Recent Publications

Publications by faculty, post-doctoral associates, students, and staff of Biochemistry and Molecular Biophysics.

More can be found in the Archives.

Frieden C. (2019). “Protein oligomerization as a metabolic control mechanism. Application to apoE.” Protein Sci. 2019 Jan 30. doi: 10.1002/pro.3583. [Epub ahead of print] (Abstract)

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)

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)

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 Jan 23. doi: 10.1093/nar/gkz023. [Epub ahead of print] (Abstract)

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. (Abstract)

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 Jan 7. pii: jbc.RA118.007048. doi: 10.1074/jbc.RA118.007048. [Epub ahead of print] (Abstract)

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)

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 Jan 3. doi: 10.1093/nar/gky1321. [Epub ahead of print] (Abstract)

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. (2018). “Discovery of Selective Matriptase and Hepsin Serine Protease Inhibitors: Useful Chemical Tools for Cancer Cell Biology.” J Med Chem. 2018 Dec 20. doi: 10.1021/acs.jmedchem.8b01536. [Epub ahead of print] (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)

Knoverek C.R., Amarasinghe G.K., & Bowman G.R. (2018). “Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.” Trends Biochem Sci. 2018 Dec 13. pii: S0968-0004(18)30248-2. doi: 10.1016/j.tibs.2018.11.007. [Epub ahead of print] (Abstract)

Maddirala A., Klein R.D., Pinkner J., Kalas V., Hultgren S.J., & Janetka J.W. (2018). “Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through iterative rational drug design.” J Med Chem. 2018 Dec 12. doi: 10.1021/acs.jmedchem.8b01561. [Epub ahead of print] (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)

Dubiel K., Myers A.R., Kozlov A.G., Yang O., Zhang J., Ha T., Lohman T.M., & Keck J.L. (2018). “Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins.” J Mol Biol. 2018 Nov 22. pii: S0022-2836(18)31046-5. doi: 10.1016/j.jmb.2018.11.019. [Epub ahead of print] (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)

More can be found in the Archives.