A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2.
Biophysics
Protein Biochemistry
Structural Biology
Journal
STAR protocols
ISSN: 2666-1667
Titre abrégé: STAR Protoc
Pays: United States
ID NLM: 101769501
Informations de publication
Date de publication:
17 06 2022
17 06 2022
Historique:
entrez:
21
3
2022
pubmed:
22
3
2022
medline:
9
4
2022
Statut:
epublish
Résumé
The present protocol describes the computational design of the SARS-CoV-2 receptor binding motif (RBD) to identify mutations that can potentially improve binding affinity for the human ACE2 (hACE2) receptor. We focus on four positions located at the interface with the hACE2 receptor in the RBD:hACE2 complex. We conduct the design with a high-throughput computational protein design (CPD) program, Proteus, incorporating an adaptive Monte Carlo (MC) protocol that promotes the selection of sequences with good binding affinities. For complete details on the use and execution of this protocol, please refer to Polydorides and Archontis (2021).
Identifiants
pubmed: 35310078
doi: 10.1016/j.xpro.2022.101254
pii: S2666-1667(22)00134-4
pmc: PMC8890969
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
ACE2 protein, human
EC 3.4.17.23
Angiotensin-Converting Enzyme 2
EC 3.4.17.23
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
101254Informations de copyright
© 2022 The Author(s).
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
J Comput Chem. 2017 Oct 30;38(28):2396-2410
pubmed: 28749575
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
J Comput Chem. 2008 Aug;29(11):1859-65
pubmed: 18351591
J Chem Theory Comput. 2017 Oct 10;13(10):4932-4943
pubmed: 28886244
J Phys Chem A. 2020 Dec 24;124(51):10637-10648
pubmed: 33170681
PLoS Comput Biol. 2020 Jan 9;16(1):e1007600
pubmed: 31917825
Biophys J. 2021 Jul 20;120(14):2859-2871
pubmed: 33984310
J Phys Chem B. 2005 Dec 1;109(47):22667-73
pubmed: 16853951
J Comput Chem. 2017 Nov 5;38(29):2509-2519
pubmed: 28786118
Proteins. 2006 Nov 15;65(3):712-25
pubmed: 16981200
J Chem Phys. 2018 Aug 21;149(7):072302
pubmed: 30134674
Nature. 2020 May;581(7807):215-220
pubmed: 32225176
J Comput Chem. 2011 Apr 30;32(6):1183-94
pubmed: 21387345