Computational modeling of viral assembly: encapsulation of nucleic acids and env

描述（由申请人提供）：在许多病毒家族中，复制需要数百至数千个蛋白质围绕病毒核酸（NA）组装，以形成称为衣壳的蛋白质外壳。此外，许多动物病毒使用蛋白质组装来驱动衣壳从细胞膜出芽。了解控制NA周围和膜上组装的机制将确定抑制NA包装或萌芽的新型抗病毒疗法的靶点，并将指导利用病毒作为靶向运输工具的努力。仅从实验中推断的组装机制是不完整的，因为中间体是短暂的。因此，该项目开发并应用了衣壳蛋白、NA和脂质的计算模型，这些模型揭示了实验无法获得的组装和膜出芽的细节。为了理解病毒NA的性质如何促进组装，开发了衣壳蛋白和NA的模型，所述模型开始以线性双链（没有碱基配对）开始，然后系统地添加由于碱基配对而产生的NA的几何和静电特征。预测的组装动力学和热力学的比较，每个模型确定的贡献的碱基配对组装。针对由合作实验室对围绕相应分子的衣壳组装（例如，合成聚电解质、异源NA和病毒基因组NA）。本文还研究了衣壳形成不同二十面体形态以容纳不同大小的核抗原的机制。采用的模拟技术包括布朗动力学和平衡计算。对于一些包膜病毒（例如，HIV）衣壳组装驱动细胞膜出芽，而对于其他（例如，甲病毒）膜蛋白的组装驱动预组装衣壳的出芽。模拟被用来研究这两类组装驱动的出芽过程如何依赖于蛋白质相互作用和膜刚性等特性，以及为什么许多病毒优先从特定的膜微区出芽。预测将与甲病毒出芽的实验进行比较。除了确定可以被操纵以防止或利用病毒组装的因素外，拟议的模拟将阐明生物学如何利用膜和丝状支架组装多大分子复合物。该研究结合了由原子模拟和实验提供信息的粗粒度模型，以及GPU和分布式计算的最新进展，以模拟相关的时间和长度尺度。提出了一种将马尔可夫状态模型应用于装配反应的新方法。

DESCRIPTION (provided by applicant): In many virus families, replication requires that hundreds to thousands of proteins assemble around the viral nucleic acid (NA) to form a protein shell called a capsid. Furthermore, many animal viruses use protein assembly to drive budding of the capsid from a cell membrane. Understanding the mechanisms that control assembly around NAs and on membranes would identify targets for novel antivirus therapies that inhibit NA packaging or budding, and would guide efforts to exploit viruses as targeted transport vehicles. Assembly mechanisms inferred from experiments alone are incomplete because intermediates are transient. Therefore, this project develops and applies computational models for capsid proteins, NAs, and lipids that reveal details of assembly and membrane budding not accessible to experiments. To understand how the properties of viral NAs facilitate assembly, models are developed for capsid proteins and NAs that begin with a linear polyelectrolyte (without base-pairing) and then systematically add the geometric and electrostatic features of NAs that arise due to base-pairing. Comparison of predicted assembly kinetics and thermodynamics for each model identifies the contributions of base-pairing to assembly. Predictions for each model are tested against experiments performed by collaborating labs on capsid assembly around corresponding molecules (e.g., synthetic polyelectrolytes, heterologous NAs, and viral genomic NAs). The mechanism by which capsids form different icosahedral morphologies to accommodate NAs with different sizes is also studied. Employed simulation techniques include Brownian dynamics and equilibrium calculations. For some enveloped viruses (e.g., HIV) capsid assembly drives budding from a cell membrane, while for others (e.g., alphaviruses) assembly of membrane proteins drives budding of a pre-assembled capsid. Simulations are used to investigate how these two classes of assembly-driven budding processes depend on properties such as protein interactions and membrane rigidity, and why many viruses preferentially bud from particular membrane microdomains. Predictions will be compared to experiments on alphavirus budding. In addition to identifying factors that can be manipulated to prevent or exploit viral assembly, the proposed simulations will elucidate how biology employs membranes and filamentous scaffolds to assemble multi- macromolecular complexes. The research combines coarse-grained models that are informed by atomistic simulations and experiments with recent advances in GPUs and distributed computing to simulate relevant time and length scales. A new method to apply Markov state models to assembly reactions is developed.