Li Tanping, Hassanali Ali A, Singer Sherwin J
Biophysics Program and Department of Chemistry, Ohio State University, Columbus, Ohio, USA.
J Phys Chem B. 2008 Dec 18;112(50):16121-34. doi: 10.1021/jp803042u.
Molecular dynamics simulations are used to calculate the time-dependent Stokes shift following photoexcitation of Trp-7 (W7) in myoglobin. In agreement with experiment, a long time (approximately 60 ps) component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of photoexcitation, we firmly establish that protein flexibility is required to observe slow Stokes shift dynamics in this case. A transition between sub-states near the middle of a 30 ns ground-state trajectory gave us an opportunity to compare solvation dynamics in two different environments. While some of the superficial features are different, we find that the underlying dynamics are shared by the two isomers. It is necessary to look beyond a decomposition of the Stokes shift into protein and water contributions and probe the underlying dynamics of protein side groups, backbone, and water dynamics to obtain a full picture of the relaxation process. We analyze water residence times, diffusion, and reorientation dynamics in the hydration layer. We find slow components in each of these quantities and critically examine their origin and how they affect the observed Stokes shift.
分子动力学模拟用于计算肌红蛋白中色氨酸-7（W7）光激发后的时间相关斯托克斯位移。与实验结果一致，观察到一个长时间（约60皮秒）的分量。由于当我们在光激发瞬间将蛋白质冻结并重复计算时，长时间的斯托克斯位移分量不存在，我们坚定地确定在这种情况下观察到缓慢的斯托克斯位移动力学需要蛋白质的柔韧性。在30纳秒基态轨迹中间附近的亚态之间的转变为我们提供了一个机会来比较两种不同环境中的溶剂化动力学。虽然一些表面特征不同，但我们发现两种异构体的潜在动力学是相同的。有必要超越将斯托克斯位移分解为蛋白质和水的贡献，深入探究蛋白质侧链基团、主链和水动力学的潜在动力学，以全面了解弛豫过程。我们分析了水在水化层中的停留时间、扩散和重新取向动力学。我们在这些量中都发现了缓慢的分量，并严格检查它们的来源以及它们如何影响观察到的斯托克斯位移。
