Recent Publications


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

More can be found in the Archives.


Evelyn Ploetz, Benjamin Ambrose, Anders Barth, Richard Börner, Felix Erichson, Achillefs N. Kapanidis, Harold D. Kim, Marcia Levitus, Timothy M. Lohman, Abhishek Mazumder, David S. Rueda, Fabio D. Steffen, Thorben Cordes, Steven W. Magennis, & Eitan Lerner (2023). “A new twist on PIFE: photoisomerisation-related fluorescence enhancement” ArXiv. 2023 Jul 10;arXiv:2302.12455v2. (Abstract)

Min Kyung Shinn, Sumit K. Chaturvedi, Alexander G. Kozlov, & Timothy M. Lohman (2023). “Allosteric effects of E. coli SSB and RecR proteins on RecO protein binding to DNA” Nucleic Acids Res. 2023 Mar 21;51(5):2284-2297. doi: 10.1093/nar/gkad084. (Abstract)

Zev J. Greenberg, Darlene Monlish, Luana Chiquetto Paracatu, Qian Dong, Michael P. Rettig, Nate Dee Roundy, Rofaida Gaballa, Weikai Li, Wei Yang, Cliff J. Luke, & Laura Schuettpelz (2022). “The tetraspanin CD53 protects stressed hematopoietic stem cells via promotion of DREAM complex- mediated quiescence” Blood. 2022 Dec 21;blood.2022016929. doi: 10.1182/blood.2022016929. Online ahead of print. (Abstract)

Garrett M. Ginell & Alex S. Holehouse (2022). “An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates” Methods Mol Biol. 2023;2563:95-116. doi: 10.1007/978-1-0716-2663-4_4. (Abstract)

Nicolás S. González-Foutel, Juliana Glavina, Wade M. Borcherds, Matías Safranchik, Susana Barrera-Vilarmau, Amin Sagar, Alejandro Estaña, Amelie Barozet, Nicolás A. Garrone, Gregorio Fernandez-Ballester, Clara Blanes-Mira, Ignacio E. Sánchez, Gonzalo de Prat-Gay, Juan Cortés, Pau Bernadó, Rohit V. Pappu, Alex S. Holehouse, Gary W. Daughdrill, & Lucía B. Chemes (2022). “Conformational buffering underlies functional selection in intrinsically disordered protein regions” Nat Struct Mol Biol. 2022 Aug;29(8):781-790. doi: 10.1038/s41594-022-00811-w. Epub 2022 Aug 10. (Abstract)

Liana Beld, Hyeim Jung, Christina A. Bulman, Bruce A. Rosa, Peter U. Fischer, James W. Janetka, Sara Lustigman, Judy A. Sakanari, and Makedonka Mitreva (2022). “Aspartyl Protease Inhibitors as Anti-Filarial Drugs” Pathogens. 2022 Jun 18;11(6):707. doi: 10.3390/pathogens11060707. (Abstract)

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, 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” 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)

Hema Adhikari, Walaa E. Kattan, Shivesh Kumar, Pei Zhou, John F. Hancock, & Christopher M. Counter (2021). “Oncogenic KRAS is dependent upon an EFR3A-PI4KA signaling axis for potent tumorigenic activity” Nat Commun. 2021 Sep 9;12(1):5248. doi: 10.1038/s41467-021-25523-5. (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)

More can be found in the Archives.