三聚体刺突与德尔塔毒株(B.1.617.2)和奥密克戎毒株(BA.2、BA.5和BQ.1)的传染性和抗体逃逸的协同和结构关系。

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Anacleto Silva de Souza, Robson Francisco de Souza, Cristiane Rodrigues Guzzo
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引用次数: 0

摘要

在此,我们对几种严重急性呼吸系统综合征冠状病毒2变异毒株(德尔塔和奥密克戎亚变种BA.2、BA.5和BQ.1)的三聚体尖峰进行了模拟,并研究了特定突变赋予中和抗体耐药性的机制。我们观察到,突变主要影响原聚体内和原聚体之间蛋白质结构域之间的合作。取代K417N和L452R扩大了氢键相互作用,减少了它们与中和抗体的相互作用。通过与附近的残基相互作用,SpikeBQ.1变体中的K444T和N460K突变可能减少溶剂暴露,从而促进对抗体的抵抗。我们还研究了D614G、P681R和P681H取代对可能与传染性有关的刺突蛋白结构的影响。D614G取代影响甘氨酸残基和相邻结构域之间的通讯,影响RBD上下状态之间的转换。在德尔塔变异株中发现的P681R突变增强了蛋白质亚基之间的相关性,而奥密克戎亚变异株中的P681H突变削弱了可能与融合原性降低有关的长程相互作用。使用多元线性回归模型,我们建立了原体间通讯和对中和抗体敏感性丧失之间的联系。我们的发现强调了蛋白质结构域之间结构通信的重要性,并为严重急性呼吸系统综合征冠状病毒2型免疫逃避的潜在机制提供了见解。总的来说,这项研究加深了我们对特定突变如何影响严重急性呼吸系统综合征冠状病毒2型传染性的理解,并揭示了病毒如何逃避免疫系统。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)

Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)

Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.

Graphical abstract

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来源期刊
Journal of Computer-Aided Molecular Design
Journal of Computer-Aided Molecular Design 生物-计算机:跨学科应用
CiteScore
8.00
自引率
8.60%
发文量
56
审稿时长
3 months
期刊介绍: The Journal of Computer-Aided Molecular Design provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. The scope of the journal encompasses papers which report new and original research and applications in the following areas: - theoretical chemistry; - computational chemistry; - computer and molecular graphics; - molecular modeling; - protein engineering; - drug design; - expert systems; - general structure-property relationships; - molecular dynamics; - chemical database development and usage.
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