RAPID: Structural Refinement and Intramolecular Binding in SARS-CoV-2 Spike Protein

非技术性摘要当前的COVID-19大流行对人类健康构成严重威胁，导致全球社会和经济出现前所未有的混乱。不同学科的所有科学组织都被充分动员起来，以各种身份与这一可怕的流行病作斗争。该奖项侧重于对这种病毒的性质以及它如何攻击人类细胞的基本理解，从而找到减轻其有害影响的方法。该研究利用大规模计算建模，针对一种关键的COVID-19蛋白质的结构和特性。其目标是获得高度准确和可靠的结构数据，并在原子尺度上研究分子间和分子内的结合机制。所支持的研究对于理解病毒攻击下人类细胞的修饰至关重要，通过计算补充实验数据，以更低的成本为疫苗开发和抗病毒药物设计提供见解。对COVID-19病毒的基本认识将在国内和国际上产生深远的社会经济影响。技术总结该奖项支持SARS-CoV-2刺突蛋白的计算建模和结构优化。由于结构复杂，需要处理大量原子，有意义的解释所需的准确性以及与COVID-19大流行相关的紧迫性，该研究具有挑战性。 这项研究包括使用第一性原理密度泛函理论计算电子结构和原子间键合，该理论基于唯一适合此目的的方法。 SARS-COV-2中的刺突（S）糖蛋白（S-蛋白）是理解病毒解剖结构的关键要素，因为它首次与人类细胞中的血管紧张素转换酶（ACE 2）接触。用冷冻电镜技术测定了S蛋白的结构，分辨率为3.5 μ m。该分辨率对于针对药物设计的详细计算来说不够精细。 这项研究在计算上解决了这一缺陷。S蛋白由三条链（A、B、C）组成，每条链由四个结构域组成：受体结合域（RBD）、N-末端结构域（NTD）和亚结构域S1和S2。该项目将主要关注RBD，它有144个氨基酸，共有2100个原子。刺突蛋白中的整个A链的结构具有959个氨基酸和14482个原子。细化这些域的结构和调查的电子结构和原子间键合，包括氢键，在融合前和融合后的构象的刺突蛋白提供了迫切需要的信息缺乏在以前的研究。在此获得的结构数据将存入适当的数据库，供科学界使用。该奖项支持使用大规模从头计算结合实验验证的研究，以识别新型复杂病毒系统的显著特征。这种策略随着高精度cyro-EM测量的使用而越来越受欢迎。计算建模、形式化理论和实验探索之间的紧密耦合反馈对于生物材料和物理病毒学的基础研究具有重要意义。所支持的研究具有广泛的影响。首先，研究产生的新见解为疫苗开发和药物设计的应用铺平了道路。其次，计划中的研究通过涉及博士后研究员，研究生和本科生以及外部合作者来实现教育目标。这个获奖项目强调了妇女和少数民族的包容性，学生们在现代科学和工程的无边界环境中作为一个团队工作。这个奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

NONTECHNICAL SUMMARYThe current COVID-19 pandemic is a severe threat to human health leading to unprecedented social and economic disruption all over the world. All scientific organizations in different disciplines are fully mobilized to combat this terrible pandemic in various capacities. This award focuses on the fundamental understanding of the nature of this virus and how it attacks the human cell, leading to means to mitigate its detrimental effects. The research targets the structure and properties of a crucial COVID-19 protein using large-scale computational modeling. The objective is to obtain highly accurate and reliable structure data and investigate both inter-molecular and intra-molecular binding mechanisms at the atomic scale.The supported research is critically important in understanding the modification of the human cell under virus attack, providing insights for vaccine development and antivirus drug design at a much reduced cost by supplementing experimental data with computation. The fundamental understanding of the COVID-19 virus will have a profound socioeconomic impact domestically and internationally.TECHNICAL SUMMARYThis award supports the computational modeling and structure refinement of the SARS-CoV-2 spike protein. The research is challenging because of the structural complexity, the large number of atoms to be dealt with, the accuracy required for meaningful interpretation and the urgency associated with COVID-19 pandemic. This research includes the calculation of the electronic structure and interatomic bonding using first-principles density functional theory based on methods uniquely suited for this purpose. The spike (S) glycoprotein (S-protein) in SARS-COV-2 is the key element in understanding the anatomy of the virus, since it makes the first contact with the angiotensin converting enzyme (ACE2) in the human cell. The structure of the S-protein was determined by cryo-EM technique with a resolution of 3.5 Å. This resolution is not sufficiently fine for detailed calculations aimed at drug design. This research addresses that deficiency computationally. The S-protein consists of three chains (A, B, C), each consisting of four structural domains: receptor binding domain (RBD), N-terminal domain (NTD), and subdomains S1 and S2. This project will mostly focus on the RBD, which has 144 amino acids with a total of 2100 atoms. The structure of the entire Chain A in the spike protein has 959 amino acids and 14482 atoms. Refinement of the structures of these domains and investigation of the electronic structure and interatomic bonding, including hydrogen bonding, of the spike protein in both the pre- and post-fusion conformations provides the urgently needed information lacking in prior research. The structural data obtained here are to be deposited in an appropriate data bank and made available to the scientific community. This award supports the research using large-scale ab-initio computation, in conjunction with experimental verification, to identify the salient features in novel complex virus systems. Such a strategy is increasingly popular with the use of high accuracy cyro-EM measurements. The tightly coupled feedback between computational modeling, formal theory and experimental exploration is important for fundamental research in biomaterials and physical virology. The supported research has a wide range of broader impacts. First, novel insights generated from the research paves the way for applications in vaccine development and drug design. Second, the planned research aligns with educational goals by involving a postdoctoral fellow, graduate and undergraduate students, and external collaborators. This awarded project emphasizes the inclusion of women and minorities, where students work as a team in a boundary-free environment of modern science and engineering.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.