McCammon J A, Wolynes P G, Karplus M
Biochemistry. 1979 Mar 20;18(6):927-42. doi: 10.1021/bi00573a001.
To probe the details of small amplitude motions in proteins, a dynamical analysis of the orientation fluctuations of two tyrosine side chains in the bovine pancreatic trypsin inhibitor is presented. Detailed results are given for the time history and correlation functions obtained for the ring motion from a molecular dynamics simulation of the entire protein. It is shown that even on a picosecond time scale orientational fluctuations of +/-30 degrees from the average position occur for the tyrosine rings in the interior of the protein. It is found that the Langevin equation is applicable to the ring torsional motion, which corresponds to that of an angular harmonic oscillator with near-critical damping. Two possible microscopic models for the observed damping effects are outlined. One of these, analogous to liquid behavior, is based on kinetic theory and takes account of the collisions which occur between atoms of the protein; the other, more analogous to solid behavior, involves the coupling among a large number of harmonic oscillators. The collisional model with parameters obtained from theoretical estimates leads to good agreement with the correlation functions from the dynamic simulation. However, the dephasing of harmonic oscillations can yield similar short-time results so that a distinction between the two models is difficult. The importance of damping effects on the motions involved in conformational transitions and enzymatic reactions is discussed.
为了探究蛋白质中小幅度运动的细节，本文对牛胰蛋白酶抑制剂中两个酪氨酸侧链的取向涨落进行了动力学分析。给出了从整个蛋白质的分子动力学模拟中获得的环运动的时间历程和相关函数的详细结果。结果表明，即使在皮秒时间尺度上，蛋白质内部酪氨酸环相对于平均位置也会出现±30度的取向涨落。研究发现，朗之万方程适用于环扭转运动，该运动对应于具有近临界阻尼的角谐振荡器的运动。概述了两种可能的微观模型来解释观察到的阻尼效应。其中一种类似于液体行为，基于动力学理论并考虑了蛋白质原子之间发生的碰撞；另一种更类似于固体行为，涉及大量谐振荡器之间的耦合。用理论估计得到的参数的碰撞模型与动态模拟的相关函数结果吻合良好。然而，谐振荡的去相移也能产生类似的短期结果，因此很难区分这两种模型。文中还讨论了阻尼效应在构象转变和酶促反应所涉及的运动中的重要性。
