstract)
Continue reading →Yen M., Qi Z., Chen X., Cooper J.A., Mitra R.D., & Onken M.D. (2018). “Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma.” BMC Med Genomics. 2018 Nov 6;11(1):97. doi: 10.1186/s12920-018-0424-0. (Abstract)
Continue reading →Robertson J.L. (2018). “The lipid bilayer membrane and its protein constituents.” J Gen Physiol. 2018 Nov 5;150(11):1472-1483. doi: 10.1085/jgp.201812153. Epub 2018 Sep 25. (Abstract)
Continue reading →Johnston A.B., Hilton D.M., McConnell P., Johnson B., Harris M.T., Simone A., Amarasinghe G.K., Cooper J.A., & Goode B.L. (2018). “A novel mode of capping protein-regulation by twinfilin.” Elife. 2018 Oct 23;7. pii: e41313. doi: 10.7554/eLife.41313. (Abstract)
Continue reading →Sun X., Singh S., Blumer K.J., & Bowman G.R. (2018). “Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding.” Elife. 2018 Oct 5;7. pii: e38465. doi: 10.7554/eLife.38465. (Abstract)
Continue reading →Kelly R Karch, Mariel Coradin, Levani Zandarashvili, Zhong-Yuan Kan, Morgan Gerace, S Walter Englander, Ben E Black & Benjamin A Garcia (2018). “Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly” Structure. 2018 Dec 4;26(12):1651-1663.e3. doi: 10.1016/j.str.2018.08.006. Epub 2018 Oct 4. (Abstract)
Continue reading →Axelrod D., Elson E.L., Schlessinger J., & Koppel D.E. (2018). “Reminiscences on the “Classic” 1976 FRAP Article in Biophysical Journal.” Biophys J. 2018 Oct 2;115(7):1156-1159. doi: 10.1016/j.bpj.2018.08.037. Epub 2018 Sep 4. (Abstract)
Continue reading →Welty R., Pabit S.A., Katz A.M., Calvey G.D., Pollack L., & Hall K.B. (2018). “Divalent ions tune the kinetics of a bacterial GTPase Center rRNA folding transition from secondary to tertiary structure.” RNA. 2018 Dec;24(12):1828-1838. doi: 10.1261/rna.068361.118. Epub 2018 Sep 25. (Abstract)
Continue reading →Woody M.S., Greenberg M.J., Barua B., Winkelmann D.A., Goldman Y.E., & Ostap E.M. (2018). “Positive cardiac inotrope omecamtiv mecarbil activates muscle despite suppressing the myosin working stroke.” Nat Commun. 2018 Sep 21;9(1):3838. doi: 10.1038/s41467-018-06193-2. (Abstract)
Continue reading →Greenberg M.J., Daily N.J., Wang A., Conway M.K., & Wakatsuki T. (2018). “Genetic and Tissue Engineering Approaches to Modeling the Mechanics of Human Heart Failure for Drug Discovery.” Front Cardiovasc Med. 2018 Sep 19;5:120. doi: 10.3389/fcvm.2018.00120. eCollection 2018. (Abstract)
Continue reading →Geronimo C.L., Singh S.P., Galletto R., & Zakian V.A. (2018). “The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity.” Nucleic Acids Res. 2018 Sep 19;46(16):8357-8370. doi: 10.1093/nar/gky655. (Abstract)
Continue reading →Justin R Porter, Katelyn E Moeder, Carrie A Sibbald, Maxwell I Zimmerman, Kathryn M Hart, Michael J Greenberg, & Gregory R Bowman (2018). “Cooperative changes in solvent exposure identify cryptic pockets, conformational switches, and allosteric coupling” bioRxiv. September 18, 2018. doi.org/10.1101/323568. (Abstract)
Continue reading →Hema Adhikari & Christopher M. Counter (2018). “Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability” Nat Commun. 2018 Sep 7;9(1):3646. doi: 10.1038/s41467-018-05692-6. (Abstract)
Continue reading →Rezaei-Ghaleh N., Parigi G., Soranno A., Holla A., Becker S., Schuler B., Luchinat C., & Zweckstetter M. (2018). “Local and Global Dynamics in Intrinsically Disordered Synuclein.” Angew Chem Int Ed Engl. 2018 Sep 5. doi: 10.1002/anie.201808172. [Epub ahead of print] (Abstract)
Continue reading →Onken M.D., Makepeace C.M., Kaltenbronn K.M., Kanai S.M., Todd T.D., Wang S., Broekelmann T.J., Rao P.K., Cooper J.A., & Blumer K.J. (2018). “Targeting nucleotide exchange to inhibit constitutively active G protein α subunits in cancer cells.” Sci Signal. 2018 Sep 4;11(546). pii: eaao6852. doi: 10.1126/scisignal.aao6852. (Abstract)
Continue reading →Macdonald-Obermann J.L. & Pike L.J. (2018). “Allosteric regulation of epidermal growth factor (EGF) receptor ligand binding by tyrosine kinase inhibitors.” J Biol Chem. 2018 Aug 31;293(35):13401-13414. doi: 10.1074/jbc.RA118.004139. (Abstract)
Continue reading →Ordabayev Y.A., Nguyen B., Niedziela-Majka A., & Lohman T.M. (2018). “Regulation of UvrD Helicase Activity by MutL.” J Mol Biol. 2018 Aug 29. pii: S0022-2836(18)30591-6. doi: 10.1016/j.jmb.2018.08.022. (Abstract)
Continue reading →Singh S.P., Kukshal V., De Bona P., Antony E., & Galletto R. (2018). “The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers.” Nucleic Acids Res. 2018 Aug 21;46(14):7193-7205. doi: 10.1093/nar/gky530. (Abstract)
Continue reading →Sukumar N., Liu S., Li W., Mathews F.S., Mitra B., & Kandavelu P. (2018). “Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2Å resolution.” Biochimie. 2018 Jul 30. pii: S0300-9084(18)30212-8. doi: 10.1016/j.biochi.2018.07.017. (Abstract)
Continue reading →Michael D. Onken, Carol M. Makepeace, Shiqi Wang, Kevin M. Kaltenbronn, Stanley M. Kanai, Tom J. Broekelmann, John A. Cooper, & Kendall J. Blumer (2018). “Pharmacologic targeting of Gq reveals new pathways in uveal melanoma” AACR, July 2018, Volume 78, Issue 13 Supplement (Abstract)
Continue reading →Klein R.D., Shu Q., Cusumano Z.T., Nagamatsu K., Gualberto N.C., Lynch A.J.L., Wu C., Wang W., Jain N., Pinkner J.S., Amarasinghe G.K., Hultgren S.J., Frieden C., & Chapman M.R. (2018). “Structure-Function Analysis of the Curli Accessory Protein CsgE Defines Surfaces Essential for Coordinating Amyloid Fiber Formation.” MBio. 2018 Jul 17;9(4). pii: e01349-18. doi: 10.1128/mBio.01349-18. (Abstract)
Continue reading →Song J.G., King M.R., Zhang R., Kadzik R.S., Thawani A., & Petry S. (2018) “Mechanism of how augmin directly targets the γ-tubulin ring complex to microtubules.” J Cell Biol. 2018 Jul 2;217(7):2417-2428. doi: 10.1083/jcb.201711090. Epub 2018 Jun 6. (Abstract)
Continue reading →Shen G., Li S., Cui W., Liu S., Liu Q., Yang Y., Gross M., & Li W. (2018). “Stabilization of warfarin-binding pocket of VKORC1 and VKORL1 by a peripheral region determines their different sensitivity to warfarin inhibition.” J Thromb Haemost. 2018 Jun;16(6):1164-1175. doi: 10.1111/jth.14127. Epub 2018 May 20. (Abstract)
Continue reading →Weber G., DeKoster G.T., Holton N., Hall K.B., & Wahl M.C. (2018). “Molecular principles underlying dual RNA specificity in the Drosophila SNF protein.” Nat Commun. 2018 Jun 7;9(1):2220. doi: 10.1038/s41467-018-04561-6. (Abstract)
Continue reading →Johnson B., McConnell P., Kozlov A.G., Mekel M., Lohman T.M., Gross M.L., Amarasinghe G.K., & Cooper J.A. (2018). “Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange.” Cell Rep. 2018 May 29;23(9):2795-2804. doi: 10.1016/j.celrep.2018.04.096. (Abstract)
Continue reading →Kim J. & Cooper J.A. (2019). “Septins regulate junctional integrity of endothelial monolayers.” Mol Biol Cell. 2018 Jul 15;29(13):1693-1703. doi: 10.1091/mbc.E18-02-0136. Epub 2018 May 17. (Abstract)
Continue reading →Tyagi R., Maddirala A.R., Elfawal M., Fischer C., Bulman C.A., Rosa B.A., Gao X., Chugani R., Zhou M., Helander J., Brindley P.J., Tseng C.C., Greig I.R., Sakanari J., Wildman S.A., Aroian R., Janetka J.W., & Mitreva M. (2018). “Small Molecule Inhibitors of Metabolic Enzymes Repurposed as a New Class of Anthelmintics.” ACS Infect Dis. 2018 Jul 13;4(7):1130-1145. doi: 10.1021/acsinfecdis.8b00090. Epub 2018 May 14. (Abstract)
Continue reading →Kinch M.S. & Griesenauer R.H. (2018). “2017 in review: FDA approvals of new molecular entities.” Drug Discov Today. 2018 May 8. pii: S1359-6446(18)30088-6. doi: 10.1016/j.drudis.2018.05.011. (Abstract)
Continue reading →Chen J., Castelvecchi G.D., Li-Villarreal N., Raught B., Krezel A.M., McNeill H., & Solnica-Krezel L. (2018). “Atypical Cadherin Dachsous1b Interacts with Ttc28 and Aurora B to Control Microtubule Dynamics in Embryonic Cleavages.” Dev Cell. 2018 May 7;45(3):376-391.e5. doi: 10.1016/j.devcel.2018.04.009. (Abstract)
Continue reading →Lobysheva E., Taylor C.M., Marshall G.R., & Kisselev O.G. (2018). “Tauroursodeoxycholic acid binds to the G-protein site on light activated rhodopsin.” Exp Eye Res. 2018 May;170:51-57. doi: 10.1016/j.exer.2018.02.015. Epub 2018 Feb 16. (Abstract)
Continue reading →Prusa J., Jensen D., Santiago-Collazo G., Pope S.S., Garner A.L., Miller J.J., Ruiz Manzano A., Galburt E.A., & Stallings C.L. (2018). “Domains within RbpA serve specific functional roles that regulate the expression of distinct mycobacterial gene subsets.” J Bacteriol. 2018 Apr 23. pii: JB.00690-17. doi: 10.1128/JB.00690-17. (Abstract)
Continue reading →Rocha A.G., Franco A., Krezel A.M., Rumsey J.M., Alberti J.M., Knight W.C., Biris N., Zacharioudakis E., Janetka J.W., Baloh R.H., Kitsis R.N., Mochly-Rosen D., Townsend R.R., Gavathiotis E., & Dorn G.W. 2nd (2018). “MFN2 agonists reverse mitochondrial defects in preclinical models of Charcot-Marie-Tooth disease type 2A.” Science. 2018 Apr 20;360(6386):336-341. doi: 10.1126/science.aao1785. (Abstract)
Continue reading →Bodmer N.K. & Havranek J.J. (2018). “Efficient minimization of multipole electrostatic potentials in torsion space.” PLoS One. 2018 Apr 11;13(4):e0195578. doi: 10.1371/journal.pone.0195578. eCollection 2018. (Abstract)
Continue reading →Lohman T.M. & Fazio N.T. (2018) “How Does a Helicase Unwind DNA? Insights from RecBCD Helicase.” Bioessays. 2018 Jun;40(6):e1800009. doi: 10.1002/bies.201800009. Epub 2018 Mar 30. (Abstract)
Continue reading →Antony E. & Lohman T.M. (2018) “Dynamics of E. coli single stranded DNA binding (SSB) protein-DNA complexes.” Semin Cell Dev Biol. 2018 Mar 30. pii: S1084-9521(17)30432-9. doi: 10.1016/j.semcdb.2018.03.017. [Epub ahead of print] (Abstract)
Continue reading →Soranno A., Zosel F., & Hofmann H. (2018). “Internal friction in an intrinsically disordered protein-Comparing Rouse-like models with experiments.” J Chem Phys. 2018 Mar 28;148(12):123326. doi: 10.1063/1.5009286. (Abstract)
Continue reading →Adam P. Joyce & James J. Havranek (2018). “Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors” Quantitative Biology, March 2018, Volume 6, Issue 1, pp 68–84 (Abstract)
Continue reading →Kalas V., Hibbing M.E., Maddirala A.R., Chugani R., Pinkner J.S., Mydock-McGrane L.K., Conover M.S., Janetka J.W., & Hultgren S.J. (2018). “Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection.” Proc Natl Acad Sci U S A. 2018 Mar 5. pii: 201720140. doi: 10.1073/pnas.1720140115. (Abstract)
Continue reading →James W. Janetka & Roseann M. Benson (2018). “Extracellular Targeting of Cell Signaling in Cancer: Strategies Directed at MET and RON Receptor Tyrosine Kinase Pathways” ISBN-13: 978-1119300182, ISBN-10: 1119300185 (Publisher)
Continue reading →Borgia A., Borgia M.B., Bugge K., Kissling V.M., Heidarsson P.O., Fernandes C.B., Sottini A., Soranno A., Buholzer K.J., Nettels D., Kragelund B.B., Best R.B., & Schuler B. (2018). “Extreme disorder in an ultrahigh-affinity protein complex.” Nature. 2018 Mar 1;555(7694):61-66. doi: 10.1038/nature25762. Epub 2018 Feb 21. (Abstract)
Continue reading →Michael S. Woody, Michael J. Greenberg, Bipasha Barua, Donald A. Winkelmann, Yale E. Goldman, & E. Michael Ostap (2018). “Single Molecule, Optical Trapping Studies of Omecamtiv Mercarbil on Human Cardiac Myosin’s Force Production” Biophysical Journal, Volume 114, Issue 3, Supplement 1, 2 February 2018, Pages 317a-318a. doi.org/10.1016/j.bpj.2017.11.1787 (Abstract)
Continue reading →Spaulding C.N., Klein R.D., Schreiber H.L. 4th, Janetka J.W., & Hultgren S.J. (2018). “Precision antimicrobial therapeutics: the path of least resistance?” NPJ Biofilms Microbiomes. 2018 Feb 27;4:4. doi: 10.1038/s41522-018-0048-3. eCollection 2018. (Abstract)
Continue reading →Su Z., Wu C., Shi L., Luthra P., Pintilie G.D., Johnson B., Porter J.R., Ge P., Chen M., Liu G., Frederick T.E., Binning J.M., Bowman G.R., Zhou Z.H., Basler C.F., Gross M.L., Leung D.W., Chiu W., & Amarasinghe G.K. (2018). “Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.” Cell. 2018 Feb 22;172(5):966-978.e12. doi: 10.1016/j.cell.2018.02.009. (Abstract)
Continue reading →Reddy D.N., Singh S., Ho C.M.W., Patel J., Schlesinger P., Rodgers S., Doctor A., & Marshall G.R. (2018). “Design, synthesis, and biological evaluation of stable β6.3-Helices: Discovery of non-hemolytic antibacterial peptides.” Eur J Med Chem. 2018 Apr 10;149:193-210. doi: 10.1016/j.ejmech.2018.02.057. Epub 2018 Feb 20. (Abstract)
Continue reading →Sarah R. Clippinger, Lina Greenberg, & Michael J. Greenberg (2018). “Dissecting the Molecular Mechanism for Familial Cardiomyopathies” Biophysical Journal. Volume 114, Issue 3, Supplement 1, p139a–140a, 2 February 2018. doi: 10.1016/j.bpj.2017.11.787 (Abstract)
Continue reading →Paige E. Cloonan, Lina Greenberg, & Michael J.Greenberg (2018). “Mechanical and Structural Analysis of Cardiomyopathies at the Single Cell Level” Biophysical Journal, Volume 114, Issue 3, Supplement 1, 2 February 2018, Page 314a. doi.org/10.1016/j.bpj.2017.11.1771 (Abstract)
Continue reading →Min Kyung Shinn, Alexander G. Kozlov, & Timothy M. Lohman (2018). “Allosteric Effect of E. coli SSB C-Terminal Tails on RecOR Binding to DNA” Biophysical Journal, Volume 114, Issue 3, Supplement 1, 2 February 2018, Page 441a (Abstract)
Continue reading →Yang B., Vasbinder M., Hird A.W., Su Q., Wang H., Yu Y., Toader D., Lyne P.D., Read J.A., Breed J., Ioannidis S., Deng C., Grondine M., DeGrace N., Whitston D., Brassil P., & Janetka J.W. (2018). “Adventures in Scaffold Morphing: Discovery of Fused Ring Heterocyclic Checkpoint Kinase 1 (CHK1) Inhibitors.” J Med Chem. doi: 10.1021/acs.jmedchem.7b01490. (Abstract)
Continue reading →Stodola J.L. & Burgers P.M. (2017). “Mechanism of Lagging-Strand DNA Replication in Eukaryotes.” Adv Exp Med Biol. 2017;1042:117-133. doi: 10.1007/978-981-10-6955-0_6. (Abstract)
Continue reading →Michael Kinch (2018). “Between Hope and Fear: A History of Vaccines and Human Immunity” ISBN-13: 978-1681777511, ISBN-10: 1681777517
Continue reading →Bartels P.L., Stodola J.L., Burgers P.M.J., & Barton J.K. (2017). “A Redox Role for the [4Fe4S] Cluster of Yeast DNA Polymerase δ.” J Am Chem Soc. 2017 Dec 20;139(50):18339-18348. doi: 10.1021/jacs.7b10284. Epub 2017 Dec 6. (Abstract)
Continue reading →Shen G., Li S., Cui W., Liu S., Yang Y., Gross M., & Li W. (2017). “Membrane Protein Structure in Live Cells: Methodology for Studying Drug Interaction by Mass Spectrometry-Based Footprinting.” Biochemistry. 2018 Jan 23;57(3):286-294. doi: 10.1021/acs.biochem.7b00874. Epub 2017 Dec 20. (Abstract)
Continue reading →Zimmerman M.I., Hart K.M., Sibbald C.A., Frederick T.E., Jimah J.R., Knoverek C.R., Tolia N.H., & Bowman G.R. (2017). “Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models.” ACS Cent Sci. 2017 Dec 27;3(12):1311-1321. doi: 10.1021/acscentsci.7b00465. Epub 2017 Nov 21. (Abstract)
Continue reading →Halstead A.M., Kapadia C.D., Bolzenius J., Chu C.E., Schriefer A., Wartman L.D., Bowman G.R., & Arora V.K. (2017). “Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation.” Elife. 2017 Nov 16;6. pii: e30862. doi: 10.7554/eLife.30862. (Abstract)
Continue reading →Griesenauer R.H., Moore R., & Kinch M.S. (2017). “NIH Support for FDA-Approved Medicines.” Cell Chem Biol. 2017 Nov 16;24(11):1315-1316. doi: 10.1016/j.chembiol.2017.11.002. (Abstract)
