2020 Publications

Vishnu C. Damalanka, Amarendar Reddy Maddirala, & James W. Janetka (2020). “Novel approaches to glycomimetic design: Development of small molecular weight lectin antagonists” Expert Opin Drug Discov. 2020 Dec 18. doi: 10.1080/17460441.2021.1857721. Online ahead of print. (Abstract)

Jesse G. Meyer, Natalie M. Niemi, David J. Pagliarini, & Joshua J. Coon (2020). “Quantitative shotgun proteome analysis by direct infusion” Nat Methods. 2020 Dec;17(12):1222-1228. doi: 10.1038/s41592-020-00999-z. Epub 2020 Nov 23. (Abstract)

Miao Gui, Meisheng Ma, Erica Sze-Tu, Xiangli Wang, Fujiet Koh, Ellen D. Zhong, Bonnie Berger, Joseph H. Davis, Susan K. Dutcher, Rui Zhang, & Alan Brown (2020). “Structures of radial spokes and associated complexes important for ciliary motility” Nat Struct Mol Biol. 2021 Jan;28(1):29-37. doi: 10.1038/s41594-020-00530-0. Epub 2020 Dec 14. (Abstract)

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman, & Judith Klein-Seetharaman (2020). “Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 -human interactome” Pac Symp Biocomput. 2021;26:154-165. (Abstract)

Melanie A. Sparks, Peter M. Burgers, & Roberto Galletto (2020). “Pif1, RPA and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis” J Biol Chem. 2020 Nov 20;295(47):15883-15891. doi: 10.1074/jbc.RA120.015699. Epub 2020 Sep 10. (Abstract)

Joanna Kim & John A. Cooper (2020). “Junctional Localization of Septin 2 Is Required for Organization of Junctional Proteins in Static Endothelial Monolayers” Arterioscler Thromb Vasc Biol. 2020 Nov 5;ATVBAHA120315472. doi: 10.1161/ATVBAHA.120.315472. Online ahead of print. (Abstract)

Michael S. Kinch, Zachary Kraft, & Tyler Schwartz (2020). “Sources of innovation for new medicines: questions of sustainability” Drug Discov Today. 2020 Nov 2;S1359-6446(20)30443-8. doi: 10.1016/j.drudis.2020.10.026. Online ahead of print. (Abstract)

Daniel L. Kober, Melissa D. Stuchell-Brereton, Colin E. Kluender, Hunter B. Dean, Michael R. Strickland, Deborah F. Steinberg, Samantha S. Nelson, Berevan Baban, David M. Holtzman, Carl Frieden, Jennifer Alexander-Brett, Erik D. Roberson, Yuhua Song, & Tom J. Brett (2020). “Functional insights from biophysical study of TREM2 interactions with apoE and Aβ 1-42” Alzheimers Dement. 2020 Oct 8. doi: 10.1002/alz.12194. Online ahead of print. (Abstract)

James R. Riehl, Maxwell I. Zimmerman, Matthew F. Singh, Gregory R. Bowman, & ShiNung Ching (2020). “Computing and Optimizing Over All Fixed-Points of Discrete Systems on Large Networks” J R Soc Interface. 2020 Sep;17(170):20200126. doi: 10.1098/rsif.2020.0126. Epub 2020 Sep 9. (Abstract)

Kory J. Lavine & Michael J. Greenberg. (2020). “Beyond genomics-technological advances improving the molecular characterization and precision treatment of heart failure” Heart Fail Rev. 2020 Sep 3. doi: 10.1007/s10741-020-10021-5. Online ahead of print. (Abstract)

Mathivanan Chinnaraj, David A. Barrios, Carl Frieden, Tomasz Heyduk, Robert Flaumenhaft, & Nicola Pozzi. (2020). “Bioorthogonal Chemistry Enables Single-Molecule FRET Measurements of Catalytically Active Protein Disulfide Isomerase” Chembiochem. 2020 Aug 28. doi: 10.1002/cbic.202000537. Online ahead of print. (Abstract)

