全原子力场的最新发展与天然无序蛋白质的模拟

Recent development of atomistic force fields and simulations of intrinsically disordered proteins

天然无序蛋白质是一类特殊的蛋白质,在天然条件下不会折叠成特定的结构,却有着重要的生物学功能.分子动力学模拟是研究天然无序蛋白质的强大工具,能够提供实验无法观测到的结构和动力学信息.本文先总结了近年来全原子力场的发展以及不同力场在天然无序蛋白质体系中的表现,然后概述了水模型对蛋白质模拟的影响,最后介绍了分子动力学模拟在天然无序蛋白质结合过程研究上的应用.

Intrinsically disordered proteins(IDPs) are a special class of proteins which lack well-defined structures under native conditions while performing essential biological functions. Molecualr dynamics(MD) simulation is a powerful tool to unravel the atomistic details on IDPs’ structures and dynamics, which cannot be obtained from experiments. In this review, we first review the recent development of protein force fields and some benchmark studies.Then, we discuss the effect of water model choice on protein simulations. Finally, we introduce some MD applications in studying IDPs’ binding process.