Continue reading →Nguyen B., Ordabayev Y., Sokoloski J.E., Weiland E., & Lohman T.M. (2017). “Large domain movements upon UvrD dimerization and helicase activation.” Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12178-12183. doi: 10.1073/pnas.1712882114. Epub 2017 Oct 30. (Abstract)
Continue reading →Li S., Shen G., & Li W. (2017). “Intramembrane thiol oxidoreductases: evolutionary convergence and structural controversy.” Biochemistry. 2018 Jan 23;57(3):258-266. doi: 10.1021/acs.biochem.7b00876. Epub 2017 Nov 7. (Abstract)
Continue reading →Tomko E.J., Fishburn J., Hahn S., & Galburt E.A. (2017). “TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning.” Nat Struct Mol Biol. 2017 Dec;24(12):1139-1145. doi: 10.1038/nsmb.3500. Epub 2017 Nov 6. (Abstract)
Continue reading →Niu H., Fujiwara H., di Martino O., Hadwiger G., Frederick T.E., Menéndez-Gutiérrez M.P., Ricote M., Bowman G.R., & Welch J.S. (2017). “Endogenous retinoid X receptor ligands in mouse hematopoietic cells.” Sci Signal. 2017 Oct 31;10(503). pii: eaan1011. doi: 10.1126/scisignal.aan1011. (Abstract)
Continue reading →Patrick G.J., Fang L., Schaefer J., Singh S., Bowman G.R., & Wencewicz T.A. (2017). “Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-lactam.” Biochemistry. 2018 Jan 9;57(1):117-135. doi: 10.1021/acs.biochem.7b00838. Epub 2017 Oct 31. (Abstract)
Continue reading →Johayra Simithy, Simone Sidoli, Zuo-Fei Yuan, Mariel Coradin, Natarajan V Bhanu, Dylan M Marchione, Brianna J Klein, Gleb A Bazilevsky, Cheryl E McCullough, Robert S Magin, Tatiana G Kutateladze, Nathaniel W Snyder, Ronen Marmorstein & Benjamin A Garcia (2017). “Characterization of histone acylations links chromatin modifications with metabolism” Nat Commun. 2017 Oct 26;8(1):1141. doi: 10.1038/s41467-017-01384-9. (Abstract)
Continue reading →Gill K., Macdonald-Obermann J.L., & Pike L.J. (2017). “Epidermal growth factor receptors containing a single tyrosine in their C-terminal tail bind different effector molecules and are signaling-competent.” J Biol Chem. 2017 Dec 15;292(50):20744-20755. doi: 10.1074/jbc.M117.802553. Epub 2017 Oct 26. (Abstract)
Continue reading →Zosel F., Haenni D., Soranno A., Nettels D., & Schuler B. (2017). “Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein.” J Chem Phys. 2017 Oct 21;147(15):152708. doi: 10.1063/1.4992800. (Abstract)
Continue reading →Tomko E.J. & Lohman T.M. (2017). “Modulation of Escherichia coli UvrD Single-Stranded DNA Translocation by DNA Base Composition.” Biophys J. 2017 Oct 3;113(7):1405-1415. doi: 10.1016/j.bpj.2017.08.023. (Abstract)
Continue reading →Griesenauer R.H. & Kinch M.S. (2017). “An overview of FDA-approved vaccines & their innovators.” Expert Rev Vaccines. 2017 Dec;16(12):1253-1266. doi: 10.1080/14760584.2017.1383159. Epub 2017 Sep 25. (Abstract)
Continue reading →Rutaganira F.U., Barks J., Dhason M.S., Wang Q., Lopez M.S., Long S., Radke J.B., Jones N.G., Maddirala A.R., Janetka J.W., El Bakkouri M., Hui R., Shokat K.M., & Sibley L.D. (2017). “Inhibition of calcium dependent protein kinase 1 (CDPK1) by pyrazolopyrimidine analogs decreases establishment and reoccurrence of central nervous system disease by Toxoplasma gondii.” J Med Chem. 2017 Dec 28;60(24):9976-9989. doi: 10.1021/acs.jmedchem.7b01192. Epub 2017 Oct 9. (Abstract)
Continue reading →Wang H., Rempel D.L., Giblin D., Frieden C., & Gross M.L. (2017). “Peptide-Level Interactions between Proteins and Small-Molecule Drug Candidates by Two Hydrogen-Deuterium Exchange MS-Based Methods: The Example of Apolipoprotein E3.” Anal Chem. 2017 Oct 17;89(20):10687-10695. doi: 10.1021/acs.analchem.7b01121. Epub 2017 Sep 25. (Abstract)
Continue reading →Marshall G.R. & Ballante F. (2017). “Limiting Assumptions in the Design of Peptidomimetics.” Drug Dev Res. 2017 Sep;78(6):245-267. doi: 10.1002/ddr.21406. Epub 2017 Sep 6. (Abstract)
Continue reading →Wang H., Shu Q., Rempel D.L., Frieden C., & Gross M.L. (2017). “Understanding Curli Amyloid-Protein Aggregation by Hydrogen-Deuterium Exchange and Mass Spectrometry.” Int J Mass Spectrom. 2017 Sep;420:16-23. doi: 10.1016/j.ijms.2016.10.006. Epub 2016 Oct 11. (Abstract)
Continue reading →Kunkel T.A. & Burgers P.M. (2017). “Arranging eukaryotic nuclear DNA polymerases for replication: Specific interactions with accessory proteins arrange Pols α, δ, and ϵ in the replisome for leading-strand and lagging-strand DNA replication.” Bioessays. 2017 Aug;39(8). doi: 10.1002/bies.201700070. (Abstract)
Continue reading →Albert B.J., Niu A., Ramani R., Marshall G.R., Wender P.A., Williams R.M., Ratner L., Barnes A.B., & Kyei G.B. (2017), “Combinations of isoform-targeted histone deacetylase inhibitors and bryostatin analogues display remarkable potency to activate latent HIV without global T-cell activation.” Sci Rep. 2017 Aug 7;7(1):7456. doi: 10.1038/s41598-017-07814-4. (Abstract)
Continue reading →Kozlov A.G., Shinn M.K., Weiland E.A., & Lohman T.M. (2017). “Glutamate promotes SSB protein-protein Interactions via intrinsically disordered regions.” J Mol Biol. 2017 Sep 1;429(18):2790-2801. doi: 10.1016/j.jmb.2017.07.021. Epub 2017 Aug 3. (Abstract)
Continue reading →McCune B.T., Tang W., Lu J., Eaglesham J.B., Thorne L., Mayer A.E., Condiff E., Nice T.J., Goodfellow I., Krezel A.M., & Virgin H.W. (2017). “Noroviruses Co-opt the Function of Host Proteins VAPA and VAPB for Replication via a Phenylalanine-Phenylalanine-Acidic-Tract-Motif Mimic in Nonstructural Viral Protein NS1/2.” MBio. 2017 Jul 11;8(4). pii: e00668-17. doi: 10.1128/mBio.00668-17. (Abstract)
Continue reading →Griesenauer R.H. and Kinch M.S. (2017). “2016 in review: FDA approvals of new molecular entities.” Drug Discov Today. 2017 Nov;22(11):1593-1597. doi: 10.1016/j.drudis.2017.06.011. Epub 2017 Jul 4. (Abstract)
Continue reading →Green J.M., Barratt M.J., Kinch M., and Gordon J.I. (2017) “Food and microbiota in the FDA regulatory framework.” Science. 2017 Jul 7;357(6346):39-40. doi: 10.1126/science.aan0836. (Abstract)
Continue reading →Stark B.C., Lanier M.H., & Cooper J.A. (2017). “CARMIL family proteins as multidomain regulators of actin-based motility.” Mol Biol Cell. 2017 Jul 1;28(13):1713-1723. doi: 10.1091/mbc.E17-01-0019. (Abstract)
Continue reading →Kinch M.S. and Woodard P.K. (2017) “Analysis of FDA-approved imaging agents.” Drug Discov Today. 2017 Jul;22(7):1077-1083. doi: 10.1016/j.drudis.2017.03.006. Epub 2017 Mar 21. (Abstract)
Continue reading →Spaulding C.N., Klein R.D., Ruer S., Kau A.L., Schreiber H.L., Cusumano Z.T., Dodson K.W., Pinkner J.S., Fremont D.H., Janetka J.W., Remaut H., Gordon J.I., & Hultgren S.J. (2017). “Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist.” Nature. 2017 Jun 22;546(7659):528-532. doi: 10.1038/nature22972. Epub 2017 Jun 14. (Abstract)
Continue reading →Stewart-Hutchinson P.J., Szasz T.P., Jaeger E.R., Onken M.D., Cooper J.A., & Morley S.C. (2017). “Technical Advance: New in vitro method for assaying the migration of primary B cells using an endothelial monolayer as substrate.” J Leukoc Biol. 2017 Sep;102(3):941-948. doi: 10.1189/jlb.1TA0117-008R. Epub 2017 Jun 21. (Abstract)
Continue reading →Hart K.M., Moeder K.E., Ho C.M.W., Zimmerman M.I., Frederick T.E., & Bowman G.R. (2017). “Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators.” PLoS One. 2017 Jun 1;12(6):e0178678. doi: 10.1371/journal.pone.0178678. eCollection 2017. (Abstract)
Continue reading →Frieden C., Wang H., & Ho C.M.W. (2017). “A mechanism for lipid binding to apoE and the role of intrinsically disordered regions coupled to domain-domain interactions.” Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6292-6297. doi: 10.1073/pnas.1705080114. Epub 2017 May 30. (Abstract)
Continue reading →Owusu B.Y., Thomas S., Venukadasula P., Han Z., Janetka J.W., Galemmo R.A. Jr., & Klampfer L. (2017). “Targeting the tumor-promoting microenvironment in MET-amplified NSCLC cells with a novel inhibitor of pro-HGF activation.” Oncotarget. 2017 May 29;8(38):63014-63025. doi: 10.18632/oncotarget.18260. eCollection 2017 Sep 8. (Abstract)
Continue reading →Wang H., Shu Q., Frieden C., & Gross M.L. (2017). “Deamidation slows Curli Amyloid-Protein Aggregation.” Biochemistry. 2017 Jun 13;56(23):2865-2872. doi: 10.1021/acs.biochem.7b00241. Epub 2017 May 26. (Abstract)
Continue reading →Mydock-McGrane L.K., Hannan T.J., & Janetka J.W. (2017). “Rational design strategies for FimH antagonists: new drugs on the horizon for urinary tract infection and Crohn’s disease.” Expert Opin Drug Discov. 2017 Jul;12(7):711-731. doi: 10.1080/17460441.2017.1331216. Epub 2017 Jun 2. (Abstract)
Continue reading →Owusu B.Y., Galemmo R., Janetka J., & Klampfer L. (2017). “Hepatocyte Growth Factor, a Key Tumor-Promoting Factor in the Tumor Microenvironment.” Cancers (Basel). 2017 Apr 17;9(4). pii: E35. doi: 10.3390/cancers9040035. (Abstract)
Continue reading →Singh S. & Bowman G.R. (2017). “Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.” J Chem Theory Comput. 2017 Apr 11;13(4):1509-1517. doi: 10.1021/acs.jctc.6b01181. Epub 2017 Mar 22. (Abstract)
Continue reading →Budelier M.M., Cheng W.W.L., Bergdoll L., Chen Z.W., Janetka J.W., Abramson J., Krishnan K., Mydock-McGrane L., Covey D.F., Whitelegge J.P., & Evers A.S. (2017). “Photoaffinity labeling with cholesterol analogues precisely maps a cholesterol-binding site in voltage-dependent anion channel-1.” J Biol Chem. 2017 Jun 2;292(22):9294-9304. doi: 10.1074/jbc.M116.773069. Epub 2017 Apr 10. (Abstract)
Continue reading →Sun X., Laroche G., Wang X., Ågren H., Bowman G.R., Giguère P.M., & Tu Y. (2017). “Propagation of the Allosteric Modulation Induced by Sodium in the δ-Opioid Receptor.” Chemistry. 2017 Apr 3;23(19):4615-4624. doi: 10.1002/chem.201605575. Epub 2017 Mar 20. (Abstract)
Continue reading →Liu G., Nash P.J., Johnson B., Pietzsch C., Ilagan M.X., Bukreyev A., Basler C.F., Bowlin T.L., Moir D.T., Leung D.W., & Amarasinghe G.K. (2017). “A Sensitive in Vitro High-Throughput Screen To Identify Pan-filoviral Replication Inhibitors Targeting the VP35-NP Interface.” ACS Infect Dis. 2017 Mar 10;3(3):190-198. doi: 10.1021/acsinfecdis.6b00209. Epub 2017 Feb 9. (Abstract)
Continue reading →Burgers P.M. & Kunkel T.A. (2017). “Eukaryotic DNA Replication Fork.” Annu Rev Biochem. 2017 Jun 20;86:417-438. doi: 10.1146/annurev-biochem-061516-044709. Epub 2017 Mar 1. (Abstract)
Continue reading →Soranno A., Holla A., Dingfelder F., Nettels D., Makarov D.E., & Schuler B. (2017). “Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations.” Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1833-E1839. doi: 10.1073/pnas.1616672114. Epub 2017 Feb 21. (Abstract)
Continue reading →Budelier M.M., Cheng W.W., Bergdoll L., Chen Z.W., Abramson J., Krishnan K., Qian M., Covey D.F., Janetka J.W., & Evers A.S. (2017). “Click Chemistry Reagent for Identification of Sites of Covalent Ligand Incorporation in Integral Membrane Proteins.” Anal Chem. 2017 Feb 21;89(4):2636-2644. doi: 10.1021/acs.analchem.6b05003. Epub 2017 Feb 9. (Abstract)
Continue reading →Reddy D.R., Ballante F., Zhou N.J., and Marshall G.R. (2017) “Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors.” Eur J Med Chem. 2017 Feb 15;127:531-553. doi: 10.1016/j.ejmech.2016.12.032. Epub 2016 Dec 18. (Abstract)
Continue reading →Ballante F., Reddy D.R., Zhou N.J., and Marshall G.R. (2017) “Structural insights of SmKDAC8 inhibitors: Targeting Schistosoma epigenetics through a combined structure-based 3D QSAR, in vitro and synthesis strategy.” Bioorg Med Chem. 2017 Apr 1;25(7):2105-2132. doi: 10.1016/j.bmc.2017.02.020. Epub 2017 Feb 13. (Abstract)
Continue reading →Kalas V., Pinkner J.S., Hannan T.J., Hibbing M.E., Dodson K.W., Holehouse A.S., Zhang H., Tolia N.H., Gross M.L., Pappu R.V., Janetka J., & Hultgren S.J. (2017). “Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions.” Sci Adv. 2017 Feb 10;3(2):e1601944. doi: 10.1126/sciadv.1601944. eCollection 2017 Feb. (Abstract)
Continue reading →Galburt E.A. & Tomko E.J. (2017). “Conformational selection and induced fit as a useful framework for molecular motor mechanisms.” Biophys Chem. 2017 Apr;223:11-16. doi: 10.1016/j.bpc.2017.01.004. Epub 2017 Feb 3. (Abstract)
Continue reading →Santiago-Tirado F.H., Onken M.D., Cooper J.A., Klein R.S., & Doering T.L. (2017). “Trojan Horse Transit Contributes to Blood-Brain Barrier Crossing of a Eukaryotic Pathogen.” MBio. 2017 Jan 31;8(1). pii: e02183-16. doi: 10.1128/mBio.02183-16. (Abstract)
Continue reading →Garner A.L., Rammohan J., Huynh J.P., Onder L.M., Chen J., Bae B., Jensen D., Weiss L.A., Ruiz Manzano A., Darst S.A., Campbell E.A., Nickels B.E., Galburt E.A., & Stallings C.L. (2016). “Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence.” J Bacteriol. 2017 Jan 30;199(4). pii: e00698-16. doi: 10.1128/JB.00698-16. Print 2017 Feb 15. (Abstract)
Continue reading →Istvan E.S., Mallari J.P., Corey V.C., Dharia N.V., Marshall G.R., Winzeler E.A., and Goldberg D.E. (2017) “Esterase mutation is a mechanism of resistance to antimalarial compounds.” Nat Commun. 2017 Jan 20;8:14240. doi: 10.1038/ncomms14240. (Abstract)
Continue reading →Chang Y.K., Srivastava Y., Hu C., Joyce A., Yang X., Zuo Z., Havranek J.J., Stormo G.D., and Jauch R. (2017) “Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.” Nucleic Acids Res. 2017 Jan 25;45(2):832-845. doi: 10.1093/nar/gkw1198. Epub 2016 Dec 2. (Abstract)
Continue reading →Hayatshahi H.S., Roe D.R., Galindo-Murillo R., Hall K.B., & Cheatham T.E. 3rd (2017). “Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in the GTPase-Associating Center RNA.” J Phys Chem B. 2017 Jan 26;121(3):451-462. doi: 10.1021/acs.jpcb.6b08764. Epub 2017 Jan 17. (Abstract)
Continue reading →Greenberg M.J., Shuman H., & Ostap E.M. (2017). “Measuring the Kinetic and Mechanical Properties of Non-processive Myosins Using Optical Tweezers.” Methods Mol Biol. 2017;1486:483-509. doi: 10.1007/978-1-4939-6421-5_19. (Abstract)
Continue reading →Galburt E.A. & Rammohan J. (2016). “A Kinetic Signature for Parallel Pathways: Conformational Selection and Induced Fit. Links and Disconnects between Observed Relaxation Rates and Fractional Equilibrium Flux under Pseudo-First-Order Conditions.” Biochemistry. 2016 Dec 20;55(50):7014-7022. Epub 2016 Dec 8. (Abstract)
Continue reading →Yang Y., Ke N., Liu S., & Li W. (2016). “Methods for Structural and Functional Analyses of Intramembrane Prenyltransferases in the UbiA Superfamily.” Methods Enzymol. 2017;584:309-347. doi: 10.1016/bs.mie.2016.10.032. Epub 2016 Dec 7. (Abstract)
Continue reading →Brosey C.A., Ho C., Long W.Z., Singh S., Burnett K., Hura G.L., Nix J.C., Bowman G.R., Ellenberger T., & Tainer J.A. (2016). “Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor” Structure. 2016 Dec 6;24(12):2067-2079. doi: 10.1016/j.str.2016.09.012. Epub 2016 Nov 3. (Abstract)
Continue reading →Shen G., Cui W., Zhang H., Zhou F., Huang W., Liu Q., Yang Y., Li S., Bowman G.R., Sadler J.E., Gross M.L., & Li W. (2017). “Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer.” Nat Struct Mol Biol. 2017 Jan;24(1):69-76. doi: 10.1038/nsmb.3333. Epub 2016 Dec 5. (Abstract)
