Recent Publications


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

More can be found in the Archives.


Daniel Griffith & Alex S. Holehouse (2021). “PARROT is a flexible recurrent neural network framework for analysis of large protein datasets” Elife. 2021 Sep 17;10:e70576. doi: 10.7554/eLife.70576. (Abstract)

Nicole R. Wong, Jay Mohan, Benjamin J. Kopecky, Shuchi Guo, Lixia Du, Jamison Leid, Guoshuai Feng, Inessa Lokshina, Oleksandr Dmytrenko, Hannah Luehmann, Geetika Bajpai, Laura Ewald, Lauren Bell, Nikhil Patel, Andrea Bredemeyer, Carla J. Weinheimer, Jessica M. Nigro, Attila Kovacs, Sachio Morimoto, Peter O. Bayguinov, Max R. Fisher, W. Tom Stump, Michael Greenberg, James A. J. Fitzpatrick, Slava Epelman, Daniel Kreisel, Rajan Sah, Yongjian Liu, Hongzhen Hu, & Kory J. Lavine (2021). “Resident cardiac macrophages mediate adaptive myocardial remodeling” Immunity. 2021 Sep 14;54(9):2072-2088.e7. doi: 10.1016/j.immuni.2021.07.003. Epub 2021 Jul 27. (Abstract)

Ishan Taneja & Alex S. Holehouse (2021). “Folded domain charge properties influence the conformational behavior of disordered tails” Curr Res Struct Biol. 2021 Sep 7;3:216-228. doi: 10.1016/j.crstbi.2021.08.002. eCollection 2021. (Abstract)

Linxuan Hao, Rui Zhang, & Timothy M. Lohman (2021). “Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting” J Mol Biol. 2021 Sep 3;433(18):167147. doi: 10.1016/j.jmb.2021.167147. Epub 2021 Jul 9. (Abstract)

Maria Papadaki, Theerachat Kampaengsri, Samantha K. Barrick, Stuart G. Campbell, Dirk von Lewinski, Peter P. Rainer, Samantha P. Harris, Michael J. Greenberg, & Jonathan A. Kirk (2021). “Myofilament glycation in diabetes reduces contractility by inhibiting tropomyosin movement, is rescued by cMyBPC domains” J Mol Cell Cardiol. 2021 Sep 3;162:1-9. doi: 10.1016/j.yjmcc.2021.08.012. Online ahead of print. (Abstract)

Ryan J. Emenecker, Daniel Griffith, & Alex S. Holehouse (2021). “Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure” Biophys J. 2021 Sep 2;S0006-3495(21)00725-6. doi: 10.1016/j.bpj.2021.08.039. Online ahead of print. (Abstract)

Fengbo Zhou, Yihu Yang, Saketh Chemuru, Weidong Cui, Shixuan Liu, Michael Gross, & Weikai Li (2021). “Footprinting Mass Spectrometry of Membrane Proteins: Ferroportin Reconstituted in Saposin A Picodiscs” Anal Chem. 2021 Aug 24;93(33):11370-11378. doi: 10.1021/acs.analchem.1c02325. Epub 2021 Aug 12. (Abstract)

Yanniv Dorone, Steven Boeynaems, Eduardo Flores, Benjamin Jin, Shannon Hateley, Flavia Bossi, Elena Lazarus, Janice G. Pennington, Emiel Michiels, Mathias De Decker, Katlijn Vints, Pieter Baatsen, George W. Bassel, Marisa S. Otegui, Alex S. Holehouse, Moises Exposito-Alonso, Shahar Sukenik, Aaron D. Gitler, Seung Y. Rhee (2021). “A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation” Cell. 2021 Aug 5;184(16):4284-4298.e27. doi: 10.1016/j.cell.2021.06.009. Epub 2021 Jul 6. (Abstract)

Neha Vithani, Michael D. Ward, Maxwell I. Zimmerman, Borna Novak, Jonathan H. Borowsky, Sukrit Singh, & Gregory R. Bowman (2021). “SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential” Biophys J. 2021 Jul 20;120(14):2880-2889. doi: 10.1016/j.bpj.2021.03.024. Epub 2021 Mar 29. (Abstract)

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)

Shubhanjali Minhas & Alex S. Holehouse (2021). “Step on the cGAS! Viral inhibition of cGAS phase separation with cytosolic DNA” Mol Cell. 2021 Jul 1;81(13):2688-2689. doi: 10.1016/j.molcel.2021.06.007. (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)

Ryan J. Emenecker, Alex S. Holehouse, & Lucia C. Strader (2021). “Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis” Cell Commun Signal. 2021 Jun 5;19(1):65. doi: 10.1186/s12964-021-00744-9. (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)

E. Sethe Burgie, Zachary T. K. Gannam, Katrice E. McLoughlin, Christopher D. Sherman, Alex S. Holehouse, Robert J. Stankey, & Richard D. Vierstra (2021). “Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families” Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2105649118. doi: 10.1073/pnas.2105649118. (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)

More can be found in the Archives.