Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.
Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.
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DOI：
10.1021/jp2119247
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发表时间：
2012-07-26
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通讯作者：
Ortoleva PJ
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作者：
Singharoy A;Joshi H;Miao Y;Ortoleva PJ
大分子组装体的粗粒度特征是通过一组有序参数（OP）来理解的，这些有序参数是根据它们的全原子构型来构造的。OP被证明是缓慢变化的时间和捕获大规模的空间功能的大分子组装。这些变量的经典概念的对称性破缺相变的基础上的OP的关系进行了讨论。详细分析了基于空间扭曲变换的OP，因为它们自然地提供了组装体的整体结构与全原子配置之间的连接。这些OP作为多尺度分析的基础，产生OP动力学的Langevin方程。在此背景下，OP和PCA模式的特性进行了比较。的OP使有效的全原子多尺度模拟响应微环境条件的变化，大分子组件的动力学，表现在豇豆褪绿斑驳病毒衣壳（CCMV）和RNA的卫星烟草花叶病毒（STMV）的结构转变。
Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of these variables to the classic notion of OPs based on symmetry breaking phase transitions is discussed. OPs based on space warping transformations are analyzed in detail as they naturally provide a connection between overall structure of an assembly and all-atom configuration. These OPs serve as the basis of a multiscale analysis that yields Langevin equations for OP dynamics. In this context, the characteristics of OPs and PCA modes are compared. The OPs enable efficient all-atom multiscale simulations of the dynamics of macromolecular assemblies in response to changes in microenvironmental conditions, as demonstrated on the structural transitions of cowpea chlorotic mottle virus capsid (CCMV) and RNA of the satellite tobacco mosaic virus (STMV).