Continue reading →Kochenova O.V., Bezalel-Buch R., Tran P., Makarova A.V., Chabes A., Burgers P.M., & Shcherbakova P.V. (2016). “Yeast DNA polymerase ζ maintains consistent activity and mutagenicity across a wide range of physiological dNTP concentrations.” Nucleic Acids Res. 2017 Feb 17;45(3):1200-1218. doi: 10.1093/nar/gkw1149. (Abstract)
Continue reading →Kraft T.E., Heitmeier M.R., Putanko M., Edwards R.L., Ilagan M.X., Payne M.A., Autry J.M., Thomas D.D., Odom A.R., and Hruz P.W. (2016) “A Novel Fluorescence Resonance Energy Transfer-Based Screen in High-Throughput Format To Identify Inhibitors of Malarial and Human Glucose Transporters.” Antimicrob Agents Chemother. 2016 Nov 21;60(12):7407-7414. Print 2016 Dec. (Abstract)
Continue reading →Michael Kinch (2016) “A Prescription for Change: The Looming Crisis in Drug Development” (ISBN-13: 978-1469630625, ISBN-10: 1469630621)
Continue reading →Needham S.R., Roberts S.K., Arkhipov A., Mysore V.P., Tynan C.J., Zanetti-Domingues L.C., Kim E.T., Losasso V., Korovesis D., Hirsch M., Rolfe D.J., Clarke D.T., Winn M.D., Lajevardipour A., Clayton A.H., Pike L.J., Perani M., Parker P.J., Shan Y., Shaw D.E., & Martin-Fernandez M.L. (2016). “EGFR oligomerization organizes kinase-active dimers into competent signalling platforms.” Nat Commun. 2016 Oct 31;7:13307. doi: 10.1038/ncomms13307. (Abstract)
Continue reading →Mydock-McGrane L., Cusumano Z., Han Z., Binkley J., Kostakioti M., Hannan T., Pinkner J.S., Klein R.D., Kalas V., Crowley J., Rath N.P., Hultgren S.J., & Janetka J.W. (2016). “Antivirulence C-Mannosides as Antibiotic-Sparing, Oral Therapeutics for Urinary Tract Infections.” J Med Chem. 2016 Oct 27;59(20):9390-9408. Epub 2016 Oct 14. (Abstract)
Continue reading →Zhou J.Y., Szasz T.P., Stewart-Hutchinson P.J., Sivapalan J., Todd E.M., Deady L.E., Cooper J.A., Onken M.D., & Morley S.C. (2016). “L-Plastin promotes podosome longevity and supports macrophage motility.” Mol Immunol. 2016 Oct;78:79-88. doi: 10.1016/j.molimm.2016.08.012. Epub 2016 Sep 7. (Abstract)
Continue reading →Hart K.M., Ho C.M., Dutta S., Gross M.L., & Bowman G.R. (2016). “Modelling proteins’ hidden conformations to predict antibiotic resistance.” Nat Commun. 2016 Oct 6;7:12965. doi: 10.1038/ncomms12965. (Abstract)
Continue reading →Welty R. & Hall K.B. (2016). “Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.” J Mol Biol. 2016 Nov 6;428(22):4490-4502. doi: 10.1016/j.jmb.2016.09.015. Epub 2016 Sep 29. (Abstract)
Continue reading →Thomas J.J., Abed M., Heuberger J., Novak R., Zohar Y., Beltran Lopez A.P., Trausch-Azar J.S., Ilagan M.X., Benhamou D., Dittmar G., Kopan R., Birchmeier W., Schwartz A.L., and Orian A. (2016) “RNF4-Dependent Oncogene Activation by Protein Stabilization.” Cell Rep. 2016 Sep 20;16(12):3388-3400. doi: 10.1016/j.celrep.2016.08.024. (Abstract)
Continue reading →Xu X., Wang X., Todd E.M., Jaeger E.R., Vella J.L., Mooren O.L., Feng Y., Hu J., Cooper J.A., Morley S.C., & Huang Y.H. (2016). “Mst1 Kinase Regulates the Actin-Bundling Protein L-Plastin To Promote T Cell Migration.” J Immunol. 2016 Sep 1;197(5):1683-91. doi: 10.4049/jimmunol.1600874. Epub 2016 Jul 27. (Abstract)
Continue reading →Mi Y., Coonce M., Fiete D., Steirer L., Dveksler G., Townsend R.R., & Baenziger J.U. (2016). “Functional Consequences of Mannose and Asialoglycoprotein Receptor Ablation.” J Biol Chem. 2016 Sep 2;291(36):18700-17. doi: 10.1074/jbc.M116.738948. Epub 2016 Jul 12. (Abstract)
Continue reading →Borgia A., Zheng W., Buholzer K., Borgia M.B., Schüler A., Hofmann H., Soranno A., Nettels D., Gast K., Grishaev A., Best R.B., & Schuler B. (2016). “Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.” J Am Chem Soc. 2016 Sep 14;138(36):11714-26. doi: 10.1021/jacs.6b05917. Epub 2016 Sep 1. (Abstract)
Continue reading →Pascolutti R., Sun X., Kao J., Maute R., Ring A.M., Bowman G.R., & Kruse A.C. (2016). “Structure and Dynamics of PD-L1 and an Ultra High-Affinity PD-1 Receptor Mutant.” Structure. 2016 Oct 4;24(10):1719-1728. doi: 10.1016/j.str.2016.06.026. Epub 2016 Sep 8. (Abstract)
Continue reading →Xiao Z., Banan B., Xu M., Jia J., Manning P.T., Hiebsch R.R., Gunasekaran M., Upadhya G.A., Frazier W.A., Mohanakumar T., Lin Y., & Chapman W.C. (2016). “Attenuation of Ischemia-Reperfusion Injury and Improvement of Survival in Recipients of Steatotic Rat Livers Using CD47 Monoclonal Antibody.” Transplantation. 2016 Jul;100(7):1480-9. doi: 10.1097/TP.0000000000001186. (Abstract)
Continue reading →Smith J.A., Xu G., Feng R., Janetka J.W., & Moeller, K.D. (2016). “C‐Glycosides, Array‐based Addressable Libraries, and the Versatility of Constant Current Electrochemistry” Electroanalysis. 2016, Volume 28, Issue 11, Pages: 2808-2817. DOI: 10.1002/elan.201600200 (Abstract)
Continue reading →Woody M.S., Lewis J.H., Greenberg M.J., Goldman Y.E., & Ostap E.M. (2016). “MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood Estimation.” Biophys J. 2016 Jul 26;111(2):273-282. doi: 10.1016/j.bpj.2016.06.019. (Abstract)
Continue reading →Simon M., Sokoloski J., Hao L., Weiland E., & Lohman T. (2016). “Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation.” J Mol Biol. 2016 Jul 31;428(15):2997-3012. doi: 10.1016/j.jmb.2016.07.002. Epub 2016 Jul 14. (Abstract)
Continue reading →Bergonzo C., Hall K.B, & Cheatham T.E. (2016). “Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.” J Chem Theory Comput. 2016 Jul 12;12(7):3382-9. doi: 10.1021/acs.jctc.6b00173. Epub 2016 Jun 28. (Abstract)
Continue reading →Schuler B., Soranno A., Hofmann H., & Nettels D. (2016). “Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.” Annu Rev Biophys. 2016 Jul 5;45:207-31. doi: 10.1146/annurev-biophys-062215-010915. Epub 2016 May 2. (Abstract)
Continue reading →Stojkovic G., Makarova A.V., Wanrooij P.H., Forslund J., Burgers P.M., & Wanrooij S. (2016). “Oxidative DNA damage stalls the human mitochondrial replisome.” Sci Rep. 2016 Jul 1;6:28942. doi: 10.1038/srep28942. (Abstract)
Continue reading →Shu Q., Krezel A.M., Cusumano Z.T., Pinkner J.S., Klein R., Hultgren S.J., & Frieden C. (2016). “Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.” Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7130-5. doi: 10.1073/pnas.1607222113. Epub 2016 Jun 13. (Abstract)
Continue reading →Rammohan J., Ruiz Manzano A., Garner A.L., Prusa J. Stallings C.L., & Galburt E.A. (2016). “Cooperative stabilization of Mycobacterium tuberculosis rrnAP3 promoter open complexes by RbpA and CarD.” Nucleic Acids Res. 2016 Sep 6;44(15):7304-13. doi: 10.1093/nar/gkw577. Epub 2016 Jun 24. (Abstract)
Continue reading →Kinch M.S. and Moore R. (2016) “Innovator Organizations in New Drug Development: Assessing the Sustainability of the Biopharmaceutical Industry.” Cell Chem Biol. 2016 Jun 23;23(6):644-53. doi: 10.1016/j.chembiol.2016.05.013. (Abstract)
Continue reading →Greenberg M.J., Arpag G., Tuzel E., & Ostap E.M. (2016). “A Perspective on the Role of Myosins as Mechanosensors.” Biophys J. 2016 Jun 21;110(12):2568-2576. doi: 10.1016/j.bpj.2016.05.021. (Abstract)
Continue reading →Fishburn J., Galburt E., & Hahn S. (2016). “Transcription Start Site Scanning and the Requirement for ATP during Transcription Initiation by RNA Polymerase II.” J Biol Chem. 2016 Jun 17;291(25):13040-7. doi: 10.1074/jbc.M116.724583. Epub 2016 Apr 17. (Abstract)
Continue reading →Babaei B., Davarian A., Lee S.L., Pryse K.M., McConnaughey W.B., Elson E.L., & Genin G.M. (2016). “Remodeling by fibroblasts alters the rate-dependent mechanical properties of collagen.” Acta Biomater. 2016 Jun;37:28-37. doi: 10.1016/j.actbio.2016.03.034. Epub 2016 Mar 23. (Abstract)
Continue reading →Cho J.E., Huang S.N., Burgers P.M., Shuman S., Pommier Y., & Jinks-Robertson S. (2016). “Parallel analysis of ribonucleotide-dependent deletions produced by yeast Top1 in vitro and in vivo.” Nucleic Acids Res. 2016 Sep 19;44(16):7714-21. doi: 10.1093/nar/gkw495. Epub 2016 Jun 1. (Abstract)
Continue reading →Stodola J.L., Stith C.M., & Burgers P.M. (2016). “Proficient Replication of the Yeast Genome by a Viral DNA Polymerase.” J Biol Chem. 2016 May 27;291(22):11698-705. doi: 10.1074/jbc.M116.728741. Epub 2016 Apr 12. (Abstract)
Continue reading →Stodola J.L. & Burgers P.M. (2016). “Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale.” Nat Struct Mol Biol. 2016 May;23(5):402-8. doi: 10.1038/nsmb.3207. Epub 2016 Apr 11. (Abstract)
Continue reading →Waldman V.M., Weiland E., Kozlov A.G., & Lohman T.M. (2016). “Is a fully wrapped SSB-DNA complex essential for Escherichia coli survival?” Nucleic Acids Res. 2016 May 19;44(9):4317-29. doi: 10.1093/nar/gkw262. Epub 2016 Apr 15. (Abstract)
Continue reading →Sokoloski J.E., Kozlov A.G., Galletto R., & Lohman T.M. (2016). “Chemo-mechanical pushing of proteins along single-stranded DNA.” Proc Natl Acad Sci U S A. 2016 May 31;113(22):6194-9. doi: 10.1073/pnas.1602878113. Epub 2016 May 16. (Abstract)
Continue reading →Chowdhury F., Li I., Ngo T., Leslie B., Kim B., Sokoloski J., Weiland E., Wang X., Chemla Y., Lohman T., & Ha T. (2016). “Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo.” Nano Lett. 2016 Jun 8;16(6):3892-7. doi: 10.1021/acs.nanolett.6b01403. Epub 2016 May 12. (Abstract)
Continue reading →Krishna U., Romero-Gallo J., Suarez G., Azah A., Krezel A.M., Varga M.G., Forsyth M.H., & Peek R.M. Jr. (2016). “Genetic Evolution of a Helicobacter pylori Acid-Sensing Histidine Kinase and Gastric Disease.” J Infect Dis. 2016 Aug 15;214(4):644-8. doi: 10.1093/infdis/jiw189. Epub 2016 May 10. (Abstract)
Continue reading →Koc K.N., Singh S.P., Stodola J.L., Burgers P.M., & Galletto R. (2016). “Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ.” Nucleic Acids Res. 2016 May 5;44(8):3811-9. doi: 10.1093/nar/gkw181. Epub 2016 Mar 21. (Abstract)
Continue reading →Sawicka, M., Wanrooij, P.H., Darbari, V.C., Tannous, E., Hailemariam, S., Bose, D., Makarova, A.V., Burgers, P.M. and Zhang, X.
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The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization.
J Biol Chem 291:13436-47 (2016) (Abstract)Mondal T., Wang H., DeKoster G.T., Baban B., Gross M.L., & Frieden C. (2016). “ApoE: In Vitro Studies of a Small Molecule Effector.” Biochemistry. 2016 May 10;55(18):2613-21. doi: 10.1021/acs.biochem.6b00324. Epub 2016 Apr 27. (Abstract)
Continue reading →Weikai Li
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Bringing Bioactive Compounds into Membranes: The UbiA Superfamily of Intramembrane Aromatic Prenyltransferases.
Trends Biochem Sci. 41(4):356-70. (2016) (Abstract)Wang Q., Heizer E., Rosa B.A., Wildman S.A., Janetka J.W., & Mitreva, M. (2016). “Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.” Infect Genet Evol. 2016 Apr;39:201-211. doi: 10.1016/j.meegid.2016.01.025. Epub 2016 Jan 30. (Abstract)
Continue reading →Wang X., Galletta B.J., Cooper J.A., & Carlsson A.E. (2016). “Actin-Regulator Feedback Interactions during Endocytosis.”
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Biophys J. 2016 Mar 29;110(6):1430-43. doi: 10.1016/j.bpj.2016.02.018. (Abstract)Singh, S.P., Koc, K.N., Stodola, J.L. and Galletto, R.
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A Monomer of Pif1 Unwinds Double-Stranded DNA and It Is Regulated by the Nature of the Non-Translocating Strand at the 3′-End.
J Mol Biol 428:1053-1067 (2016). (Abstract)Han Z., Harris P.K.W., Karmakar P., Kim T., Owusu B.Y., Wildman S.A., Klampfer, L., & Janetka J.W. (2016). “α-Ketobenzothiazole Serine Protease Inhibitors of Aberrant HGF/c-MET and MSP/RON Kinase Pathway Signaling in Cancer.” ChemMedChem. 2016 Mar 17;11(6):585-99. doi: 10.1002/cmdc.201500600. Epub 2016 Feb 17. (Abstract)
Continue reading →Simpson C., Jones N.G., Hull-Ryde E.A., Kireev D., Stashko M., Tang K., Janetka J., Wildman S.A., Zuercher W.J., Schapira M., Hui R., Janzen W., & Sibley L.D. (2016). “Identification of small molecule inhibitors that block the Toxoplasma gondii rhoptry kinase ROP18.” ACS Infect Dis. 2016 Mar 11;2(3):194-206. Epub 2015 Dec 28. (Abstract)
Continue reading →Ronan T., Macdonald-Obermann J.L., Huelsmann L., Bessman N.J., Naegle K.M., & Pike L.J. (2016). “Different Epidermal Growth Factor Receptor (EGFR) Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Proteins.” J Biol Chem. 2016 Mar 11;291(11):5528-40. doi: 10.1074/jbc.M115.710087. Epub 2016 Jan 19. (Abstract)
Continue reading →Bowman G.R.
Continue reading →
Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation.
J Comput Chem. 37(6):558-66. (2016) (Abstract)Lisica A., Engel C., Jahnel M., Roldán É., Galburt E.A., Cramer P., & Grill S.W. (2016). “Mechanisms of backtrack recovery by RNA polymerases I and II.” Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2946-51. doi: 10.1073/pnas.1517011113. Epub 2016 Feb 29. (Abstract)
Continue reading →Reddy D.N., Ballante F., Chuang T., Pirolli A., Marrocco B., and Marshall G.R. (2016) “Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors.” J Med Chem. 2016 Feb 25;59(4):1613-33. doi: 10.1021/acs.jmedchem.5b01632. Epub 2016 Jan 7. (Abstract)
Continue reading →Burgers, P.M., Gordenin, D. and Kunkel, T.A.
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Who Is Leading the Replication Fork, Pol ε or Pol δ?
Mol Cell. 61:492-493 (2016). (Abstract)Elson E.L. & Genin G.M. (2016). “Tissue constructs: platforms for basic research and drug discovery.” Interface Focus. 2016 Feb 6;6(1):20150095. doi: 10.1098/rsfs.2015.0095. (Abstract)
Continue reading →Li Y., Huang G., Li M., Wang L., Elson E.L., Lu T.J., Genin G.M., & Xu F. (2016). “An approach to quantifying 3D responses of cells to extreme strain.” Sci Rep. 2016 Feb 18;6:19550. doi: 10.1038/srep19550. (Abstract)
Continue reading →Jarvis C., Han Z., Kalas V., Klein R., Pinkner J.S., Ford B., Binkley J., Cusumano C.K., Cusumano Z., Mydock-McGrane L., Hultren S.J., & Janetka J.W. (2016). “Antivirulence Isoquinolone Mannosides: Optimization of the Biaryl Aglycone for FimH Lectin Binding Affinity and Efficacy in the Treatment of Chronic UTI.” ChemMedChem. 2016 Feb 17;11(4):367-73. doi: 10.1002/cmdc.201600006. Epub 2016 Jan 26. (Abstract)
Continue reading →Ballante F. and Marshall G.R. (2016) “An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design.” J Chem Inf Model. 2016 Jan 25;56(1):54-72. doi: 10.1021/acs.jcim.5b00603. Epub 2016 Jan 6. (Abstract)
Continue reading →Mydock-McGrane L.K., Cusumano Z.T., & Janetka J.W. (2016). “Mannose-derived FimH antagonists: a promising anti-virulence therapeutic strategy for urinary tract infections and Crohn’s disease.” Expert Opin Ther Pat. 2016;26(2):175-97. doi: 10.1517/13543776.2016.1131266. Epub 2016 Jan 22. (Abstract)
Continue reading →Wanrooij, P.H, Tannous, E., Kumar, S., Navadgi-Patil, V.M. and Burgers, P.M.
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Probing the Mec1ATR Checkpoint Activation Mechanism with Small Peptides.
J Biol Chem 291:1076-1091 (2016). (Abstract)Babaei B., Abramowitch S.D., Elson E.L., Thomopoulos S., & Genin G.M. (2015). “A discrete spectral analysis for determining quasi-linear viscoelastic properties of biological materials.” J R Soc Interface. 2015 Dec 6;12(113):20150707. doi: 10.1098/rsif.2015.0707. (Abstract)
Continue reading →Zimmerman, M.I. and Bowman, G.R.
