MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
Biophys J. 2013 Sep 3;105(5):1248-57. doi: 10.1016/j.bpj.2013.07.033.
Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin-Debye model and the Poisson-Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.
尽管通过隐式描述溶剂的连续模型可以将分子动力学模拟加速一个数量级以上，但目前大多数可用的隐式溶剂模拟方法都无法稳健地模拟核酸的结构和动力学。对于 RNA 来说，这些困难变得更加严重，这表明先前用于描述溶剂和抗衡离子对核酸影响的连续模型存在严重的物理缺陷。我们提出了一种新颖的隐式溶剂模型，通过将 Langevin-Debye 模型和泊松-玻尔兹曼方程相结合，来模拟核酸，从而更好地估计水和抗衡离子的静电屏蔽。模型的测试涉及对三个具有 20、29 和 75 个核苷酸的 RNA 靶标进行隐式和显式溶剂模拟的比较。该模型与显式溶剂模拟具有合理的一致性，并指出了未来改进的方向。
