Han M, DeDecker B S, Smith S O
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.
Biophys J. 1993 Aug;65(2):899-906. doi: 10.1016/S0006-3495(93)81117-2.
Semiempirical molecular orbital calculations are combined with 13C NMR chemical shifts to localize the counterion in the retinal binding site of vertebrate rhodopsin. Charge densities along the polyene chain are calculated for an 11-cis-retinylidene protonated Schiff base (11-cis-RPSB) chromophore with 1) a chloride counterion at various distances from the Schiff base nitrogen, 2) one or two chloride counterions at different positions along the retinal chain from C10 to C15 and at the Schiff base nitrogen, and 3) a carboxylate counterion out of the retinal plane near C12. Increasing the distance of the negative counterion from the Schiff base results in an enhancement of alternating negative and positive partial charge on the even- and odd-numbered carbons, respectively, when compared to the 11-cis-RPSB chloride model compound. In contrast, the observed 13C NMR data of rhodopsin exhibit downfield chemical shifts from C8 to C13 relative to the 11-cis-RPSB.Cl corresponding to a net increase of partial positive or decrease of partial negative charge at these positions (Smith, S. O., I. Palings, M. E. Miley, J. Courtin, H. de Groot, J. Lugtenburg, R. A. Mathies, and R. G. Griffin. 1990. Biochemistry. 29:8158-8164). The anomalous changes in charge density reflected in the rhodopsin NMR chemical shifts can be qualitatively modeled by placing a single negative charge above C12. The calculated fit improves when a carboxylate counterion is used to model the retinal binding site. Inclusion of water in the model does not alter the fit to the NMR data, although it is consistent with observations based on other methods. These data constrain the location and the orientation of the Glu113 side chain, which is known to be the counterion in rhodopsin, and argue for a strong interaction centered at C12 of the retinylidene chain.
半经验分子轨道计算与碳-13核磁共振化学位移相结合，以确定反离子在脊椎动物视紫红质视网膜结合位点中的位置。对于11-顺式视黄醛质子化席夫碱（11-cis-RPSB）发色团，计算了沿多烯链的电荷密度，其中：1）氯离子反离子与席夫碱氮原子的距离各不相同；2）一个或两个氯离子反离子位于视网膜链上从C10到C15的不同位置以及席夫碱氮原子处；3）一个羧酸根反离子位于靠近C12的视网膜平面外。与11-cis-RPSB氯化物模型化合物相比，增加负反离子与席夫碱的距离会分别导致偶数和奇数碳上交替出现的负电荷和正电荷增强。相比之下，视紫红质的碳-13核磁共振数据显示，相对于11-cis-RPSB.Cl，从C8到C13的化学位移向低场移动，这对应于这些位置上部分正电荷的净增加或部分负电荷的减少（史密斯，S.O.，I.帕林格斯，M.E.米利，J.库尔廷，H.德格鲁特，J.卢滕堡，R.A.马西斯，和R.G.格里芬。1990年。《生物化学》。29:8158 - 8164）。视紫红质核磁共振化学位移中反映出的电荷密度异常变化，可以通过在C12上方放置一个负电荷进行定性模拟。当使用羧酸根反离子来模拟视网膜结合位点时，计算得到的拟合度会提高。尽管这与基于其他方法的观察结果一致，但在模型中加入水并不会改变对核磁共振数据的拟合。这些数据限制了已知为视紫红质中反离子的Glu113侧链的位置和方向，并支持以视黄醛链的C12为中心的强相互作用。
