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For: Woo H, Park SJ, Choi YK, Park T, Tanveer M, Cao Y, Kern NR, Lee J, Yeom MS, Croll TI, Seok C, Im W. Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane. J Phys Chem B 2020;124:7128-7137. [PMID: 32559081 PMCID: PMC7341691 DOI: 10.1021/acs.jpcb.0c04553] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/18/2020] [Indexed: 12/27/2022]
Number Cited by Other Article(s)
1
Casalino L, Ramos-Guzmán CA, Amaro RE, Simmerling C, Lodola A, Mulholland AJ, Świderek K, Moliner V. A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats. J Phys Chem Lett 2025;16:3249-3263. [PMID: 40118074 PMCID: PMC11973918 DOI: 10.1021/acs.jpclett.4c03654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Revised: 02/19/2025] [Accepted: 02/26/2025] [Indexed: 03/23/2025]
2
Cheng RL, Lim JPL, Fortuna MA, Reyes DV, Hans EADR, Nellas RB. Exploring the effects of N234 and N343 linked glycans to SARS CoV 2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations. Sci Rep 2025;15:7052. [PMID: 40016249 PMCID: PMC11868416 DOI: 10.1038/s41598-025-85153-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 01/01/2025] [Indexed: 03/01/2025]  Open
3
Neander L, Hannemann C, Netz RR, Sahoo AK. Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD. JACS AU 2025;5:204-216. [PMID: 39886596 PMCID: PMC11775700 DOI: 10.1021/jacsau.4c00886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 12/20/2024] [Accepted: 12/26/2024] [Indexed: 02/01/2025]
4
Isaković S, Senćanski M, Perović V, Stevanović K, Prodić I. Bioinformatic Selection of Mannose-Specific Lectins from Allium genus as SARS-CoV-2 Inhibitors Analysing Protein-Protein Interaction. Life (Basel) 2025;15:162. [PMID: 40003571 PMCID: PMC11856470 DOI: 10.3390/life15020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/13/2025] [Accepted: 01/20/2025] [Indexed: 02/27/2025]  Open
5
Lall S, Balaram P, Mathew MK, Gosavi S. Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics. J Phys Chem B 2025;129:194-209. [PMID: 39692154 DOI: 10.1021/acs.jpcb.4c05270] [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: 12/19/2024]
6
Furnon W, Cowton VM, De Lorenzo G, Orton R, Herder V, Cantoni D, Ilia G, Mendonca DC, Kerr K, Allan J, Upfold N, Meehan GR, Bakshi S, Das UR, Molina Arias S, McElwee M, Little S, Logan N, Kwok K, Smollett K, Willett BJ, Da Silva Filipe A, Robertson DL, Grove J, Patel AH, Palmarini M. Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic. Nat Microbiol 2025;10:77-93. [PMID: 39753670 PMCID: PMC11726466 DOI: 10.1038/s41564-024-01878-5] [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: 04/17/2024] [Accepted: 11/11/2024] [Indexed: 01/12/2025]
7
Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024;128:9976-10042. [PMID: 39303207 PMCID: PMC11492285 DOI: 10.1021/acs.jpcb.4c04100] [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: 06/20/2024] [Revised: 08/15/2024] [Accepted: 08/22/2024] [Indexed: 09/22/2024]
8
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
9
Stafford P, Sherma ND, Peterson M, Diehnelt CW. A Peptide Microarray Platform Approach for Discovery of Immunodominant Antibody Epitopes. Anal Chem 2024;96:14524-14530. [PMID: 39207871 DOI: 10.1021/acs.analchem.4c02806] [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: 09/04/2024]
10
Otazu K, Olivos-Ramirez GE, Fernández-Silva PD, Vilca-Quispe J, Vega-Chozo K, Jimenez-Avalos GM, Chenet-Zuta ME, Sosa-Amay FE, Cárdenas Cárdenas RG, Ropón-Palacios G, Dattani N, Camps I. The Malaria Box molecules: a source for targeting the RBD and NTD cryptic pocket of the spike glycoprotein in SARS-CoV-2. J Mol Model 2024;30:217. [PMID: 38888748 DOI: 10.1007/s00894-024-06006-y] [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: 08/21/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
11
Shahriari M, Jafari M, Doustdar F, Mehrnejad F. Comparative study of the interactions between C60 fullerene and SARS-CoV-2, HIV, eukaryotic, and bacterial model membranes: Insights into antimicrobial strategies with C60-peptide hybrids. Int J Biol Macromol 2024;271:132399. [PMID: 38754684 DOI: 10.1016/j.ijbiomac.2024.132399] [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: 11/19/2023] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
12
