How complex is the dynamics of peptide folding?
How complex is the dynamics of peptide folding?
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DOI：
10.1103/physrevlett.98.028102
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发表时间：
2007-01-12
影响因子：
8.6
通讯作者：
Stock, Gerhard
中科院分区：
文献类型：
--
作者：
Hegger, Rainer;Altis, Alexandros;Stock, Gerhard
经典的分子动力学模拟的丙氨酸肽在水溶液中的折叠进行了分析，通过构建一个确定性的动力学模型，使用非线性时间序列分析的方法。虽然自由能景观的维度随着系统尺寸的增加而增加，但李雅普诺夫分析表明动力系统的有效维度相当小，甚至随着链长的增加而减少。所观察到的相空间的减少是由稳定肽的二级结构的分子内氢键引起的非线性协同效应。
Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with system size, a Lyapunov analysis shows that the effective dimension of the dynamic system is rather small and even decreases with chain length. The observed reduction of phase space is a nonlinear cooperative effect that is caused by intramolecular hydrogen bonds that stabilize the secondary structure of the peptides.