Tournier Alexander L, Xu Jiancong, Smith Jeremy C
Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, 69120 Heidelberg, Germany.
Biophys J. 2003 Sep;85(3):1871-5. doi: 10.1016/S0006-3495(03)74614-1.
Experimental and computer simulation studies have revealed the presence of a glass-like transition in the internal dynamics of hydrated proteins at approximately 200 K involving an increase of the amplitude of anharmonic dynamics. This increase in flexibility has been correlated with the onset of protein activity. Here, we determine the driving force behind the protein transition by performing molecular dynamics simulations of myoglobin surrounded by a shell of water. A dual heat bath method is used with which, in any given simulation, the protein and solvent are held at different temperatures, and sets of simulations are performed varying the temperature of the components. The results show that the protein transition is driven by a dynamical transition in the hydration water that induces increased fluctuations primarily in side chains in the external regions of the protein. The water transition involves activation of translational diffusion and occurs even in simulations where the protein atoms are held fixed.
实验和计算机模拟研究表明，水合蛋白质内部动力学在约200 K时存在类似玻璃态的转变，涉及非谐动力学振幅的增加。这种灵活性的增加与蛋白质活性的开始相关。在此，我们通过对被水壳包围的肌红蛋白进行分子动力学模拟，确定蛋白质转变背后的驱动力。使用双热浴方法，在任何给定模拟中，蛋白质和溶剂保持在不同温度，并进行多组模拟来改变各组分的温度。结果表明，蛋白质转变是由水合水的动力学转变驱动的，这主要导致蛋白质外部区域侧链的波动增加。水的转变涉及平动扩散的激活，甚至在蛋白质原子保持固定的模拟中也会发生。