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FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs
J. Chem. Theory Comput. 11:5747-5757 (2015). (Abstract)Stark B.C. & Cooper J.A. (2015). “Differential expression of CARMIL-family genes during zebrafish development.” Cytoskeleton (Hoboken). 2015 Oct;72(10):534-41. doi: 10.1002/cm.21257. Epub 2015 Oct 23. (Abstract)
Continue reading →Zhang C., Myers C.A., Qi Z., Mitra R.D., Corbo J.C., and Havranek J.J. (2015) “Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex.” Nucleic Acids Res. 2015 Oct 15;43(18):9076-85. doi: 10.1093/nar/gkv901. Epub 2015 Sep 13. (Abstract)
Continue reading →Wang H., Shu Q., Rempel D.L., Frieden C., & Gross M.L. (2015). “Continuous and pulsed hydrogen-deuterium exchange and mass spectrometry characterize CsgE oligomerization.” Biochemistry. 2015 Oct 27;54(42):6475-81. doi: 10.1021/acs.biochem.5b00871. Epub 2015 Oct 14. (Abstract)
Continue reading →Wang Q., Rosa B.A., Nare B., Powell K., Valente S., Rotili D., Mai A., Marshall G.R., and Mitreva M. (2015) “Targeting Lysine Deacetylases (KDACs) in Parasites.” PLoS Negl Trop Dis. 2015 Sep 24;9(9):e0004026. doi: 10.1371/journal.pntd.0004026. eCollection 2015. (Abstract)
Continue reading →Bergonzo C., Hall K.B., & Cheatham T.E. 3rd. (2015). “Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions.” J Phys Chem B. 2015 Sep 24;119(38):12355-64. doi: 10.1021/acs.jpcb.5b05190. Epub 2015 Sep 14. (Abstract)
Continue reading →Liu X., Pu Y., Cron K., Deng L., Kline J., Frazier W.A., Xu H., Peng H., Fu Y.X., & Xu M.M. (2015). “CD47 blockade triggers T cell-mediated destruction of immunogenic tumors.” Nat Med. 2015 Oct;21(10):1209-15. doi: 10.1038/nm.3931. Epub 2015 Aug 31. (Abstract)
Continue reading →Suksombat S., Khafizov R., Kozlov A.G., Lohman T.M., & Chemla Y.R. (2015). “Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways.” Elife. 2015 Aug 25;4. doi: 10.7554/eLife.08193. (Abstract)
Continue reading →Zhang R., Alushin G.M., Brown A., & Nogales E. (2015) “Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins.” Cell. 2015 Aug 13;162(4):849-59. doi: 10.1016/j.cell.2015.07.012. Epub 2015 Jul 30. (Abstract)
Continue reading →Rau M.J., Welty R., Stump T.W., & Hall K.B. (2015). “Formation of Tertiary Interactions during rRNA GTPase Center Folding.” J Mol Biol. 2015 Aug 28;427(17):2799-815. doi: 10.1016/j.jmb.2015.07.013. Epub 2015 Jul 22. (Abstract)
Continue reading →Kee A.J., Yang L., Lucas C.A., Greenberg M.J., Martel N., Leong G.M., Hughes W.E., Cooney G.J., James D.E., Ostap E.M., Han W., Gunning P.W., & Hardeman E.C. (2015). “An actin filament population defined by the tropomyosin Tpm3.1 regulates glucose uptake.” Traffic. 2015 Jul;16(7):691-711. doi: 10.1111/tra.12282. Epub 2015 Apr 29. (Abstract)
Continue reading →Sasaki Y., Margolin Z., Borgo B., Havranek J.J., & Milbrandt J. (2015). “Characterization of Leber Congenital Amaurosis-associated NMNAT1 Mutants.” J Biol Chem. 2015 Jul 10;290(28):17228-38. doi: 10.1074/jbc.M115.637850. Epub 2015 May 27. (Abstract)
Continue reading →Greene S.E., Hibbing M.E., Janetka J., Chen S.L., & Hultgren S.J. (2015). “Human Urine Decreases Function and Expression of Type 1 Pili in Uropathogenic Escherichia coli.” MBio. 2015 Jun 30;6(4):e00820. doi: 10.1128/mBio.00820-15. (Abstract)
Continue reading →Greenberg M.J., Lin T., Shuman H., & Ostap E.M. (2015). “Mechanochemical tuning of myosin-I by the N-terminal region.” Proc Natl Acad Sci U S A. 2015 Jun 30;112(26):E3337-44. doi: 10.1073/pnas.1506633112. Epub 2015 Jun 8. (Abstract)
Continue reading →Kukshal V., Kim I.K., Hura G.L., Tomkinson A.E., Tainer J.A., & Ellenberger T. (2015). “Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining.” Nucleic Acids Res. 2015 Aug 18;43(14):7021-31. doi: 10.1093/nar/gkv652. Epub 2015 Jun 29. (Abstract)
Continue reading →Liu K.E. & Frazier W.A. (2015). “Phosphorylation of the BNIP3 C-Terminus Inhibits Mitochondrial Damage and Cell Death without Blocking Autophagy.” PLoS One. 2015 Jun 23;10(6):e0129667. doi: 10.1371/journal.pone.0129667. eCollection 2015. (Abstract)
Continue reading →Bowman, G.R.
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Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation.
J Comput Chem 37:558-566 (2016) (Abstract)Rowe R.A., Pryse K.M., Asnes C.F., Elson E.L., & Genin G.M. (2015). “Collective matrix remodeling by isolated cells: unionizing home improvement do-it-yourselfers.” Biophys J. 2015 Jun 2;108(11):2611-2. doi: 10.1016/j.bpj.2015.04.026. (Abstract)
Continue reading →Chen X., Kim I.K., Honaker Y., Paudval S.C., Koh W.K., Sparks M., Lis S., Piwnica-Worms H., Ellenberger T., & You Z. (2015). “14-3-3 proteins restrain the Exo1 nuclease to prevent overresection. J Biol Chem. 2015 May 8;290(19):12300-12. doi: 10.1074/jbc.M115.644005. Epub 2015 Apr 1. (Abstract)
Continue reading →Pascal J.M., & Ellenberger T. (2015). “The rise and fall of poly(ADP-ribose): An enzymatic perspective. DNA Repair (Amst). 2015 Aug;32:10-6. doi: 10.1016/j.dnarep.2015.04.008. Epub 2015 May 1. (Abstract)
Continue reading →Franco F.M., Jones D.E., Harris P.K., Han Z., Wildman S.A., Jarvis C.M., & Janetka J.W. (2015). “Structure-based discovery of small molecule hepsin and HGFA protease inhibitors: Evaluation of potency and selectivity derived from distinct binding pockets.” Bioorg Med Chem. 2015 May 15;23(10):2328-43. doi: 10.1016/j.bmc.2015.03.072. Epub 2015 Apr 4. (Abstract)
Continue reading →Feldmann, E.A., De Bona, P. and Galletto, R.
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The wrapping loop and Rap1 C-terminal (RCT) domain of yeast Rap1 modulate access to different DNA binding modes.
Journal of Biological Chemistry 290:11455-11466 (2015). (Abstract)Wanrooij, P.H. and Burgers, P.M.
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Yet another job for Dna2: Checkpoint activation.
DNA Repair 43:4179-4190 (2015). (Abstract)Koc, K.N., Stodola, J.L, Burgers, P.M. and Galletto, R.
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Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5′-flaps.
Nucleic Acid Research 43:4179-4190. (2015). (Abstract)Petrova V., Chen S.H., Molzberger E.T., Tomko E., Chitteni-Pattu S., Jia H., Ordabayev Y., Lohman T.M., & Cox M.M. (2015). “Active displacement of RecA filaments by UvrD translocase activity.” Nucleic Acids Res. 2015 Apr 30;43(8):4133-49. doi: 10.1093/nar/gkv186. Epub 2015 Mar 30. (Abstract)
Continue reading →Hall K.B. (2015). “Mighty tiny.” RNA. 2015 Apr;21(4):630-1. doi: 10.1261/rna.050567.115. (Abstract)
Continue reading →Kuster D.J., Liu C., Ponder J.W., & Marshall G.R. (2015). “High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.” PLoS One. 2015 Apr 20;10(4):e0123146. doi: 10.1371/journal.pone.0123146. eCollection 2015. (Abstract)
Continue reading →Comstock M.J., Whitley K.D., Jia H., Sokoloski J., Lohman T.M., Ha T., & Chemla Y.R. (2015). “Protein structure. Direct observation of structure-function relationship in a nucleic acid-processing enzyme.” Science. 2015 Apr 17;348(6232):352-4. doi: 10.1126/science.aaa0130. Epub 2015 Apr 16. (Abstract)
Continue reading →Koc, K.N., Stodola, J.L., Burgers, P.M., and Galletto, R.
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Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5′-flaps.
Nucleic Acid Research 43:4179-4190 (2015). (Abstract)Ghisays F., Brace C.S., Yackly S.M., Kwon H.J., Mills K.F., Kashentseva E., Dmitriev I.P., Curiel D.T., Imai S.I., & Ellenberger T. (2015). “The N-Terminal Domain of SIRT1 Is a Positive Regulator of Endogenous SIRT1-Dependent Deacetylation and Transcriptional Outputs.” Cell Rep. 2015 Mar 10. pii: S2211-1247(15)00182-5. doi: 10.1016/j.celrep.2015.02.036. (Abstract)
Continue reading →Fishburn J., Tomko E., Galburt E., & Hahn S. (2015). “Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation.” Proc Natl Acad Sci U S A. 2015 Mar 31;112(13):3961-6. doi: 10.1073/pnas.1417709112. Epub 2015 Mar 16. (Abstract)
Continue reading →Sparks, J.L. and Burgers, P.M.
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Error-free and mutagenic processing of topoisomerase 1-provoked damage at genomic ribonucleotides.
EMBO J. 34:1259-1269 (2015). (Abstract)Williams, J.S., Clausen, A.R., Lujan, S.A., Marjavaara, L., Clark, A.B., Burgers, P.M., Chabes, A. and Kunkel, T.A.
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Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific.
Nat Struct Mol Biol. 22:291-297 (2015). (Abstract)Babaei B., Davarian A., Pryse K.M., Elson E.L., & Genin G.M. (2015). “Efficient and optimized identification of generalized Maxwell viscoelastic relaxation spectra.” J Mech Behav Biomed Mater. 2015 Mar;55:32-41. doi: 10.1016/j.jmbbm.2015.10.008. Epub 2015 Oct 17. (Abstract)
Continue reading →Melnykov A.V., Nayak R.K., Hall K.B., & Van Orden A. (2015). “Effect of loop composition on the stability and folding kinetics of RNA hairpins with large loops.” Biochemistry. 2015 Mar 17;54(10):1886-96. doi: 10.1021/bi5014276. Epub 2015 Mar 4. (Abstract)
Continue reading →Rau M.J. & Hall K.B. (2015). “2-Aminopurine Fluorescence as a Probe of Local RNA Structure and Dynamics and Global Folding.” Methods Enzymol. 2015;558:99-124. doi: 10.1016/bs.mie.2015.01.006. Epub 2015 Mar 3. (Abstract)
Continue reading →Feldmann, E.A., Koc, K.N. and Galletto, R.
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Alternative arrangements of telomeric recognition sites regulate the binding mode of the DNA-binding domain of yeast Rap1.
Biophysical Chemistry 198:1-8 (2015). (Abstract)Kozlov A.G., Weiland E., Mittal A., Waldman V., Antony E., Fazio N., Pappu R.V., & Lohman T.M. (2015). “Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA.” J Mol Biol. 2015 Feb 27;427(4):763-74. doi: 10.1016/j.jmb.2014.12.020. Epub 2015 Jan 3. (Abstract)
Continue reading →Kim I.K., Stegeman R.A., Brosey C.A., & Ellenberger T. (2015). “A quantitative assay reveals ligand specificity of the DNA scaffold repair protein XRCC1 and efficient disassembly of complexes of XRCC1 and the poly(ADP-ribose) polymerase 1 by poly(ADP-ribose) glycohydrolase.” J Biol Chem. 2015 Feb 6;290(6):3775-83. doi: 10.1074/jbc.M114.624718. Epub 2014 Dec 4. (Abstract)
Continue reading →Xiao Z.Y., Chung H., Banan B., Manning P.T., Ott K.C., Lin S., Capoccia B.J., Subramanian V., Hiebsch R.R., Upadhya G., Mohanakumar T., Frazier W.A., Lin Y., & Chapman W.C. (2015). “Antibody mediated therapy targeting CD47 inhibits tumor progression of hepatocellular carcinoma.” Cancer Lett. 2015 May 1;360(2):302-9. doi: 10.1016/j.canlet.2015.02.036. Epub 2015 Feb 23. (Abstract)
Continue reading →Rammohan J., Ruiz Manzano A., Garner A.L., Stallings C.L., & Galburt E.A. (2015). “CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism.” Nucleic Acids Res. 2015 Mar 31;43(6):3272-85. doi: 10.1093/nar/gkv078. Epub 2015 Feb 19. (Abstract)
Continue reading →Makarova, A.V. and Burgers, P.M.
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Eukaryotic DNA polymerase ζ.
DNA Repair S1568-7864:00048 (2015). (Abstract)DuBay, K.H., Bowman, G.R. and Geissler, P.L.
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Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation
Acc. Chem. Res. 48:1098-1105 (2015). (Abstract)Amend S.R., Uluckan O., Hurchla M., Leib D., Novack D.V., Silva M., Frazier W., & Weilbaecher K.N. (2015). “Thrombospondin-1 regulates bone homeostasis through effects on bone matrix integrity and nitric oxide signaling in osteoclasts.” J Bone Miner Res. 2015 Jan;30(1):106-15. doi: 10.1002/jbmr.2308. (Abstract)
Continue reading →Xiao Z.Y., Banan B., Jia J., Manning P.T., Hiebsch R.R., Gunasekaran M., Upadhya G., Frazier W.A., Mohanakumar T., & Chapman W.C. (2015). “CD47 blockade reduces ischemia/reperfusion injury and improves survival in a rat liver transplantation model.” Liver Transpl. 2015 Apr;21(4):468-477. doi: 10.1002/lt.24059. Epub 2015 Jan 29. (Abstract)
Continue reading →Bowman, G.R. Bolin, E.R., Hart, K.M., Maguire, B.C. and Marqusee, S.
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Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
PNAS 112:2734-2739 (2015). (Abstract)Wu E.Y., Walsh A.R., Materne E.C., Hiltner E.P., Zielinski B., Miller B.R. 3rd, Mawby L., Modeste E., Parish C.A., Barnes W.M., & Kermekchiev M.B. (2015). “A conservative isoleucine to leucine mutation causes major rearrangements and cold sensitivity in KlenTaq1 DNA polymerase.” Biochemistry. 2015 Jan 27;54(3):881-9. doi: 10.1021/bi501198f. Epub 2015 Jan 9. (Abstract)
Continue reading →Joyce A.P., Zhang C., Bradley P., & Havranek J.J. (2015). “Structure-based modeling of protein: DNA specificity.” Brief Funct Genomics. 2015 Jan;14(1):39-49. doi: 10.1093/bfgp/elu044. Epub 2014 Nov 19. (Abstract)
Continue reading →Greenberg M.J., Shuman H., & Ostap E.M. (2014). “Inherent force-dependent properties of β-cardiac myosin contribute to the force-velocity relationship of cardiac muscle.” Biophys J. 2014 Dec 16;107(12):L41-4. doi: 10.1016/j.bpj.2014.11.005. (Abstract)
Continue reading →Feldmann, E.A. and Galletto, R.
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The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes.
Biochemistry 33:7471-7483 (2014). (Abstract)Frieden C. (2015). “ApoE: the role of conserved residues in defining function.” Protein Sci. 2015 Jan;24(1):138-44. doi: 10.1002/pro.2597. Epub 2014 Dec 9. (Abstract)
Continue reading →Liu C., Ponder J.W., and Marshall G.R. (2014) “Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence.” Proteins. 2014 Nov;82(11):3043-61. doi: 10.1002/prot.24665. Epub 2014 Sep 20. (Abstract)
Continue reading →Han Z., Harris P.K., Jones D.E., Chugani R., Kim T., Agarwal M., Shen W., Wildman S.A., & Janetka J.W. (2014). “Inhibitors of HGFA, Matriptase, and Hepsin Serine Proteases: A Nonkinase Strategy to Block Cell Signaling in Cancer.” ACS Med Chem Lett. 2014 Oct 9;5(11):1219-24. doi: 10.1021/ml500254r. eCollection 2014 Nov 13. (Abstract)
Continue reading →Galburt E.A. (2014). “Magnetic Tweezers Force Spectroscopy” Handbook of Imaging in Biological Mechanics. Chapter 38. DOI: 10.1201/b17566-51. ISBN: 9781466588134. (Abstract)
Continue reading →Garai K., Verghese P.B., Baban B., Holtzman D.M., & Frieden C. (2014). “The binding of apolipoprotein E to oligomers and fibrils of amyloid-β alters the kinetics of amyloid aggregation.” Biochemistry. 2014 Oct 14;53(40):6323-31. doi: 10.1021/bi5008172. Epub 2014 Sep 25. (Abstract)
Continue reading →Nguyen B., Sokoloski J.E., Galletto R., Elson E.L., Wold M.S., & Lohman T.M. (2014). “Diffusion of human replication protein A along single-stranded DNA.” J Mol Biol. 2014 Sep 23;426(19):3246-3261. doi: 10.1016/j.jmb.2014.07.014. Epub 2014 Jul 22. (Abstract)
Continue reading →Macdonald-Obermann J.L. & Pike L.J. (2014). “Different epidermal growth factor (EGF) receptor ligands show distinct kinetics and biased or partial agonism for homodimer and heterodimer formation.” J Biol Chem. 2014 Sep 19;289(38):26178-88. doi: 10.1074/jbc.M114.586826. Epub 2014 Aug 1. (Abstract)
Continue reading →Dovrat, D., Stodola, J.L., Burgers, P.M. and Aharoni, A.
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Sequential switching of binding partners on PCNA during in vitro Okazaki fragment maturation.
PNAS 111:14118-14123 (2014). (Abstract)Hammes G. & Frieden C. (2014). “Robert A. Alberty” National Academy of Sciences. Biographical Memoirs. (Article)
Continue reading →Lin Y., Manning P.T., Jia J., Gaut J.P., Xiao Z., Capoccia B.J., Chen C.C., Hiebsch R.R., Upadhya G., Mohanakumar T., Frazier W.A., & Chapman W.C. (2014). “CD47 blockade reduces ischemia-reperfusion injury and improves outcomes in a rat kidney transplant model.” Transplantation. 2014 Aug 27;98(4):394-401. doi: 10.1097/TP.0000000000000252. (Abstract)
Continue reading →Kunkel, T.A. and Burgers, P.M.
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Delivering nonidentical twins.
Nat Struct Mol Biol 21:649-651 (2014). (Abstract)Garner A.L., Weiss L., Manzano A.R., Galburt E.A., & Stallings C.L. (2014). “CarD integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria.” Mol Microbiol. 2014 Aug;93(4):682-97. doi: 10.1111/mmi.12681. Epub 2014 Jul 16. (Abstract)
Continue reading →DeKoster G.T., Delaney K.J., & Hall K.B. (2014). “A compare-and-contrast NMR dynamics study of two related RRMs: U1A and SNF.” Biophys J. 2014 Jul 1;107(1):208-19. doi: 10.1016/j.bpj.2014.05.026. (Abstract)
Continue reading →Lee K.S., Marciel A.B., Kozlov A.G., Schroeder C.M., Lohman T.M., & Ha T. (2014). “Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer.” J Mol Biol. 2014 Jun 26;426(13):2413-21. doi: 10.1016/j.jmb.2014.04.023. Epub 2014 May 2. (Abstract)
Continue reading →Ilagan M.X. and Kopan R. (2014) “Monitoring Notch activation in cultured mammalian cells: luciferase complementation imaging assays.” Methods Mol Biol. 2014;1187:155-68. doi: 10.1007/978-1-4939-1139-4_12. (Abstract)
Continue reading →Williams S.G. & Hall K.B. (2014). “Binding affinity and cooperativity control U2B″/snRNA/U2A’ RNP formation.” Biochemistry. 2014 Jun 17;53(23):3727-37. doi: 10.1021/bi500438e. Epub 2014 Jun 5. (Abstract)
Continue reading →Williams S.G. & Hall K.B. (2014). “Linkage and allostery in snRNP protein/RNA complexes.” Biochemistry. 2014 Jun 10;53(22):3529-39. doi: 10.1021/bi500192a. Epub 2014 May 29. (Abstract)
Continue reading →Delaney K.J., Williams S.G., Lawler M., & Hall K.B. (2014). “Climbing the vertebrate branch of U1A/U2B″ protein evolution.” RNA. 2014 Jul;20(7):1035-45. doi: 10.1261/rna.044255.114. Epub 2014 May 19. (Abstract)
Continue reading →Lin, Y.C., Li, L., Makarova, A.V., Burgers, P.M. and Lloyd, R.S.
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Error-prone replication bypass of the primary aflatoxin B1 DNA adduct, AFB1-N7-Gua.
J Biol Chem 289:18497-18506 (2014). (Abstract)Makarova, A.V., McElhinny, S.A., Watts, B.E., Kunkel, T.A. and Burgers, P.M.
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Ribonucleotide incorporation by yeast DNA polymerase ζ.
DNA Repair 18:63-67 (2014). (Abstract)Borgo B. and Havranek J.J. (2014) “Motif-directed redesign of enzyme specificity.” Protein Sci. 2014 Mar;23(3):312-20. doi: 10.1002/pro.2417. Epub 2014 Feb 4. (Abstract)
Continue reading →Bowman, G.R. and Geissler, P.L.
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Extensive Conformational Heterogeneity within Protein Cores
J Phys Chem B 118:6417-6423.(2014). (Abstract)Cheng W. and Li W.
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Structural insights into ubiquinone biosynthesis in membranes.
