2018 Publications

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Michael Kinch (2018). “Between Hope and Fear: A History of Vaccines and Human Immunity” ISBN-13: 978-1681777511, ISBN-10: 1681777517