De Greve H, Fioravanti A. Single domain antibodies from camelids in the treatment of microbial infections. Front Immunol 2024;15:1334829. [PMID: 38827746 PMCID: PMC11140111 DOI: 10.3389/fimmu.2024.1334829] [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: 11/07/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024]  Open
13
Romeo A, Cappelli G, Iacovelli F, Colizzi V, Falconi M. Computational and experimental validation of phthalocyanine and hypericin as effective SARS-CoV-2 fusion inhibitors. J Biomol Struct Dyn 2024;42:3920-3934. [PMID: 37235773 DOI: 10.1080/07391102.2023.2216276] [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: 02/02/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
14
Yu I, Mori T, Matsuoka D, Surblys D, Sugita Y. SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. J Comput Chem 2024;45:498-505. [PMID: 37966727 DOI: 10.1002/jcc.27260] [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: 08/22/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
15
Haynes CA, Keppel TR, Mekonnen B, Osman SH, Zhou Y, Woolfitt AR, Baudys J, Barr JR, Wang D. Inclusion of deuterated glycopeptides provides increased sequence coverage in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike glycoprotein. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024;38:e9690. [PMID: 38355883 PMCID: PMC10871554 DOI: 10.1002/rcm.9690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 02/16/2024]
16
Roy R. Cancer cells and viruses share common glycoepitopes: exciting opportunities toward combined treatments. Front Immunol 2024;15:1292588. [PMID: 38495885 PMCID: PMC10940920 DOI: 10.3389/fimmu.2024.1292588] [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: 09/11/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024]  Open
17
Samsudin F, Zuzic L, Marzinek JK, Bond PJ. Mechanisms of allostery at the viral surface through the eyes of molecular simulation. Curr Opin Struct Biol 2024;84:102761. [PMID: 38142635 DOI: 10.1016/j.sbi.2023.102761] [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: 10/10/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
18
Hsieh MK, Klauda JB. Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2. J Phys Chem B 2024;128:150-162. [PMID: 38147592 DOI: 10.1021/acs.jpcb.3c07105] [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: 12/28/2023]
19
Gasparello J, Verona M, Chilin A, Gambari R, Marzaro G. Assessing the interaction between hemoglobin and the receptor binding domain of SARS-CoV-2 spike protein through MARTINI coarse-grained molecular dynamics. Int J Biol Macromol 2023;253:127088. [PMID: 37774812 DOI: 10.1016/j.ijbiomac.2023.127088] [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: 07/10/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
20
Popov P, Kalinin R, Buslaev P, Kozlovskii I, Zaretckii M, Karlov D, Gabibov A, Stepanov A. Unraveling viral drug targets: a deep learning-based approach for the identification of potential binding sites. Brief Bioinform 2023;25:bbad459. [PMID: 38113077 PMCID: PMC10783863 DOI: 10.1093/bib/bbad459] [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: 08/07/2023] [Revised: 11/10/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]  Open
21
Aliper ET, Efremov RG. Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain. Int J Mol Sci 2023;24:16421. [PMID: 38003610 PMCID: PMC10671605 DOI: 10.3390/ijms242216421] [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: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]  Open
22
Chmielewski D, Wilson EA, Pintilie G, Zhao P, Chen M, Schmid MF, Simmons G, Wells L, Jin J, Singharoy A, Chiu W. Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans. Nat Commun 2023;14:7175. [PMID: 37935678 PMCID: PMC10630519 DOI: 10.1038/s41467-023-42836-9] [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: 02/05/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]  Open
23
Hsiao YW, Bray DJ, Taddese T, Jiménez-Serratos G, Crain J. Structure adaptation in Omicron SARS-CoV-2/hACE2: Biophysical origins of evolutionary driving forces. Biophys J 2023;122:4057-4067. [PMID: 37717145 PMCID: PMC10624932 DOI: 10.1016/j.bpj.2023.09.003] [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: 12/14/2022] [Revised: 05/20/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023]  Open
24