Science. 343(6173):878-81. doi: 10.1126/science.1246774. (2014) (Abstract)Hall K.B. (2014). “Molecular biology: Protein binding cannot subdue a lively RNA.” Nature. 2014 Feb 20;506(7488):303-4. doi: 10.1038/nature13055. Epub 2014 Feb 12. (Abstract)
Continue reading →Shuman H., Greenberg M.J., Zwolak A., Lin T., Sindelar C.V., Dominguez R., & Ostap E.M. (2014). “A vertebrate myosin-I structure reveals unique insights into myosin mechanochemical tuning.” Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2116-21. doi: 10.1073/pnas.1321022111. Epub 2014 Jan 27. (Abstract)
Continue reading →Genin G.M. & Elson E.L. (2014). “Mechanically guided cell migration: less of a stretch than ever.” Biophys J. 2014 Feb 18;106(4):776-7. doi: 10.1016/j.bpj.2014.01.016. (Abstract)
Continue reading →Park E., Ménétret J.F., Gumbart J.C., Ludtke S.J., Li W., Whynot A., Rapoport T.A., and Akey C.W.
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Structure of the SecY channel during initiation of protein translocation.
Nature. 506(7486):102-6. doi: 10.1038/nature12720. (2014) (Abstract)Borin B.N., Tang W., & Krezel A.M. (2014). “Helicobacter pylori RNA polymerase α-subunit C-terminal domain shows features unique to ɛ-proteobacteria and binds NikR/DNA complexes.” Protein Sci. 2014 Apr;23(4):454-63. doi: 10.1002/pro.2427. Epub 2014 Feb 4. (Abstract)
Continue reading →Liu S., Cheng W., Fowle Grider R., Shen G., and Li W.
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Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer.
Nat Commun. 5:3110. doi: 10.1038/ncomms4110. (2014) (Abstract)Kohlhoff, K.J., Shukla, D., Lawrenz, M., Bowman, G.R., Konerding, D.E., Belov, D., Altman, R.B. and Pande, V.S.
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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Nature Chemistry 6:15-21 (2014). (Abstract)Galburt E.A., Tomko E.J., Stump W.T., & Ruiz Manzano A. (2014). “Force-dependent melting of supercoiled DNA at thermophilic temperatures.” Biophys Chem. 2014 Mar-Apr;187-188:23-8. doi: 10.1016/j.bpc.2014.01.001. Epub 2014 Jan 17. (Abstract)
Continue reading →Lin, Y.C., Li, L., Makarova, A.V., Burgers, P.M., Stone, M.P. and Lloyd, R.S.
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Molecular basis of aflatoxin-induced mutagenesis-role of the aflatoxin B1-formamidopyrimidine adduct.
Carcinogenesis 35:1461-1468 (2014). (Abstract)Borin B.N., Tang W., Nice T.J., McCune B.T., Virgin H.W., & Krezel A.M. (2013). “Murine norovirus protein NS1/2 aspartate to glutamate mutation, sufficient for persistence, reorients side chain of surface exposed tryptophan within a novel structured domain.” Proteins. 2014 Jul;82(7):1200-9. doi: 10.1002/prot.24484. Epub 2013 Dec 26. (Abstract)
Continue reading →Frieden, C. and Garai, K.
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Concerning the structure of apoE.
Protein Sci. 22:1820-1825 (2013). (Abstract)Crick, S.L., Ruff, K.M., Garai, K., Frieden, C. and Pappu, R.V.
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Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation.
PNAS 110:20075-20080 (2013). (Abstract)Zheleznyak A., Ikotun O.F., Dimitry J., Frazier W.A., & Lapi S.E. (2013). “Imaging of CD47 expression in xenograft and allograft tumor models.” Mol Imaging. 2013 Nov-Dec;12(8). doi: 10.2310/7290.2013.00069. (Abstract)
Continue reading →Macdonald-Obermann J.L., Adak S., Landgraf R., Piwnica-Worms D., & Pike L.J. (2013). “Dynamic analysis of the epidermal growth factor (EGF) receptor-ErbB2-ErbB3 protein network by luciferase fragment complementation imaging.” J Biol Chem. 2013 Oct 18;288(42):30773-84. doi: 10.1074/jbc.M113.489534. Epub 2013 Sep 6. (Abstract)
Continue reading →Elson E.L. & Genin G.M. (2013). “The role of mechanics in actin stress fiber kinetics.” Exp Cell Res. 2013 Oct 1;319(16):2490-500. doi: 10.1016/j.yexcr.2013.06.017. Epub 2013 Jul 29. (Abstract)
Continue reading →Hall K.B. (2013). “RNA does the folding dance of twist, turn, stack.” Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16706-7. doi: 10.1073/pnas.1316029110. Epub 2013 Sep 26. (Abstract)
Continue reading →Northam, M.R., Moore, E.A., Mertz, T.M., Binz, S.K., Stith, C.M., Stepchenkova, E.I., Wendt, K.L., Burgers, P.M., and Shcherbakova, P.V.
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DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures.
Nucleic Acids Res. 42:290-306 (2014). (Abstract)Qiao, Q., Bowman G.R., Huang X.
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Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation
J Am Chem Soc 135:16092-16101. (2013). (Abstract)Antony E., Weiland E., Yuan Q., Manhart C.M., Nguyen B., Kozlov A.G., McHenry C.S., & Lohman T.M. (2013). “Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair.” J Mol Biol. 2013 Nov 29;425(23):4802-19. doi: 10.1016/j.jmb.2013.08.021. Epub 2013 Sep 7. (Abstract)
Continue reading →Azcutia V., Routledge M., Williams M.R., Newton G., Frazier W.A., Manica A., Croce K.J., Parkos C.A., Schmider A.B., Turman M.V., Soberman R.J., & Luscinskas F.W. (2013). “CD47 plays a critical role in T-cell recruitment by regulation of LFA-1 and VLA-4 integrin adhesive functions.” Mol Biol Cell. 2013 Nov;24(21):3358-68. doi: 10.1091/mbc.E13-01-0063. Epub 2013 Sep 4. (Abstract)
Continue reading →Qiu Y., Antony E., Doganay S., Koh H.R., Lohman T.M., & Myong S. (2013). “Srs2 prevents Rad51 filament formation by repetitive motion on DNA.” Nat Commun. 2013;4:2281. doi: 10.1038/ncomms3281. (Abstract)
Continue reading →Bowman, G.R., Meng, L. and Huang, X.
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Quantitative comparison of alternative methods for coarse-graining biological networks
J Chem Phys 139:121905. (2013). (Abstract)Wallen J.R., Majka J., & Ellenberger T. (2013). “Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase.” Biochemistry. 2013 Jun 11;52(23):4026-36. doi: 10.1021/bi400284j. Epub 2013 May 31. (Abstract)
Continue reading →Williams S.G., Harms M.J., & Hall K.B. (2013). “Resurrection of an Urbilaterian U1A/U2B″/SNF protein.” J Mol Biol. 2013 Oct 23;425(20):3846-62. doi: 10.1016/j.jmb.2013.05.031. Epub 2013 Jun 22. (Abstract)
Continue reading →Totsika M., Kostakioti M., Hannan T.J., Upton M., Beatson S.A., Janetka J.W., Hultgren S.J., & Schembri M.A. (2013). “A FimH inhibitor prevents acute bladder infection and treats chronic cystitis caused by multidrug-resistant uropathogenic Escherichia coli ST131.” J Infect Dis. 2013 Sep;208(6):921-8. doi: 10.1093/infdis/jit245. Epub 2013 Jun 3. (Abstract)
Continue reading →Lyskov S., Chou F.C., Conchúir S.Ó., Der B.S., Drew K., Kuroda D., Xu J., Weitzner B.D., Renfrew P.D., Sripakdeevong P., Borgo B., Havranek J.J., Kuhlman B., Kortemme T., Bonneau R., Gray J.J., and Das R. (2013) “Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).” PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. (Abstract)
Continue reading →Lee K.S., Balci H., Jia H., Lohman T.M., & Ha T. (2013). “Direct imaging of single UvrD helicase dynamics on long single-stranded DNA.” Nat Commun. 2013;4:1878. doi: 10.1038/ncomms2882. (Abstract)
Continue reading →Verghese, P.B., Castellano, J.M., Garai, K., Wang, Y., Jiang, H., Shah, A., Bu, G., Frieden, C. and Holtzmann, D.M.
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ApoE influences amyloid-β (Aβ) clearance despite minimal apoE/Aβ association in physiological conditions.
PNAS 110:E1807-1816 (2013). (Abstract)Yao, Y., Cui, R.Z., Bowman, G.R., Silva, D.A., Sun, J. and Huang, X.
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Hierarchical Nyström methods for constructing Markov state models for conformational dynamics
J Chem Phys 138:174106. (2013). (Abstract)Galletto, R. and Tomko, E.
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Translocation of Saccharomyces cerevisiae Pif1 helicase monomers on single-stranded DNA.
Nucleic Acids Res. 41:4613-4627 (2013). (Abstract)Greenberg M.J. & Ostap E.M. (2013). “Regulation and control of myosin-I by the motor and light chain-binding domains.” Trends Cell Biol. 2013 Feb;23(2):81-9. doi: 10.1016/j.tcb.2012.10.008. Epub 2012 Nov 29. (Abstract)
Continue reading →Leaver-Fay A., O’Meara M.J., Tyka M., Jacak R., Song Y., Kellogg E.H., Thompson J., Davis I.W., Pache R.A., Lyskov S., Gray J.J., Kortemme T., Richardson J.S, Havranek J.J., Snoeyink J., Baker D., and Kuhlman B. (2013) “Scientific benchmarks for guiding macromolecular energy function improvement.” Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0. (Abstract)
Continue reading →Antony E. & Lohman T.M. (2013). “Nonhexameric SF1 DNA Helicases/Translocases” Encyclopedia of Biological Chemistry, 2nd Edition, 2013, Pages 261-265. doi: 10.1016/B978-0-12-378630-2.00393-5. (Abstract)
Continue reading →Garai, K. and Frieden, C.
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Quantitative analysis of the time course of Aβ oligomerization and subsequent growth steps using tetramethylrhodamine-labeled Aβ.
PNAS 110:3321-3326 (2013). (Abstract)Marshall, G.R. (2013) “Limiting assumptions in molecular modeling: electrostatics.” J Comput Aided Mol Des. 2013 Feb;27(2):107-14. doi: 10.1007/s10822-013-9634-x. Epub 2013 Jan 26. (Abstract)
Continue reading →Kumar, S. and Burgers, P.M.
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Lagging strand maturation factor Dna2 is a component of the replication checkpoint initiation machinery.
Genes Dev 27:313-321 (2013). (Abstract)Chon, H., Sparks, J.L., Rychlik, M., Nowotny, M., Burgers, P.M., Crouch, R.J. and Cerritelli, S.M.
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RNase H2 roles in genome integrity revealed by unlinking its activities.
Nucleic Acids Res. 41:3130-3143 (2013). (Abstract)Elson E.L. (2013). “Brief introduction to fluorescence correlation spectroscopy.” Methods Enzymol. 2013;518:11-41. doi: 10.1016/B978-0-12-388422-0.00002-9. (Abstract)
Continue reading →Elson E.L. (2013). “40 years of FCS: how it all began.” Methods Enzymol. 2013;518:1-10. doi: 10.1016/B978-0-12-388422-0.00001-7. (Abstract)
Continue reading →Lee S.L., Nekouzadeh A., Butler B., Pryse K.M., McConnaughey W.B., Nathan A.C., Legant W.R., Schaefer P.M., Pless R.B., Elson E.L., & Genin G.M. (2012). “Physically-induced cytoskeleton remodeling of cells in three-dimensional culture.” PLoS One. 2012;7(12):e45512. doi: 10.1371/journal.pone.0045512. Epub 2012 Dec 27. (Abstract)
Continue reading →Xie F., Wu C.G., Weiland E., & Lohman T.M. (2012). “Asymmetric regulation of bipolar single-stranded DNA translocation by the two motors within Escherichia coli RecBCD helicase.” J Biol Chem. 2013 Jan 11;288(2):1055-64. doi: 10.1074/jbc.M112.423384. Epub 2012 Nov 27. (Abstract)
Continue reading →Della-Maria J., Hegde M.L., McNeill D.R., Matsumoto Y., Tsai M.S., Ellenberger T., Wilson D.M., Mitra S., & Tomkinson, A.E. (2012). “The interaction between polynucleotide kinase phosphatase and the DNA repair protein XRCC1 is critical for repair of DNA alkylation damage and stable association at DNA damage sites.” J Biol Chem. 2012 Nov 9;287(46):39233-44. doi: 10.1074/jbc.M112.369975. Epub 2012 Sep 19. (Abstract)
Continue reading →Clausen, A.R., Zhang, S., Burgers, P.M., Lee, M.Y. and Kunkel, T.A.
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Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ.
DNA Repair (Amst) 12:121-127 (2012). (Abstract)Kozlov A.G., Galletto R., & Lohman T.M. (2012). “SSB-DNA binding monitored by fluorescence intensity and anisotropy.” Methods Mol Biol. 2012;922:55-83. doi: 10.1007/978-1-62703-032-8_4. (Abstract)
Continue reading →Ring, A.M., Lin, J., Feng, D., Mitra, S., Rickert, M., Bowman, G.R., Pande, V.S., Li, P, Moraga, I., Spolski, R., Özkan, E.,Leonard, W.J. and Garcia, K.C.
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Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15
Nature Immunology 13:1187-1195. (2012). (Abstract)Wu C.G., Xie F., & Lohman T.M. (2012). “The primary and secondary translocase activities within E. coli RecBC helicase are tightly coupled to ATP hydrolysis by the RecB motor.” J Mol Biol. 2012 Oct 26;423(3):303-14. doi: 10.1016/j.jmb.2012.07.009. Epub 2012 Jul 20. (Abstract)
Continue reading →Sparks, J.L., Kumar, R., Singh, M., Wold, M.S., Pandita, T.K. and Burgers, P.M.
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Human exonuclease 5 is a novel sliding exonuclease required for genome stability.
J Biol Chem 287:42773-42783 (2012). (Abstract)Soto-Pantoja D.R., Miller T.W., Frazier W.A., & Roberts D.D. (2012). “Inhibitory signaling through signal regulatory protein-α is not sufficient to explain the antitumor activities of CD47 antibodies.” Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):E2842; author reply E2844-5. doi: 10.1073/pnas.1205441109. Epub 2012 Aug 24. (Abstract)
Continue reading →Makarova, A.V., Stodola, J.L. and Burgers, P.M.
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A four-subunit DNA polymerase ζ complex containing Pol δ accessory subunits is essential for PCNA-mediated mutagenesis.
Nucleic Acids Res. 40:11618-11626 (2012). (Abstract)Bowman, G.R.
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Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
J Chem Phys 137:134111. (2012). (Abstract)Zheng X., Wu C., Ponder J.W., and Marshall G.R. (2012) “Molecular dynamics of β-hairpin models of epigenetic recognition motifs.” J Am Chem Soc. 2012 Sep 26;134(38):15970-8. Epub 2012 Sep 17. (Abstract)
Continue reading →Rau M., Stump W.T., & Hall K.B. (2012). “Intrinsic flexibility of snRNA hairpin loops facilitates protein binding.” RNA. 2012 Nov;18(11):1984-95. doi: 10.1261/rna.035006.112. Epub 2012 Sep 25. (Abstract)
Continue reading →Greenberg M.J., Lin T., Goldman Y.E., Shuman H., & Ostap E.M. (2012). “Myosin IC generates power over a range of loads via a new tension-sensing mechanism.” Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):E2433-40. doi: 10.1073/pnas.1207811109. Epub 2012 Aug 20. (Abstract)
Continue reading →Li Y., Macdonald-Obermann J., Westfall C., Piwnica-Worms D., & Pike L.J. (2012). “Quantitation of the effect of ErbB2 on epidermal growth factor receptor binding and dimerization.” J Biol Chem. 2012 Sep 7;287(37):31116-25. doi: 10.1074/jbc.M112.373647. Epub 2012 Jul 20. (Abstract)
Continue reading →Pryse K.M., Rong X., Whisler J.A., McConnaughey W.B., Jiang Y.F., Melnykov A.V., Elson E.L., & Genin G.M. (2012). “Confidence intervals for concentration and brightness from fluorescence fluctuation measurements.” Biophys J. 2012 Sep 5;103(5):898-906. (Abstract)
Continue reading →Silvestri L., Ballante F., Mai A., Marshall G.R., and Ragno R. (2012) “Histone deacetylase inhibitors: structure-based modeling and isoform-selectivity prediction.” J Chem Inf Model. 2012 Aug 27;52(8):2215-35. doi: 10.1021/ci300160y. Epub 2012 Jul 19. (Abstract)
Continue reading →Sparks, J.L., Chon, H., Cerritelli, S.M., Kunkel, T.A., Johansson, E., Crouch, R.J. and Burgers, P.M.
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RNase H2-initiated ribonucleotide excision repair.
Mol Cell. 47:980-986 (2012). (Abstract)Kozlov A.G. & Lohman T.M. (2012). “SSB binding to ssDNA using isothermal titration calorimetry.” Methods Mol Biol. 2012;922:37-54. doi: 10.1007/978-1-62703-032-8_3. (Abstract)
Continue reading →Cui, R.Z., Silva, D.A., Song, J., Bowman, G.R., Zhuang, W. and Huang, X.
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Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics
Curr Phys Chem 2:45-58. (2012). (Abstract)Ballante F., Musmuca I., Marshall G.R., and Ragno R. (2012) “Comprehensive model of wild-type and mutant HIV-1 reverse transciptases.” J Comput Aided Mol Des. 2012 Aug;26(8):907-19. doi: 10.1007/s10822-012-9586-6. Epub 2012 Jul 26. (Abstract)
Continue reading →Antony E., Weiland E.A., Korolev S., & Lohman T.M. (2012). “Plasmodium falciparum SSB tetramer wraps single-stranded DNA with similar topology but opposite polarity to E. coli SSB.” J Mol Biol. 2012 Jul 20;420(4-5):269-83. doi: 10.1016/j.jmb.2012.04.021. Epub 2012 Apr 27. (Abstract)
Continue reading →Antony E., Kozlov A.G., Nguyen B., & Lohman T.M. (2012). “Plasmodium falciparum SSB tetramer binds single-stranded DNA only in a fully wrapped mode.” J Mol Biol. 2012 Jul 20;420(4-5):284-95. doi: 10.1016/j.jmb.2012.04.022. Epub 2012 Apr 26. (Abstract)
Continue reading →Yang B., Hird A.W., Russell D.J., Fauber B.P., Dakin L.A., Zheng X., Su Q., Godin R., Brassil P., Devereaux E., and Janetka J.W. (2012) “Discovery of novel hedgehog antagonists from cell-based screening: Isosteric modification of p38 bisamides as potent inhibitors of SMO.” Bioorg Med Chem Lett. 2012 Jul 15;22(14):4907-11. doi: 10.1016/j.bmcl.2012.04.104. Epub 2012 Apr 30. (Abstract)
Continue reading →Voelz, V.A., Jager, M., Yao, S., Chen, Y., Zhu, L., Waldauer, S.A., Bowman, G.R., Friedrichs, M., Bakajin, O., Lapidus, L.J., Weiss, S., and Pande, V.S.
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Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment
J Am Chem Soc 134:12565-12577. (2012). (Abstract)Bowman, G.R. and Geissler, P.L.
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Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
Proc Natl Acad Sci U S A 109:11681-11686. (2012). (Abstract)Guiton P.S., Cusumano C.K., Kline K.A., Dodson K.W., Han Z., Janetka J.W., Henderson J.P., Caparon M.G., & Hultgren S.J. (2012). “Combinatorial small-molecule therapy prevents uropathogenic Escherichia coli catheter-associated urinary tract infections in mice.” Antimicrob Agents Chemother. 2012 Sep;56(9):4738-45. doi: 10.1128/AAC.00447-12. Epub 2012 Jun 25.
