AMS Department, Khalifa University, 127788, Abu Dhabi, UAE,
Adv Exp Med Biol. 2014;805:171-97. doi: 10.1007/978-3-319-02970-2_8.
Molecular dynamics simulations have become an invaluable tool in investigating the dynamics of protein folding. However, most computational studies of protein folding assume dilute aqueous simulation conditions in order to reduce the complexity of the system under study and enhance the efficiency. Nowadays, it is evident that environmental conditions encountered in vivo (or even in vitro) play a major role in regulating the dynamics of protein folding especially when one considers the highly condensed environment in the cellular cytoplasm. In order to factor in these conditions, we can utilize the high efficiency of well-designed low resolution (coarse-grained) simulation models to reduce the complexity of these added protein-milieu interactions involving different time and length scales. The goal of this chapter is to describe some recently developed coarse-grained simulation techniques that are specifically designed to go beyond traditional aqueous solvent conditions. The chapter also gives the reader a flavor of the things that we can study using such "smart" low resolution models.
分子动力学模拟已成为研究蛋白质折叠动力学的宝贵工具。然而，为了降低研究系统的复杂性并提高效率，大多数蛋白质折叠的计算研究都假设在稀水溶液模拟条件下进行。如今，显然在体内（甚至在体外）遇到的环境条件在调节蛋白质折叠动力学方面起着主要作用，特别是当考虑到细胞细胞质中高度浓缩的环境时。为了考虑这些条件，我们可以利用精心设计的低分辨率（粗粒化）模拟模型的高效率来降低涉及不同时间和长度尺度的这些添加的蛋白质-环境相互作用的复杂性。本章的目的是描述一些最近开发的粗粒化模拟技术，这些技术专门用于超越传统的水溶剂条件。本章还使读者了解到我们可以使用这种“智能”低分辨率模型来研究的内容。
