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For: Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core. Nat Commun 2022;13:1002. [PMID: 35194049 PMCID: PMC8863989 DOI: 10.1038/s41467-022-28654-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/03/2022] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
1
Akıl C, Xu J, Shen J, Zhang P. Unveiling the Complete Spectrum of SARS-CoV-2 Fusion Stages by In Situ Cryo-ET. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.25.640151. [PMID: 40060467 PMCID: PMC11888396 DOI: 10.1101/2025.02.25.640151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
2
Sahrmann PG, Voth GA. Understanding the coarse-grained free energy landscape of phospholipids and their phase separation. Biophys J 2025;124:620-636. [PMID: 39982441 PMCID: PMC11900191 DOI: 10.1016/j.bpj.2024.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 11/15/2024] [Accepted: 12/30/2024] [Indexed: 02/22/2025]  Open
3
Cecil AJ, Sogues A, Gurumurthi M, Lane KS, Remaut H, Pak AJ. Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies. PNAS NEXUS 2024;3:pgae538. [PMID: 39660065 PMCID: PMC11631148 DOI: 10.1093/pnasnexus/pgae538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 11/04/2024] [Indexed: 12/12/2024]
4
Roytenberg R, Yue H, DeHart A, Kim E, Bai F, Kim Y, Denning K, Kwei A, Zhang Q, Liu J, Zheng XL, Li W. Thymidine phosphorylase mediates SARS-CoV-2 spike protein enhanced thrombosis in K18-hACE2TG mice. Thromb Res 2024;244:109195. [PMID: 39442286 PMCID: PMC11585440 DOI: 10.1016/j.thromres.2024.109195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 09/09/2024] [Accepted: 10/17/2024] [Indexed: 10/25/2024]
5
Asor R, Olerinyova A, Burnap SA, Kushwah MS, Soltermann F, Rudden LS, Hensen M, Vasiljevic S, Brun J, Hill M, Chang L, Dejnirattisai W, Supasa P, Mongkolsapaya J, Zhou D, Stuart DI, Screaton GR, Degiacomi MT, Zitzmann N, Benesch JLP, Struwe WB, Kukura P. Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition. Proc Natl Acad Sci U S A 2024;121:e2403260121. [PMID: 39298475 PMCID: PMC11459207 DOI: 10.1073/pnas.2403260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/28/2024] [Indexed: 09/21/2024]  Open
6
Grunst MW, Qin Z, Dodero-Rojas E, Ding S, Prévost J, Chen Y, Hu Y, Pazgier M, Wu S, Xie X, Finzi A, Onuchic JN, Whitford PC, Mothes W, Li W. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science 2024;385:757-765. [PMID: 39146425 PMCID: PMC11449073 DOI: 10.1126/science.adn5658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/15/2024] [Indexed: 08/17/2024]
7
Benlarbi M, Ding S, Bélanger É, Tauzin A, Poujol R, Medjahed H, El Ferri O, Bo Y, Bourassa C, Hussin J, Fafard J, Pazgier M, Levade I, Abrams C, Côté M, Finzi A. Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission. mBio 2024;15:e0090724. [PMID: 38953636 PMCID: PMC11323525 DOI: 10.1128/mbio.00907-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024]  Open
8
Wen CY, Luo YL, Madsen JJ. Optimizing Coarse-Grained Models for Large-Scale Membrane Protein Simulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.594009. [PMID: 38798639 PMCID: PMC11118278 DOI: 10.1101/2024.05.13.594009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
9
Patarca R, Haseltine WA. Forty years of HIV research inspires the development of SARS-CoV-2 therapy. J Mol Cell Biol 2024;15:mjad065. [PMID: 37873695 PMCID: PMC11137671 DOI: 10.1093/jmcb/mjad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/24/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]  Open
10
Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024;16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024]  Open
11
Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024;128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
12
Hudait A, Voth GA. HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex. Proc Natl Acad Sci U S A 2024;121:e2313737121. [PMID: 38241438 PMCID: PMC10823262 DOI: 10.1073/pnas.2313737121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024]  Open
13
Biskupek I, Gieldon A. Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2). Int J Mol Sci 2024;25:679. [PMID: 38203850 PMCID: PMC10779479 DOI: 10.3390/ijms25010679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]  Open
14
de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023;37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
15
Kumar S, Delipan R, Chakraborty D, Kanjo K, Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. J Virol 2023;97:e0092223. [PMID: 37861334 PMCID: PMC10688319 DOI: 10.1128/jvi.00922-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023]  Open
16
Onigbinde S, Reyes CDG, Fowowe M, Daramola O, Atashi M, Bennett AI, Mechref Y. Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants. Biomolecules 2023;13:1467. [PMID: 37892149 PMCID: PMC10604390 DOI: 10.3390/biom13101467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023]  Open