Continue reading →Lewis J.H., Greenberg M.J., Laakso J.M., Shuman H., & Ostap E.M. (2012). “Calcium regulation of myosin-I tension sensing.” Biophys J. 2012 Jun 20;102(12):2799-807. doi: 10.1016/j.bpj.2012.05.014. Epub 2012 Jun 19. (Abstract)
Continue reading →Oza V., Ashwell S., Almeida L., Brassil P., Breed J., Deng C., Gero T., Grondine M., Horn C., Ioannidis S., Liu D., Lyne P., Newcombe N., Pass M., Read J., Ready S., Rowsell S., Su M., Toader D., Vasbinder M., Yu D., Yu Y., Xue Y., Zabludoff S., and Janetka J. (2012) “Discovery of checkpoint kinase inhibitor (S)-5-(3-fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by structure-based design and optimization of thiophenecarboxamide ureas.” J Med Chem. 2012 Jun 14;55(11):5130-42. doi: 10.1021/jm300025r. Epub 2012 Jun 4. (Abstract)
Continue reading →Kostakioti M., Hadjifrangiskou M., Cusumano C.K., Hannan T.J., Janetka J.W., & Hultgren S.J. (2012). “Distinguishing the contribution of type 1 pili from that of other QseB-misregulated factors when QseC is absent during urinary tract infection.” Infect Immun. 2012 Aug;80(8):2826-34. doi: 10.1128/IAI.00283-12. Epub 2012 Jun 4. (Abstract)
Continue reading →Kim I.K., Kiefer J.R., Ho C.M., Stegeman R.A., Classen S., Tainer J.A., & Ellenberger, T. (2012). “Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element.” Nat Struct Mol Biol. 2012 May 20;19(6):653-6. doi: 10.1038/nsmb.2305. (Abstract)
Continue reading →Frieden C. & Garai K. (2012). “Structural differences between apoE3 and apoE4 may be useful in developing therapeutic agents for Alzheimer’s disease.” Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):8913-8. doi: 10.1073/pnas.1207022109. Epub 2012 May 21. (Abstract)
Continue reading →Chen Z.W., Vignaud C., Jaafar A., Levy B., Gueritte F., Guenard D., Lederer F., & Mathews F.S. (2012). “High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole. Implications for inhibitor specificity and drug design.” Biochimie. 2012 May;94(5):1172-9. doi: 10.1016/j.biochi.2012.02.003. Epub 2012 Feb 9. (Abstract)
Continue reading →Levin, A.M., Bates, D.L., Ring, A.M., Krieg, C., Lin, J.T., Su, L., Moraga, I., Raeber, M.E., Bowman, G.R., Novick, P., Pande, V.S., Fathman, C.G., Boyman, O. and Garcia, K.C.
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Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’
Nature 484:529-533. (2012). (Abstract)Han Z., Pinkner J.S., Ford B., Chorell E., Crowley J.M., Cusumano C.K., Campbell S., Henderson J.P., Hultgren S.J., and Janetka J.W. (2012) “Lead optimization studies on FimH antagonists: discovery of potent and orally bioavailable ortho-substituted biphenyl mannosides.” J Med Chem. 2012 Apr 26;55(8):3945-59. doi: 10.1021/jm300165m. Epub 2012 Apr 13. (Abstract)
Continue reading →Ellenberger, T. (2012). “An arresting development in transcription.” Mol Cell. 2012 Apr 13;46(1):3-4. doi: 10.1016/j.molcel.2012.03.025. (Abstract)
Continue reading →Tomko E.J., Fischer C.J., & Lohman T.M. (2012). “Single-stranded DNA translocation of E. coli UvrD monomer is tightly coupled to ATP hydrolysis.” J Mol Biol. 2012 Apr 20;418(1-2):32-46. doi: 10.1016/j.jmb.2012.02.013. Epub 2012 Feb 14. (Abstract)
Continue reading →Shu Q., Crick S.L., Pinkner J.S., Ford B., Hultgren S.J., & Frieden C. (2012). “The E. coli CsgB nucleator of curli assembles to β-sheet oligomers that alter the CsgA fibrillization mechanism.” Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6502-7. doi: 10.1073/pnas.1204161109. Epub 2012 Apr 9. (Abstract)
Continue reading →Chen, C., Greenberg, M.J., Laakso, J.M., Ostap, E.M., Goldman, Y.E and Shuman, H.
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Kinetic schemes for post-synchronized single molecule dynamics.
Biophys J. 102:L23-L25 (2012). (Abstract)Tang Y.T., Gao R., Havranek J.J., Groisman E.A., Stock A.M., and Marshall G.R. (2012) “Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator.” Chem Biol Drug Des. 2012 Jun;79(6):1007-17. doi: 10.1111/j.1747-0285.2012.01362.x. Epub 2012 Mar 21. (Abstract)
Continue reading →Hall K.B. (2012). “Spectroscopic probes of RNA structure and dynamics.” Methods Mol Biol. 2012;875:67-84. doi: 10.1007/978-1-61779-806-1_4. (Abstract)
Continue reading →Fischer C.J., Tomko E.J., Wu C.G., & Lohman T.M. (2012). “Fluorescence methods to study DNA translocation and unwinding kinetics by nucleic acid motors.” Methods Mol Biol. 2012;875:85-104. doi: 10.1007/978-1-61779-806-1_5. (Abstract)
Continue reading →Ha T., Kozlov A.G., & Lohman T.M. (2012). “Single-molecule views of protein movement on single-stranded DNA.” Annu Rev Biophys. 2012;41:295-319. doi: 10.1146/annurev-biophys-042910-155351. Epub 2012 Feb 23. (Abstract)
Continue reading →Pike L.J. (2012). “Negative co-operativity in the EGF receptor.” Biochem Soc Trans. 2012 Feb;40(1):15-9. doi: 10.1042/BST20110610. (Abstract)
Continue reading →Borgo B. and Havranek J.J. (2012) “Automated selection of stabilizing mutations in designed and natural proteins.” Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1494-9. doi: 10.1073/pnas.1115172109. Epub 2012 Jan 17. (Abstract)
Continue reading →Nayak R.K., Peersen O.B., Hall K.B., & Van Orden A. (2012). “Millisecond time-scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics.” J Am Chem Soc. 2012 Feb 8;134(5):2453-6. doi: 10.1021/ja208490w. Epub 2012 Jan 30. (Abstract)
Continue reading →Lazzaro, F., Novarina, D., Amara, F., Watt, D.L., Stone, J.E., Costanzo, V., Burgers, P.M., Kunkel, T.A., Plevani, P. and Mulzi-Falconi, M.
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RNase H and postreplication repair protect cells from ribonucleotides incorporated in DNA.
Mol Cell. 45:99-110 (2012). (Abstract)Macdonald-Obermann J.L, Piwnica-Worms D., & Pike L.J. (2012). “Mechanics of EGF receptor/ErbB2 kinase activation revealed by luciferase fragment complementation imaging.” Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):137-42. doi: 10.1073/pnas.1111316109. Epub 2011 Dec 21. (Abstract)
Continue reading →Marshall G.R. (2012) “Limiting assumptions in structure-based design: binding entropy.” J Comput Aided Mol Des. 2012 Jan;26(1):3-8. doi: 10.1007/s10822-011-9494-1. Epub 2012 Jan 3. (Abstract)
Continue reading →Adak S., Yang K.S., Macdonald-Obermann J., & Pike L.J. (2011). “The membrane-proximal intracellular domain of the epidermal growth factor receptor underlies negative cooperativity in ligand binding.” J Biol Chem. 2011 Dec 30;286(52):45146-55. doi: 10.1074/jbc.M111.274175. Epub 2011 Nov 8. (Abstract)
Continue reading →Elson E. (2011). “Fluorescence correlation spectroscopy: past, present, future.” Biophys J. 2011 Dec 21;101(12):2855-70. doi: 10.1016/j.bpj.2011.11.012. Epub 2011 Dec 20. (Abstract)
Continue reading →Netz, D.J., Stith, C.M., Stümpfig, M., Köpf, G., Vogel, D., Genau, H.M., Stodola, J.L., Burgers, P.M. and Pierik, A.J.
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Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes.
Nat Chem Biol 8:125-132 (2011). (Abstract)Cusumano C.K., Pinkner J.S., Han Z., Greene S.E., Ford B.A., Crowley J.R., Henderson J.P., Janetka J.W., and Hultgren S.J.
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Treatment and prevention of urinary tract infection with orally active FimH inhibitors.
Sci Transl Med. 3(109):109ra115. doi: 10.1126/scitranslmed.3003021. (2011) (Abstract)Huang R.Y., Garai K., Frieden C., & Gross M.L. (2011). “Hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry determine the interface and dynamics of apolipoprotein E oligomerization.” Biochemistry. 2011 Nov 1;50(43):9273-82. doi: 10.1021/bi2010027. Epub 2011 Oct 5. (Abstract)
Continue reading →Navadgi-Patil, V.M., Kumar, S. and Burgers, P.M.
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The unstructured C-terminal tail of yeast Dpb11 (human TopBP1) protein is dispensable for DNA replication and the S phase checkpoint but required for the G2/M checkpoint.
J Biol Chem 286:40999-41007 (2011). (Abstract)Niedziela-Majka A., Maluf N.K., Antony E., & Lohman T.M. (2011). “Self-assembly of Escherichia coli MutL and its complexes with DNA.” Biochemistry. 2011 Sep 20;50(37):7868-80. doi: 10.1021/bi200753b. Epub 2011 Aug 26. (Abstract)
Continue reading →Gau B.C., Garai K., Frieden C., & Gross M.L. (2011). “Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3, and E4.” Biochemistry. 2011 Sep 27;50(38):8117-26. doi: 10.1021/bi200911c. Epub 2011 Sep 2. (Abstract)
Continue reading →Collier I.E., Legant W., Marmer B., Lubman O., Saffarian S., Wakatsuki T., Elson E., & Goldberg G.I. (2011). “Diffusion of MMPs on the surface of collagen fibrils: the mobile cell surface-collagen substratum interface.” PLoS One. 2011;6(9):e24029. doi: 10.1371/journal.pone.0024029. Epub 2011 Sep 1. (Abstract)
Continue reading →Burgers, P.M.
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It’s all about flaps: Dna2 and checkpoint activation.
Cell Cycle 10:2417-2418 (2011). (Abstract)Wildman S.A., Zheng X., Sept D., Auletta J.T., Rosenberry T.L., and Marshall G.R. (2011) “Drug-like leads for steric discrimination between substrate and inhibitors of human acetylcholinesterase.” Chem Biol Drug Des. 2011 Oct;78(4):495-504. doi: 10.1111/j.1747-0285.2011.01157.x. Epub 2011 Aug 22. (Abstract)
Continue reading →Jia H., Korolev S., Niedziela-Majka A., Maluf N.K., Gauss G.H., Myong S., Ha T., Waksman G., & Lohman T.M. (2011). “Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding.” J Mol Biol. 2011 Aug 19;411(3):633-48. doi: 10.1016/j.jmb.2011.06.019. Epub 2011 Jun 17. (Abstract)
Continue reading →Balci H., Arslan S., Myong S., Lohman T.M., & Ha T. (2011). “Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis.” Biophys J. 2011 Aug 17;101(4):976-84. doi: 10.1016/j.bpj.2011.07.010. (Abstract)
Continue reading →Nikiforovich G.V., Taylor C.M., Marshall G.R., and Baranski T.J. (2011) “Difference between restoring and predicting 3D structures of the loops in G-protein-coupled receptors by molecular modeling.” Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):E341; author reply E342. doi: 10.1073/pnas.1107702108. Epub 2011 Jul 1. (Abstract)
Continue reading →Zhou R., Kozlov A.G., Roy R., Zhang J., Korolev S., Lohman T.M., & Ha T. (2011). “SSB functions as a sliding platform that migrates on DNA via reptation.” Cell. 2011 Jul 22;146(2):222-32. doi: 10.1016/j.cell.2011.06.036. (Abstract)
Continue reading →Garai K., Baban B., & Frieden C. (2011). “Self-association and stability of the ApoE isoforms at low pH: implications for ApoE-lipid interactions.” Biochemistry. 2011 Jul 26;50(29):6356-64. doi: 10.1021/bi2006702. Epub 2011 Jun 29. (Abstract)
Continue reading →Watt, D.L., Johansson, E., Burgers, P.M. and Kunkel, T.A.
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Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases.
DNA Repair 10:897-902 (2011). (Abstract)Kommoju P.R., Chen Z.W., Bruckner R.C., Mathews F.S., & Jorns, M.S. (2011). “Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate.” Biochemistry. 2011 Jun 21;50(24):5521-34. doi: 10.1021/bi200388g. Epub 2011 May 26. (Abstract)
Continue reading →Silva, D., Bowman, G.R., Sosa-Peinado, A. and Huang, X.
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A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
PLoS Comput Biol 21:4-11. (2011). (Abstract)Sperry, J.B., Smith, C.L., Caparon, M.G., Ellenberger, T. and Gross, M.L.
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Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes.
Biochem 50:4038-4045 (2011). (Abstract)Stone, J.E., Kumar, D., Binz, S.K., Inase, A., Iwai, S., Chabes, A., Burgers, P.M. and Kunkel, T.A.
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Lesion bypass by S. cerevisiae Pol ζ alone.
DNA Repair (Amst). 10:826-834 (2011). ( Abstract)Williams S.G. & Hall K.B. (2011). “Human U2B″ protein binding to snRNA stemloops.” Biophys Chem. 2011 Nov;159(1):82-9. doi: 10.1016/j.bpc.2011.05.010. Epub 2011 May 16. (Abstract)
Continue reading →Navadgi-Patil, V.M. and Burgers, P.M.
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Cell-cycle-specific activators of the Mec1/ATR checkpoint kinase.
Biochem Soc Trans. 39:600-605 (2011). ( Abstract)Thomopoulos S., Das R., Birman V., Smith L., Ku K., Elson E., Pryse K.M., Marquez P., & Genin G.M. (2011). “Fibrocartilage tissue engineering: the role of the stress environment on cell morphology and matrix expression.” Tissue Eng Part A. 2011 Apr;17(7-8):1039-53. doi: 10.1089/ten.TEA.2009.0499. Epub 2011 Jan 9. (Abstract)
Continue reading →Galburt E.A., Parrondo J.M., & Grill S.W. (2011). “RNA polymerase pushing.” Biophys Chem. 2011 Aug;157(1-3):43-7. doi: 10.1016/j.bpc.2011.04.009. Epub 2011 Apr 16. (Abstract)
Continue reading →Frazier E.P., Isenberg J.S., Shiva S., Zhao L., Schlesinger P., Dimitry J., Abu-Asab M.S., Tsokoa M., Roberts D.D., & Frazier W.A. (2011). “Age-dependent regulation of skeletal muscle mitochondria by the thrombospondin-1 receptor CD47.” Matrix Biol. 2011 Mar;30(2):154-61. doi: 10.1016/j.matbio.2010.12.004. Epub 2011 Jan 20. (Abstract)
Continue reading →Lin, T., Greenberg, M.J., Moore, J.R. and Ostap, E.M.
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A hearing loss-associated myo1c mutation (R156W) decreases the myosin duty ratio and force sensitivity.
Biochemistry 50:1831-1838 (2011). (Abstract)Garai K., Baban B., & Frieden C. (2011). “Dissociation of apolipoprotein E oligomers to monomer is required for high-affinity binding to phospholipid vesicles.” Biochemistry. 2011 Apr 5;50(13):2550-8. doi: 10.1021/bi1020106. Epub 2011 Feb 28. (Abstract)
Continue reading →Tang Y.T. and Marshall G.R. (2011) “PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.” J Chem Inf Model. 2011 Feb 28;51(2):214-28. doi: 10.1021/ci100257s. Epub 2011 Jan 7. (Abstract)
Continue reading →Li J., Gan J.H., Mathews F.S., & Xia Z.X. (2011). “The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase.” Biochem Biophys Res Commun. 2011 Mar 25;406(4):621-6. doi: 10.1016/j.bbrc.2011.02.107. Epub 2011 Feb 26. (Abstract)
Continue reading →Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T.
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Structural basis of Streptococcus pyogenes immunity to its NAD+ glycohydrolase toxin.
Structure 19:192-202 (2011). (Abstract)Li W. and Li F.
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Cross-crystal averaging with search models to improve molecular replacement phases.
Structure. 19(2):155-61. doi: 10.1016/j.str.2010.12.007. (2011) (Abstract)Ma C.X., Janetka J.W., and Piwnica-Worms H.
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Death by releasing the breaks: CHK1 inhibitors as cancer therapeutics.
Trends Mol Med. 17(2):88-96. doi: 10.1016/j.molmed.2010.10.009. (2011) (Abstract)Choi M., Sukumar N., Mathews F.S., Liu A., & Davidson V.L. (2011). “Proline 96 of the copper ligand loop of amicyanin regulates electron transfer from methylamine dehydrogenase by positioning other residues at the protein-protein interface.” Biochemistry. 2011 Feb 22;50(7):1265-73. doi: 10.1021/bi101794y. Epub 2011 Jan 26. (Abstract)
Continue reading →Adak S., Deandrade D., & Pike L.J. (2012). “The tethering arm of the EGF receptor is required for negative cooperativity and signal transduction.” J Biol Chem. 2011 Jan 14;286(2):1545-55. doi: 10.1074/jbc.M110.182899. Epub 2010 Nov 3. (Abstract)
Continue reading →Tang Y.T. and Marshall G.R. (2011) “Virtual screening for lead discovery.” Methods Mol Biol. 2011;716:1-22. doi: 10.1007/978-1-61779-012-6_1. (Abstract)
Continue reading →Bowman, G.R., Voelz, V.A. and Pande, V.S.
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Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85
J Am Chem Soc 133:664-667. (2011). (Abstract)Leaver-Fay A., Tyka M., Lewis S.M., Lange O.F., Thompson J., Jacak R., Kaufman K., Renfrew P.D., Smith C.A., Sheffler W., Davis I.W., Cooper S., Treuille A., Mandell D.J., Richter F., Ban Y.E., Fleishman S.J., Corn J.E., Kim D.E., Lyskov S., Berrondo M., Mentzer S., Popović Z., Havranek J.J., Karanicolas J., Das R., Meiler J., Kortemme T., Gray J.J., Kuhlman B., Baker D., and Bradley P. (2011) “ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.” Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6. (Abstract)
Continue reading →Niu W., Shu, Q., Chen Z., Mathews F.S., Di Cera E., & Frieden C. (2010). “The role of Zn2+ on the structure and stability of murine adenosine deaminase.” J Phys Chem B. 2010 Dec 16;114(49):16156-65. doi: 10.1021/jp106041v. Epub 2010 Sep 3. (Abstract)
Continue reading →Tomko E.J., Jia H., Park J., Maluf N.K., Ha T., & Lohman T.M. (2010). “5′-Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase.” EMBO J. 2010 Nov 17;29(22):3826-39. doi: 10.1038/emboj.2010.242. Epub 2010 Sep 28. (Abstract)
Continue reading →Feng J.A. and Marshall G.R. (2010) “SKATE: a docking program that decouples systematic sampling from scoring.” J Comput Chem. 2010 Nov 15;31(14):2540-54. doi: 10.1002/jcc.21545. (Abstract)
Continue reading →Bowman, G.R., Voelz, V.A. and Pande, V.S.
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Taming the complexity of protein folding
Curr Opin Struct Biol 21:4-11. (2011). (Abstract)Garai K. & Frieden C. (2010). “The association−dissociation behavior of the ApoE proteins: kinetic and equilibrium studies.” Biochemistry. 2010 Nov 9;49(44):9533-41. doi: 10.1021/bi101407m. (Abstract)
Continue reading →Pike, J.E., Henry, R.A., Burgers, P.M., Campbell, J.L. and Bambara, R.A.
