Recent Publications


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

More can be found in the Archives.


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)

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)

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 Nov 21. pii: 201809454. doi: 10.1073/pnas.1809454115. [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)

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 Nov 5. doi: 10.1093/nar/gky1065. [Epub ahead of print] (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)

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)

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)

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 Jun 21. doi: 10.1093/nar/gky530. (Abstract)


More can be found in the Archives.