配体解结合的反应坐标应该有多湿？
How wet should be the reaction coordinate for ligand unbinding?
摘要：
我们使用最近提出的称为序参量的光谱间隙优化（SGOOP）的方法（Tiwary和Berne，Proc.Natl. Acad. Sci 2016，113，2839（2016）），以确定用于将巴基球从显式水中的口袋中解绑的最佳一维反应坐标（RC）。该RC被估计为多个可用的序参量的线性组合，这些顺序参数可以共同用于区分与解约束相关的各种稳定状态。我们特别注意确定和量化水分子应包含在RC中的程度。使用SGOOP与欠采样偏置模拟，我们预测，水发挥了独特的作用，在反应坐标解结合的情况下，当配体的空间约束沿对称轴移动。该预测是通过广泛的计算的解结合时间通过metadaptics，并通过比较，通过细致平衡与无偏分子动力学估计的结合时间。然而，当空间限制被删除，我们发现，水在反应坐标的作用减弱。在这里，而不是SGOOP确定了一个很好的一维钢筋混凝土涉及各种运动自由度。
英文摘要：
We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics, and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.
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