A novel severe acute respiratory syndrome (SARS)‐like coronavirus (SARS‐CoV‐2) has emerged as a human pathogen, causing global pandemic and resulting in over 400 000 deaths worldwide. The surface spike protein of SARS‐CoV‐2 mediates the process of coronavirus entry into human cells by binding angiotensin‐converting enzyme 2 (ACE2). Due to the critical role in viral‐host interaction and the exposure of spike protein, it has been a focus of most vaccines' developments. However, the structural and biochemical studies of the spike protein are challenging because it is thermodynamically metastable. Here, we develop a new pipeline that automatically identifies mutants that thermodynamically stabilize the spike protein. Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We then utilize our previously developed protein design tool, Eris, to predict thermodynamically stabilizing mutations in proteins. We validate the ability of our pipeline to identify protein stabilization mutants through known prefusion spike protein mutants. We finally utilize the pipeline to identify new prefusion spike protein stabilization mutants.

中文翻译：

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通过计算诱变稳定融合前刺突蛋白

一种新型严重急性呼吸系统综合症 (SARS) 样冠状病毒 (SARS-CoV-2) 已作为人类病原体出现，导致全球大流行并导致全球超过 40 万人死亡。SARS-CoV-2 的表面刺突蛋白通过结合血管紧张素转换酶 2 (ACE2) 介导冠状病毒进入人体细胞的过程。由于在病毒与宿主相互作用中的关键作用和刺突蛋白的暴露，它一直是大多数疫苗开发的重点。然而，刺突蛋白的结构和生化研究具有挑战性，因为它是热力学亚稳态的。在这里，我们开发了一个新的管道，可以自动识别热力学稳定刺突蛋白的突变体。我们的管道整合了保守残基的生物信息学分析、分子动力学模拟的运动动力学、和其他结构分析，以确定对刺突蛋白的热力学稳定性有显着贡献的残基。然后，我们利用我们之前开发的蛋白质设计工具 Eris 来预测蛋白质中的热力学稳定突变。我们验证了我们的管道通过已知的融合前刺突蛋白突变体识别蛋白质稳定突变体的能力。我们最终利用该管道来识别新的融合前刺突蛋白稳定突变体。我们验证了我们的管道通过已知的融合前刺突蛋白突变体识别蛋白质稳定突变体的能力。我们最终利用该管道来识别新的融合前刺突蛋白稳定突变体。我们验证了我们的管道通过已知的融合前刺突蛋白突变体识别蛋白质稳定突变体的能力。我们最终利用该管道来识别新的融合前刺突蛋白稳定突变体。