Efficiency of the local torsional deformations method for identifying the stable structures of cyclic molecules
Efficiency of the local torsional deformations method for identifying the stable structures of cyclic molecules
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DOI：
10.1021/jp9627537
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发表时间：
1997-03-13
影响因子：
2.9
通讯作者：
Meirovitch, H
中科院分区：
文献类型：
--
作者：
Baysal, C;Meirovitch, H
我们最近提出了一种产生链状分子低能结构的新方法。这是一个随机过程，在每个步骤中，通过沿链进行几个局部扭转变形(LTD)来改变能量最小化的结构，这些局部扭转变形暂时破坏了旋转键的邻居。然后能量被最小化，被破坏的键返回到它们通常的几何形状(根据键的长度和角度)，而链呈现新的构象。这种构象被接受(然后变形)或被拒绝，借助于优先接受较低能量结构并将搜索引向包括全局能量最小(GEM)结构的最低能量区域的“选择过程”。被测试的选择程序是Li和Scheraga的蒙特卡罗最小化(MCM)方法和Sist的小组的使用指导(UD)方法。LTD是一种通用的方法，其参数可以对任何链条系统进行优化。然而，由于构象变化的局部性，它有望对环肽、蛋白质中的环和致密的多链系统特别有效。本文将LTD方法应用于环十七烷的MM2力场模拟，并对其参数进行了优化，结果表明该方法比其他方法更有效。对该分子和线性五肽亮氨酸脑啡肽的ECEPP模型的结果表明，MCM和UD的效率几乎相当，但MCM略有优势。
A new method for generating the low-energy structures of a chain molecule was proposed recently by us. This is a stochastic process where at each step an energy-minimized structure is changed by carrying out several local torsional deformations (LTDs) along the chain, which temporarily disrupt neighbors of the rotated bonds. The energy is then minimized and the disrupted bonds return to their usual geometry (in terms of bond lengths and angles) while the chain assumes a new conformation. This conformation is accepted (and then deformed) or rejected with the help of a ''selection procedure'' that gives preference to accepting the lower energy structures and, thug, directs the search toward the lowest energy regions, which include the global energy minimum (GEM) structure. The selection procedures tested are the Mont Carlo minimization (MCM) method of Li and Scheraga and the ''usage directed'' (UD) method of Still's group. LTD is a general method whose parameters can be optimized for any chain system. However, because of the local character of the conformational change, it is expected to be especially efficient for cyclic peptides, loops in proteins, and dense multichain systems. In this paper, LTD is applied to cycloheptadecane modeled by the MM2 force field, its parameters are optimized, and it is found to be more efficient than other methods. The results for this molecule and for an ECEPP model of the linear pentapeptide Leu-enkephalin show that MCM and UD are almost comparable in efficiency, with a slight advantage for MCM.