蛋白质折叠动力学无序与有序的比较研究
A Comparative Study of Disordered and Ordered Protein Folding Dynamics Using Computational Simulation
摘要：
折叠蛋白质动力学一直是一个领域的高度兴趣了相当一段时间，特别是考虑到越来越多的关注生物物理学领域。由于折叠动力学发生在如此短的时间尺度上，为更“静态”的蛋白质事件开发的经验技术，如X射线晶体学，核磁共振和绿色荧光蛋白（GFP）标记，并不适用。相反，必须经常使用计算方法来模拟这些短暂但高度动态的事件。分子动力学模拟（MD Simulation）就是这样一种计算方法，它被证明可以为蛋白质折叠动力学提供非常有价值的见解。这种模拟方法在计算上要求很高，但在蛋白质物理行为的建模方面非常准确。除了MD模拟之外，模拟通常在这些蛋白质事件的背景下非常适用。例如，简单的Gillespie算法，一种几乎可以在任何个人计算机上执行的计算技术，由于其计算简单，提供了相当强大的蛋白质动力学视图。本文将比较两种模拟的结果，一种是无序的六残基致癌蛋白质片段的MD模拟，另一种是基于Gillespie算法的有序折叠蛋白质的模拟：预测致癌蛋白质系统时间序列的确切行为的野生型的渐近随机双曲正切动力学的Gillespie算法时间序列的数学上相同的性质将显示计算功率模拟提供用于分析无序和有序的蛋白质系统。
英文摘要：
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for more "static" protein events, such as X-ray crystallography, nuclear magnetic resonance, and green fluorescent protein (GFP) labelling, aren't as applicable. Instead, computational methods must often be used to simulate these short lived yet highly dynamic events. One such computational method that is proven to provide much valuable insight into protein folding dynamics is Molecular Dynamics Simulation (MD Simulation). This simulation method is both highly computationally demanding, yet highly accurate in its modelling of a proteins physical behaviour. Besides MD Simulation, simulations in general are quite applicable in the context of these protein events. For example, the simple Gillespie algorithm, a computational technique which can be executed on almost any personal computer, provides quite the robust view into protein dynamics given its computational simplicity. This paper will compare the results of two simulations, an MD simulation of a disordered, six-residue, carcinogenic protein fragment, and a Gillespie algorithm based simulation of an ordered folding protein: the mathematically identical nature of the Gillespie algorithm time series of the asymptotically stochastic hyperbolic tangent dynamics for the wild type predicting the exact behaviour of the carcinogenic protein system time series will show the computational power simulations provide for analyzing both disordered and ordered protein systems.
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