Recent Publications

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

More can be found in the Archives.

Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, & Gregory R. Bowman (2021). “SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome” Nat Chem. 2021 Jul;13(7):651-659. doi: 10.1038/s41557-021-00707-0. Epub 2021 May 24. (Abstract)

Samantha K. Barrick, Lina Greenberg, & Michael J. Greenberg (2021). “A Troponin T Variant Linked with Pediatric Dilated Cardiomyopathy Reduces the Coupling of Thin Filament Activation to Myosin and Calcium Binding” Mol Biol Cell. 2021 Jun 23;mbcE21020082. doi: 10.1091/mbc.E21-02-0082. Online ahead of print. (Abstract)

Elias A. Tannous & Peter M. Burgers (2021). “Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)” Crit Rev Biochem Mol Biol. 2021 Jun 20;1-14. doi: 10.1080/10409238.2021.1925218. Online ahead of print. (Abstract)

George R. Heath, Ekaterina Kots, Janice L. Robertson, Shifra Lansky, George Khelashvili, Harel Weinstein, & Simon Scheuring (2021). “Localization atomic force microscopy” Nature. 2021 Jun;594(7863):385-390. doi: 10.1038/s41586-021-03551-x. Epub 2021 Jun 16. (Abstract)

Melanie Ernst & Janice L. Robertson (2021). “The Role of the Membrane in Transporter Folding and Activity” J Mol Biol. 2021 Jun 15;167103. doi: 10.1016/j.jmb.2021.167103. Online ahead of print.

Mattia Bernetti, Kathleen B. Hall, & Giovanni Bussi (2021). “Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles” Nucleic Acids Res. 2021 Jun 9;gkab459. doi: 10.1093/nar/gkab459. Online ahead of print. (Abstract)

Denis A. Kiktev, Margaret Dominska, Tony Zhang, Joseph Dahl, Elena I. Stepchenkova, Piotr Mieczkowski, Peter M. Burgers, Scott Lujan, Adam Burkholder, Thomas A. Kunkel, & Thomas D. Petes (2021). “The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ” Nucleic Acids Res. 2021 Jun 4;49(10):5623-5636. doi: 10.1093/nar/gkab371. (Abstract)

Binh Nguyen, Min Kyung Shinn, Elizabeth Weiland, & Timothy M. Lohman (2021). “Regulation of E. coli Rep helicase activity by PriC” J Mol Biol. 2021 Jun 1;433(15):167072. doi: 10.1016/j.jmb.2021.167072. Online ahead of print. (Abstract)

Xiangli Wang, Yong Fu, Wandy L. Beatty, Meisheng Ma, Alan Brown, L. David Sibley, & Rui Zhang (2021). “Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins” Nat Commun. 2021 May 24;12(1):3065. doi: 10.1038/s41467-021-23351-1. (Abstract)

Michael D. Ward, Maxwell I. Zimmerman, Artur Meller, Moses Chung, S. J. Swamidass, & Gregory R. Bowman (2021). “Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets” Nat Commun. 2021 May 21;12(1):3023. doi: 10.1038/s41467-021-23246-1. (Abstract)

Matthew Mahoney, Vishnu C. Damalanka, Michael A. Tartell, Dong Hee Chung, André Luiz Lourenco, Dustin Pwee, Anne E. Mayer Bridwell, Markus Hoffmann, Jorine Voss, Partha Karmakar, Nurit Azouz, Andrea M. Klingler, Paul W. Rothlauf, Cassandra E. Thompson, Melody Lee, Lidija Klampfer, Christina Stallings, Marc E. Rothenberg, Stefan Pöhlmann, Sean P. Whelan, Anthony J. O’Donoghue, Charles S. Craik, & James W. Janetka (2021). “A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells” bioRxiv. 2021 May 6;2021.05.06.442935. doi: 10.1101/2021.05.06.442935. Preprint (Abstract)

Sarah R. Clippinger, Paige E. Cloonan, Wei Wang, Lina Greenberg, W. Tom Stump, Paweorn Angsutararux, Jeanne M. Nerbonne, & Michael J. Greenberg (2021). “Mechanical dysfunction of the sarcomere induced by a pathogenic mutation in troponin T drives cellular adaptation” J Gen Physiol. 2021 May 3;153(5):e202012787. doi: 10.1085/jgp.202012787. (Abstract)

Alexander G. Kozlov & Timothy M. Lohman (2021). “Probing E. coli SSB Protein-DNA topology by reversing DNA backbone polarity” Biophys J. 2021 Apr 20;120(8):1522-1533. doi: 10.1016/j.bpj.2021.02.025. Epub 2021 Feb 23. (Abstract)

Rahul Chadda, Nathan Bernhardt, Elizabeth G. Kelley, Susana Cm. Teixeira, Kacie Griffith, Alejandro Gil-Ley, Tuğba N. Öztürk, Lauren E. Hughes, Ana Forsythe, Venkatramanan Krishnamani, José D. Faraldo-Gómez, & Janice L. Robertson (2021). “Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states” Elife. 2021 Apr 7;10:e63288. doi: 10.7554/eLife.63288. (Abstract)

