Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions
Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions
复制标题
DOI：
10.1021/acs.jctc.6b00702
复制
发表时间：
2017-01-01
影响因子：
5.5
通讯作者：
Polimeno, Antonino
中科院分区：
文献类型：
--
作者：
Calligari, Paolo;Gerolin, Marco;Polimeno, Antonino
在本文中，我们提出了一种基于对 MD 模拟计算出的原子间距离相关函数的相关时间的分析的蛋白质中原子的聚类方法。目标是用更少的元素提供蛋白质的粗粒度描述，这些元素可以被视为动态独立的亚基。重要的是，这种结构域分解方法没有考虑蛋白质的结构特性。相反，根据动态相关域网络的蛋白质残基聚类是基于成对距离相关函数的有效相关时间来定义的。对于这些特性，我们的方法是对准刚性、基于结构域的常规蛋白质分解的补充分析。原型蛋白质结构获得的结果说明了所提出的方法。
In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.