Principal component analysis for protein folding dynamics.
Principal component analysis for protein folding dynamics.
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DOI：
10.1016/j.jmb.2008.10.018
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发表时间：
2009-01-09
影响因子：
5.6
通讯作者：
Scheraga, Harold A.
中科院分区：
文献类型：
--
作者：
Maisuradze, Gia G.;Liwo, Adam;Scheraga, Harold A.
本文通过研究来自形成蛋白结合蛋白28（FBP）的三重β链WW结构域的折叠动力学来考虑蛋白质折叠。从展开状态开始，在本地或非本地构象状态结束，轨迹生成与粗粒联合残留（UNRES）力场。主成分分析（PCA），一个已经建立的数学技术，寻找全球性的，相关的运动在原子模拟蛋白质的有效性，在这里评估粗粒度的轨迹。讨论了主成分分析的相关问题及其解决方法。蛋白质的折叠和非折叠与自由能景观检查。通过对不同温度下蛋白质折叠和非折叠轨迹的详细分析表明，PCA方法可以有效地表征蛋白质的一般折叠和非折叠特征。它示出的第一主成分捕捉和详细描述了系统的动态。异常扩散的折叠/非折叠动力学检查的均方位移，（MSD），分数扩散和分数动力学方程。多肽经历布朗运动沿着前几个主成分的无碰撞（或弹道）行为。
Protein folding is considered here by studying the dynamics of the folding of the triple β-strand WW domain from the Formin binding protein 28 (FBP). Starting from the unfolded state and ending either in the native or nonnative conformational states, trajectories are generated with the coarse-grained united residue (UNRES) force field. The effectiveness of principal component analysis (PCA), an already-established mathematical technique for finding global, correlated motions in atomic simulations of proteins, is evaluated here for coarse-grained trajectories. The problems related to PCA and their solutions are discussed. The folding and non-folding of proteins are examined with free energy landscapes. Detailed analyses of many folding and non-folding trajectories at different temperatures show that PCA is very efficient for characterizing the general folding and non-folding features of proteins. It is shown that the first principal component captures and describes in detail the dynamics of a system. Anomalous diffusion in the folding/non-folding dynamics is examined by the mean-square displacement, (MSD), and the fractional diffusion and fractional kinetic equations. The collision-less (or ballistic) behavior of a polypeptide undergoing Brownian motion along the first few principal components is accounted for.
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影响因子：
3.3
作者：
Khalili, M;Liwo, A;Scheraga, HA
通讯作者：
Scheraga, HA
影响因子：
4.4
作者：
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通讯作者：
Stock, Gerhard
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2.4
作者：
Hess, B
通讯作者：
Hess, B
影响因子：
56.9
作者：
FRAUENFELDER, H;SLIGAR, SG;WOLYNES, PG
通讯作者：
WOLYNES, PG
影响因子：
8.6
作者：
Hegger, Rainer;Altis, Alexandros;Stock, Gerhard
通讯作者：
Stock, Gerhard