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刺突蛋白 RBD 结合位点处的低熵水合壳可能揭示 SARS-CoV-2 变体的传染性。

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

机构信息

National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China.

School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia.

出版信息

Biomolecules. 2023 Nov 7;13(11):1628. doi: 10.3390/biom13111628.

Abstract

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.

摘要

严重急性呼吸综合征冠状病毒 2(SARS-CoV-2)的传染性主要取决于其刺突蛋白受体结合域(RBD)与血管紧张素转换酶 2(ACE2)受体之间的结合亲和力。在这里,通过筛选蛋白质表面上的假亲水基团,展示了 ACE2 受体和多种 SARS-CoV-2 变体的 RBD 水合壳中低熵区域的分布。鉴定出多种 SARS-CoV-2 变体的低熵水合壳之间的形状匹配是驱动 RBD 与 ACE2 受体之间疏水吸引的机制,从而估计了结合亲和力。展示了在确定其他病毒及其受体结合中起重要作用的水合壳的低熵区域。因此,发现 RBD-ACE2 的结合受蛋白质水合壳的形状匹配的低熵区域之间的疏水塌陷的指导。可以通过计算结合位点内的真正亲水基团来估计水合壳的低熵状态的度量。SARS-CoV-2 变体的传染性的一个重要指标是其在刺突蛋白结合位点上水合壳的低熵水平。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2782/10669249/61b55c208144/biomolecules-13-01628-g001.jpg

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