Engels M, Gerwert K, Bashford D
Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037, USA.
Biophys Chem. 1995 Sep-Oct;56(1-2):95-104. doi: 10.1016/0301-4622(95)00020-x.
Starting from a refined model of bacteriorhodopsin's ground state, alternative models of the K and L intermediates with retinal in either 13-cis or 13-14-dicis configuration have been generated by molecular dynamics simulations. All models have been submitted to electrostatic calculations in order to determine the pK1/2 values of particular residues of interest in the active site. Our pK1/2 calculations for the refined ground state can reestablish our former results, this time without adjusting the intrinsic pK of the Schiff base. For the K intermediate the electrostatic calculations show no significant change in the pK1/2 values compared to the ground state for most of the titrating groups in the active site. For the L intermediate where retinal possesses a 13-cis configuration, we found that electrostatic factors decrease the pK1/2 value of the Schiff base by 4-5 pK-units compared to the ground state. The calculations suggest that changes of the electrostatic environment via a pure 13-cis model are sufficient to produce a pK reduction of the Schiff base that will promote subsequent proton transfer steps.
从细菌视紫红质基态的精确模型出发，通过分子动力学模拟生成了视黄醛处于13-顺式或13,14-二顺式构型的K和L中间体的替代模型。所有模型都已进行静电计算，以确定活性位点中特定感兴趣残基的pK1/2值。我们对精确基态的pK1/2计算能够重现我们之前的结果，这次无需调整席夫碱的固有pK值。对于K中间体，静电计算表明，与基态相比，活性位点中大多数滴定基团的pK1/2值没有显著变化。对于视黄醛具有13-顺式构型 的L中间体，我们发现与基态相比，静电因素使席夫碱的pK1/2值降低了4-5个pK单位。计算结果表明，通过纯13-顺式模型改变静电环境足以使席夫碱的pK降低，从而促进后续的质子转移步骤。
