Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA.
Proteins. 2013 Jul;81(7):1200-11. doi: 10.1002/prot.24269. Epub 2013 Apr 10.
We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics.
我们开发了一个粗粒模型，其中溶剂被隐式考虑，静电相互作用被视为短程相互作用，侧链被粗粒化为单个珠子。该模型取决于三个主要参数：疏水性、静电和侧链氢键强度。这些参数是通过考虑三个近似层次并对三个选定的蛋白质（训练集）的折叠进行特征化来确定的。另外九个蛋白质（包含多达 126 个残基）以及突变版本（测试集）用给定的参数进行折叠。在所有折叠模拟中，初始状态是一个随机卷曲配置。除了天然状态，一些蛋白质折叠成一个额外的状态，在拓扑结构（螺旋束的结构）上有所不同。我们讨论了天然状态的稳定性，并将我们的模型的动力学与全原子分子动力学模拟以及一些控制折叠动力学的相互作用的一般性质进行了比较。
