The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
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DOI：
10.1063/1.473299
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发表时间：
1997-01-22
影响因子：
4.4
通讯作者：
Karplus, M
中科院分区：
文献类型：
--
作者：
Becker, OM;Karplus, M
探讨了多维势能面的拓扑特征，并将全构象空间映射到局部极小点集上。该映射将构象空间划分为能量依赖或温度依赖的“吸引盆地”，并生成反映盆地连通性和表征多维表面形状的“不连通性”图。构造空间的分区是用来表示的时间行为的系统在盆地到盆地的动力学，而不是通常的状态到状态的转换。为此，系统的过渡矩阵表示在盆地到盆地的过渡和相应的主方程求解。例如，该方法应用于四肽，异丁酰基-（ala）（3）-NH-甲基（IAN），其是可以形成完整螺旋转角的最短肽。从Czerminiski和Elber的工作中，可以获得这个系统的几乎完整的最小值和障碍列表。肽的多维势能面显示出整体的“漏斗”形状。研究了二面角空间中连通性与空间邻近性之间的关系。据发现，虽然两者是相似的，在一个接近并不总是意味着在另一个接近。盆地到盆地的动力学检查使用主方程和动力学连通性方面的结果进行解释。肽的构象空间根据表面形貌进行划分，以模拟其“折叠"行为。即使在这个非常简单的系统中，动力学也表现出一种“捕获”状态，它表现为一种“动力学中间体”，就像蛋白质折叠一样。本文所述的方法可更普遍地用于复杂系统的多维势能面和时间发展的分类。(C)1997年美国物理学会。
Topological characteristics of multidimensional potential energy surfaces are explored and the full conformation space is mapped on the set of local minima. This map partitions conformation space into energy-dependent or temperature-dependent ''attraction basins'' and generates ''disconnectivity'' graph that reflects the basin connectivity and characterizes the shape of the multidimensional surface. The partitioning of the conformation space is used to express the temporal behavior of the system in terms of basin-to-basin kinetics instead of the usual state-to-state transitions. For this purpose the transition matrix of the system is expressed in terms of basin-to-basin transitions and the corresponding master equation is solved. As an example, the approach is applied to the tetrapeptide, isobutyryl-(ala)(3)-NH-methyl (IAN), which is the shortest peptide that can form a full helical turn. A nearly complete List of minima and barriers is available for this system from the work of Czerminiski and Elber. The multidimensional potential energy surface of the peptide is shown to exhibit an overall ''funnel'' shape. The relation between connectivity and spatial proximity in dihedral angle space is examined. It is found that, although the two are similar, closeness in one does not always imply closeness in the other. The basin to basin kinetics is examined using a master equation and the results are interpreted in terms of kinetic connectivity. The conformation space of the peptide is divided up in terms of the surface topography to model its ''folding'' behavior. Even in this very simple system, the kinetics exhibit a ''trapping'' state which appears as a ''kinetic intermediate,'' as in the folding of proteins. The approach described here can be used more generally to classify multidimensional potential energy surface sand the time development of complex systems. (C) 1997 American Institute of Physics.