Cargando…

Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants

The infectivity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily determined by the binding affinity between the receptor-binding domain (RBD) of the spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. Here, through screening off pseudo hydrophilic g...

Descripción completa

Detalles Bibliográficos
Autores principales: Yang, Lin, Guo, Shuai, Hou, Chengyu, Jiang, Shenda, Shi, Liping, Ma, Xiaoliang, Zheng, Bing, Fang, Yi, Ye, Lin, He, Xiaodong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10669249/
https://www.ncbi.nlm.nih.gov/pubmed/38002310
http://dx.doi.org/10.3390/biom13111628
_version_ 1785139651378413568
author Yang, Lin
Guo, Shuai
Hou, Chengyu
Jiang, Shenda
Shi, Liping
Ma, Xiaoliang
Zheng, Bing
Fang, Yi
Ye, Lin
He, Xiaodong
author_facet Yang, Lin
Guo, Shuai
Hou, Chengyu
Jiang, Shenda
Shi, Liping
Ma, Xiaoliang
Zheng, Bing
Fang, Yi
Ye, Lin
He, Xiaodong
author_sort Yang, Lin
collection PubMed
description The infectivity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily determined by the binding affinity between the receptor-binding domain (RBD) of the spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. Here, through screening off pseudo hydrophilic groups on protein surfaces, the distribution of low-entropy regions on hydration shells of the ACE2 receptor and the RBDs of multiple SARS-CoV-2 variants was demonstrated. Shape matching between the low-entropy hydration shells of multiple SARS-CoV-2 variants and the ACE2 receptor has been identified as a mechanism that drives hydrophobic attraction between the RBDs and the ACE2 receptor, which estimates the binding affinity. Low-entropy regions of the hydration shells, which play important roles in determining the binding of other viruses and their receptors, are demonstrated. The RBD–ACE2 binding is thus found to be guided by hydrophobic collapse between the shape-matched low-entropy regions of the hydration shells of the proteins. A measure of the low-entropy status of the hydration shells can be estimated by calculating genuine hydrophilic groups within the binding sites. An important indicator of the contagiousness of SARS-CoV-2 variants is the low-entropy level of its hydration shells at the spike protein binding site.
format Online
Article
Text
id pubmed-10669249
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-106692492023-11-07 Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants Yang, Lin Guo, Shuai Hou, Chengyu Jiang, Shenda Shi, Liping Ma, Xiaoliang Zheng, Bing Fang, Yi Ye, Lin He, Xiaodong Biomolecules Article The infectivity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily determined by the binding affinity between the receptor-binding domain (RBD) of the spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. Here, through screening off pseudo hydrophilic groups on protein surfaces, the distribution of low-entropy regions on hydration shells of the ACE2 receptor and the RBDs of multiple SARS-CoV-2 variants was demonstrated. Shape matching between the low-entropy hydration shells of multiple SARS-CoV-2 variants and the ACE2 receptor has been identified as a mechanism that drives hydrophobic attraction between the RBDs and the ACE2 receptor, which estimates the binding affinity. Low-entropy regions of the hydration shells, which play important roles in determining the binding of other viruses and their receptors, are demonstrated. The RBD–ACE2 binding is thus found to be guided by hydrophobic collapse between the shape-matched low-entropy regions of the hydration shells of the proteins. A measure of the low-entropy status of the hydration shells can be estimated by calculating genuine hydrophilic groups within the binding sites. An important indicator of the contagiousness of SARS-CoV-2 variants is the low-entropy level of its hydration shells at the spike protein binding site. MDPI 2023-11-07 /pmc/articles/PMC10669249/ /pubmed/38002310 http://dx.doi.org/10.3390/biom13111628 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Yang, Lin
Guo, Shuai
Hou, Chengyu
Jiang, Shenda
Shi, Liping
Ma, Xiaoliang
Zheng, Bing
Fang, Yi
Ye, Lin
He, Xiaodong
Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants
title Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants
title_full Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants
title_fullStr Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants
title_full_unstemmed Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants
title_short Low-Entropy Hydration Shells at the Spike RBD’s Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants
title_sort low-entropy hydration shells at the spike rbd’s binding site may reveal the contagiousness of sars-cov-2 variants
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10669249/
https://www.ncbi.nlm.nih.gov/pubmed/38002310
http://dx.doi.org/10.3390/biom13111628
work_keys_str_mv AT yanglin lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT guoshuai lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT houchengyu lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT jiangshenda lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT shiliping lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT maxiaoliang lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT zhengbing lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT fangyi lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT yelin lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants
AT hexiaodong lowentropyhydrationshellsatthespikerbdsbindingsitemayrevealthecontagiousnessofsarscov2variants