2016 Publications

The following is a partial list of publications by faculty, post-doctoral associates, students, and staff of Biochemistry and Molecular Biophysics.


Galburt E.A. & Rammohan J. (2016). “A Kinetic Signature for Parallel Pathways: Conformational Selection and Induced Fit. Links and Disconnects between Observed Relaxation Rates and Fractional Equilibrium Flux under Pseudo-First-Order Conditions.” Biochemistry. 2016 Dec 20;55(50):7014-7022. Epub 2016 Dec 8. (Abstract)

Yang Y., Ke N., Liu S., & Li W. (2016). “Methods for Structural and Functional Analyses of Intramembrane Prenyltransferases in the UbiA Superfamily.” Methods Enzymol. 2017;584:309-347. doi: 10.1016/bs.mie.2016.10.032. Epub 2016 Dec 7. (Abstract)

Brosey C.A., Ho C., Long W.Z., Singh S., Burnett K., Hura G.L., Nix J.C., Bowman G.R., Ellenberger T., & Tainer J.A. (2016). “Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor” Structure. 2016 Dec 6;24(12):2067-2079. doi: 10.1016/j.str.2016.09.012. Epub 2016 Nov 3. (Abstract)

Shen G., Cui W., Zhang H., Zhou F., Huang W., Liu Q., Yang Y., Li S., Bowman G.R., Sadler J.E., Gross M.L., & Li W. (2017). “Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer.” Nat Struct Mol Biol. 2017 Jan;24(1):69-76. doi: 10.1038/nsmb.3333. Epub 2016 Dec 5. (Abstract)

Kochenova O.V., Bezalel-Buch R., Tran P., Makarova A.V., Chabes A., Burgers P.M., & Shcherbakova P.V. (2016). “Yeast DNA polymerase ζ maintains consistent activity and mutagenicity across a wide range of physiological dNTP concentrations.” Nucleic Acids Res. 2017 Feb 17;45(3):1200-1218. doi: 10.1093/nar/gkw1149. (Abstract)

Kraft T.E., Heitmeier M.R., Putanko M., Edwards R.L., Ilagan M.X., Payne M.A., Autry J.M., Thomas D.D., Odom A.R., and Hruz P.W. (2016) “A Novel Fluorescence Resonance Energy Transfer-Based Screen in High-Throughput Format To Identify Inhibitors of Malarial and Human Glucose Transporters.” Antimicrob Agents Chemother. 2016 Nov 21;60(12):7407-7414. Print 2016 Dec. (Abstract)

Michael Kinch (2016) “A Prescription for Change: The Looming Crisis in Drug Development” (ISBN-13: 978-1469630625, ISBN-10: 1469630621)

Needham S.R., Roberts S.K., Arkhipov A., Mysore V.P., Tynan C.J., Zanetti-Domingues L.C., Kim E.T., Losasso V., Korovesis D., Hirsch M., Rolfe D.J., Clarke D.T., Winn M.D., Lajevardipour A., Clayton A.H., Pike L.J., Perani M., Parker P.J., Shan Y., Shaw D.E., & Martin-Fernandez M.L. (2016). “EGFR oligomerization organizes kinase-active dimers into competent signalling platforms.” Nat Commun. 2016 Oct 31;7:13307. doi: 10.1038/ncomms13307. (Abstract)

Mydock-McGrane L., Cusumano Z., Han Z., Binkley J., Kostakioti M., Hannan T., Pinkner J.S., Klein R.D., Kalas V., Crowley J., Rath N.P., Hultgren S.J., & Janetka J.W. (2016). “Antivirulence C-Mannosides as Antibiotic-Sparing, Oral Therapeutics for Urinary Tract Infections.” J Med Chem. 2016 Oct 27;59(20):9390-9408. Epub 2016 Oct 14. (Abstract)

