Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, United States of America.
PLoS Comput Biol. 2020 Oct 20;16(10):e1008357. doi: 10.1371/journal.pcbi.1008357. eCollection 2020 Oct.
Icosahedral viruses are under a micrometer in diameter, their infectious genome encapsulated by a shell assembled by a multiscale process, starting from an integer multiple of 60 viral capsid or coat protein (VP) monomers. We predict and validate inter-atomic hotspot interactions between VP monomers that are important for the assembly of 3 types of icosahedral viral capsids: Adeno Associated Virus serotype 2 (AAV2) and Minute Virus of Mice (MVM), both T = 1 single stranded DNA viruses, and Bromo Mosaic Virus (BMV), a T = 3 single stranded RNA virus. Experimental validation is by in-vitro, site-directed mutagenesis data found in literature. We combine ab-initio predictions at two scales: at the interface-scale, we predict the importance (cruciality) of an interaction for successful subassembly across each interface between symmetry-related VP monomers; and at the capsid-scale, we predict the cruciality of an interface for successful capsid assembly. At the interface-scale, we measure cruciality by changes in the capsid free-energy landscape partition function when an interaction is removed. The partition function computation uses atlases of interface subassembly landscapes, rapidly generated by a novel geometric method and curated opensource software EASAL (efficient atlasing and search of assembly landscapes). At the capsid-scale, cruciality of an interface for successful assembly of the capsid is based on combinatorial entropy. Our study goes all the way from resource-light, multiscale computational predictions of crucial hotspot inter-atomic interactions to validation using data on site-directed mutagenesis' effect on capsid assembly. By reliably and rapidly narrowing down target interactions, (no more than 1.5 hours per interface on a laptop with Intel Core i5-2500K @ 3.2 Ghz CPU and 8GB of RAM) our predictions can inform and reduce time-consuming in-vitro and in-vivo experiments, or more computationally intensive in-silico analyses.
二十面体病毒的直径小于一微米，其感染性基因组被一个由多层次过程组装而成的壳所包裹，该过程从整数倍的 60 个病毒衣壳或外壳蛋白 (VP) 单体开始。我们预测并验证了 VP 单体之间的原子间热点相互作用，这些相互作用对于 3 种二十面体病毒衣壳的组装很重要：腺相关病毒血清型 2 (AAV2) 和小鼠微小病毒 (MVM)，均为 T = 1 单链 DNA 病毒，以及 Bromo Mosaic Virus (BMV)，一种 T = 3 单链 RNA 病毒。实验验证是通过文献中发现的体外、定点诱变数据进行的。我们结合了两种尺度的从头预测：在界面尺度上，我们预测了在每个对称相关 VP 单体之间的界面上，成功组装亚基所需的相互作用的重要性（关键性）；在衣壳尺度上，我们预测了界面对于成功组装衣壳的关键性。在界面尺度上，我们通过当去除相互作用时衣壳自由能景观分区函数的变化来测量关键性。分区函数计算使用接口子组装景观图集，该图集由一种新颖的几何方法快速生成，并使用开源软件 EASAL（高效组装景观图集和搜索）进行了整理。在衣壳尺度上，界面对于衣壳成功组装的关键性基于组合熵。我们的研究从资源轻量化、多层次计算预测关键性原子间热点相互作用开始，一直到使用定点诱变对衣壳组装影响的数据进行验证。通过可靠而快速地缩小目标相互作用的范围（在配备 Intel Core i5-2500K @ 3.2 Ghz CPU 和 8GB RAM 的笔记本电脑上，每个界面不超过 1.5 小时），我们的预测可以为体外和体内实验或更计算密集型的计算分析提供信息并减少时间。
