The European Physical Journal B ( IF 1.6 ) Pub Date : 2021-09-14 , DOI: 10.1140/epjb/s10051-021-00186-9 Mattia Bernetti 1 , Giovanni Bussi 1
|
Abstract
Small-angle X-ray scattering (SAXS) experiments are arising as an effective instrument in the structural characterization of biomolecules in solution. However, they suffer from limited resolution, and complementing them with molecular dynamics (MD) simulations can be a successful strategy to obtain information at a finer scale. To this end, tools that allow computing SAXS spectra from MD-sampled structures have been designed over the years, mainly differing in how the solvent contribution is accounted for. In this context, RNA molecules represent a particularly challenging case, as they can have a remarkable effect on the surrounding solvent. Herein, we provide a comparison of SAXS spectra computed through different available software packages for a prototypical RNA system. RNA conformational dynamics is intentionally neglected so as to focus on solvent effects. The results highlight that solvent effects are important also at relatively low scattering vector, suggesting that approaches explicitly modeling solvent contribution are advisable when comparing with experimental data, while more efficient implicit-solvent methods can be a better choice as reaction coordinates to improve MD sampling on-the-fly.
Graphic abstract
中文翻译：
比较从原子分子动力学模拟反算 SAXS 光谱的最新方法
摘要
小角度 X 射线散射 (SAXS) 实验正在成为解决溶液中生物分子结构表征的有效工具。然而，它们的分辨率有限，用分子动力学 (MD) 模拟对它们进行补充可能是获得更精细信息的成功策略。为此，多年来设计了允许从 MD 采样结构计算 SAXS 光谱的工具，主要区别在于如何解释溶剂贡献。在这种情况下，RNA 分子代表了一个特别具有挑战性的案例，因为它们可以对周围的溶剂产生显着的影响。在此，我们提供了通过原型 RNA 系统的不同可用软件包计算的 SAXS 光谱的比较。RNA 构象动力学被有意忽略，以关注溶剂效应。结果强调溶剂效应在相对较低的散射矢量下也很重要，这表明在与实验数据进行比较时，明确建模溶剂贡献的方法是可取的，而更有效的隐式溶剂方法可能是更好的选择，作为反应坐标以改善 MD 采样-苍蝇。
京公网安备 11010802027423号