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An alternative pathway for Okazaki fragment processing: resolution of fold-back flaps by Pif1 helicase.
J Biol Chem 285:41712-41723 (2010). (Abstract)Baldwin R.L., Frieden C., & Rose G.D. (2010). “Dry molten globule intermediates and the mechanism of protein unfolding.” Proteins. 2010 Oct;78(13):2725-37. doi: 10.1002/prot.22803. (Abstract)
Continue reading →Barranco-Medina, S. and Galletto, R.
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DNA binding induces dimerization of Saccharomyces cerevisiae Pif1.
Biochemistry 49:8445-8454 (2010). (Abstract)Greenberg, M.J., Kazmierczak, K., Szczesna-Cordary, D. and Moore JR.
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Cardiomyopathy-linked myosin regulatory light chain mutations disrupt myosin strain-dependent biochemistry.
Proc Natl Acad Sci U S A 107:17403-17408 (2010). (Abstract)Fischer C.J., Wooten L., Tomko E.J., and Lohman T.M.
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Kinetics of motor protein translocation on single-stranded DNA.
Methods Mol Biol. 587:45-56. doi: 10.1007/978-1-60327-355-8_4. (2010) (Abstract)Kozlov A.G., Eggington J.M., Cox M.M., & Lohman T.M. (2010). “Binding of the dimeric Deinococcus radiodurans single-stranded DNA binding protein to single-stranded DNA.” Biochemistry. 2010 Sep 28;49(38):8266-75. doi: 10.1021/bi100920w. (Abstract)
Continue reading →Wu C.G., Bradford C., & Lohman T.M. (2010). “Escherichia coli RecBC helicase has two translocase activities controlled by a single ATPase motor.” Nat Struct Mol Biol. 2010 Oct;17(10):1210-7. doi: 10.1038/nsmb.1901. Epub 2010 Sep 19. (Abstract)
Continue reading →Frieden C. (2010). “Sidney Frederick Velick” National Academy of Sciences. Biographical Memoir (Article)
Continue reading →Qui H., Zhu Y., Sun Z., Trzeciakowski J.P., Gansner M., Depre C., Resuello R.R., Natividad F.F., Hunter W.C., Genin G.M., Elson E.L., Vatner D.E., Meininger G.A., & Vatner S.F. (2010). “Short communication: vascular smooth muscle cell stiffness as a mechanism for increased aortic stiffness with aging.” Circ Res. 2010 Sep 3;107(5):615-9. doi: 10.1161/CIRCRESAHA.110.221846. Epub 2010 Jul 15. (Abstract)
Continue reading →Oza V., Ashwell S., Brassil P., Breed J., Deng C., Ezhuthachan J., Haye H., Horn C., Janetka J., Lyne P., Newcombe N., Otterbien L., Pass M., Read J., Roswell S., Su M., Toader D., Yu D., Yu Y., Valentine A., Webborn P., White A., Zabludoff S., and Zheng X.
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Discovery of a novel class of triazolones as checkpoint kinase inhibitors–hit to lead exploration.
Bioorg Med Chem Lett. 20(17):5133-8. doi: 10.1016/j.bmcl.2010.07.015. (2010) (Abstract)Chen Z., Datta S., Dubois J.L., Klinman J.P., & Mathews F.S. (2010). “Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity.” Biochemistry. 2010 Aug 31;49(34):7393-402. doi: 10.1021/bi100643y. (Abstract)
Continue reading →Schulman S., Wang B., Li W., and Rapoport T.A.
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Vitamin K epoxide reductase prefers ER membrane-anchored thioredoxin-like redox partners.
Proc Natl Acad Sci U S A. 107(34):15027-32. doi: 10.1073/pnas.1009972107. (2010) (Abstract)Park J., Myong S., Niedziela-Majka A., Lee K.S., Yu J., Lohman T.M., & Ha T. (2010). “PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps.” Cell. 2010 Aug 20;142(4):544-55. doi: 10.1016/j.cell.2010.07.016. (Abstract)
Continue reading →Van Eps N., Anderson L.L., Kisselev O.G., Baranski T.J., Hubbell W.L., and Marshall G.R. (2010) “Electron paramagnetic resonance studies of functionally active, nitroxide spin-labeled peptide analogues of the C-terminus of a G-protein alpha subunit.” Biochemistry. 2010 Aug 17;49(32):6877-86. doi: 10.1021/bi100846c. (Abstract)
Continue reading →Updegrove, T.B., Correia, J.J., Galletto, R., Bujalowski, W. and Wartell, R.M.
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E. coli DNA associated with isolated Hfq interacts with Hfq’s distal surface and C-terminal domain.
Biochim Biophys Acta 1799:588-596 (2010). (Abstract)Yang K.S., Macdonald-Obermann J., Piwnica-Worms D., & Pike L.J. (2010). “Asp-960/Glu-961 controls the movement of the C-terminal tail of the epidermal growth factor receptor to regulate asymmetric dimer formation.” J Biol Chem. 2010 Jul 30;285(31):24014-22. doi: 10.1074/jbc.M110.103317. Epub 2010 May 27. (Abstract)
Continue reading →Bourne G.T., Kuster D.J., and Marshall G.R. (2010) “Synthesis of the phenylpyridal scaffold as a helical peptide mimetic.” Chemistry. 2010 Jul 26;16(28):8439-45. doi: 10.1002/chem.201000315. (Abstract)
Continue reading →Cotner-Gohara, E., Kim, I.K., Tainer, J.A., Tomkinson, A.E. and Ellenberger, T.
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Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states.
Biochemistry 49:6165-6176 (2010). (Abstract)Brown, J.A., Zhang, L., Sherrer, S.M., Taylor, J.S., Burgers, P.M. and Suo, Z.
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Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta.
J Nucleic Acids 2010:1-11 (2010). (Abstract)Yang R.Y., Yang K.S., Pike L.J., and Marshall G.R. (2010) “Targeting the dimerization of epidermal growth factor receptors with small-molecule inhibitors.” Chem Biol Drug Des. 2010 Jul;76(1):1-9. doi: 10.1111/j.1747-0285.2010.00986.x. Epub 2010 May 4. (Abstract)
Continue reading →Tomko E.J., Fischer C.J., and Lohman T.M. (2010) “Ensemble methods for monitoring enzyme translocation along single stranded nucleic acids.” Methods. 2010 Jul;51(3):269-76. doi: 10.1016/j.ymeth.2010.03.010. Epub 2010 Apr 3. (Abstract)
Continue reading →Perry, J.J. and Cotner-Gohara, E., Ellenberger, T. and Tainer, J.A.
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Structural dynamics in DNA damage signaling and repair.
Curr Opin Struct Biol 20:283-294 (2010). (Abstract)Lydeard, J.R., Lipkin-Moore, Z., Sheu, Y.J., Stillman, B., Burgers, P.M. and Haber, J.E.
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Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly.
Genes Dev 24:1133-1144 (2010). (Abstract)Lohman T.M. (2010). “Clipping along.” J Mol Biol. 2010 Jun 25;399(5):663-4. doi: 10.1016/j.jmb.2010.04.063. Epub 2010 May 4. (Abstract)
Continue reading →Han, Z., Pinkner, J.S., Ford, B., Obermann, R., Nolan, W., Wildman, S.A., Hobbs, D., Ellenberger, T., Cusumano, C.K., Hultgren, S.J. and Janetka, J.W.
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Structure-based drug design and optimization of mannoside bacterial FimH antagonists.
J Med Chem. 53(12):4779-92. doi: 10.1021/jm100438s. (2010) (Abstract)Williams S.G. & Hall K.B. (2010). “Coevolution of Drosophila snf protein and its snRNA targets.” Biochemistry. 2010 Jun 8;49(22):4571-82. doi: 10.1021/bi100374d. (Abstract)
Continue reading →Mustafi S.M., Garai K., Crick S.L., Baban B., & Frieden C. (2010). “Substoichiometric inhibition of Abeta(1-40) aggregation by a tandem Abeta(40-1-Gly8-1-40) peptide.” Biochem Biophys Res Commun. 2010 Jul 2;397(3):509-12. doi: 10.1016/j.bbrc.2010.05.144. Epub 2010 May 31. (Abstract)
Continue reading →Kozlov A.G., Cox M.M., and Lohman T.M. (2010) “Regulation of single-stranded DNA binding by the C termini of Escherichia coli single-stranded DNA-binding (SSB) protein.” J Biol Chem. 2010 May 28;285(22):17246-52. doi: 10.1074/jbc.M110.118273. Epub 2010 Apr 1. (Abstract)
Continue reading →Kozlov A.G. & Lohman T.M. (2010). “E. coli SSB tetramer binds the first and second molecules of (dT)(35) with heat capacities of opposite sign.” Biophys Chem. 2011 Nov;159(1):48-57. doi: 10.1016/j.bpc.2011.05.005. Epub 2011 May 12. (Abstract)
Continue reading →Jorns M.S., Chen Z.W., & Mathews F.S. (2010). “Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase.” Biochemistry. 2010 May 4;49(17):3631-9. doi: 10.1021/bi100160j. (Abstract)
Continue reading →Kozlov A.G., Jezewska M.J., Bujalowski W., and Lohman T.M. (2010) “Binding specificity of Escherichia coli single-stranded DNA binding protein for the chi subunit of DNA pol III holoenzyme and PriA helicase.” Biochemistry. 2010 May 4;49(17):3555-66. doi: 10.1021/bi100069s. (Abstract)
Continue reading →Liu F., Maynard C., Scott G., Melnykov A., Hall K.B., & Gruebele M. (2010). “A natural missing link between activated and downhill protein folding scenarios.” Phys Chem Chem Phys. 2010 Apr 14;12(14):3542-9. doi: 10.1039/b925033f. Epub 2010 Feb 11. (Abstract)
Continue reading →Sukumar N., Mathews F.S., Langan P., & Davidson V.L. (2010). “A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer.” Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6817-22. doi: 10.1073/pnas.0912672107. Epub 2010 Mar 29. (Abstract)
Continue reading →Burgers, P.M., Stith, C.M., Yoder, B.L. and Sparks, J.L.
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Yeast exonuclease 5 is essential for mitochondrial genome maintenance.
Mol Cell Biol 30:1457-1466 (2010). (Abstract)Dallmann, H.G., Fackelmayer, O.J., Tomer, G., Chen, J., Wiktor-Becker, A., Ferrara, T., Pope, C., Oliveira, M.T., Burgers, P.M., Kaguni, L.S. and McHenry, C.S.
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Parallel multiplicative target screening against divergent bacterial replicases: identification of specific inhibitors with broad spectrum potential.
Biochemistry. 49:2551-2562 (2010). (Abstract)Nick McElhinny, S.A., Watts, B.E., Kumar, D, Watt, D.L., Lundstrom, E.B., Burgers, P.M., Johansson, E., Chabes, A. and Kunkel, T.A.
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Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases.
Proc Natl Acad Sci USA 107:4949-4954 (2010). (Abstract)Taylor C.M., Rockweiler N.B., Liu C., Rikimaru L., Tunemalm A.K., Kisselev O.G., and Marshall G.R. (2010) “Using ligand-based virtual screening to allosterically stabilize the activated state of a GPCR.” Chem Biol Drug Des. 2010 Mar;75(3):325-32. doi: 10.1111/j.1747-0285.2009.00944.x. Epub 2010 Jan 19. (Abstract)
Continue reading →Zhang Z., Kermekchiev M.B., & Barnes W.M. (2010). “Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq.” J Mol Diagn. 2010 Mar;12(2):152-61. doi: 10.2353/jmoldx.2010.090070. Epub 2010 Jan 14. (Abstract)
Continue reading →Orelli, B., McClendon, T.B., Tsodikov, O.V., Ellenberger, T., Niedernhofer, L.J. and Scharer, O.D.
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The XPA-binding domain of ERCC1 is required for nucleotide excision repair but not other DNA repair pathways.
J Biol Chem 285:3705-3712 (2010). (Abstract)Marquez J.P., Elson E.L., & Genin G.M. (2010). “Whole cell mechanics of contractile fibroblasts: relations between effective cellular and extracellular matrix moduli.” Philos Trans A Math Phys Eng Sci. 2010 Feb 13;368(1912):635-54. doi: 10.1098/rsta.2009.0240. (Abstract)
Continue reading →Loh J.T., Gupta S.S., Friedman D.B., Krezel A.M., & Cover T.L. (2010). “Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system.” J Bacteriol. 2010 Apr;192(8):2034-43. doi: 10.1128/JB.01703-08. Epub 2010 Feb 12. (Abstract)
Continue reading →Stewart C.R., Stuart L.M., Wilkinson K., van Gils J.M., Deng J., Halle A., Rayner K.J., Boyer L., Zhong R., Frazier W.A., Lacy-Hulbert A., Khoury J.E., Golenbock D.T., & Moore K.J. (2010). “CD36 ligands promote sterile inflammation through assembly of a Toll-like receptor 4 and 6 heterodimer.” Nat Immunol. 2010 Feb;11(2):155-61. doi: 10.1038/ni.1836. Epub 2009 Dec 27. (Abstract)
Continue reading →Elson E.L., Fried E., Dolbow J.E., & Genin G.M. (2010). “Phase separation in biological membranes: integration of theory and experiment.” Annu Rev Biophys. 2010;39:207-26. doi: 10.1146/annurev.biophys.093008.131238. (Abstract)
Continue reading →Nikiforovich G.V., Taylor C.M., Marshall G.R., and Baranski T.J.
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Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors.
Proteins. 2010 Feb 1;78(2):271-85. doi: 10.1002/prot.22537. (2010) (Abstract)Li W., Schulman S., Dutton R.J., Boyd D., Beckwith J., and Rapoport T.A.
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Structure of a bacterial homologue of vitamin K epoxide reductase.
Nature. 463(7280):507-12. doi: 10.1038/nature08720. (2010) (Abstract)Garai, K., Mustafi, S.M., Baban, B. and Frieden, C.
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Structural differences between apolipoprotein E3 and E4 as measured by (19)F NMR.
Protein Sci. 19:66-74. (2010). (Abstract)Maynard C.M. & Hall K.B. (2010). “Interactions between PTB RRMs induce slow motions and increase RNA binding affinity.” J Mol Biol. 2010 Mar 19;397(1):260-77. doi: 10.1016/j.jmb.2009.12.051. Epub 2010 Jan 18. (Abstract)
Continue reading →Wu K., Li W., Peng G., and Li F.
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Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor.
Proc Natl Acad Sci U S A. 106(47):19970-4. doi: 10.1073/pnas.0908837106. (2009) (Abstract)Sukumar N., Mathews F.S., Gordon M.M., Ealik S.E., & Alpers D.H. (2009). “Postcrystallization Analysis of the Irreproducibility of the Human Intrinsic Factor-Cobalamin Complex Crystals.” Cryst Growth Des. 2009;9(1):348-351. (Abstract)
Continue reading →Kommoju P.R., Bruckner R.C., Ferreira P., Carrell C.J., Mathews F.S., & Jorns M.S. (2009). “Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.” Biochemistry. 2009 Oct 13;48(40):9542-55. doi: 10.1021/bi901056a. (Abstract)
Continue reading →Kurz L.C., Constantine C.Z., Jiang H., & Kappock T.J. (2009). “The partial substrate dethiaacetyl-coenzyme A mimics all critical carbon acid reactions in the condensation half-reaction catalyzed by Thermoplasma acidophilum citrate synthase.” Biochemistry. 2009 Aug 25;48(33):7878-91. doi: 10.1021/bi9006447. (Abstract)
Continue reading →Sukumar N., Dewanti A., Merli A., Rossi G.L., Mitra B., & Mathews F.S. (2009). “Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates.” Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):543-52. doi: 10.1107/S0907444909010270. Epub 2009 May 15. (Abstract)
Continue reading →Andreeva, I.E., Szymanski, M.R., Jezewska, M.J., Galletto, R. and Bujalowski, W.
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Dynamics of the ssDNA recognition by the RepA hexameric helicase of plasmid RSF1010: analyses using fluorescence stopped-flow intensity and anisotropy methods.
J Mol Biol 388:751-775 (2009). (Abstract)Macdonald-Obermann J.L. & Pike L.J. (2009). “The intracellular juxtamembrane domain of the epidermal growth factor (EGF) receptor is responsible for the allosteric regulation of EGF binding.” J Biol Chem. 2009 May 15;284(20):13570-6. doi: 10.1074/jbc.M109.001487. Epub 2009 Mar 31. (Abstract)
Continue reading →Galburt E.A., Grill S.W., & Bustamante C. (2009). “Single molecule transcription elongation.” Methods. 2009 Aug;48(4):323-32. doi: 10.1016/j.ymeth.2009.04.021. Epub 2009 May 6. (Abstract)
Continue reading →Pike L.J. (2009). “The challenge of lipid rafts.” J Lipid Res. 2009 Apr;50 Suppl:S323-8. doi: 10.1194/jlr.R800040-JLR200. Epub 2008 Oct 27. (Abstract)
Continue reading →Kermekchiev M.B., Kirilova L.I., Vail E.E., & Barnes W.M. (2009). “Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples.” Nucleic Acids Res. 2009 Apr;37(5):e40. doi: 10.1093/nar/gkn1055. Epub 2009 Feb 10. (Abstract)
Continue reading →Uluckan O., Becker S.N., Deng H., Zou W., Prior J.L., Piwnica-Worms D., Frazier W.A., & Weilbaecher K.N. (2009). “CD47 regulates bone mass and tumor metastasis to bone.” Cancer Res. 2009 Apr 1;69(7):3196-204. doi: 10.1158/0008-5472.CAN-08-3358. Epub 2009 Mar 10. (Abstract)
Continue reading →Macdonald-Obermann J.L. & Pike L.J. (2009). “Palmitoylation of the EGF receptor impairs signal transduction and abolishes high-affinity ligand binding.” Biochemistry. 2009 Mar 24;48(11):2505-13. doi: 10.1021/bi802249x. (Abstract)
Continue reading →Yang K.S., Ilagan M.X., Pinica-Worms D. and Pike L.J. (2009) “Luciferase fragment complementation imaging of conformational changes in the epidermal growth factor receptor.” J Biol Chem. 2009 Mar 20;284(12):7474-82. doi: 10.1074/jbc.M808041200. Epub 2009 Jan 26. (Abstract)
Continue reading →Depken M., Galburt E.A., & Grill S.W. (2009). “The origin of short transcriptional pauses.” Biophys J. 2009 Mar 18;96(6):2189-93. doi: 10.1016/j.bpj.2008.12.3918. (Abstract)
Continue reading →Gupta S.S., Borin B.N., Cover T.L., & Krezel A.M. (2009). “Structural analysis of the DNA-binding domain of the Helicobacter pylori response regulator ArsR.” J Biol Chem. 2009 Mar 6;284(10):6536-45. doi: 10.1074/jbc.M804592200. Epub 2008 Dec 30. (Abstract)
Continue reading →Ramamoorthy A., Lee D.K., Santos J.S., & Henzler-Wildman K.A. (2008). “Nitrogen-14 solid-state NMR spectroscopy of aligned phospholipid bilayers to probe peptide-lipid interaction and oligomerization of membrane associated peptides.” J Am Chem Soc. 2008 Aug 20;130(33):11023-9. doi: 10.1021/ja802210u. Epub 2008 Jul 23. (Abstract)
Continue reading →Eiblmaier M., Meyer L.A., Watson M.A., Fracasso P.M., Pike L.J. & Anderson C.J. (2008). “Correlating EGFR expression with receptor-binding properties and internalization of 64Cu-DOTA-cetuximab in 5 cervical cancer cell lines.” J Nucl Med. 2008 Sep;49(9):1472-9. doi: 10.2967/jnumed.108.052316. Epub 2008 Aug 14. (Abstract)
Continue reading →Borin B.N. & Krezel A.M. (2008). “Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator.” Proteins. 2008 Oct;73(1):265-8. doi: 10.1002/prot.22159. (Abstract)
Continue reading →Porcelli F., Verardi R., Shi L., Henzler-Wildman K.A., Ramamoorthy A., & Veglia G. (2008). “NMR structure of the cathelicidin-derived human antimicrobial peptide LL-37 in dodecylphosphocholine micelles.” Biochemistry. 2008 May 20;47(20):5565-72. doi: 10.1021/bi702036s. Epub 2008 Apr 26. (Abstract)
Continue reading →Macdonald J.L. & Pike L.J. (2008). “Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system.” Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):112-7. doi: 10.1073/pnas.0707080105. Epub 2007 Dec 28. (Abstract)
Continue reading →Henzler-Wildman K. & Kern D. (2007). “Dynamic personalities of proteins.” Nature. 2007 Dec 13;450(7172):964-72. (Abstract)
Continue reading →Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., Pozharski E., Wilson M.A., Petsko G.A., Karplus M., Hübner C.G., & Kern D. (2007). “Intrinsic motions along an enzymatic reaction trajectory.” Nature. 2007 Dec 6;450(7171):838-44. Epub 2007 Nov 18. (Abstract)
Continue reading →Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., & Kern D. (2007). “A hierarchy of timescales in protein dynamics is linked to enzyme catalysis.” Nature. 2007 Dec 6;450(7171):913-6. Epub 2007 Nov 18. (Abstract)
Continue reading →Li W., Schulman S., Boyd D., Erlandson K., Beckwith J., and Rapoport T.A.
