Nano-Biotechnology Department, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
Department of Genetics and Advanced Medical Technology, Medical Biotechnology Research Center, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran.
J Mol Graph Model. 2018 Sep;84:43-53. doi: 10.1016/j.jmgm.2018.06.009. Epub 2018 Jun 9.
Recently protein engineering has been used as a pivotal tool for designing proteins with improved characteristics. While the experimental methods might be laborious and time-consuming, in silico protein design is a time and cost-effective approach. Moreover, in some cases, protein modeling might be the only way to obtain structural information where the experimental techniques are inapplicable. Molecular dynamics (MD) simulation is a method that allows the motion of protein to be simulated in defined conditions on the basis of classical molecular dynamics. MD simulation could widely be used when protein design needs accurate modeling of the target protein dynamics and also descriptions of the relation between conformational changes and function of protein at the atomic level. In this review, the effectiveness and the power of MD simulation in designing proteins with improved characteristics will be discussed.
最近，蛋白质工程已被用作设计具有改良特性的蛋白质的关键工具。虽然实验方法可能繁琐且耗时，但计算蛋白质设计是一种节省时间和成本的方法。此外，在某些情况下，蛋白质建模可能是获得实验技术不适用的结构信息的唯一方法。分子动力学 (MD) 模拟是一种方法，它可以根据经典分子动力学在定义的条件下模拟蛋白质的运动。当蛋白质设计需要准确建模目标蛋白质动力学并描述构象变化与蛋白质原子水平功能之间的关系时，MD 模拟可以广泛使用。在本文综述中，将讨论 MD 模拟在设计具有改良特性的蛋白质方面的有效性和强大功能。
