RAPID--Physical principles of self-assembly of SARS-CoV-2: Theory with input from experiment

非技术性总结本奖项是针对冠状病毒病2019年的快速提案而颁发的亲爱的同事们的信。SARS-CoV-2属于冠状病毒家族，是目前疫情的罪魁祸首。解开病毒组件如何自我组装以制造它的步骤和阶段是具有挑战性的。与二十面体病毒不同的是，二十面体病毒的形状像一个有20个三角形边的测地圆顶，冠状病毒在大小和形态上都是不同的，这使得它们的统计重建变得复杂。虽然已经对二十面体病毒的组装进行了相当多的理论研究，但还没有人尝试对伴随其复杂性的冠状病毒进行这样的分析。由于病毒没有独立的能源，组装和萌芽策略主要依赖于平衡统计物理和开发为形成病毒而劫持的活跃细胞过程的组合。本项目从理论和计算机模拟两个方面对SARS-CoV-2病毒的组装进行了研究。由于缺乏理论所需的数据，本项目还包含一个实验部分。该项目的重点是通过实验促进对SARS-CoV2结构蛋白在其自组装中的作用的理解。特别是，PI将使用显微镜研究病毒在人类细胞和体外模型中的组装，并对从细胞中收集的颗粒进行表征。实验的目的是为理论研究提供必要的基本参数。通过理论和实验的协调开展，私人投资机构将对SARS-CoV-2的形成和组装获得更深入和更机械的了解，这有助于快速设计有效的药物治疗方法，从而在抗击目前和未来此类冠状病毒全球大流行爆发的威胁方面发挥关键作用。技术总结通过快速提案获得这项奖项的支持，将能够开发粗粒度模拟程序，以研究导致SARS-CoV-2形成的几种蛋白质的作用，该病毒正在世界各地迅速传播，对健康和经济造成巨大的不利影响。由于这一问题的紧迫性，应采取许多相辅相成的战略来解决这一问题，并改善知识和信息基础。SARS-CoV-2病毒形成于高尔基体内质网中间隔膜(ERGIC)。与许多其他病毒相比，SARS-CoV-2的组装是独特的，因为组装和萌发都同时发生在ERGIC膜上。尽管进行了一些研究，但对组装途径或机制知之甚少。该项目旨在促进对SARS-CoV-2如何组装的了解，并为其他基础研究提供一个平台，以开发药物和其他治疗策略。更好地了解SARS-CoV-2形成过程中涉及的物理原理将推进战胜该病毒的方法。研究小组将使用软凝聚物质和病毒组装的统计力学方法，使用平衡和非平衡方法。由于病毒组装类似于热力学相变，因此将使用成核和生长理论来描述动力学。利用质量作用定律和经典成核理论，PI研究了蛋白质浓度、溶液条件，即pH和盐浓度，如何影响组装和萌发的程度。分析理论将被宏正则系综中的蒙特卡罗模拟所增强。该奖项还有一个由理论和模拟工作的需要指导的实验部分。这一提议的特殊智力价值是发展了膜的耦合形状波动和结合在其上的蛋白质的扩散的动力学理论，并通过对所提议的实验的分析来检验这些结果。该奖项反映了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 SUMMARYThis award is made on a RAPID proposal in response to the Coronavirus Disease 2019 Dear Colleague Letter. SARS-CoV-2 belongs to the family of coronaviruses and is responsible for the current pandemic. Untangling the steps and stages of how the components of the virus assemble themselves to make it is challenging. In contrast to icosahedral viruses which are shaped like a geodesic dome with 20 triangular sides, coronaviruses are heterogeneous both in size and morphology complicating their statistical reconstruction. While a fair amount of theory has been done for the assembly of icosahedral viruses, such an analysis has not been attempted for coronaviruses with their attendant complexities. Since viruses have no independent energy source, assembly and budding strategies rely mainly on a combination of equilibrium statistical physics and the exploitation of active cellular processes hijacked for the formation of the virus. This project is focused on the investigating the assembly of SARS-CoV-2 both theoretically and through computer simulations. Due to the lack of data necessary for the theory, this project also contains an experimental component. The project is focused on advancing understanding of the role of SARS-CoV2 structural proteins in its self-assembly using experiments. In particular, the PIs will use microscopy to study viral assembly within human cells and in vitro models, and to characterize particles collected from cells. The goal of experiments is to provide the basic necessary parameters for the theoretical investigation. By carrying out theory and experiment in concert, the PIs will obtain a deeper and more mechanistic understanding of the formation and assembly of SARS-CoV-2, which can contribute to the rapid design of effective drug therapies and thus will have a crucial role in combating the threat of the present and future global pandemic outbreaks of such coronaviruses.TECHNICAL SUMMARYThe research supported through this award made on RAPID proposal will enable the development of coarse-grained simulations to study the role of several proteins involved in the formation of SARS-CoV-2 responsible for the Coronavirus Disease 2019 (COVID-19), which is spreading rapidly across the world, with tremendous adverse impact on health and the economy. Due to the urgency of the issue, numerous complementary strategies should be employed to tackle the problem and to improve the knowledge and information base. SARS-CoV-2 forms at the membrane of the Endoplasmic Reticulum Golgi Intermediate Compartment (ERGIC). The assembly of SARS-CoV-2 is unique compared to many other viruses as both the assembly and budding occur simultaneously at the ERGIC membrane. Despite some investigation, very little is known of the assembly pathway or mechanism. This project is aimed to advance understanding of how SARS-CoV-2 assembles and provides a platform for other fundamental investigations to develop drugs and other strategies for treatment. A better understanding of physical principles involved in the formation of SARS-CoV-2 will advance the means of defeating the virus. The research team will employ the methods of soft condensed matter and statistical mechanics of virus assembly, using both equilibrium and nonequilibrium approaches. Since virus assembly is akin to a thermodynamic phase transition, nucleation and growth theory will be used for the kinetics. Using the law of mass action and classical nucleation theory the PIs explore how the protein concentration, solution condition, that is, pH and salt concentration, influence the degree of assembly and budding. The analytical theory will be augmented by Monte Carlo simulations in grand canonical ensembles. This award also has an experimental component guided by the needs of the theory and simulation effort.The particular intellectual merit of this proposal is the development of a dynamical theory of the coupled shape fluctuations of the membrane and the diffusion of proteins bound to it, and the testing of these results by the analysis of the experiments proposed.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.