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通过分子模拟对SARS-CoV-2尖端蛋白变体的形态和稳定性分析

Gustavo E Olivos-Ramirez¹, Luis F Cofas-Vargas¹, Tobias Madl²

¹Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, ul. Pawińskiego 5B, 02-106 Warsaw, Poland.

Pathogens (Basel, Switzerland)

|March 26, 2025

概括

分子动力学模拟显示,SARS-CoV-2尖端蛋白变体如XBB.1.5和JN.1采用紧状态. 特定突变增强了宿主受体相互作用,并改变了抗体结合部位.

科学领域:

结构生物学是结构生物学.
计算生物物理学的计算生物物理.
病毒学病毒学

背景情况:

SARS-CoV-2 尖端蛋白对于病毒进入至关重要,也是疫苗和治疗的关键目标.
新兴变种表现出改变的结构和功能性质,需要持续调查.
了解尖端蛋白的结构动态对于预测病毒进化和免疫逃避至关重要.

研究的目的:

与野生型相比,全面分析SARS-CoV-2尖端蛋白变体 (Delta,BA.1,XBB.1.5,JN.1) 的结构格局.
确定与结构转型相关的稳定本地联系和构造状态.
阐明特定突变对尖端蛋白结构,功能和抗体可访问性的影响.

主要方法:

用分子动力学 (MD) 模拟来探索尖端蛋白变体的结构空间.
对集体变量 (CVs) 的分析,包括域间距离 (RBD-NTD),特征性构造状态.
进行了稳定这些构造的本地接触 (NCs) 的识别和表征.

主要成果:

遗传上相距较远的变种 (XBB.1.5,BA.1,JN.1) 显示出比野生类型更紧的构造状态.
这些变体显示了新的本地接触特征,增加了离子,极和非极相互作用.
关键突变 (T478K,N500Y,Y504H) 增强了宿主受体的结合,并引入了稳定接触,可能会影响抗体可访问性.

结论:

SARS-CoV-2 尖端蛋白质变体表现出由遗传分歧和特定突变驱动的独特的结构偏好.
变体中的新型本地接触模式有助于改变结构稳定性和受体相互作用.
了解这些结构性适应对于开发有效的抗病毒策略和预测未来变种演变至关重要.

关键词:

这就是SARS-CoV-2病毒.集体变量是一个集体变量.构造空间的构造空间.分子动力学分子动力学本地人接触地图概率状态表示概率状态.蛋白质的稳定性蛋白质的稳定性

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