Zhou J.Y., Szasz T.P., Stewart-Hutchinson P.J., Sivapalan J., Todd E.M., Deady L.E., Cooper J.A., Onken M.D., & Morley S.C. (2016). “L-Plastin promotes podosome longevity and supports macrophage motility.” Mol Immunol. 2016 Oct;78:79-88. doi: 10.1016/j.molimm.2016.08.012. Epub 2016 Sep 7. (Abstract)

Hart K.M., Ho C.M., Dutta S., Gross M.L., & Bowman G.R. (2016). “Modelling proteins’ hidden conformations to predict antibiotic resistance.” Nat Commun. 2016 Oct 6;7:12965. doi: 10.1038/ncomms12965. (Abstract)

Welty R. & Hall K.B. (2016). “Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.” J Mol Biol. 2016 Nov 6;428(22):4490-4502. doi: 10.1016/j.jmb.2016.09.015. Epub 2016 Sep 29. (Abstract)

Thomas J.J., Abed M., Heuberger J., Novak R., Zohar Y., Beltran Lopez A.P., Trausch-Azar J.S., Ilagan M.X., Benhamou D., Dittmar G., Kopan R., Birchmeier W., Schwartz A.L., and Orian A. (2016) “RNF4-Dependent Oncogene Activation by Protein Stabilization.” Cell Rep. 2016 Sep 20;16(12):3388-3400. doi: 10.1016/j.celrep.2016.08.024. (Abstract)

Xu X., Wang X., Todd E.M., Jaeger E.R., Vella J.L., Mooren O.L., Feng Y., Hu J., Cooper J.A., Morley S.C., & Huang Y.H. (2016). “Mst1 Kinase Regulates the Actin-Bundling Protein L-Plastin To Promote T Cell Migration.” J Immunol. 2016 Sep 1;197(5):1683-91. doi: 10.4049/jimmunol.1600874. Epub 2016 Jul 27. (Abstract)

Mi Y., Coonce M., Fiete D., Steirer L., Dveksler G., Townsend R.R., & Baenziger J.U. (2016). “Functional Consequences of Mannose and Asialoglycoprotein Receptor Ablation.” J Biol Chem. 2016 Sep 2;291(36):18700-17. doi: 10.1074/jbc.M116.738948. Epub 2016 Jul 12. (Abstract)

Borgia A., Zheng W., Buholzer K., Borgia M.B., Schüler A., Hofmann H., Soranno A., Nettels D., Gast K., Grishaev A., Best R.B., & Schuler B. (2016). “Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.” J Am Chem Soc. 2016 Sep 14;138(36):11714-26. doi: 10.1021/jacs.6b05917. Epub 2016 Sep 1. (Abstract)

Pascolutti R., Sun X., Kao J., Maute R., Ring A.M., Bowman G.R., & Kruse A.C. (2016). “Structure and Dynamics of PD-L1 and an Ultra High-Affinity PD-1 Receptor Mutant.” Structure. 2016 Oct 4;24(10):1719-1728. doi: 10.1016/j.str.2016.06.026. Epub 2016 Sep 8. (Abstract)

Xiao Z., Banan B., Xu M., Jia J., Manning P.T., Hiebsch R.R., Gunasekaran M., Upadhya G.A., Frazier W.A., Mohanakumar T., Lin Y., & Chapman W.C. (2016). “Attenuation of Ischemia-Reperfusion Injury and Improvement of Survival in Recipients of Steatotic Rat Livers Using CD47 Monoclonal Antibody.” Transplantation. 2016 Jul;100(7):1480-9. doi: 10.1097/TP.0000000000001186. (Abstract)

Smith J.A., Xu G., Feng R., Janetka J.W., & Moeller, K.D. (2016). “C‐Glycosides, Array‐based Addressable Libraries, and the Versatility of Constant Current Electrochemistry” Electroanalysis. 2016, Volume 28, Issue 11, Pages: 2808-2817. DOI: 10.1002/elan.201600200 (Abstract)

Woody M.S., Lewis J.H., Greenberg M.J., Goldman Y.E., & Ostap E.M. (2016). “MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood Estimation.” Biophys J. 2016 Jul 26;111(2):273-282. doi: 10.1016/j.bpj.2016.06.019. (Abstract)

