Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Bioinformatics advances Pub Date : 2024-04-08 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae053
Anže Božič, Rudolf Podgornik
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Abstract

Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution.

Results: We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2200 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment.

Availability and implementation: The data underlying the article are available in the Supplementary material.

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SARS-CoV-2 新血统尖峰蛋白总电荷的变化。
研究动机严重急性呼吸系统综合征冠状病毒2(SARS-CoV-2)尖峰蛋白上的带电荷氨基酸残基已被证明会影响其与不同细胞表面受体的结合、与环境的非特异性静电相互作用以及其结构稳定性和构象。因此,充分了解在病毒进化过程中不同 SARS-CoV-2 世系中出现的影响尖峰蛋白总电荷的氨基酸突变非常重要:我们分析了病毒大流行期间出现的近 2200 个 SARS-CoV-2 株系中可电离氨基酸数量的变化以及尖峰蛋白上相应的总电荷。我们的研究结果表明,以前观察到的 SARS-CoV-2 变异株尖峰蛋白正电荷增加的趋势随着早期奥米克龙变异株的出现而基本停止。此外,最近出现的变种在可离子化氨基酸的组成方面表现出更大的多样性。我们还证明,尖峰蛋白上可电离氨基酸数量的变化规律是 SARS-CoV-2 系统发生树更广泛支系划分中相关支系的特征。由于静电相互作用在生物环境中无处不在,我们的发现对涉及 SARS-CoV-2 结构稳定性及其与环境相互作用的广泛研究具有重要意义:文章的基础数据见补充材料。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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