Molecular dynamics simulations of biological reactions.
Molecular dynamics simulations of biological reactions.
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生物反应的分子动力学模拟。
DOI：
10.1021/ar010033z
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发表时间：
2002
影响因子：
18.3
通讯作者：
Warshel,Arieh
中科院分区：
文献类型：
--
作者：
Warshel,Arieh
本文综述了作者对生物过程分子动力学（MD）模拟出现的看法。它始于1976年对视紫红质中主要事件的模拟，然后是对酶反应和电子转移反应的最早模拟，最后是对蛋白质中质子易位和离子转运的最新模拟。重点放在我们在模拟实际生物反应和功能特性方面的进展，而不是对结构和热运动等一般性质的研究。在大多数情况下，已经有可能制定特殊的战略，捕捉特定生物过程的相关动态。指出了我们早期对快速生物过程（如视觉和光合作用）的模拟的预测能力以及从这些研究中获得的见解。综述了不同生物过程中动力学效应的重要研究。这包括动力学效应不太可能对酶催化或其他具有显著活化障碍的过程有显著贡献的发现。即使在离子通道的情况下，它被发现，最重要的影响是与能量，而不是动态。然而，MD模拟提供了可能是最真实的描述实际反应事件。由此产生的洞察力是至关重要的快速光生物学反应的研究和指导的情况下，较慢的过程。
This review considers the author perspective on the emergence of molecular dynamics (MD) simulations of biological processes. It starts with the 1976 simulation of the primary event in rhodopsin, moves to the earliest simulations of enzymatic reactions and electron transfer reactions and ends up with recent simulations of proton translocations and ion transport in proteins. The emphasis is placed on our progress in simulations of actual biological reactions and functional properties, rather than on studies of general properties such as structure and thermal motions. In most cases it has been possible to develop special strategies that capture the relevant dynamics of the given biological process. The predictive power of our early simulations of fast biological process (e.g. vision and photosynthesis) and the insight obtained from these studies is pointed out. Critical examinations of dynamical effects in different biological processes is reviewed. This includes the finding that dynamical effects are unlikely to contribute significantly to enzyme catalysis or to other processes with significant activation barriers. Even in the case of ion channels it is found that the most important effects are associated with energetics rather than dynamics. Nevertheless, MD simulations provide what is probably the most realistic description of the actual reactive events. The resulting insight is crucial in studies of fast photobiological reactions and instructive in cases of slower processes.