The protein folding network
The protein folding network
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DOI：
10.1016/j.jmb.2004.06.063
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发表时间：
2004-09-03
影响因子：
5.6
通讯作者：
Caflisch, A
中科院分区：
文献类型：
--
作者：
Rao, F;Caflisch, A
通过分子动力学模拟，将20个残基反平行β -片肽的构象空间映射到一个网络中。沿轨迹保存的快照按二级结构分组为网络节点，节点之间的过渡为链路。构象空间网络描述了显著的自由能最小值及其动态连通性，而不需要任意选择反应坐标。正如之前在互联网和万维网以及社会和生物网络中发现的那样，构象空间网络是无标度的，并且包含高度连接的枢纽，例如人口最多的自由能源盆地的原生状态。此外，天然盆地表现出层次化的组织，这是缺乏主要自由能最小值的随机杂多聚合物所没有的。该网络拓扑用于识别折叠过渡态（TS）系综中的构象，为理解TS和变性态系综的异质性以及多路径的存在提供了基础。(C) 2004 Elsevier Ltd.版权所有。
The conformation space of a 20 residue antiparallel beta-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Snapshots saved along the trajectory are grouped according to secondary structure into nodes of the network and the transitions between them are links. The conformation space network describes the significant free energy minima and their dynamic connectivity without requiring arbitrarily chosen reaction coordinates. As previously found for the Internet and the World-Wide Web as well as for social and biological networks, the conformation space network is scale-free and contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the native basin exhibits a hierarchical organization, which is not found for a random heteropolymer lacking a predominant free-energy minimum. The network topology is used to identify conformations in the folding transition state (TS) ensemble, and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways. (C) 2004 Elsevier Ltd. All rights reserved.