Henke Paul S, Mak Chi H
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
J Chem Phys. 2016 Mar 14;144(10):105104. doi: 10.1063/1.4943387.
How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg(2+) screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.
在诸如核酸等聚电解质的分子动力学模拟中，如何恰当地考虑多价反离子仍是一个悬而未决的问题。诸如Mg(2+)等反离子不仅会屏蔽静电相互作用，还会产生吸引性的链内相互作用，从而稳定二级和三级结构。在此，我们展示了如何将源自最近报道的隐式反离子模型的简单力场整合到RNA的分子动力学模拟中，以逼真地再现单链和碱基配对RNA构建体的关键结构细节。这种二价反离子模型计算效率高。它可与现有的原子力场配合使用，或者粗粒度模型也可进行调整以与之配合。我们为利用这种新反离子力场的粗粒度RNA模型提供了优化参数。使用新模型，我们说明了在不同盐条件下RNA双向接头的结构灵活性是如何被改变的。
