2017 Publications

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)