Weikai Li, Russell E. Bishop, & Filippo Mancia. (2020). “Integral Membrane Enzymes (2020)” J Mol Biol. 2020 Aug 21;432(18):4943-4945. doi: 10.1016/j.jmb.2020.07.022. Epub 2020 Jul 30. (Abstract)

Yihu Yang, Xiaoran Roger Liu, Zev J. Greenberg, Fengbo Zhou, Peng He, Lingling Fan, Shixuan Liu, Guomin Shen, Takeshi Egawa, Michael L. Gross, Laura G. Schuettpelz, & Weikai Li (2020). “Open conformation of tetraspanins shapes interaction partner networks on cell membranes” EMBO J (2020) e105246. 2020-08-16. doi: 10.15252/embj.2020105246. (Abstract)

Wenwen Gao, Yaqi Xu, Hongli Liu, Meng Gao, Qing Cao, Yiyi Wang, Longteng Cui, Rong Huang, Yan Shen, Sanqiang Li, Haiping Yang, Yixiang Chen, Chaokun Li, Haichuan Yu, Weikai Li, & Guomin Shen. (2020). “Characterization of missense mutations in the signal peptide and propeptide of FIX in hemophilia B by a cell-based assay” Blood Adv. 2020 Aug 11;4(15):3659-3667. doi: 10.1182/bloodadvances.2020002520. (Abstract)

Rachel Bezalel-Buch, Young K. Cheun, Upasana Roy, Orlando D. Schärer, & Peter M. Burgers (2020). “Bypass of DNA interstrand crosslinks by a Rev1-DNA polymerase ζ complex” Nucleic Acids Res. 2020 Jul 7;gkaa580. doi: 10.1093/nar/gkaa580. Online ahead of print. (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 (2020). “Citizen Scientists Create an Exascale Computer to Combat COVID-19” bioRxiv. 2020 Jun 28;2020.06.27.175430. doi: 10.1101/2020.06.27.175430. Preprint (Abstract)

Katarzyna Dubiel, Camille Henry, Lisanne M. Spenkelink, Alexander G. Kozlov, Elizabeth A. Wood, Slobodan Jergic, Nicholas E. Dixon, Antoine M. van Oijen, Michael M. Cox, Timothy M. Lohman, Steven J. Sandler, & James L. Keck (2020). “Development of a Single-Stranded DNA-binding Protein Fluorescent Fusion Toolbox” Nucleic Acids Res. 2020 Jun 19;48(11):6053-6067. doi: 10.1093/nar/gkaa320. (Abstract)

Shuang Li, Shixuan Liu, Xiaoran Roger Liu, Mengru Mira Zhang, and Weikai Li. (2020). “Competitive tight-binding inhibition of VKORC1 underlies warfarin dosage variation and antidotal efficacy” Blood Adv. 2020 May 26; 4(10): 2202–2212. Published online 2020 May 20. doi: 10.1182/bloodadvances.2020001750 (Abstract)

Jason D Fernandes, Sarvenaz Sarabipour, Christopher T Smith, Natalie M Niemi, Nafisa M Jadavji, Ariangela J Kozik, Alex S Holehouse, Vikas Pejaver, Orsolya Symmons, Alexandre W Bisson Filho, & Amanda Haage (2020). “A survey-based analysis of the academic job market” Elife. 2020 Jun 12;9:e54097. doi: 10.7554/eLife.54097. Online ahead of print. (Abstract)

Eliza A. Ruben, Prafull S. Gandhi, Zhiwei Chen, Sarah K. Koester, Gregory T. DeKoster, Carl Frieden, & Enrico Di Cera. (2020). “19 F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2” J Biol Chem. 2020 Jun 12;295(24):8227-8235. doi: 10.1074/jbc.RA120.013419. Epub 2020 May 1. (Abstract)

