Faculty of Chemistry, Biological and Chemical Research Center , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland.
J Chem Theory Comput. 2018 Apr 10;14(4):2277-2287. doi: 10.1021/acs.jctc.7b01242. Epub 2018 Mar 6.
We recently developed a new coarse-grained model of protein structure and dynamics [ Dawid et al. J. Chem. Theory Comput. 2017 , 13 ( 11 ), 5766 - 5779 ]. The model assumed a single bead representation of amino acid residues, where positions of such united residues were defined by centers of mass of four amino acid fragments. Replica exchange Monte Carlo sampling of the model chains provided good pictures of modeled structures and their dynamics. In its generic form the statistical knowledge-based force field of the model has been dedicated for single-domain globular proteins. Sequence-specific interactions are defined by three-letter secondary structure data. In the present work we demonstrate that different assignments and/or predictions of secondary structures are usually sufficient for enforcing cooperative formation of native-like folds of SURPASS chains for the majority of single-domain globular proteins. Simulations of native-like structure assembly for a representative set of globular proteins have shown that the accuracy of secondary structure data is usually not crucial for model performance, although some specific errors can strongly distort the obtained three-dimensional structures.
我们最近开发了一种新的蛋白质结构和动力学的粗粒模型[Dawid 等人，J. Chem. Theory Comput.，2017，13（11），5766-5779]。该模型假设氨基酸残基的单个珠状表示，其中这些联合残基的位置由四个氨基酸片段的质心定义。对模型链进行 replica exchange Monte Carlo 采样提供了模型结构及其动力学的良好图像。在其通用形式中，该模型的基于统计知识的力场已专门用于单域球状蛋白质。序列特异性相互作用由三字母二级结构数据定义。在本工作中，我们证明对于大多数单域球状蛋白质，不同的二级结构分配和/或预测通常足以强制 SURPASS 链形成类似于天然的折叠。对一组代表性球状蛋白质的天然样结构组装的模拟表明，二级结构数据的准确性通常对于模型性能不是至关重要的，尽管一些特定的错误可能会强烈扭曲所得到的三维结构。
