The Nature of the Complex Counterion of the Chromophore in Rhodopsin
The Nature of the Complex Counterion of the Chromophore in Rhodopsin
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视紫红质中发色团复杂抗衡离子的性质
DOI：
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发表时间：
2004
期刊：
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通讯作者：
J. Hafner
中科院分区：
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作者：
M. Sugihara;V. Buss;P. Entel;J. Hafner
利用密度泛函理论方法研究了视紫红质发色团与不同反离子的相互作用，并进行了能量最小化和分子动力学计算。Palczewski等人从视紫红质的X射线结构中获得了连接到Lys 296的视网膜发色团和靠近视网膜结合位点的其他氨基酸残基的初始几何形状。我们还考虑了Okada等人在最近的研究中发现的一个水分子（Wat 2b）的存在。研究了以下抗衡离子（按照复杂性增加的顺序）：Glu 113; Glu 113和Thr 94; Glu 113和Wat 2b; Glu 113、Thr 94和Wat 2b; Glu 113、Thr 94、Wat 2b和Cys 187。仅使用谷氨酸盐时，质子化的发色团不稳定，并且质子快速地转移到谷氨酸盐抗衡离子。Thr 94通过与Glu 113的氧形成氢键来稳定质子化的发色团。Wat 2b通过相同的机制起作用，尽管效果较弱，并且发色团在两个波长之间振荡。
The interaction of the rhodopsin chromophore with different complex counterions has been investigated using density functional theory methodology for both energy minimization and molecular dynamics calculations. The initial geometry of the retinal chromophore attached to Lys296 and of other amino acid residues close to the retinal binding site was taken from the rhodopsin X-ray structure by Palczewski et al. We also considered the presence of one water molecule (Wat2b) found in a recent study by Okada et al. The following counterions were studied (in order of increasing complexity): Glu113; Glu113 and Thr94; Glu113 and Wat2b; Glu113, Thr94, and Wat2b; Glu113, Thr94, Wat2b, and Cys187. With glutamate only, the protonated chromophore is not stable, and the proton is shifted rapidly to the glutamate counterion. Thr94 stabilizes the protonated chromophore by engaging the oxygen of Glu113 in hydrogen bonding. Wat2b works by the same mechanism, though the effect is weaker, and the chromophore oscillates betwee...