2021 Publications

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)

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)

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)

Jasmine Cubuk, Jhullian J. Alston, J. Jeremías Incicco, Sukrit Singh, Melissa D. Stuchell-Brereton, Michael D. Ward, Maxwell I. Zimmerman, Neha Vithani, Daniel Griffith, Jason A. Wagoner, Gregory R. Bowman, Kathleen B. Hall, Andrea Soranno, & Alex S. Holehouse. (2021). “The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA” Nat Commun. 2021 Mar 29;12(1):1936. doi: 10.1038/s41467-021-21953-3. (Abstract)

Drake Jensen & Eric A. Galburt (2021). “The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation” J Bacteriol. 2021 Mar 23;203(8):e00512-20. doi: 10.1128/JB.00512-20. Print 2021 Mar 23. (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)

Rahul Tyagi, Christina A. Bulman, Fidelis Cho-Ngwa, Chelsea Fischer, Chris Marcellino, Michelle R. Arkin, James H. McKerrow, Case W. McNamara, Matthew Mahoney, Nancy Tricoche, Shabnam Jawahar, James W. Janetka, Sara Lustigman, Judy Sakanari, & Makedonka Mitreva (2021). “An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease” Pathogens. 2021 Jan 14;10(1):71. doi: 10.3390/pathogens10010071. (Abstract)

Michael D. Onken, Kendall J. Blumer, & John A. Cooper (2021). “Uveal melanoma cells use ameboid and mesenchymal mechanisms of cell motility crossing the endothelium” Mol Biol Cell. 2021 Jan 6;mbcE20040241. doi: 10.1091/mbc.E20-04-0241. Online ahead of print. (Abstract)

Thomas Blackwell, W. Tom Stump, Sarah R. Clippinger, & Michael J. Greenberg (2021). “Computational Tool for Ensemble Averaging of Single-Molecule Data” Biophys J. 2021 Jan 5;120(1):10-20. doi: 10.1016/j.bpj.2020.10.047. Epub 2020 Nov 26. (Abstract)

Shixuan Liu, Shuang Li, Guomin Shen, Narayanasami Sukumar, Andrzej M. Krezel, & Weikai Li (2021). “Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation” Science. 2021 Jan 1;371(6524):eabc5667. doi: 10.1126/science.abc5667. Epub 2020 Nov 5. (Abstract)