Recent Publications


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

More can be found in the Archives.


Alexander G. Kozlov, Xian Cheng, Hongshan Zhang, Min Kyung Shinn, Elizabeth Weiland, Binh Nguyen, Irina A. Shkel, Emily Zytkiewicz, Ilya J. Finkelstein, M. Thomas Record Jr., & Timothy M. Lohman (2022). “How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein” J Mol Biol. 2022 Mar 26;434(9):167562. doi: 10.1016/j.jmb.2022.167562. Online ahead of print.

Jie Sun, Weikai Li, & Michael L. Gross (2022). “Advances in mass spectrometry-based footprinting of membrane proteins” Proteomics. 2022 Apr;22(8):e2100222. doi: 10.1002/pmic.202100222. (Abstract)

Upasana L. Mallimadugula & Eric A. Galburt (2022). “Parallel path mechanisms lead to nonmonotonic force-velocity curves and an optimum load for molecular motor function” Phys Rev E. 2022 Mar;105(3-1):034405. doi: 10.1103/PhysRevE.105.034405. (Abstract)

Shixuan Liu, Shuang Li, Andrzej M. Krezel, & Weikai Li (2022). “Stabilization and structure determination of integral membrane proteins by termini restraining” Nat Protoc. 2022 Jan 17. doi: 10.1038/s41596-021-00656-5. Online ahead of print. (Abstract)

Jie Sun, Xiaoran Roger Liu, Shuang Li, Peng He, Weikai Li, & Michael L. Gross (2021). “Nanoparticles and photochemistry for native-like transmembrane protein footprinting” Nat Commun. 2021 Dec 14;12(1):7270. doi: 10.1038/s41467-021-27588-8. (Abstract)

Vishnu C. Damalanka, Jorine J. L. P. Voss, Matthew W. Mahoney, Tina Primeau, Shunqiang Li, Lidija Klampfer, & James W. Janetka (2021). “Macrocyclic Inhibitors of HGF-Activating Serine Proteases Overcome Resistance to Receptor Tyrosine Kinase Inhibitors and Block Lung Cancer Progression” J Med Chem. 2021 Dec 13. doi: 10.1021/acs.jmedchem.1c01671. Online ahead of print. (Abstract)

Maya Topf, Edina Rosta, Gregory R. Bowman, & Massimiliano Bonomi (2021). “Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function” Front Mol Biosci. 2021 Nov 29;8:799406. doi: 10.3389/fmolb.2021.799406. eCollection 2021. (Abstract)

Matthew Mahoney, Vishnu C. Damalanka, Michael A. Tartell, Dong Hee Chung, AndrĂ© 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” Proc Natl Acad Sci U S A. 2021 Oct 26;118(43):e2108728118. doi: 10.1073/pnas.2108728118. (Abstract)

Samantha K. Barrick & Michael J. Greenberg (2021). “Cardiac myosin contraction and mechanotransduction in health and disease” J Biol Chem. 2021 Nov;297(5):101297. doi: 10.1016/j.jbc.2021.101297. Epub 2021 Oct 9. (Abstract)

Benjamin C. Stark, Yuanyuan Gao, Diane S. Sepich, Lakyn Belk, Matthew A. Culver, Bo Hu, Marlene Mekel, Wyndham Ferris, Jimann Shin, Lilianna Solnica-Krezel, Fang Lin, & John A. Cooper (2021). “CARMIL3 is important for cell migration and morphogenesis during early development in zebrafish” Dev Biol. 2022 Jan;481:148-159. doi: 10.1016/j.ydbio.2021.09.008. Epub 2021 Sep 30. (Abstract)

Chia-Chen Liu, Melissa E. Murray, Xia Li, Na Zhao, Na Wang, Michael G. Heckman, Francis Shue, Yuka Martens, Yonghe Li, Ana-Caroline Raulin, Cassandra L. Rosenberg, Sydney V. Doss, Jing Zhao, Melissa C. Wren, Lin Jia, Yingxue Ren, Tadafumi C. Ikezu, Wenyan Lu, Yuan Fu, Thomas Caulfield, Zachary A. Trottier, Joshua Knight, Yixing Chen, Cynthia Linares, Xue Wang, Aishe Kurti, Yan W. Asmann, Zbigniew K. Wszolek, Glenn E. Smith, Prashanthi Vemuri, Kejal Kantarci, David S. Knopman, Val J. Lowe, Clifford R. Jack Jr., Joseph E. Parisi, Tanis J. Ferman, Bradley F. Boeve, Neill R. Graff-Radford, Ronald C. Petersen, Steven G. Younkin, John D. Fryer, Hu Wang, Xianlin Han, Carl Frieden, Dennis W. Dickson, Owen A. Ross, & Guojun Bu (2021). “APOE3-Jacksonville (V236E) variant reduces self-aggregation and risk of dementia” Sci Transl Med. 2021 Sep 29;13(613):eabc9375. doi: 10.1126/scitranslmed.abc9375. Epub 2021 Sep 29. (Abstract)

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)

More can be found in the Archives.