McCammon J A, Karplus M
Proc Natl Acad Sci U S A. 1979 Aug;76(8):3585-9. doi: 10.1073/pnas.76.8.3585.
A procedure for the dynamical simulation of activated processes, such as ligand binding and enzymatic reactions, in a globular protein is outlined. Preliminary calculations of the transition state geometry and barrier crossing trajectories are presented for a model reaction, the rotation of an aromatic ring in the bovine pancreatic trypsin inhibitor. The results show that repulsive nonbonded interactions between the ring atoms and the atoms in the surrounding protein matrix determine the dynamical character of the reorientation process; the nonbonded interactions are the source of the rotational barrier and of the impulses that speed up or slow down the ring motion during the barrier crossings.
概述了一种用于动态模拟球状蛋白质中活化过程（如配体结合和酶促反应）的程序。针对一个模型反应——牛胰蛋白酶抑制剂中芳香环的旋转，给出了过渡态几何结构和越过势垒轨迹的初步计算结果。结果表明，环原子与周围蛋白质基质中的原子之间的排斥性非键相互作用决定了重新定向过程的动力学特征；非键相互作用是旋转势垒以及在越过势垒过程中加速或减慢环运动的冲量的来源。
