Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.
COVID-19
SARS-CoV-2
coronavirus
databases
evolution
molecular
pandemics
protein
viral proteins
Journal
Proteins
ISSN: 1097-0134
Titre abrégé: Proteins
Pays: United States
ID NLM: 8700181
Informations de publication
Date de publication:
05 2022
05 2022
Historique:
revised:
26
08
2021
received:
21
12
2020
accepted:
16
09
2021
pubmed:
29
9
2021
medline:
14
4
2022
entrez:
28
9
2021
Statut:
ppublish
Résumé
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
Identifiants
pubmed: 34580920
doi: 10.1002/prot.26250
pmc: PMC8661935
mid: NIHMS1743413
doi:
Substances chimiques
Amino Acids
0
Proteome
0
Viral Proteins
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1054-1080Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM135141
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM132565
Pays : United States
Organisme : NIMH NIH HHS
ID : U24 MH068457
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008339
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM133198
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM128596
Pays : United States
Organisme : NIAID NIH HHS
ID : R37 AI027690
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM136431
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2021 Wiley Periodicals LLC.
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