Pattis Jason G, May Eric R
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut.
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut.
Biophys J. 2016 Mar 29;110(6):1246-54. doi: 10.1016/j.bpj.2016.02.008.
Lassa virus protects its viral genome through the formation of a ribonucleoprotein complex in which the nucleoprotein (NP) encapsidates the single-stranded RNA genome. Crystal structures provide evidence that a conformational change must occur to allow for RNA binding. In this study, the mechanism by which NP binds to RNA and how the conformational changes in NP are achieved was investigated with molecular-dynamics simulations. NP was structurally characterized in an open configuration when bound to RNA and in a closed form in the absence of RNA. Our results show that when NP is bound to RNA, the protein is highly dynamic and the system undergoes spontaneous deviations away from the open-state configuration. The equilibrium simulations are supported by free-energy calculations that quantify the influence of RNA on the free-energy surface, which governs NP dynamics. We predict that the globally stable states are qualitatively in agreement with the observed crystal structures, but that both open and closed conformations are thermally accessible in the presence of RNA. The free-energy calculations also provide a prediction of the location of the transition state for RNA binding and identify an intermediate metastable state that exhibits correlated motions that could promote RNA binding.
拉沙病毒通过形成核糖核蛋白复合体来保护其病毒基因组，其中核蛋白（NP）包裹着单链RNA基因组。晶体结构提供了证据，表明必须发生构象变化才能实现RNA结合。在本研究中，利用分子动力学模拟研究了NP与RNA结合的机制以及NP构象变化是如何实现的。NP在与RNA结合时呈开放构象，在没有RNA时呈封闭形式。我们的结果表明，当NP与RNA结合时，蛋白质具有高度的动态性，系统会自发地偏离开放状态构象。平衡模拟得到了自由能计算的支持，自由能计算量化了RNA对自由能表面的影响，而自由能表面决定了NP的动力学。我们预测，全局稳定状态在定性上与观察到的晶体结构一致，但在有RNA存在的情况下，开放和封闭构象在热动力学上都是可及的。自由能计算还预测了RNA结合的过渡态位置，并确定了一个中间亚稳态，该亚稳态表现出可能促进RNA结合的相关运动。
