A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2

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...

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Autores principales: Polydorides, Savvas, Archontis, Georgios
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8890969/
https://www.ncbi.nlm.nih.gov/pubmed/35310078
http://dx.doi.org/10.1016/j.xpro.2022.101254
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author Polydorides, Savvas
Archontis, Georgios
author_facet Polydorides, Savvas
Archontis, Georgios
author_sort Polydorides, Savvas
collection PubMed
description 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).
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spelling pubmed-88909692022-03-04 A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2 Polydorides, Savvas Archontis, Georgios STAR Protoc Protocol 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). Elsevier 2022-03-03 /pmc/articles/PMC8890969/ /pubmed/35310078 http://dx.doi.org/10.1016/j.xpro.2022.101254 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Polydorides, Savvas
Archontis, Georgios
A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
title A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
title_full A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
title_fullStr A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
title_full_unstemmed A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
title_short A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2
title_sort computational protein design protocol for optimization of the sars-cov-2 receptor-binding-motif affinity for human ace2
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8890969/
https://www.ncbi.nlm.nih.gov/pubmed/35310078
http://dx.doi.org/10.1016/j.xpro.2022.101254
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