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

非技术摘要当前的 COVID-19 大流行对人类健康构成严重威胁，导致世界各地前所未有的社会和经济混乱。所有不同学科的科学组织都充分动员起来，以各种能力抗击这一可怕的流行病。该奖项的重点是对这种病毒的性质及其如何攻击人体细胞的基本了解，从而找到减轻其有害影响的方法。该研究利用大规模计算模型来研究关键的 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。支持的研究对于了解病毒攻击下人体细胞的修饰至关重要，通过补充实验数据和计算，以大大降低的成本为疫苗开发和抗病毒药物设计提供见解。对 COVID-19 病毒的基本了解将对国内外产生深远的社会经济影响。技术摘要该奖项支持 SARS-CoV-2 刺突蛋白的计算建模和结构细化。这项研究具有挑战性，因为结构复杂、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。 这项研究包括使用第一原理密度泛函理论以及独特适合此目的的方法来计算电子结构和原子间键合。 SARS-COV-2 中的刺突 (S) 糖蛋白（S 蛋白）是了解病毒解剖结构的关键元素，因为它首先与人体细胞中的血管紧张素转换酶 (ACE2) 接触。 S 蛋白的结构通过冷冻电镜技术测定，分辨率为 3.5 Å。对于针对药物设计的详细计算而言，该分辨率不够精细。 这项研究通过计算解决了这一缺陷。 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端域（NTD）以及子域S1和S2。该项目将主要关注 RBD，它有 144 个氨基酸，总共 2100 个原子。刺突蛋白中整个A链的结构有959个氨基酸和14482个原子。对这些结构域结构的细化以及对融合前和融合后构象中刺突蛋白的电子结构和原子间键合（包括氢键合）的研究提供了先前研究中缺乏的迫切需要的信息。这里获得的结构数据将存放在适当的数据库中并提供给科学界。该奖项支持使用大规模从头计算与实验验证相结合的研究，以识别新型复杂病毒系统的显着特征。随着高精度冷冻电镜测量的使用，这种策略越来越受欢迎。计算模型、形式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非常重要。所支持的研究具有广泛的影响。首先，研究产生的新颖见解为疫苗开发和药物设计的应用铺平了道路。其次，计划中的研究与教育目标保持一致，涉及博士后研究员、研究生和本科生以及外部合作者。该获奖项目强调包容女性和少数族裔，学生在现代科学和工程的无边界环境中作为一个团队工作。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力优点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.