17
Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023;52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
18
Zaporozhets I, Clementi C. Multibody Terms in Protein Coarse-Grained Models: A Top-Down Perspective. J Phys Chem B 2023;127:6920-6927. [PMID: 37499123 DOI: 10.1021/acs.jpcb.3c04493] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
19
Wrobel AG. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Curr Opin Struct Biol 2023;81:102619. [PMID: 37285618 PMCID: PMC10183628 DOI: 10.1016/j.sbi.2023.102619] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023]
20
Hudait A, Hurley JH, Voth GA. Dynamics of upstream ESCRT organization at the HIV-1 budding site. Biophys J 2023;122:2655-2674. [PMID: 37218128 PMCID: PMC10397573 DOI: 10.1016/j.bpj.2023.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023]  Open
21
Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK. hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics. ACS Infect Dis 2023;9:1180-1189. [PMID: 37166130 PMCID: PMC10228703 DOI: 10.1021/acsinfecdis.3c00010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Indexed: 05/12/2023]
22
Huang L, Mao X, Li J, Li Q, Shen J, Liu M, Fan C, Tian Y. Nanoparticle Spikes Enhance Cellular Uptake via Regulating Myosin IIA Recruitment. ACS NANO 2023;17:9155-9166. [PMID: 37171255 DOI: 10.1021/acsnano.2c12660] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
23
El-Baba T, Lutomski CA, Burnap SA, Bolla JR, Baker LA, Baldwin AJ, Struwe WB, Robinson CV. Uncovering the Role of N-Glycan Occupancy on the Cooperative Assembly of Spike and Angiotensin Converting Enzyme 2 Complexes: Insights from Glycoengineering and Native Mass Spectrometry. J Am Chem Soc 2023;145:8021-8032. [PMID: 37000485 PMCID: PMC10103161 DOI: 10.1021/jacs.3c00291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/01/2023]
24
Durumeric AEP, Charron NE, Templeton C, Musil F, Bonneau K, Pasos-Trejo AS, Chen Y, Kelkar A, Noé F, Clementi C. Machine learned coarse-grained protein force-fields: Are we there yet? Curr Opin Struct Biol 2023;79:102533. [PMID: 36731338 PMCID: PMC10023382 DOI: 10.1016/j.sbi.2023.102533] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 02/04/2023]
25
Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney KE, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel AG, Benton DJ, Nawrath P, Flitsch SL, Joshi D, González-Ramírez A, Wilkinson KA, Wilkinson RJ, Wall EC, Hurtado-Guerrero R, Malaker SA, Schumann B. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS CENTRAL SCIENCE 2023;9:393-404. [PMID: 36968546 PMCID: PMC10037455 DOI: 10.1021/acscentsci.2c01349] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 06/18/2023]
26
Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023;14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023]  Open
27
Mironov AA, Savin MA, Beznoussenko GV. COVID-19 Biogenesis and Intracellular Transport. Int J Mol Sci 2023;24:ijms24054523. [PMID: 36901955 PMCID: PMC10002980 DOI: 10.3390/ijms24054523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]  Open
28
Fantini J, Chahinian H, Yahi N. Convergent Evolution Dynamics of SARS-CoV-2 and HIV Surface Envelope Glycoproteins Driven by Host Cell Surface Receptors and Lipid Rafts: Lessons for the Future. Int J Mol Sci 2023;24:1923. [PMID: 36768244 PMCID: PMC9915253 DOI: 10.3390/ijms24031923] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]  Open
29
Yan ZS, Li XL, Ma YQ, Ding HM. Effect of the Graphene Nanosheet on Functions of the Spike Protein in Open and Closed States: Comparison between SARS-CoV-2 Wild Type and the Omicron Variant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022;38:13972-13982. [PMID: 36318181 PMCID: PMC9662070 DOI: 10.1021/acs.langmuir.2c02316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/05/2022] [Indexed: 05/24/2023]
30
Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022;14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022]  Open
31
Su L, Hendrikse SIS, Meijer EW. Supramolecular glycopolymers: How carbohydrates matter in structure, dynamics, and function. Curr Opin Chem Biol 2022;69:102171. [PMID: 35749930 DOI: 10.1016/j.cbpa.2022.102171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
32
Li T, Zhou B, Li Y, Huang S, Luo Z, Zhou Y, Lai Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D. Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Int J Biol Macromol 2022;209:1379-1388. [PMID: 35460753 PMCID: PMC9020654 DOI: 10.1016/j.ijbiomac.2022.04.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022]
33
Fighting SARS-CoV-2 with structural biology methods. Nat Methods 2022;19:381-383. [PMID: 35396469 DOI: 10.1038/s41592-022-01448-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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