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CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Res Sq. 2021 May 19.
Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, Lam V, Li F, Li Y, Nguyen H, Nowotny C, Owens T, Peters J, Rizo A, Schulze-Gahmen U, Smith A, Young I, Yu Z, Asarnow D, Billesbølle C, Campbell M, Chen J, Chen KH, Chio US, Dickinson M, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez K, Mancino A, Iii FM, Paul M, Pawar K, Pelin A, Pospiech T, Puchades C, Remesh S, Safari M, Schaefer K, Sun M, Tabios M, Thwin A, Titus E, Trenker R, Tse E, Tsui TKM, Feng F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, Agard D, Cheng Y, Fraser J, Jura N, Kortemme T, Manglik A, Southworth D, Stroud R, Swaney D, Krogan N, Frost A, Rosenberg O. PMID: 34031651.
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An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science. 2020 12 18; 370(6523):1473-1479.
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium , Walter P, Manglik A. PMID: 33154106.
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47 Fields:
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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521).
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium , Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium , Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. PMID: 33060197.
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69 Fields:
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General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Proc Natl Acad Sci U S A. 2020 09 29; 117(39):24269-24273.
Wang F, Liu Y, Yu Z, Li S, Feng S, Cheng Y, Agard DA. PMID: 32913054.
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1 Fields:
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The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis. BMC Biol. 2020 01 27; 18(1):10.
Joshi A, Dai L, Liu Y, Lee J, Ghahhari NM, Segala G, Beebe K, Jenkins LM, Lyons GC, Bernasconi L, Tsai FTF, Agard DA, Neckers L, Picard D. PMID: 31987035.
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4 Fields:
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Designed peptides that assemble into cross-a amyloid-like structures. Nat Chem Biol. 2018 09; 14(9):870-875.
Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. PMID: 30061717.
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12 Fields:
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Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1. Elife. 2017 07 25; 6.
Elnatan D, Betegon M, Liu Y, Ramelot T, Kennedy MA, Agard DA. PMID: 28742020.
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17 Fields:
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HumansAnimalsCells
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Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase. Science. 2016 Jun 24; 352(6293):1542-7.
Verba KA, Wang RY, Arakawa A, Liu Y, Shirouzu M, Yokoyama S, Agard DA. PMID: 27339980.
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110 Fields:
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Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations. J Am Chem Soc. 2015 Jun 10; 137(22):7152-7159.
Wirth AJ, Liu Y, Prigozhin MB, Schulten K, Gruebele M. PMID: 25988868.
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15 Fields:
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Stable small quantum dots for synaptic receptor tracking on live neurons. Angew Chem Int Ed Engl. 2014 Nov 10; 53(46):12484-8.
Cai E, Ge P, Lee SH, Jeyifous O, Wang Y, Liu Y, Wilson KM, Lim SJ, Baird MA, Stone JE, Lee KY, Davidson MW, Chung HJ, Schulten K, Smith AM, Green WN, Selvin PR. PMID: 25255882.
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25 Fields:
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Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIa. Nat Commun. 2014 Mar 28; 5:3552.
Zhou Q, Li J, Yu H, Zhai Y, Gao Z, Liu Y, Pang X, Zhang L, Schulten K, Sun F, Chen C. PMID: 24675427.
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14 Fields:
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Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel. Elife. 2014 Feb 18; 3:e01834.
Wang Y, Liu Y, Deberg HA, Nomura T, Hoffman MT, Rohde PR, Schulten K, Martinac B, Selvin PR. PMID: 24550255.
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48 Fields:
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Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. J Am Chem Soc. 2014 Mar 19; 136(11):4265-72.
Liu Y, Prigozhin MB, Schulten K, Gruebele M. PMID: 24437525.
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7 Fields:
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Flexible interwoven termini determine the thermal stability of thermosomes. Protein Cell. 2013 Jun; 4(6):432-44.
Zhang K, Wang L, Liu Y, Chan KY, Pang X, Schulten K, Dong Z, Sun F. PMID: 23709365.
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3 Fields:
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Misplaced helix slows down ultrafast pressure-jump protein folding. Proc Natl Acad Sci U S A. 2013 May 14; 110(20):8087-92.
Prigozhin MB, Liu Y, Wirth AJ, Kapoor S, Winter R, Schulten K, Gruebele M. PMID: 23620522.
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17 Fields:
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Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. PLoS Pathog. 2013 Jan; 9(1):e1003132.
Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker TS, Schulten K, Zheng D, Pang H, Sun F. PMID: 23341770.
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45 Fields:
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Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1333-8.
Lai Y, Diao J, Liu Y, Ishitsuka Y, Su Z, Schulten K, Ha T, Shin YK. PMID: 23300284.
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48 Fields:
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Structural Characterization of ?-Repressor Folding from All-Atom Molecular Dynamics Simulations. J Phys Chem Lett. 2012 May 03; 3(9):1117-1123.
Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K. PMID: 22737279.
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18 Fields:
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Extension of a three-helix bundle domain of myosin VI and key role of calmodulins. Biophys J. 2011 Jun 22; 100(12):2964-73.
Liu Y, Hsin J, Kim H, Selvin PR, Schulten K. PMID: 21689530.
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6 Fields:
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Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain. Structure. 2010 Nov 10; 18(11):1443-9.
Kim H, Hsin J, Liu Y, Selvin PR, Schulten K. PMID: 21070943.
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14 Fields:
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Challenges in protein folding simulations: Timescale, representation, and analysis. Nat Phys. 2010 Oct 01; 6(10):751-758.
Freddolino PL, Harrison CB, Liu Y, Schulten K. PMID: 21297873.
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Flow-induced beta-hairpin folding of the glycoprotein Ibalpha beta-switch. Biophys J. 2010 Aug 09; 99(4):1182-91.
Zou X, Liu Y, Chen Z, Cárdenas-Jirón GI, Schulten K. PMID: 20713002.
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6 Fields:
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Stabilization of native and non-native structures by salt bridges in a lattice model of the GCN4 leucine dimer. J Phys Chem B. 2010 Jan 21; 114(2):796-803.
Liu Y, Chapagain PP, Gerstman BS. PMID: 20038147.
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The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization. J Chem Phys. 2008 Nov 07; 129(17):175103.
Chapagain PP, Liu Y, Gerstman BS. PMID: 19045375.
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Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper. J Chem Phys. 2008 Jan 28; 128(4):045106.
Liu Y, Chapagain PP, Parra JL, Gerstman BS. PMID: 18248013.
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Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide. J Chem Phys. 2007 Aug 21; 127(7):075103.
Chapagain PP, Parra JL, Gerstman BS, Liu Y. PMID: 17718634.
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2 Fields:
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The study of I-V characteristics of single electron triple-barrier tunnel-junction. Acta Physica Sinica. 2004; 53(8):2734-2740.
Yanxin Liu, Yongchang Wang, and Shaoyi Du. View Publication.