Dynamics of essential collective motions in proteins: Theory
Dynamics of essential collective motions in proteins: Theory
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DOI：
10.1103/physreve.76.051918
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发表时间：
2007-11-01
影响因子：
2.4
通讯作者：
Stepanova, Maria
中科院分区：
文献类型：
--
作者：
Stepanova, Maria
介绍了蛋白质分子构象运动表征的一般理论背景，以及基于其相轨迹的统计分析构建蛋白质的简化粗粒度模型。利用投影算子技术，对分子动力学轨迹的主成分分析得到的基本集体坐标导出了一组耦合广义朗之万方程。基本自由度的个数在理论上是不受限制的。建立了基本集体坐标的广义朗之万方程与基本集体自由度子空间上全原子相轨迹的广义朗之万方程的显式解析关系。所介绍的理论被应用于识别大分子中的相关动态域，并构建粗粒度模型，通过嵌入在耗散介质中的几个相互作用域来表示蛋白质中的构象运动。为大分子中动态相关结构域的识别提供了严格的理论背景。给出了G蛋白结构域识别的实例，并应用于核磁共振实验的解释。讨论了该理论的挑战和潜在结果。
A general theoretical background is introduced for characterization of conformational motions in protein molecules, and for building reduced coarse-grained models of proteins, based on the statistical analysis of their phase trajectories. Using the projection operator technique, a system of coupled generalized Langevin equations is derived for essential collective coordinates, which are generated by principal component analysis of molecular dynamic trajectories. The number of essential degrees of freedom is not limited in the theory. An explicit analytic relation is established between the generalized Langevin equation for essential collective coordinates and that for the all-atom phase trajectory projected onto the subspace of essential collective degrees of freedom. The theory introduced is applied to identify correlated dynamic domains in a macromolecule and to construct coarse-grained models representing the conformational motions in a protein through a few interacting domains embedded in a dissipative medium. A rigorous theoretical background is provided for identification of dynamic correlated domains in a macromolecule. Examples of domain identification in protein G are given and employed to interpret NMR experiments. Challenges and potential outcomes of the theory are discussed.