Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide
Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide
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DOI：
10.1063/1.4764868
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发表时间：
2012-11-21
影响因子：
4.4
通讯作者：
Rao, Francesco
中科院分区：
文献类型：
--
作者：
Berezovska, Ganna;Prada-Gracia, Diego;Rao, Francesco
分子模拟以及单分子实验已在有序参数方面得到了广泛的分析，后者代表了相关自由度的候选探针。尽管这种方法非常直观，但越来越多的证据表明这种描述是不准确的，导致状态定义不明确和动力学错误。为了克服这些限制，研究了一种利用阶次参数波动与复杂网络分析相结合的框架。这种方法源自单分子时间轨迹分析的最新进展，考虑了每个时间点周围的波动，以区分具有相似序参数值但不同动力学的状态。具有相似波动的快照被用作转换网络的节点，其状态的聚类提供了所研究系统的准确的马尔可夫状态模型。该方法应用于具有噪声有序参数的理论模型以及无序肽的动力学，说明了仅在有序参数时间序列的基础上建立分子过程的准确描述而不使用任何补充信息的可能性。 (C) 2012 年美国物理研究所。 [http://dx.doi.org/10.1063/1.4764868]
Molecular simulations as well as single molecule experiments have been widely analyzed in terms of order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive, mounting evidence showed that such descriptions are inaccurate, leading to ambiguous definitions of states and wrong kinetics. To overcome these limitations a framework making use of order parameter fluctuations in conjunction with complex network analysis is investigated. Derived from recent advances in the analysis of single molecule time traces, this approach takes into account the fluctuations around each time point to distinguish between states that have similar values of the order parameter but different dynamics. Snapshots with similar fluctuations are used as nodes of a transition network, the clusterization of which into states provides accurate Markov-state-models of the system under study. Application of the methodology to theoretical models with a noisy order parameter as well as the dynamics of a disordered peptide illustrates the possibility to build accurate descriptions of molecular processes on the sole basis of order parameter time series without using any supplementary information. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4764868]