Romeo A, Pellegrini R, Gualtieri M, Benassi B, Santoro M, Iacovelli F, Stracquadanio M, Falconi M, Marino C, Zanini G, Arcangeli C. Experimental and in silico evaluations of the possible molecular interaction between airborne particulate matter and SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023;895:165059. [PMID: 37353034 PMCID: PMC10284444 DOI: 10.1016/j.scitotenv.2023.165059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
25
Samanta P, Mishra SK, Pomin VH, Doerksen RJ. Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein. Molecules 2023;28:6413. [PMID: 37687244 PMCID: PMC10490367 DOI: 10.3390/molecules28176413] [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: 07/17/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]  Open
26
Brunetti NS, Davanzo GG, de Moraes D, Ferrari AJR, Souza GF, Muraro SP, Knittel TL, Boldrini VO, Monteiro LB, Virgílio-da-Silva JV, Profeta GS, Wassano NS, Nunes Santos L, Carregari VC, Dias AHS, Veras FP, Tavares LA, Forato J, Castro IMS, Silva-Costa LC, Palma AC, Mansour E, Ulaf RG, Bernardes AF, Nunes TA, Ribeiro LC, Agrela MV, Moretti ML, Buscaratti LI, Crunfli F, Ludwig RG, Gerhardt JA, Munhoz-Alves N, Marques AM, Sesti-Costa R, Amorim MR, Toledo-Teixeira DA, Parise PL, Martini MC, Bispos-Dos-Santos K, Simeoni CL, Granja F, Silvestrini VC, de Oliveira EB, Faca VM, Carvalho M, Castelucci BG, Pereira AB, Coimbra LD, Dias MMG, Rodrigues PB, Gomes ABSP, Pereira FB, Santos LMB, Bloyet LM, Stumpf S, Pontelli MC, Whelan S, Sposito AC, Carvalho RF, Vieira AS, Vinolo MAR, Damasio A, Velloso L, Figueira ACM, da Silva LLP, Cunha TM, Nakaya HI, Marques-Souza H, Marques RE, Martins-de-Souza D, Skaf MS, Proenca-Modena JL, Moraes-Vieira PMM, Mori MA, Farias AS. SARS-CoV-2 uses CD4 to infect T helper lymphocytes. eLife 2023;12:e84790. [PMID: 37523305 PMCID: PMC10390044 DOI: 10.7554/elife.84790] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/13/2023] [Indexed: 08/02/2023]  Open
27
Dokainish HM, Sugita Y. Structural effects of spike protein D614G mutation in SARS-CoV-2. Biophys J 2023;122:2910-2920. [PMID: 36397671 PMCID: PMC9671695 DOI: 10.1016/j.bpj.2022.11.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]  Open
28
Iannucci S, Harvey WT, Hughes J, Robertson DL, Poyade M, Hutchinson E. The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. J Vis Commun Med 2023;46:122-132. [PMID: 37526402 PMCID: PMC10726978 DOI: 10.1080/17453054.2023.2237087] [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: 09/15/2022] [Accepted: 06/23/2023] [Indexed: 08/02/2023]
29
Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023;19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Indexed: 04/06/2023]
30
Parker JE, Rodriguez RA. Development of a charged model of the SARS-CoV-2 viral surface. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023;1865:184136. [PMID: 36746311 PMCID: PMC9898061 DOI: 10.1016/j.bbamem.2023.184136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/06/2023]
31
Investigation of the effects of N-Acetylglucosamine on the stability of the spike protein in SARS-CoV-2 by molecular dynamics simulations. COMPUT THEOR CHEM 2023;1222:114049. [PMID: 36743995 PMCID: PMC9890939 DOI: 10.1016/j.comptc.2023.114049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
32
Zhao Y, Zhao Y, Xie L, Li Q, Zhang Y, Zang Y, Li X, Zhang L, Yang Z. Identification of Potential Lead Compounds Targeting Novel Druggable Cavity of SARS-CoV-2 Spike Trimer by Molecular Dynamics Simulations. Int J Mol Sci 2023;24:6281. [PMID: 37047254 PMCID: PMC10094189 DOI: 10.3390/ijms24076281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/07/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]  Open
33
Hsu YP, Frank M, Mukherjee D, Shchurik V, Makarov A, Mann BF. Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor-binding affinity. Glycobiology 2023;33:126-137. [PMID: 36370046 PMCID: PMC9990995 DOI: 10.1093/glycob/cwac077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/14/2022]  Open
34
Pezeshkian W, Grünewald F, Narykov O, Lu S, Arkhipova V, Solodovnikov A, Wassenaar TA, Marrink SJ, Korkin D. Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. Structure 2023;31:492-503.e7. [PMID: 36870335 DOI: 10.1016/j.str.2023.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
35
Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike. iScience 2023;26:105981. [PMID: 36694788 PMCID: PMC9851991 DOI: 10.1016/j.isci.2023.105981] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/05/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023]  Open
36
