论文标题
通过通过诱变验证的能量景观来快速预测至关重要的热点相互作用。
Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis
论文作者
论文摘要
二十面体病毒具有由多尺度工艺组装的壳封装的传染性基因组，从60个病毒衣壳或外套蛋白（VP）单体的整数倍数开始。 我们预测并验证了对3种二十面体病毒衣壳组装至关重要的VP单体之间的原子间热点相互作用：adeno相关病毒血清型2（AAV2）和小鼠的微小病毒（MVM）（MVM），t = 1个单链DNA病毒病毒病毒病毒和Bromo Mosaic Viruus，以及Bromo Mosaic Viruus（BMNA），bmmvA（BMV）。实验验证是通过文献中发现的，位于位置定向的诱变数据的验证。 我们将AB-Initio预测在两个量表上结合在一起：在界面尺度上，我们预测了相互作用的重要性（至关重要）对于在VP单体之间的每个接口上成功的子组件的相互作用的重要性（至关重要）；在衣壳尺度上，我们预测了成功的衣壳组件的界面的关键。 在界面尺度上，我们通过在删除相互作用时通过Capsid自由能景观分区函数的变化来测量关键性。分区函数计算使用界面子组装景观的图书馆，该景观是通过新颖的几何方法和策划的OpenSource软件Easal（有效的地拨号和搜索组装景观的搜索）迅速生成的。在衣壳尺度上，成功组装的界面的关键性是基于组合熵的。 我们的研究从对关键热点间相互作用的资源光，多尺度计算预测到使用有关位置定向诱变对capsid组装的影响的数据的验证。通过可靠，快速缩小目标相互作用（使用Intel Core i5-2500k 3.2GHz CPU和8GB RAM的笔记本电脑上的每个界面不超过1.5小时），我们的预测可以告知和减少时间耗时的体内和VIVO内实验，或者更多的计算强度强度强度。
Icosahedral viruses have 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 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 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 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 3.2Ghz 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.
