2015 Publications

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)

Zimmerman, M.I. and Bowman, G.R.
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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Bowman, G.R.
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)

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)

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)

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)

Feldmann, E.A., De Bona, P. and Galletto, R.
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.
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.
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)

Hall K.B. (2015). “Mighty tiny.” RNA. 2015 Apr;21(4):630-1. doi: 10.1261/rna.050567.115. (Abstract)

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)

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)

Koc, K.N., Stodola, J.L., Burgers, P.M., and Galletto, R.
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)

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)

Sparks, J.L. and Burgers, P.M.
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.
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)

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)

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)

Feldmann, E.A., Koc, K.N. and Galletto, R.
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)

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)

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)

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)

Makarova, A.V. and Burgers, P.M.
Eukaryotic DNA polymerase ζ.
DNA Repair S1568-7864:00048 (2015). (Abstract)

DuBay, K.H., Bowman, G.R. and Geissler, P.L.
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)

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)

Bowman, G.R. Bolin, E.R., Hart, K.M., Maguire, B.C. and Marqusee, S.
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)

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)