Simon M., Sokoloski J., Hao L., Weiland E., & Lohman T. (2016). “Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation.” J Mol Biol. 2016 Jul 31;428(15):2997-3012. doi: 10.1016/j.jmb.2016.07.002. Epub 2016 Jul 14. (Abstract)

Bergonzo C., Hall K.B, & Cheatham T.E. (2016). “Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.” J Chem Theory Comput. 2016 Jul 12;12(7):3382-9. doi: 10.1021/acs.jctc.6b00173. Epub 2016 Jun 28. (Abstract)

Schuler B., Soranno A., Hofmann H., & Nettels D. (2016). “Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.” Annu Rev Biophys. 2016 Jul 5;45:207-31. doi: 10.1146/annurev-biophys-062215-010915. Epub 2016 May 2. (Abstract)

Stojkovic G., Makarova A.V., Wanrooij P.H., Forslund J., Burgers P.M., & Wanrooij S. (2016). “Oxidative DNA damage stalls the human mitochondrial replisome.” Sci Rep. 2016 Jul 1;6:28942. doi: 10.1038/srep28942. (Abstract)

Shu Q., Krezel A.M., Cusumano Z.T., Pinkner J.S., Klein R., Hultgren S.J., & Frieden C. (2016). “Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.” Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7130-5. doi: 10.1073/pnas.1607222113. Epub 2016 Jun 13. (Abstract)

Rammohan J., Ruiz Manzano A., Garner A.L., Prusa J. Stallings C.L., & Galburt E.A. (2016). “Cooperative stabilization of Mycobacterium tuberculosis rrnAP3 promoter open complexes by RbpA and CarD.” Nucleic Acids Res. 2016 Sep 6;44(15):7304-13. doi: 10.1093/nar/gkw577. Epub 2016 Jun 24. (Abstract)

Kinch M.S. and Moore R. (2016) “Innovator Organizations in New Drug Development: Assessing the Sustainability of the Biopharmaceutical Industry.” Cell Chem Biol. 2016 Jun 23;23(6):644-53. doi: 10.1016/j.chembiol.2016.05.013. (Abstract)

Greenberg M.J., Arpag G., Tuzel E., & Ostap E.M. (2016). “A Perspective on the Role of Myosins as Mechanosensors.” Biophys J. 2016 Jun 21;110(12):2568-2576. doi: 10.1016/j.bpj.2016.05.021. (Abstract)

Fishburn J., Galburt E., & Hahn S. (2016). “Transcription Start Site Scanning and the Requirement for ATP during Transcription Initiation by RNA Polymerase II.” J Biol Chem. 2016 Jun 17;291(25):13040-7. doi: 10.1074/jbc.M116.724583. Epub 2016 Apr 17. (Abstract)

Babaei B., Davarian A., Lee S.L., Pryse K.M., McConnaughey W.B., Elson E.L., & Genin G.M. (2016). “Remodeling by fibroblasts alters the rate-dependent mechanical properties of collagen.” Acta Biomater. 2016 Jun;37:28-37. doi: 10.1016/j.actbio.2016.03.034. Epub 2016 Mar 23. (Abstract)

Cho J.E., Huang S.N., Burgers P.M., Shuman S., Pommier Y., & Jinks-Robertson S. (2016). “Parallel analysis of ribonucleotide-dependent deletions produced by yeast Top1 in vitro and in vivo.” Nucleic Acids Res. 2016 Sep 19;44(16):7714-21. doi: 10.1093/nar/gkw495. Epub 2016 Jun 1. (Abstract)

Stodola J.L., Stith C.M., & Burgers P.M. (2016). “Proficient Replication of the Yeast Genome by a Viral DNA Polymerase.” J Biol Chem. 2016 May 27;291(22):11698-705. doi: 10.1074/jbc.M116.728741. Epub 2016 Apr 12. (Abstract)

