An approximate DFT method for QM/MM simulations of biological structures and processes
An approximate DFT method for QM/MM simulations of biological structures and processes
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DOI：
10.1016/s0166-1280(03)00286-0
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发表时间：
2003-08-01
影响因子：
--
通讯作者：
Suhai, S
中科院分区：
文献类型：
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作者：
Elstner, M;Frauenheim, T;Suhai, S
在过去的几年里，我们已经开发了一个计算效率高的近似密度泛函理论，所谓的自洽电荷密度泛函紧束缚计划（SCC-DFTB）。为了将其适用性扩展到生物分子结构，这种方法已被实施到量子力学/分子力学（QM/MM）和线性缩放计划，并增加了经验处理的色散力。本文综述了SCC-DFTB QM/MM方法在肝醇脱氢酶和磷酸丙糖异构酶等酶的质子转移反应中的应用。SCC-DFTB的计算速度不仅允许计算PT的最小能量路径，还允许计算平均力的潜力。进一步的应用涉及溶液中多肽的动力学以及其生物环境中配体的动力学。审查的发展允许第一次现实的QM模拟多肽，蛋白质和DNA十二聚体在纳秒的时间尺度。(C)2003 Elsevier B. V.保留所有权利。
In the last years, we have developed a computationally efficient approximation to density functional theory, the so called self-consistent charge density functional tight-binding scheme (SCC-DFTB). To extend its applicability to biomolecular structures, this method has been implemented into quantum mechanical/molecular mechanics (QM/MM) and linear scaling schemes and augmented with an empirical treatment of the dispersion forces. We review here applications of the SCC-DFTB QM/MM method to proton transfer (PT) reactions in enzymes like liver alcohol dehydrogenase and triosephosphate isomerase. The computational speed of SCC-DFTB allows not only to compute minimum energy pathways for the PT but also the potential of mean force. Further applications concern the dynamics of polypeptides in solution and of ligands in their biological environment. The developments reviewed allowed for the first time realistic QM simulations of polypeptides, a protein and a DNA dodecamer in the nanosecond time scale. (C) 2003 Elsevier B.V. All rights reserved.