Sugihara Minoru, Buss Volker, Entel Peter, Elstner Marcus, Frauenheim Thomas
Institute of Theoretical Low-Temperature Physics, University of Duisburg, D47048 Duisburg, Germany.
Biochemistry. 2002 Dec 24;41(51):15259-66. doi: 10.1021/bi020533f.
Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.7 kcal/mol in favor of the former. Of the two possible 6-s-cis conformations, the one with a negative twist angle (optimized value: -35 degrees ) is strongly favored, by 3.6 kcal/mol, relative to the one in which the dihedral is positive. (ii) Out-of-plane twist of the chromophore. The environment induces a nonplanar helical deformation of the chromophore, with the distortions concentrated in the central region of the chromophore, from C10 to C13. The dihedral angle between the planes formed by the bonds from C7 to C10 and from C13 to C15 is 42 degrees. (iii) The absolute configuration of the chromophore. The dihedral angle about the C12-C13 bond is +170 degrees from planar s-cis, which imparts a positive helicity on the chromophore, in agreement with earlier considerations based on theoretical and spectroscopic evidence.
基于自洽电荷紧束缚近似的密度泛函理论（DFT）计算已被用于研究蛋白质口袋对11-顺式视黄醛席夫碱（SB）发色团三维结构的影响。从嵌入由27个次近邻氨基酸组成的蛋白质口袋中的有效平面发色团开始，通过能量优化和分子动力学（MD）模拟得到的松弛发色团几何结构，对于以下问题产生了新的见解：（i）β-紫罗兰酮环的构象。蛋白质口袋能够容纳6-s-顺式和6-s-反式两种构象，总能量差为0.7千卡/摩尔，前者更占优势。在两种可能的6-s-顺式构象中，扭转角为负（优化值：-35度）的构象比扭转角为正的构象更受青睐，优势为3.6千卡/摩尔。（ii）发色团的面外扭转。环境诱导发色团发生非平面螺旋变形，变形集中在发色团从C10到C13的中心区域。由C7到C10和C13到C15的键形成的平面之间的二面角为42度。（iii）发色团的绝对构型。关于C12 - C13键的二面角相对于平面s-顺式为+170度，这赋予发色团正螺旋性，与基于理论和光谱证据的早期考虑一致。