Stodola J.L. & Burgers P.M. (2016). “Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale.” Nat Struct Mol Biol. 2016 May;23(5):402-8. doi: 10.1038/nsmb.3207. Epub 2016 Apr 11. (Abstract)

Waldman V.M., Weiland E., Kozlov A.G., & Lohman T.M. (2016). “Is a fully wrapped SSB-DNA complex essential for Escherichia coli survival?” Nucleic Acids Res. 2016 May 19;44(9):4317-29. doi: 10.1093/nar/gkw262. Epub 2016 Apr 15. (Abstract)

Sokoloski J.E., Kozlov A.G., Galletto R., & Lohman T.M. (2016). “Chemo-mechanical pushing of proteins along single-stranded DNA.” Proc Natl Acad Sci U S A. 2016 May 31;113(22):6194-9. doi: 10.1073/pnas.1602878113. Epub 2016 May 16. (Abstract)

Chowdhury F., Li I., Ngo T., Leslie B., Kim B., Sokoloski J., Weiland E., Wang X., Chemla Y., Lohman T., & Ha T. (2016). “Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo.” Nano Lett. 2016 Jun 8;16(6):3892-7. doi: 10.1021/acs.nanolett.6b01403. Epub 2016 May 12. (Abstract)

Krishna U., Romero-Gallo J., Suarez G., Azah A., Krezel A.M., Varga M.G., Forsyth M.H., & Peek R.M. Jr. (2016). “Genetic Evolution of a Helicobacter pylori Acid-Sensing Histidine Kinase and Gastric Disease.” J Infect Dis. 2016 Aug 15;214(4):644-8. doi: 10.1093/infdis/jiw189. Epub 2016 May 10. (Abstract)

Koc K.N., Singh S.P., Stodola J.L., Burgers P.M., & Galletto R. (2016). “Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ.” Nucleic Acids Res. 2016 May 5;44(8):3811-9. doi: 10.1093/nar/gkw181. Epub 2016 Mar 21. (Abstract)

Sawicka, M., Wanrooij, P.H., Darbari, V.C., Tannous, E., Hailemariam, S., Bose, D., Makarova, A.V., Burgers, P.M. and Zhang, X.
The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization.
J Biol Chem 291:13436-47 (2016) (Abstract)

Mondal T., Wang H., DeKoster G.T., Baban B., Gross M.L., & Frieden C. (2016). “ApoE: In Vitro Studies of a Small Molecule Effector.” Biochemistry. 2016 May 10;55(18):2613-21. doi: 10.1021/acs.biochem.6b00324. Epub 2016 Apr 27. (Abstract)

Weikai Li
Bringing Bioactive Compounds into Membranes: The UbiA Superfamily of Intramembrane Aromatic Prenyltransferases.
Trends Biochem Sci. 41(4):356-70. (2016) (Abstract)

Wang Q., Heizer E., Rosa B.A., Wildman S.A., Janetka J.W., & Mitreva, M. (2016). “Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.” Infect Genet Evol. 2016 Apr;39:201-211. doi: 10.1016/j.meegid.2016.01.025. Epub 2016 Jan 30. (Abstract)

Wang X., Galletta B.J., Cooper J.A., & Carlsson A.E. (2016). “Actin-Regulator Feedback Interactions during Endocytosis.”
Biophys J. 2016 Mar 29;110(6):1430-43. doi: 10.1016/j.bpj.2016.02.018. (Abstract)

Singh, S.P., Koc, K.N., Stodola, J.L. and Galletto, R.
A Monomer of Pif1 Unwinds Double-Stranded DNA and It Is Regulated by the Nature of the Non-Translocating Strand at the 3′-End.
J Mol Biol 428:1053-1067 (2016). (Abstract)

Han Z., Harris P.K.W., Karmakar P., Kim T., Owusu B.Y., Wildman S.A., Klampfer, L., & Janetka J.W. (2016). “α-Ketobenzothiazole Serine Protease Inhibitors of Aberrant HGF/c-MET and MSP/RON Kinase Pathway Signaling in Cancer.” ChemMedChem. 2016 Mar 17;11(6):585-99. doi: 10.1002/cmdc.201500600. Epub 2016 Feb 17. (Abstract)

