The Infrared Spectra of the Retinal Chromophore in Bacteriorhodopsin Calculated by a DFT/MM Approach
The Infrared Spectra of the Retinal Chromophore in Bacteriorhodopsin Calculated by a DFT/MM Approach
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DOI：
10.1021/jp902432e
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发表时间：
2009-07-30
影响因子：
3.3
通讯作者：
Tavan, P.
中科院分区：
文献类型：
--
作者：
Babitzki, G.;Mathias, G.;Tavan, P.
在前一篇论文(DOI 10.1021/JP902428x)中，我们用密度泛函理论和分子力学模型相结合的混合方法推导了细菌视紫红质(BR)的极化力场。这种极化的力场使得对BR的生色团结合口袋的扩展分子动力学(MD)模拟成为可能，从而紧密地保留了实验上众所周知的结构。在这里，我们使用在生理温度下普遍存在的构象亚态的PBR-MD轨迹作为DFT/MM计算生色团振动光谱的材料。通过对一个分离的发色团的结构和振动光谱的密度泛函分析结果的比较，我们确定了蛋白质环境引起的结构和光谱的变化。与文献中关于生色团振动光谱的丰富实验数据进行比较，可以估计DFT/MM描述的准确性。我们讨论了为什么高精度的DFT/MM描述有望成为解决光驱动质子泵BR实际如何工作的长期谜团的决定性工具。
In the preceding paper (DOI 10.1021/jp902428x), we have derived the polarized force field "PBR" for bacteriorhodopsin (BR) using hybrid methods which combine density functional theory (DFT) with molecular mechanics (MM) models. This polarized force field has enabled extended molecular dynamics (MD) simulations of BR's chromophore binding pocket which closely preserve the experimentally well-known structure. Here, we employ the PBR-MD trajectories obtained for the conformational substates prevalent at physiological temperatures as material for the DFT/MM computation of the chromophore's vibrational spectra. By comparison with DFT results on the structure and vibrational spectra of an isolated chromophore, we identify the structural and spectral changes induced by the protein environment. Comparisons with the wealth of experimental data available in the literature on the chromophore's vibrational spectra yield estimates on the accuracy of the DFT/MM descriptions. We discuss why highly accurate DFT/MM. descriptions are expected to become a decisive tool for solving the long-standing enigma of how the light-driven proton pump BR actually works.