水溶液中二价阳离子和氨基酸的相互作用:基于神经网络势能面的分子模拟

Interaction of Divalent Cations and Amino Acids in Bulk Water:Molecular Simulations with Neural Network Potentials

了解二价金属离子与氨基酸相互作用的机理对于理解金属离子与蛋白质之间的相互作用具有重要意义.本研究结合神经网络势能面、分子动力学模拟和伞形采样系统研究了水溶液中Mg^(2+)、Ca^(2+)和Zn^(2+)与氨基酸侧链类似物的相互作用机理.计算得到的自由能曲线不仅揭示了每个离子与氨基酸的结合过程以及最稳定的配位结构,而且还显示了不同离子之间的差异.此外,还将基于神经网络势函数得到的时又能作为标准对经典力场进行基准测试,对开发针对金属离子的力场具有重要意义.

Understanding the interaction mechanism between divalent metal ions with amino acids is of great significance to understand the interaction between metal ions with proteins.In this study,the interaction mechanisms of Mg^(2+),Ca^(2+),and Zn^(2+)with amino acid side chain analogs in water were systematically studied by combining neural network potential energy surface,molecular dynamics simulation and umbrella sampling.The calculated potential mean forces not only reveal the binding process of each ion and amino acid,the most stable coordination structure,but also show the difference between different ions.In addition,we also use the neural network based potential of mean force as a standard to benchmark classical force fields,which is also meaningful for the development of force fields targeting metal ions.