Simpson C., Jones N.G., Hull-Ryde E.A., Kireev D., Stashko M., Tang K., Janetka J., Wildman S.A., Zuercher W.J., Schapira M., Hui R., Janzen W., & Sibley L.D. (2016). “Identification of small molecule inhibitors that block the Toxoplasma gondii rhoptry kinase ROP18.” ACS Infect Dis. 2016 Mar 11;2(3):194-206. Epub 2015 Dec 28. (Abstract)

Ronan T., Macdonald-Obermann J.L., Huelsmann L., Bessman N.J., Naegle K.M., & Pike L.J. (2016). “Different Epidermal Growth Factor Receptor (EGFR) Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Proteins.” J Biol Chem. 2016 Mar 11;291(11):5528-40. doi: 10.1074/jbc.M115.710087. Epub 2016 Jan 19. (Abstract)

Bowman G.R.
Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation.
J Comput Chem. 37(6):558-66. (2016) (Abstract)

Lisica A., Engel C., Jahnel M., Roldán É., Galburt E.A., Cramer P., & Grill S.W. (2016). “Mechanisms of backtrack recovery by RNA polymerases I and II.” Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2946-51. doi: 10.1073/pnas.1517011113. Epub 2016 Feb 29. (Abstract)

Reddy D.N., Ballante F., Chuang T., Pirolli A., Marrocco B., and Marshall G.R. (2016) “Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors.” J Med Chem. 2016 Feb 25;59(4):1613-33. doi: 10.1021/acs.jmedchem.5b01632. Epub 2016 Jan 7. (Abstract)

Burgers, P.M., Gordenin, D. and Kunkel, T.A.
Who Is Leading the Replication Fork, Pol ε or Pol δ?
Mol Cell. 61:492-493 (2016). (Abstract)

Elson E.L. & Genin G.M. (2016). “Tissue constructs: platforms for basic research and drug discovery.” Interface Focus. 2016 Feb 6;6(1):20150095. doi: 10.1098/rsfs.2015.0095. (Abstract)

Li Y., Huang G., Li M., Wang L., Elson E.L., Lu T.J., Genin G.M., & Xu F. (2016). “An approach to quantifying 3D responses of cells to extreme strain.” Sci Rep. 2016 Feb 18;6:19550. doi: 10.1038/srep19550. (Abstract)

Jarvis C., Han Z., Kalas V., Klein R., Pinkner J.S., Ford B., Binkley J., Cusumano C.K., Cusumano Z., Mydock-McGrane L., Hultren S.J., & Janetka J.W. (2016). “Antivirulence Isoquinolone Mannosides: Optimization of the Biaryl Aglycone for FimH Lectin Binding Affinity and Efficacy in the Treatment of Chronic UTI.” ChemMedChem. 2016 Feb 17;11(4):367-73. doi: 10.1002/cmdc.201600006. Epub 2016 Jan 26. (Abstract)

Ballante F. and Marshall G.R. (2016) “An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design.” J Chem Inf Model. 2016 Jan 25;56(1):54-72. doi: 10.1021/acs.jcim.5b00603. Epub 2016 Jan 6. (Abstract)

Mydock-McGrane L.K., Cusumano Z.T., & Janetka J.W. (2016). “Mannose-derived FimH antagonists: a promising anti-virulence therapeutic strategy for urinary tract infections and Crohn’s disease.” Expert Opin Ther Pat. 2016;26(2):175-97. doi: 10.1517/13543776.2016.1131266. Epub 2016 Jan 22. (Abstract)

Wanrooij, P.H, Tannous, E., Kumar, S., Navadgi-Patil, V.M. and Burgers, P.M.
Probing the Mec1ATR Checkpoint Activation Mechanism with Small Peptides.
J Biol Chem 291:1076-1091 (2016). (Abstract)