Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules
Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules
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DOI：
10.1021/ct800489r
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发表时间：
2009-05-01
影响因子：
5.5
通讯作者：
Waroquier, M.
中科院分区：
文献类型：
--
作者：
Ghysels, A.;Van Speybroeck, V.;Waroquier, M.
在早期的工作中，作者开发了一种新方法，即移动块 Hessian (MBH) 方法，可以准确计算部分优化的分子结构的振动模式 [J.化学。物理。 2007, 126(22), 224102.]。它基于引入由原子团组成的块，可以像刚体一样移动。嵌段的内部几何形状不需要对应于总分子结构的整体优化状态。标准 MBH 方法考虑具有六个自由度的自由块。在本文介绍的扩展MBH方法中，块可以通过一或两个相邻原子连接，这进一步减少了自由度的数量。新方法为蛋白质等生物分子的常模分析铺平了道路。它基于这样的假设：蛋白质的低频模式可以描述为连续氨基酸残基块的纯刚体运动。该方法针对一系列小分子进行了验证，并进一步应用于丙氨酸二肽作为原型来描述两个肽单元之间的振动相互作用； Crambin，一种含有 46 个氨基酸残基的小蛋白质；以及 ICE/caspase-1，其包含 518 个氨基酸残基。
In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102.]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.