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The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal.
Mol Cell. 26(4):511-21. (2007, Cover Story) (Abstract)Saffarian S., Li Y., Elson E.L., & Pike L.J. (2007). “Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis.” Biophys J. 2007 Aug 1;93(3):1021-31. Epub 2007 May 11. (Abstract)
Continue reading →Galburt E.A., Grill S.W., Wiedmann A., Lubkowska L., Choy J., Nogales E., Kashlev M., & Bustamante C. (2007). “Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.” Nature. 2007 Apr 12;446(7137):820-3. Epub 2007 Mar 14. (Abstract)
Continue reading →Majka J. Niedziela-Majka A., & Burgers P.M. (2006). “The checkpoint clamp activates Mec1 kinase during initiation of the DNA damage checkpoint.” Mol Cell. 2006 Dec 28;24(6):891-901. (Abstract)
Continue reading →Anderson M.A., Ogbay B., Kisselev O.G., Cistola D.P., & Marshall G.R. (2006). “Alternate binding mode of C-terminal phenethylamine analogs of G(t)alpha(340-350) to photoactivated rhodopsin.” Chem Biol Drug Des. 2006 Dec;68(6):295-307. (Abstract)
Continue reading →Nikiforovich G.V., Zhang M., Yang Q., Jagadeesh G., Chen H.C., Hunyady L., Marshall G.R., & Catt K.J. (2006). “Interactions between conserved residues in transmembrane helices 2 and 7 during angiotensin AT1 receptor activation.” Chem Biol Drug Des. 2006 Nov;68(5):239-49. (Abstract)
Continue reading →Canton D.A., Olsten M.E., Niederstrasser H., Cooper J.A., & Litchfield D.W. (2006). “The role of CKIP-1 in cell morphology depends on its interaction with actin-capping protein.” J Biol Chem. 2006 Nov 24;281(47):36347-59. Epub 2006 Sep 20. (Abstract)
Continue reading →Sukumar N., Chen Z.W., Ferrari D., Merli A., Rossi G.L., Bellamy H.D., Chistoserdov A., Davidson V.L., & Mathews F.S. (2006). “Crystal structure of an electron transfer complex between aromatic amine dehydrogenase and azurin from Alcaligenes faecalis.” Biochemistry. 2006 Nov 14;45(45):13500-10. (Abstract)
Continue reading →Pascal J.M. & Ellenberger T. (2006). “RNA ligase does the AMP shuffle.” Nat Struct Mol Biol. 2006 Nov;13(11):950-1. (Abstract)
Continue reading →Crick S.L., Jayaraman M., Frieden C., Wetzel R., & Pappu R.V. (2006). “Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions.” Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16764-9. Epub 2006 Oct 30. (Abstract)
Continue reading →Pineda A.O., Chen Z.W., Bah A., Garvey L.C., Mathews F.S., & Di Cera E (2006). “Crystal structure of thrombin in a self-inhibited conformation.” J Biol Chem. 2006 Oct 27;281(43):32922-8. Epub 2006 Sep 5. (Abstract)
Continue reading →Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., & Ellenberger T. (2006). “A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.” Mol Cell. 2006 Oct 20;24(2):279-91. (Abstract)
Continue reading →Bhattacharya N., Ghosh S., Sept D., & Cooper J.A. (2006). “Binding of myotrophin/V-1 to actin-capping protein: implications for how capping protein binds to the filament barbed end.” J Biol Chem. 2006 Oct 13;281(41):31021-30. Epub 2006 Aug 7. (Abstract)
Continue reading →Wille J.J., Elson E.L., & Okamoto R.J. (2006). “Cellular and matrix mechanics of bioartificial tissues during continuous cyclic stretch.” Ann Biomed Eng. 2006 Nov;34(11):1678-90. Epub 2006 Oct 11. (Abstract)
Continue reading →Hu T., Krezel A.M., Li C., & Coffey R.J. (2006). “Structural studies of human Naked2: a biologically active intrinsically unstructured protein.” Biochem Biophys Res Commun. 2006 Dec 1;350(4):911-5. Epub 2006 Oct 2. (Abstract)
Continue reading →Hynson R.M., Mathews F.S., & Schuman Jorns M. (2006). “Identification of a stable flavin-thiolate adduct in heterotetrameric sarcosine oxidase.” J Mol Biol. 2006 Sep 29;362(4):656-63. Epub 2006 Jul 29. (Abstract)
Continue reading →Moon J.Y., Henzler-Wildman K.A., & Ramamoorthy A. (2006). “Expression and purification of a recombinant LL-37 from Escherichia coli.” Biochim Biophys Acta. 2006 Sep;1758(9):1351-8. Epub 2006 Feb 28. (Abstract)
Continue reading →Majka J., Binz S.K., Wold M.S., & Burgers P.M. (2006). “Replication protein A directs loading of the DNA damage checkpoint clamp to 5′-DNA junctions.” J Biol Chem. 2006 Sep 22;281(38):27855-61. Epub 2006 Jul 24. (Abstract)
Continue reading →Downs M.A., Arimoto R., Marshall G.R., & Kisselev O.G. (2006). “G-protein alpha and beta-gamma subunits interact with conformationally distinct signaling states of rhodopsin.” Vision Res. 2006 Dec;46(27):4442-8. Epub 2006 Sep 20. (Abstract)
Continue reading →Northam M.R., Garg P., Baitin D.M., Burgers P.M., & Shcherbakova P.V. (2006). “A novel function of DNA polymerase zeta regulated by PCNA.” EMBO J. 2006 Sep 20;25(18):4316-25. Epub 2006 Sep 7. (Abstract)
Continue reading →Zhong X., Garg P., Stith C.M., McElhinny S.A., Kissling G.E., Burgers P.M., & Kunkel T.A. (2006). “The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins.” Nucleic Acids Res. 2006;34(17):4731-42. Epub 2006 Sep 13. (Abstract)
Continue reading →Isenberg J.S., Ridnour L.A., Dimitry J., Frazier W.A., Wink D.A., & Roberts D.D. (2006). “CD47 is necessary for inhibition of nitric oxide-stimulated vascular cell responses by thrombospondin-1.” J Biol Chem. 2006 Sep 8;281(36):26069-80. Epub 2006 Jul 11. (Abstract)
Continue reading →Marquez J.P., Genin G.M., Pryse K.M., & Elson E.L. (2006). “Cellular and matrix contributions to tissue construct stiffness increase with cellular concentration.” Ann Biomed Eng. 2006 Sep;34(9):1475-82. Epub 2006 Jul 28. (Abstract)
Continue reading →Fortune J.M., Stith C.M., Kissling G.E., Burgers P.M., & Kunkel T.A. (2006). “RPA and PCNA suppress formation of large deletion errors by yeast DNA polymerase delta.” Nucleic Acids Res. 2006;34(16):4335-41. Epub 2006 Aug 26. (Abstract)
Continue reading →Macdonald J., Li Z., Su W., & Pike L.J. (2006). “The membrane proximal disulfides of the EGF receptor extracellular domain are required for high affinity binding and signal transduction but do not play a role in the localization of the receptor to lipid rafts.” Biochim Biophys Acta. 2006 Aug;1763(8):870-8. Epub 2006 May 13. (Abstract)
Continue reading →Chen Z.W., Hassan-Abdulah A., Zhao G., Jorns M.S., & Mathews F.S. (2006). “Heterotetrameric sarcosine oxidase: structure of a diflavin metalloenzyme at 1.85 A resolution.” J Mol Biol. 2006 Jul 28;360(5):1000-18. Epub 2006 Jun 15. (Abstract)
Continue reading →King D.A., Hall B.E., Iwamoto M.A., Win K.Z., Chang J.F., & Ellenberger T. (2006). “Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments.” J Biol Chem. 2006 Jul 21;281(29):20107-19. Epub 2006 May 22. (Abstract)
Continue reading →Tehrani S., Faccio R., Chandrasekar I., Ross F.P., & Cooper J.A. (2006). “Cortactin has an essential and specific role in osteoclast actin assembly.” Mol Biol Cell. 2006 Jul;17(7):2882-95. Epub 2006 Apr 12. (Abstract)
Continue reading →Bruck S., Huber T.B., Ingham R.J., Kim K., Niederstrasser H., Allen P.M., Pawson T., Cooper J.A., & Shaw A.S. (2006). “Identification of a novel inhibitory actin-capping protein binding motif in CD2-associated protein.” J Biol Chem. 2006 Jul 14;281(28):19196-203. Epub 2006 May 16. (Abstract)
Continue reading →Ma J.K., Carrell C.J., Mathews F.S., & Davidson V.L. (2006). “Site-directed mutagenesis of proline 52 to glycine in amicyanin converts a true electron transfer reaction into one that is conformationally gated.” Biochemistry. 2006 Jul 11;45(27):8284-93. (Abstract)
Continue reading →Nikiforovich G.V. & Marshall G.R. (2006). “3D modeling of the activated states of constitutively active mutants of rhodopsin.” Biochem Biophys Res Commun. 2006 Jun 23;345(1):430-7. Epub 2006 Apr 25. (Abstract)
Continue reading →Chen X., Pascal J., Vijayakumar S., Wilson G.M., Ellenberger T., & Tomkinson A.E. (2006). “Human DNA ligases I, III, and IV-purification and new specific assays for these enzymes.” Methods Enzymol. 2006;409:39-52. (Abstract)
Continue reading →Bylund G.O., Majka J., & Burgers P.M. (2006). “Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiae.” Methods Enzymol. 2006;409:1-11. (Abstract)
Continue reading →Asnes C.F., Marquez J.P., Elson E.L., & Wakatsuki T. (2006). “Reconstitution of the Frank-Starling mechanism in engineered heart tissues.” Biophys J. 2006 Sep 1;91(5):1800-10. Epub 2006 Jun 16. (Abstract)
Continue reading →Anderson M.A., Ogbay B., Arimoto R., Sha W., Kisselev O.G., Cistola D.P., & Marshall G.R. (2006). “Relative strength of cation-pi vs salt-bridge interactions: the Gtalpha(340-350) peptide/rhodopsin system.” J Am Chem Soc. 2006 Jun 14;128(23):7531-41. (Abstract)
Continue reading →Carrell C.J., Bush L.A., Mathews F.S., & Di Cera, E. (2006). “High resolution crystal structures of free thrombin in the presence of K(+) reveal the molecular basis of monovalent cation selectivity and an inactive slow form.” Biophys Chem. 2006 Jun 1;121(3):177-84. Epub 2006 Feb 17. (Abstract)
Continue reading →Våbenø J., Nikiforovich G.V., & Marshall G.R. (2006). “Insight into the binding mode for cyclopentapeptide antagonists of the CXCR4 receptor.” Chem Biol Drug Des. 2006 May;67(5):346-54. (Abstract)
Continue reading →Li H. & Frieden C. (2006). “Fluorine-19 NMR studies on the acid state of the intestinal fatty acid binding protein.” Biochemistry. 2006 May 23;45(20):6272-8. (Abstract)
Continue reading →Ye Y., Liu M., Kao J.L., & Marshall G.R. (2006). “Novel trihydroxamate-containing peptides: design, synthesis, and metal coordination.” Biopolymers. 2006;84(5):472-89. (Abstract)
Continue reading →Hagnerud S., Manna P.P., Cella M., Stenberg A., Frazier W.A., Colonna M., & Oldenborg P.A. (2006). “Deficit of CD47 results in a defect of marginal zone dendritic cells, blunted immune response to particulate antigen and impairment of skin dendritic cell migration.” J Immunol. 2006 May 15;176(10):5772-8. (Abstract)
Continue reading →Chattopadhyay K. & Frieden C. (2006). “Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein.” Proteins. 2006 May 1;63(2):327-35. (Abstract)
Continue reading →Ackers G.K. & Holt J.M. (2006). “Asymmetric cooperativity in a symmetric tetramer: human hemoglobin.” J Biol Chem. 2006 Apr 28;281(17):11441-3. Epub 2006 Jan 19. (Abstract)
Continue reading →Pike L.J. (2006). “Rafts defined: a report on the Keystone Symposium on Lipid Rafts and Cell Function.” J Lipid Res. 2006 Jul;47(7):1597-8. Epub 2006 Apr 27. (Abstract)
Continue reading →Remond M.C., Fee J.A., Elson E.L., & Taber L.A. (2006). “Myosin-based contraction is not necessary for cardiac c-looping in the chick embryo.” Anat Embryol (Berl). 2006 Oct;211(5):443-54. Epub 2006 Apr 25. (Abstract)
Continue reading →Saffarian S., Qian H., Collier I., Elson E., & Goldberg G. (2006). “Powering a burnt bridges Brownian ratchet: a model for an extracellular motor driven by proteolysis of collagen.” Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Apr;73(4 Pt 1):041909. Epub 2006 Apr 10. (Abstract)
Continue reading →Che Y. & Marshall G.R. (2006). “Impact of cis-proline analogs on peptide conformation.” Biopolymers. 2006 Apr 5;81(5):392-406. (Abstract)
Continue reading →Våbenø J., Nikiforovich G.V., & Marshall G.R. (2006). “A minimalistic 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists.” Biopolymers. 2006;84(5):459-71. (Abstract)
Continue reading →Kim K., Galletta B.J., Schmidt K.O., Chang F.S., Blumer K.J., & Cooper J.A. (2006). “Actin-based motility during endocytosis in budding yeast.” Mol Biol Cell. 2006 Mar;17(3):1354-63. Epub 2006 Jan 4. (Abstract)
Continue reading →Che Y., Brooks B.R., & Marshall G.R. (2006). “Development of small molecules designed to modulate protein-protein interactions.” J Comput Aided Mol Des. 2006 Feb;20(2):109-30. Epub 2006 Apr 19. (Abstract)
Continue reading →Zhuang Z., Yoder B.L., Burgers P.M., & Benkovic S.J. (2006). “The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer.” Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2546-51. Epub 2006 Feb 13. (Abstract)
Continue reading →Radman-Livaja M., Biswas T., Ellenberger T., Landy A., & Aihara, H. (2006). “DNA arms do the legwork to ensure the directionality of lambda site-specific recombination.” Curr Opin Struct Biol. 2006 Feb;16(1):42-50. Epub 2005 Dec 20. (Abstract)
Continue reading →Tomkinson A.E., Vijayakumar S., Pascal J.M., & Ellenberger, T. (2006). “DNA ligases: structure, reaction mechanism, and function.” Chem Rev. 2006 Feb;106(2):687-99. (Abstract)
Continue reading →Kim T.W., Brieba L.G., Ellenberger T., & Kool, E.T. (2006). “Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs.” J Biol Chem. 2006 Jan 27;281(4):2289-95. Epub 2005 Nov 27. (Abstract)
Continue reading →Li W., Kamtekar S., Xiong Y., Sarkis G.J., Grindley N.D., & Steitz T.A. (2005). “Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs.” Science. 2005 Aug 19;309(5738):1210-5. Epub 2005 Jun 30. (Abstract)
Continue reading →Kurz L.C., Fite B., Jean J., Park J., Erpelding T., & Callis P. (2005). “Photophysics of tryptophan fluorescence: link with the catalytic strategy of the citrate synthase from Thermoplasma acidophilum.” Biochemistry. 2005 Feb 8;44(5):1394-413. (Abstract)
Continue reading →Morgan J.C., Majors J.E., & Galileo D.S. (2005). “Distinct and opposite roles for SH2 and SH3 domains of v-src in embryo survival and hemangiosarcoma formation.” Clin Exp Metastasis. 2005;22(2):167-75. (Abstract)
Continue reading →Ren C.P., Chaudhuri R.R., Fivian A., Bailey C.M., Antonio M., Barnes W.M., & Pallen M.J. (2004). “The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J Bacteriol. 2004 Jun;186(11):3547-60. (Abstract)
Continue reading →Cliften P., Sudarsanam P., Desikan A., Fulton L., Fulton B., Majors J., Waterston R., Cohen B.A., & Johnston M. (2003). “Finding functional features in Saccharomyces genomes by phylogenetic footprinting.” Science. 301(5629):71-6. (Abstract)
Continue reading →Hardy R.W., Marcotrigiano J., Blight K.J., Majors J.E., & Rice C.M. (2003). “Hepatitis C virus RNA synthesis in a cell-free system isolated from replicon-containing hepatoma cells.” J Virol. 77(3):2029-37. (Abstract)
Continue reading →Kurz, L.C., Drysdale, G., Riley, M., Tomar, M.A., Chen, J., Russell, R.J.M. & Danson, M.J. (2000). “Kinetics and mechanism of the citrate synthase from the thermophilic archaeon Thermoplasma acidophilum.” Biochemistry. 2000 Mar 7;39(9):2283-96. (Abstract)
Continue reading →Gu, Z., Drueckhammer, D.G., Kurz, L., Liu, K., Martin, D.P., & McDermott, A. (1999). “Solid state NMR studies of hydrogen bonding in a citrate synthase inhibitor complex.” Biochemistry. 1999 Jun 22;38(25):8022-31. (Abstract)
Continue reading →Deng H., Kurz L.C., Rudolph F.B. & Callender R. (1998). “Characterization of hydrogen bonding in the complex of adenosine deaminase with a transition state analogue: a Raman spectroscopic study.” Biochemistry. 1998 Apr 7;37(14):4968-76. (Abstract)
Continue reading →Scott R.A., Sullivan R.J., DeWolf W.E. Jr., Dolle R.E., and Kruse L.I.
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The copper sites of dopamine beta-hydroxylase: an X-ray absorption spectroscopic study.
Biochemistry. 26;27(15):5411-7 (1988). (Abstract)Baenziger J., Kornfeld S., & Kochwa S. (1974). “Structure of the carbohydrate units of IgE immunoglobulin. II. Sequence of the sialic acid-containing glycopeptides.” J Biol Chem. 1974 Mar 25;249(6):1897-903. (Abstract)
Continue reading →Baenziger J., Kornfeld S., & Kochwa S. (1974). “Structure of the carbohydrate units of IgE immunoglobulin. I. Over-all composition, glycopeptide isolation, and structure of the high mannose oligosaccharide unit.” J Biol Chem. 1974 Mar 25;249(6):1889-96. (Abstract)
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