衣壳内类RNA聚电解质：显式静电相互作用的分子动力学
RNA-like Polyelectrolyte in a Viral Capsid: Molecular Dynamics with Explicit Electrostatic Interactions
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中文总结 AI 辅助
本研究采用含显式离子、水和全库仑静电的分子动力学模拟，揭示病毒衣壳内类RNA聚电解质的组织机制，验证平均场近似对径向组织的适用性，同时发现离散分子细节带来的偏差及盐浓度对平衡时间的影响。
中文摘要 AI 辅助
病毒衣壳内RNA基因组的组织主要由带负电的基因组与衣壳蛋白带正电的N端结构域之间的静电相互作用控制。在理论研究中，这类相互作用通常用平均场模型描述，该模型将衣壳电荷平滑到内表面，并将离子屏蔽视为连续介质。然而，电荷定位于离散的N端结合位点，而离子屏蔽则源于相关的离子分布。本研究采用包含显式离子、显式水和全库仑静电的分子动力学模拟，模拟被限定在带有类N端离散电荷位点的模型衣壳内的线性聚电解质。我们首先通过模拟本体溶液中的聚电解质验证方法，证实 persistence length（持续长度）随盐浓度升高而降低，与单链RNA的实验测量结果一致。当聚电解质被限定在衣壳内时，径向密度分布随盐浓度升高从衣壳壁系统地向内移动，与平均场预测相符。通过独立改变电荷大小、结合位点密度和N端突出长度，我们发现总静电耦合控制全局组织，而几何细节调节局部基因组-壁接触以及N端附近的基因组角向组织（本研究中针对T=3衣壳结构、线性基因组拓扑和单价盐范围）。在所有模拟中，平衡时间随盐浓度升高增加7倍，揭示了平衡理论无法获取的动力学效应。这些结果验证了径向组织的连续介质近似，同时揭示了离散分子细节导致的偏差，并为后续研究基因组二级结构、衣壳几何和组装动力学建立了框架。
英文摘要
The organization of RNA genomes within viral capsids is primarily controlled by electrostatic interactions between the negatively charged genome and positively charged N-terminal domains of coat proteins. In theoretical approaches, these interactions are commonly captured by mean-field models that smooth capsid charge over the inner surface and treat ionic screening as a continuum. However, charges are localized at discrete N-terminal binding sites and ionic screening arises from correlated ion distributions. Here we use molecular dynamics simulations with explicit ions, explicit water, and full Coulomb electrostatics to simulate a linear polyelectrolyte confined within a model capsid bearing discrete N-terminal-like charge sites. We first validate our approach by simulating a polyelectrolyte in bulk solution and demonstrating that persistence length decreases with increasing salt, matching experimental measurements for single-stranded RNA. When confined within a capsid, radial density profiles shift systematically inward from the capsid wall with increasing salt concentration, in agreement with mean-field predictions. By independently varying charge magnitude, binding-site density, and N-terminal protrusion length, we show that total electrostatic coupling governs global organization while geometric details modulate local genome-wall contact and angular genome organization near N-terminals (within the T=3 architecture, linear genome topology, and monovalent salt range studied here). Across all simulations, equilibration times increase sevenfold with salt, revealing kinetic effects inaccessible to equilibrium theory. These results validate continuum approximations for radial organization while revealing deviations arising from discrete molecular details and establishing a framework for future investigations of genome secondary structure, capsid geometry, and assembly kinetics.
