Hegger Rainer, Altis Alexandros, Nguyen Phuong H, Stock Gerhard
Institute of Physical and Theoretical Chemistry, J.W. Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany.
Phys Rev Lett. 2007 Jan 12;98(2):028102. doi: 10.1103/PhysRevLett.98.028102.
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.
通过构建动力学的确定性模型，并使用非线性时间序列分析方法，对丙氨酸肽在水溶液中折叠的经典分子动力学模拟进行了分析。虽然自由能景观的维度随系统大小增加，但李雅普诺夫分析表明，动态系统的有效维度相当小，甚至随链长减小。观察到的相空间缩减是一种非线性协同效应，由稳定肽二级结构的分子内氢键引起。
