Lin Bingbing, Gao Ya, Li Yongxiu, Zhang John Z H, Mei Ye
Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China.
J Mol Model. 2014 Apr;20(4):2189. doi: 10.1007/s00894-014-2189-5. Epub 2014 Mar 27.
Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.
在过去几年中，时间分辨超快荧光光谱法已被应用于蛋白质动力学的研究。然而，这些实验的观察结果与其他实验研究存在争议。理论方法参与这场辩论并未调和这一矛盾，因为计算机模拟预测的初始弛豫比超快荧光光谱实验快一个数量级。在那些模拟中，采用了成对力场，结果表明这种力场会低估自由能景观的粗糙度。因此，成对力场下蛋白质和水分子的弛豫速率被错误地夸大了。在这项工作中，我们在采用成对、极化和可极化力场的线性响应近似下比较了色氨酸/环境相互作用的弛豫情况。结果表明，尽管弛豫可以在一定程度上减慢，但实验与理论之间的巨大差距仍然无法填补。
