Quantum mechanical studies on the crystallographic model of bathorhodopsin.
Quantum mechanical studies on the crystallographic model of bathorhodopsin.
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DOI：
10.1002/anie.200600585
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发表时间：
2006-06
影响因子：
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通讯作者：
M. Schreiber;M. Sugihara;T. Okada;V. Buss
中科院分区：
文献类型：
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作者：
M. Schreiber;M. Sugihara;T. Okada;V. Buss
视紫红质是脊椎动物眼睛中调节明/暗视觉的色素。在光激发后，视紫红质的发色团11-顺式-视黄醛在极快的反应中异构化形成全反式异构体，从而开始一系列黑暗事件，最终达到蛋白质的信号状态并激活视觉级联。形成的第一个光产物，光视紫红质，是在200 fs内完成，并捕获超过50%的光子能量，这是在随后的事件中消耗。在几皮秒内，光视紫红质弛豫为视紫红质，视紫红质是视紫红质光循环的第一个热平衡中间体，并且可以在低温下被捕获。[1，2]前一篇论文报道了该中间体的第一次晶体学分析。[3]主要的改变被发现是从扭曲的11-顺式形式的视紫红质的扭曲的全反式形式的生色团的构型变化，与显色团的环境中的明显的，但较小的变化。理论计算可以帮助评估和改进蛋白质X射线数据。由于在精制过程中使用标准计算机软件，蛋白质基质的建模通常是可靠的。活性中心的处理，例如嵌入蛋白质中的发色团，由于其特定的电子结构，可能无法达到相同的精度水平，并且可能需要使用严格的量子力学。[4]在这里，我们描述的基础上的X-射线晶体结构的视紫红质生色团的理论研究的结果。结合袋内生色团几何结构的稳定性用DFTB测试，[5]一种自洽电荷密度泛函紧结合方法。在优化几何结构的基础上，进行DFT计算以分析特定的拉曼谱带，并进行多构型CASPT 2 [6]计算以获得UV/维斯和圆二色性（CD）光谱数据。DFTB和激发态计算的细节在实验部分中提供。结果进行了讨论，参考类似的治疗视紫红质。[7]X射线晶体结构和优化的发色团结构的比较如图1所示。视紫红质发色团[7]典型的交替键长模式保留在batho中间体中。计算的交替比实验确定的要弱，这是包括电子相关的方法通常观察到的。[8]计算出的键角与实验结果吻合得很好;仅在C7、C8和C9处注意到键角的差异。以前的视紫红质晶体模型在不同的分辨率[7]显示差异，
Rhodopsin is the pigment that mediates light/dark vision in the eyes of vertebrates. After photoexcitation, the chromophore of rhodopsin, 11-cis-retinal, isomerizes in an extremely fast reaction to form the all-trans isomer, thus starting a sequence of dark events that finally reaches the signaling state of the protein and activates the visual cascade. Formation of the first photoproduct, photorhodopsin, is complete within 200 fs and captures more than 50% of the photon energy, which is expended during the subsequent events. Within a few picoseconds photorhodopsin relaxes to bathorhodopsin, which is the first thermally equilibrated intermediate of the rhodopsin photocycle and can be trapped at cryogenic temperatures.[1, 2] The preceding paper reports the first crystallographic analysis of this intermediate.[3] The main alteration is found to be the configurational change of the chromophore from the twisted 11-cis form in rhodopsin to the distorted all-trans form, with distinct but smaller changes in the chromophore environment. Theoretical calculations can help to assess and improve protein X-ray data. Modeling the protein matrix is usually reliable owing to the use of standard computer software during the refinement process. The treatment of an active center, such as the chromophore embedded in the protein, may not reach the same level of accuracy as a result of its specific electronic structure, and the use of rigorous quantum mechanics may be required.[4] Herein, we describe the results of a theoretical study of the bathorhodopsin chromophore based on the X-ray crystal structure. The stability of the chromophore geometry inside the binding pocket was tested with DFTB,[5] a self-consistent charge density-functional tight-binding method. On the basis of the optimized geometry, DFT calculations were performed for the analysis of specific Raman bands and multiconfigurational CASPT2 [6] calculations were performed to obtain UV/Vis and circular dichroism (CD) spectral data. Details of the DFTB and the excited-state calculations are provided in the Experimental Section. The results are discussed with reference to an analogous treatment of rhodopsin.[7] A comparison of the X-ray crystal structure and the optimized chromophore structure is shown in Figure 1. The pattern of alternating bond lengths which is typical for the rhodopsin chromophore [7] is preserved in the batho intermediate. The calculated alternation is weaker than that determined experimentally, as is commonly observed for methods that include electron correlation.[8] Calculated bond angles agree well with experiment; a discrepancy is noted only for the bond angles at C7, C8, and C9. Previous crystal models of rhodopsin at different resolution [7] showed differences of