Chmielewski D, Wilson EA, Pintilie G, Zhao P, Chen M, Schmid MF, Simmons G, Wells L, Jin J, Singharoy A, Chiu W. Integrated analyses reveal a hinge glycan regulates coronavirus spike tilting and virus infectivity. RESEARCH SQUARE 2023:rs.3.rs-2553619. [PMID: 36824920 PMCID: PMC9949256 DOI: 10.21203/rs.3.rs-2553619/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
37
Ching WY, Adhikari P, Jawad B, Podgornik R. Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory. Biomedicines 2023;11:517. [PMID: 36831053 PMCID: PMC9953097 DOI: 10.3390/biomedicines11020517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]  Open
38
Kim S, Liu Y, Ziarnik M, Seo S, Cao Y, Zhang XF, Im W. Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern. J Comput Chem 2023;44:594-601. [PMID: 36398990 PMCID: PMC9825653 DOI: 10.1002/jcc.27025] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/11/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022]
39
Huerta-Miranda GA, García-García WI, Vidal-Limon A, Miranda-Hernández M. Use of simplified models for theoretical prediction of the interactions between available antibodies and the receptor-binding domain of SARS-CoV-2 spike protein. J Biomol Struct Dyn 2023;41:1018-1027. [PMID: 34935602 DOI: 10.1080/07391102.2021.2019123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
40
Liu J, Amaral LAN, Keten S. A new approach for extracting information from protein dynamics. Proteins 2023;91:183-195. [PMID: 36094321 PMCID: PMC9844508 DOI: 10.1002/prot.26421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/19/2023]
41
Hognon C, Bignon E, Monari A, Marazzi M, Garcia-Iriepa C. Revealing the Molecular Interactions between Human ACE2 and the Receptor Binding Domain of the SARS-CoV-2 Wild-Type, Alpha and Delta Variants. Int J Mol Sci 2023;24:2517. [PMID: 36768842 PMCID: PMC9916449 DOI: 10.3390/ijms24032517] [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: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]  Open
42
Maschietto F, Qiu T, Wang J, Shi Y, Allen B, Lisi GP, Lolis E, Batista VS. Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism. Comput Struct Biotechnol J 2023;21:1066-1076. [PMID: 36688026 PMCID: PMC9841741 DOI: 10.1016/j.csbj.2023.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]  Open
43
Belapure J, Sorokina M, Kastritis PL. IRAA: A statistical tool for investigating a protein-protein interaction interface from multiple structures. Protein Sci 2023;32:e4523. [PMID: 36454539 PMCID: PMC9793972 DOI: 10.1002/pro.4523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
44
Verkhivker GM, Agajanian S, Oztas D, Gupta G. Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. J Biomol Struct Dyn 2022;40:9724-9741. [PMID: 34060425 DOI: 10.1080/07391102.2021.1933594] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
45
Pipitò L, Reynolds CA, Deganutti G. Is the Stalk of the SARS-CoV-2 Spike Protein Druggable? Viruses 2022;14:2789. [PMID: 36560795 PMCID: PMC9786045 DOI: 10.3390/v14122789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]  Open
46
Sahihi M, Faraudo J. Computer Simulation of the Interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022;38:14673-14685. [PMID: 36418228 PMCID: PMC9730903 DOI: 10.1021/acs.langmuir.2c02120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/07/2022] [Indexed: 06/16/2023]
47
Mutational escape prevention by combination of four neutralizing antibodies that target RBD conserved regions and stem helix. Virol Sin 2022;37:860-873. [PMID: 36414178 PMCID: PMC9674564 DOI: 10.1016/j.virs.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022]  Open
48
Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022;24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
49
Isobe A, Arai Y, Kuroda D, Okumura N, Ono T, Ushiba S, Nakakita SI, Daidoji T, Suzuki Y, Nakaya T, Matsumoto K, Watanabe Y. ACE2 N-glycosylation modulates interactions with SARS-CoV-2 spike protein in a site-specific manner. Commun Biol 2022;5:1188. [PMID: 36335195 PMCID: PMC9637154 DOI: 10.1038/s42003-022-04170-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022]  Open
50
Li ZL, Buck M. Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity. Comput Struct Biotechnol J 2022;20:6078-6086. [PMID: 36373151 PMCID: PMC9638846 DOI: 10.1016/j.csbj.2022.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]  Open
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