Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.
Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.
复制标题
DOI：
10.1021/ct200574x
复制
发表时间：
2012-04-10
影响因子：
5.5
通讯作者：
Ortoleva, Peter J.
中科院分区：
文献类型：
--
作者：
Singharoy, Abhishek;Sereda, Yuriy;Ortoleva, Peter J.
大分子组件通常显示大分子或其子组件的分层组织。为了模拟这一点，我们制定了一种空间翘曲方法，可以通过一组粗粒度顺序参数（OPs）捕获整体大分子结构和动力学。本文是描述另一类OPs的构造和计算实现的两篇文章中的第一篇，这些OPs内置了大分子组装的层次结构。为了实现这一点，首先，将系统划分为子系统，每个子系统都通过一组具有代表性的OPs进行描述。然后，从这些以子系统为中心的OPs构建一个全局变量集，以捕获整个系统组织。将所得OPs的动力学特性与之前的非分层OPs进行了比较，并讨论了100ns， 200万原子溶剂化的人乳头瘤病毒样粒子模拟的隐含概念和计算优势。在第二篇文章中，分层OPs被证明能够从n原子Liouville方程开始进行多尺度分析，并产生随机OP动力学的严格朗之万方程。后者是通过一个基于力场的模拟算法来证明的，该算法探测了关键的结构转变途径，同时考虑了全原子细节和整体结构。
Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure.
登录
查看更多内容
影响因子：
3
作者：
Patel, S;Brooks, CL
通讯作者：
Brooks, CL
DOI：
10.1016/j.pbiomolbio.2011.07.006
发表时间：
2011-10
影响因子：
3.8
作者：
Joshi H;Singharoy A;Sereda YV;Cheluvaraja SC;Ortoleva PJ
通讯作者：
Ortoleva PJ
影响因子：
3
作者：
Miao, Yinglong;Ortoleva, Peter J.
通讯作者：
Ortoleva, Peter J.
DOI：
10.1002/prot.340230207
发表时间：
1995-10-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
HAYWARD, S;KITAO, A;GO, N
通讯作者：
GO, N
影响因子：
4.4
作者：
Miao, Yinglong;Ortoleva, Peter
通讯作者：
Ortoleva, Peter