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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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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 |
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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 |
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