Ming Cheng, Chunyang Guo, Weikai Li, & Michael L. Gross (2021). “Free-Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication” Angew Chem Int Ed Engl. 2021 Mar 10. doi: 10.1002/anie.202014096. Online ahead of print. (Abstract)

Weikai Li (2021). “Targeting multiple enzymes in vitamin K metabolism for anticoagulation” J Thromb Haemost. 2021 Mar;19(3):633-636. doi: 10.1111/jth.15212. (Abstract)

Michael J. Greenberg & Jil C. Tardiff (2021). “Complexity in genetic cardiomyopathies and new approaches for mechanism-based precision medicine” J Gen Physiol. 2021 Mar 1;153(3):e202012662. doi: 10.1085/jgp.202012662. (Abstract)

Adam L. Bailey, Oleksandr Dmytrenko, Lina Greenberg, Andrea L. Bredemeyer, Pan Ma, Jing Liu, Vinay Penna, Lulu Lai, Emma S. Winkler, Sanja Sviben, Erin Brooks, Ajith P. Nair, Kent A. Heck, Aniket S. Rali, Leo Simpson, Mehrdad Saririan, Dan Hobohm, W. Tom Stump, James A. Fitzpatrick, Xuping Xie, Pei-Yong Shi, J. Travis Hinson, Weng-Tein Gi, Constanze Schmidt, Florian Leuschner, Chieh-Yu Lin, Michael S. Diamond, Michael J. Greenberg, & Kory J. Lavine (2021). “SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis” JACC Basic Transl Sci. 2021 Feb 26. doi: 10.1016/j.jacbts.2021.01.002. Online ahead of print. (Abstract)

Min Kyung Shinn, Alexander G. Kozlov, & Timothy M. Lohman (2021). “Allosteric effects of SSB C-terminal tail on assembly of E. coli RecOR proteins” Nucleic Acids Res. 2021 Feb 26;49(4):1987-2004. doi: 10.1093/nar/gkaa1291. (Abstract)

Kacey Mersch, Tugba N. Ozturk, Kunwoong Park, Hyun-Ho Lim, & Janice L. Robertson (2021). “Altering CLC stoichiometry by reducing non-polar side-chains at the dimerization interface” J Mol Biol. 2021 Feb 20;433(8):166886. doi: 10.1016/j.jmb.2021.166886. Online ahead of print. (Abstract)

Michael D. Onken, Carol M. Makepeace, Kevin M. Kaltenbronn, Joelle Choi, Leonel Hernandez-Aya, Katherine N. Weilbaecher, Kisha D. Piggott, P. Kumar Rao, Carla M. Yuede, Alethia J. Dixon, Patrick Osei-Owusu, John A. Cooper, & Kendall J. Blumer (2021). “Targeting primary and metastatic uveal melanoma with a G protein inhibitor” J Biol Chem. 2021 Feb 9;100403. doi: 10.1016/j.jbc.2021.100403. Online ahead of print. (Abstract)

Lisa K. McLellan, Michael R. McAllaster, Arthur S. Kim, Ľubomíra Tóthová, Patrick D. Olson, Jerome S. Pinkner, Allyssa L. Daugherty, Teri N. Hreha, James W. Janetka, Daved H. Fremont, Scott J. Hultgren, Herbert W. Virgin, & David A Hunstad (2021). “A host receptor enables type 1 pilus-mediated pathogenesis of Escherichia coli pyelonephritis” PLoS Pathog. 2021 Jan 29;17(1):e1009314. doi: 10.1371/journal.ppat.1009314. eCollection 2021 Jan. (Abstract)

Elias A. Tannous, Luke A. Yates, Xiaodong Zhang, & Peter M. Burgers (2021). “Mechanism of auto-inhibition and activation of Mec1 ATR checkpoint kinase” Nat Struct Mol Biol. 2021 Jan;28(1):50-61. doi: 10.1038/s41594-020-00522-0. Epub 2020 Nov 9. (Abstract)

Jessica B. Behring, Sjoerd van der Post, Arshag D. Mooradian, Matthew J. Egan, Maxwell I. Zimmerman, Jenna L. Clements, Gregory R. Bowman, & Jason M. Held (2021). “Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation” Sci Signal. 2020 Jan 21;13(615):eaay7315. doi: 10.1126/scisignal.aay7315. (Abstract)

Wayne M. Barnes, Zhian Zhang, & Milko B. Kermekchiev (2021). “A Single Amino Acid Change to Taq DNA Polymerase Enables Faster PCR, Reverse Transcription and Strand-Displacement” Front. Bioeng. Biotechnol., 14 January 2021, doi: 10.3389/fbioe.2020.553474 (Abstract)

More can be found in the Archives.