Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics
Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics
复制标题
DOI：
10.1016/j.chemphys.2011.08.021
复制
发表时间：
2012-03-02
期刊：
影响因子：
2.3
通讯作者：
Noe, Frank
中科院分区：
文献类型：
--
作者：
Keller, Bettina G.;Prinz, Jan-Hendrik;Noe, Frank
生物分子的平衡动力学可以通过诸如温度跳跃或荧光相关光谱的技术来探测。这些测量可以通过动态指纹来描述，即，弛豫时间尺度的密度，其中每个峰对应于指数弛豫过程。在许多情况下，单峰或双峰指纹被发现，表明一个两个或三个状态的模型可以提供一个令人满意的描述研究的生物分子，而模拟往往揭示了一个更复杂的图片与许多动力学相关的状态。在这里，我们勾勒出一个方法相结合的马尔可夫模型的模拟动力学与动态指纹之间的链接仿真和实验。这种联系揭示了实验装置和实验对特定动力学过程的敏感性之间的关系。此外，我们的方法可以用来设计实验，使特定的过程出现大幅度。通过回顾荧光18-mer肽MR 121-（GS）（9）-W的分析的最新结果来说明这一点。(C)2011爱思唯尔有限公司版权所有。
The equilibrium kinetics of biomolecules can be probed by techniques such as temperature-jump or fluorescence correlation spectroscopy. These measurements can be described by dynamical fingerprints, i.e., densities of relaxation timescales where each peak corresponds to an exponential relaxation process. In many cases, single-or double-peaked fingerprints are found, suggesting that a two-or three-state model may provide a satisfactory description of the biomolecule studied, while simulations often reveal a more complex picture with many kinetically relevant states. Here we sketch an approach combining Markov models of the simulated dynamics with dynamical fingerprints to link between simulation and experiment. This link sheds light on the relation between experimental setup and sensitivity of the experiment to particular kinetic processes. Furthermore, our approach can be used to design experiments such that specific processes appear with large amplitudes. This is illustrated by reviewing recent results from the analysis of the fluorescent 18-mer peptide MR121-(GS)(9)-W. (C) 2011 Elsevier B.V. All rights reserved.