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

RAPID--SARS-CoV-2 自组装的物理原理：来自实验的理论

• 批准号: 2034794
• 负责人: Roya Zandi
• 金额: $ 20万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2034794&HistoricalAwards=false
• 关键词: RAPID; Physical; principles; self; assembly

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.

非技术性总结此奖项是针对2019年冠状病毒病致同事信的快速提案而颁发的。 SARS-CoV-2属于冠状病毒家族，是造成目前大流行的原因。解开病毒组件如何组装自己以制造病毒的步骤和阶段是具有挑战性的。与形状像具有20个三角形边的测地线圆顶的二十面体病毒相比，冠状病毒在大小和形态上都是异质的，这使得它们的统计重建变得复杂。虽然对于二十面体病毒的组装已经做了相当多的理论，但是对于冠状病毒及其伴随的复杂性还没有尝试进行这样的分析。 由于病毒没有独立的能量来源，组装和出芽策略主要依赖于平衡统计物理学和利用被劫持用于病毒形成的活跃细胞过程的组合。 本项目的重点是研究SARS-CoV-2的组装理论和计算机模拟。由于缺乏理论所需的数据，该项目还包括实验部分。该项目的重点是利用实验来推进对SARS-CoV 2结构蛋白在其自组装中的作用的理解。特别是，PI将使用显微镜研究人类细胞和体外模型中的病毒组装，并表征从细胞中收集的颗粒。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同开展，PI将对SARS-CoV-2的形成和组装获得更深入和更机理的理解，这将有助于快速设计有效的药物疗法，从而在应对目前和未来全球大流行性冠状病毒爆发的威胁方面发挥至关重要的作用。能够开发粗粒度模拟，以研究参与SARS-CoV-2形成的几种蛋白质的作用，这些蛋白质是2019年冠状病毒病（COVID-19）的原因，该疾病正在全球迅速蔓延，对健康和经济产生巨大的不利影响。由于这一问题的紧迫性，应采用许多补充战略来解决这一问题，并改进知识和信息库。SARS-CoV-2在内质网高尔基中间复合体（ERGIC）的膜上形成。与许多其他病毒相比，SARS-CoV-2的组装是独特的，因为组装和出芽同时发生在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如何组装的理解，并为其他基础研究提供平台，以开发药物和其他治疗策略。 更好地理解SARS-CoV-2形成过程中的物理原理将有助于战胜该病毒。研究小组将采用软凝聚态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，因此成核和生长理论将用于动力学。利用质量作用定律和经典成核理论，PI探索蛋白质浓度、溶液条件（即pH值和盐浓度）如何影响组装和出芽的程度。分析理论将通过巨正则系综中的蒙特卡罗模拟得到扩充。该奖项也有一个由理论和模拟工作的需要指导的实验部分。该提案的特殊智力价值是发展了膜的耦合形状波动和与其结合的蛋白质扩散的动力学理论，以及通过分析所提出的实验来检验这些结果。该奖项反映了NSF的法定使命，并被认为值得支持通过使用基金会的知识价值和更广泛的影响审查标准进行评估。

项目成果

Virus Assembly Pathways Inside a Host Cell

• DOI: 10.1021/acsnano.1c06335
• 发表时间: 2022-01-12
• 期刊: ACS NANO
• 影响因子: 17.1
• 作者: Panahandeh, Sanaz;Li, Siyu;Zandi, Roya
• 通讯作者: Zandi, Roya