Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.
Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.
复制标题
使用驱动分子动力学方法进行简正模态分析。
DOI：
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发表时间：
2004
影响因子：
4.4
通讯作者：
J. Bowman
中科院分区：
文献类型：
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作者：
Martina Kaledin;Alex Brown;A. Kaledin;J. Bowman
最近由Bowman、Zhang和Brown [J. Chem. Phys. 119，646（2003）]提出的驱动分子动力学（DMD）方法已经被实施到TINKER分子模拟程序包中。DMD方法产生的频率和正常模式没有评估的海森矩阵。它采用了一个外部的谐波驱动项，可以用来扫描频谱，并确定谐振频率。在共振频率下驱动引起的分子运动对应于简正模振动。在目前的工作中，我们将该方法应用于Neidigh、Fesinmeyer和Andersen [Nature Struct.Biol.9，425（2002）]报道的20个残基的蛋白质Trp-笼。该分子的结构和动力学性质，如B因子，均方根波动，各向异性，振动熵，和互相关系数，使用DMD方法计算。计算结果与标准简正波分析方法的计算结果吻合得很好。因此，DMD方法提供了一个可行的替代标准的海森为基础的方法，并具有相当大的潜力的大型系统的研究，海森为基础的方法是不可行的。
The driven molecular-dynamics (DMD) method, recently proposed by Bowman, Zhang, and Brown [J. Chem. Phys. 119, 646 (2003)], has been implemented into the TINKER molecular modeling program package. The DMD method yields frequencies and normal modes without evaluation of the Hessian matrix. It employs an external harmonic driving term that can be used to scan the spectrum and determine resonant absorptions. The molecular motions, induced by driving at resonant frequencies, correspond to the normal-mode vibrations. In the current work we apply the method to a 20-residue protein, Trp-cage, that has been reported by Neidigh, Fesinmeyer, and Andersen [Nature Struct. Biol. 9, 425 (2002)]. The structural and dynamical properties of this molecule, such as B-factors, root-mean square fluctuations, anisotropies, vibrational entropy, and cross-correlations coefficients, are calculated using the DMD method. The results are in very good agreement with ones calculated using standard normal-mode analysis method. Thus, the DMD method provides a viable alternative to the standard Hessian-based method and has considerable potential for the study of large systems, where the Hessian-based method is not feasible.