James W Janetka, Allen T Hopper, Ziping Yang, Jennifer Barks, Mary Savari Dhason, Qiuling Wang, & L David Sibley (2020). “Optimizing Pyrazolopyrimidine Inhibitors of Calcium Dependent Protein Kinase 1 for Treatment of Acute and Chronic Toxoplasmosis” J Med Chem. 2020 Jun 11;63(11):6144-6163. doi: 10.1021/acs.jmedchem.0c00419. Epub 2020 Jun 1. (Abstract)

Justin R. Porter, Artur Meller, Maxwell I. Zimmerman, Michael J. Greenberg, & Gregory R. Bowman (2020). “Conformational Distributions of Isolated Myosin Motor Domains Encode Their Mechanochemical Properties” Elife. 2020 May 29;9:e55132. doi: 10.7554/eLife.55132. (Abstract)

Shuang Li, Shixuan Liu, Yihu Yang, & Weikai Li (2020). “Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases” J Mol Biol. 2020 May 20;S0022-2836(20)30350-8. doi: 10.1016/j.jmb.2020.05.009. Online ahead of print. (Abstract)

James Brett Case, Paul W Rothlauf, Rita E Chen, Zhuoming Liu, Haiyan Zhao, Arthur S Kim, Louis-Marie Bloyet, Qiru Zeng, Stephen Tahan, Lindsay Droit, Ma Xenia G Ilagan, Michael A Tartell, Gaya Amarasinghe, Jeffrey P Henderson, Shane Miersch, Mart Ustav, Sachdev Sidhu, Herbert W Virgin, David Wang, Siyuan Ding, Davide Corti, Elitza S Theel, Daved H Fremont, Michael S Diamond, & Sean P J Whelan (2020). “Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2” bioRxiv. 2020 May 18;2020.05.18.102038. doi: 10.1101/2020.05.18.102038. Preprint (Abstract)

John T. Petroff 2nd, Ailing Tong, Lawrence J. Chen, Gregory T. Dekoster, Farha Khan, Jeff Abramson, Carl Frieden, & Wayland W. L. Cheng (2020). “Charge Reduction of Membrane Proteins in Native Mass Spectrometry Using Alkali Metal Acetate Salts” Anal Chem. 2020 May 5;92(9):6622-6630. doi: 10.1021/acs.analchem.0c00454. Epub 2020 Apr 14. (Abstract)

Brown C.A., Hu L., Sun Z., Patel M.P., Singh S., Porter J.R., Sankaran B., Prasad B.V.V., Bowman G.R., & Palzkill T. (2020). “Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance.” J Biol Chem. 2020 Apr 16. pii: jbc.RA119.012489. doi: 10.1074/jbc.RA119.012489. [Epub ahead of print] (Abstract)

Patrick McConnell, Marlene Mekel, Alex G. Kozlov, Olivia L. Mooren, Timothy M. Lohman, & John A. Cooper (2020). “Comparative Analysis of CPI-Motif Regulation of Biochemical Functions of Actin Capping Protein” Biochemistry. 2020 Mar 24;59(11):1202-1215. doi: 10.1021/acs.biochem.0c00092. Epub 2020 Mar 10. (Abstract)

Holehouse A.S. & Sukenik S. (2020). “Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning.” J Chem Theory Comput. 2020 Mar 10;16(3):1794-1805. doi: 10.1021/acs.jctc.9b00604. Epub 2020 Feb 17. (Abstract)

Hohl M., Mojumdar A., Hailemariam S., Kuryavyi V., Ghisays F., Sorenson K., Chang M., Taylor B.S., Patel D.J., Burgers P.M., Cobb J.A., & Petrini J.H.J. (2020). “Modeling cancer genomic data in yeast reveals selection against ATM function during tumorigenesis.” PLoS Genet. 2020 Mar 18;16(3):e1008422. doi: 10.1371/journal.pgen.1008422. [Epub ahead of print] (Abstract)

Antonija Kuzmanic, Gregory R. Bowman, Jordi Juarez-Jimenez, Julien Michel, & Francesco L. Gervasio (2020). “Investigating Cryptic Binding Sites by Molecular Dynamics Simulations” Acc Chem Res. 2020 Mar 17;53(3):654-661. doi: 10.1021/acs.accounts.9b00613. Epub 2020 Mar 5. (Abstract)

