Complex network analysis of free-energy landscapes
Complex network analysis of free-energy landscapes
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DOI：
10.1073/pnas.0608099104
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发表时间：
2007-02-06
影响因子：
11.1
通讯作者：
Rao, F.
中科院分区：
文献类型：
--
作者：
Gfeller, D.;De Los Rios, P.;Rao, F.
生物分子异构化过程的动力学，如蛋白质折叠，是由一个自由能表面的高维数和复杂性。作为一维或二维投影的替代方案，自由能表面可以映射到加权网络中，其中节点和链接分别是配置和它们之间的直接转换。在这项工作中，丙氨酸二肽的自由能盆地和障碍是使用算法定量确定的，以将网络划分为簇（即，状态）根据分子动力学采样的平衡跃迁。基于网络的方法允许生物分子异构化的热力学和动力学的分析，而不依赖于任意选择的顺序参数。此外，它表明，低维模型，这可以被视为分析，以及为丙氨酸dipeparticle，宽尾的重量分布在其网络中观察到的起源于自由能盆地，主要是dipic字符。
The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped into a weighted network where nodes and links are configurations and direct transitions among them, respectively. In this work, the free-energy basins and barriers of the alanine dipepticle are determined quantitatively using an algorithm to partition the network into clusters (i.e., states) according to the equilibrium transitions sampled by molecular dynamics. The network-based approach allows for the analysis of the thermodynamics and kinetics of bionnolecule isomerization without reliance on arbitrarily chosen order parameters. Moreover, it is shown on low-dimensional models, which can be treated analytically, as well as for the alanine dipepticle, that the broad-tailed weight distribution observed in their networks originates from freeenergy basins with mainly enthalpic character.