Kuczera K, Lambry J C, Martin J L, Karplus M
Department of Chemistry, Harvard University, Cambridge, MA 02138.
Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5805-7. doi: 10.1073/pnas.90.12.5805.
Molecular dynamics simulations of myoglobin after ligand photodissociation show that the out-of-plane motion of the heme iron has a rapid subpicosecond phase followed by a slower nonexponential process involving more global protein relaxation. Individual trajectories show rather different behavior, suggesting there is an inhomogeneous component to the relaxation. The calculated time dependence of the iron motion over 100 ps is in excellent agreement with the frequency shift of band III of the heme group [see Lim, M., Jackson, T. A. & Anfinrud, P. A. (1993) Proc. Natl. Acad. Sci. USA 90, 5801-5804]. If that the barrier to rebinding depends on the out-of-plane iron position, the time dependence obtained from the simulation can explain the nonexponential room-temperature geminate recombination of NO.
配体光解离后肌红蛋白的分子动力学模拟表明，血红素铁的平面外运动会经历一个快速的亚皮秒阶段，随后是一个较慢的非指数过程，涉及更全局性的蛋白质弛豫。单个轨迹显示出相当不同的行为，这表明弛豫过程中存在不均匀成分。计算得到的铁运动在100皮秒内的时间依赖性与血红素基团III带的频移非常吻合[见Lim, M., Jackson, T. A. & Anfinrud, P. A. (1993) Proc. Natl. Acad. Sci. USA 90, 5801 - 5804]。如果再结合的势垒取决于平面外铁的位置，那么从模拟中得到的时间依赖性可以解释一氧化氮在室温下的非指数双分子复合。