Joanna Kim & John A. Cooper (2020). “Septin Roles and Mechanisms in Organization of Endothelial Cell Junctions” bioRxiv. doi: https://doi.org/10.1101/2020.03.04.977199 (Abstract)

Jordan E. Ezekian, Sarah R. Clippinger, Jaquelin M. Garcia, Qixin Yang, Susan Denfield, Aamir Jeewa, William J. Dreyer, Wenxin Zou, Yuxin Fan, Hugh D. Allen, Jeffrey J. Kim, Michael J. Greenberg, & Andrew P. Landstrom (2020). “Variant R94C in TNNT2-Encoded Troponin T Predisposes to Pediatric Restrictive Cardiomyopathy and Sudden Death Through Impaired Thin Filament Relaxation Resulting in Myocardial Diastolic Dysfunction” J Am Heart Assoc. 2020 Mar 3;9(5):e015111. doi: 10.1161/JAHA.119.015111. Epub 2020 Feb 26. (Abstract)

Rawlings A.E., Liravi P., Corbett S., Holehouse A.S., & Staniland S.S. (2020). “Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6.” PLoS One. 2020 Feb 25;15(2):e0228708. doi: 10.1371/journal.pone.0228708. eCollection 2020. (Abstract)

Matthew A. Cruz, Thomas E. Frederick, Sukrit Singh, Neha Vithani, Maxwell I. Zimmerman, Justin R. Porter, Katelyn E. Moeder, Gaya K. Amarasinghe, & Gregory R. Bowman (2020). “Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments” bioRxiv. doi: https://doi.org/10.1101/2020.02.09.940510 (Abstract)

Martin E.W., Holehouse A.S., Peran I., Farag M., Incicco J.J., Bremer A., Grace C.R., Soranno A., Pappu R.V., & Mittag T. (2020). “Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.” Science. 2020 Feb 7;367(6478):694-699. doi: 10.1126/science.aaw8653. (Abstract)

Greig J.A., Nguyen T.A., Lee M., Holehouse A.S., Posey A.E., Pappu R.V., & Jedd G. (2020). “Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation.” Mol Cell. 2020 Feb 6. pii: S1097-2765(20)30046-0. doi: 10.1016/j.molcel.2020.01.025. [Epub ahead of print] (Abstract)

Choi J.M., Holehouse A.S., & Pappu R.V. (2020). “Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions.” Annu Rev Biophys. 2020 Jan 31. doi: 10.1146/annurev-biophys-121219-081629. [Epub ahead of print] (Abstract)

Yang B., Hird A.W., Bodnarchuk M.S., Zheng X., Dakin L., Su Q., Daly K., Godin R., Hattersley M.M., Brassil P., Redmond S., John Russell D., & Janetka J.W. (2020). “Heteroarylamide smoothened inhibitors: Discovery of N-[2,4-dimethyl-5-(1-methylimidazol-4-yl)phenyl]-4-(2-pyridylmethoxy)benzamide (AZD8542) and N-[5-(1H-imidazol-2-yl)-2,4-dimethyl-phenyl]-4-(2- pyridylmethoxy)benzamide (AZD7254).” Bioorg Med Chem. 2020 Jan 15;28(2):115227. doi: 10.1016/j.bmc.2019.115227. Epub 2019 Dec 11. (Abstract)

Zev J. Greenberg, Darlene A. Monlish, Rachel L. Bartnett, Yihu Yang, Guomin Shen, Weikai Li, Jeffrey J. Bednarski, & Laura G. Schuettpelz. (2020). “The Tetraspanin CD53 Regulates Early B Cell Development by Promoting IL-7R Signaling.” J Immunol. 2020 Jan 1;204(1):58-67. doi: 10.4049/jimmunol.1900539. Epub 2019 Nov 20. (Abstract)