Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics
Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics
复制标题
DOI：
10.1007/s12195-009-0084-4
复制
发表时间：
2009-09-01
影响因子：
2.8
通讯作者：
Delp, Scott L.
中科院分区：
文献类型：
--
作者：
Parker, David;Bryant, Zev;Delp, Scott L.
需要实验和计算方法来揭示分子马达将化学能转化为机械功的机制。在本文中，我们描述了生成与不同来源的实验数据兼容的分子运动构象的结构真实模型的方法和软件。分子结构的粗粒度模型是通过将原子组组合成由关节连接的刚体系统来构建的。刚体之间的接触强制排除体积约束，弹簧势对系统弹性进行建模。这种简化的表示允许交互式模拟复杂分子马达的构象，为模型和实验之间的假设建立和定量比较提供工具。在示例计算中，我们使用该软件构建了与其肌动蛋白轨道结合的肌球蛋白 V 分子马达的原子详细模型。该软件可从 http://www.simtk.org 获取”。
Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at http://www.simtk.org".