School of Chemistry, University of Southampton, SouthamptonSO17 1BJ, U.K.
Department of Pharmaceutical Sciences, University of California, Irvine, California92697, United States.
J Chem Theory Comput. 2023 Feb 14;19(3):1050-1062. doi: 10.1021/acs.jctc.2c00823. Epub 2023 Jan 24.
Water molecules play a key role in many biomolecular systems, particularly when bound at protein-ligand interfaces. However, molecular simulation studies on such systems are hampered by the relatively long time scales over which water exchange between a protein and solvent takes place. Grand canonical Monte Carlo (GCMC) is a simulation technique that avoids this issue by attempting the insertion and deletion of water molecules within a given structure. The approach is constrained by low acceptance probabilities for insertions in congested systems, however. To address this issue, here, we combine GCMC with nonequilibium candidate Monte Carlo (NCMC) to yield a method that we refer to as grand canonical nonequilibrium candidate Monte Carlo (GCNCMC), in which the water insertions and deletions are carried out in a gradual, nonequilibrium fashion. We validate this new approach by comparing GCNCMC and GCMC simulations of bulk water and three protein binding sites. We find that not only is the efficiency of the water sampling improved by GCNCMC but that it also results in increased sampling of ligand conformations in a protein binding site, revealing new water-mediated ligand-binding geometries that are not observed using alternative enhanced sampling techniques.
水分子在许多生物分子体系中起着关键作用,特别是在蛋白质-配体界面结合时。然而,由于蛋白质与溶剂之间的水分子交换需要相对较长的时间尺度,因此对这类体系的分子模拟研究受到了阻碍。巨正则蒙特卡罗(GCMC)是一种模拟技术,它通过在给定结构内尝试插入和删除水分子来避免这个问题。然而,在拥挤的系统中,插入的接受概率较低,这限制了该方法的应用。为了解决这个问题,我们在这里将 GCMC 与非平衡候选蒙特卡罗(NCMC)相结合,得到一种我们称之为巨正则非平衡候选蒙特卡罗(GCNCMC)的方法,其中水分子的插入和删除是以逐渐的、非平衡的方式进行的。我们通过比较 GCNCMC 和 GCMC 对体相水和三个蛋白质结合位点的模拟来验证这种新方法。我们发现,GCNCMC 不仅提高了水分子采样的效率,而且还增加了蛋白质结合位点中配体构象的采样,揭示了新的水介导的配体结合几何形状,这些几何形状是使用替代增强采样技术观察不到的。
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