Bondar Ana-Nicoleta, Smith Jeremy C, Fischer Stefan
Computational Molecular Biophysics, IWR, Heidelberg University, Im Neuenheimer Feld 368, Heidelberg, Germany.
Photochem Photobiol Sci. 2006 Jun;5(6):547-52. doi: 10.1039/b516451f. Epub 2006 Apr 4.
In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.
在光驱动的细菌视紫红质质子泵中，第一个质子转移步骤是从视黄醛席夫碱转移到附近的羧基。这一转移步骤的机制极具争议，尤其是是否允许直接质子跳跃。在此，我们回顾了使用量子力学/分子力学相结合的方法计算出的直接质子转移路径的结构和能量决定因素。蛋白质的柔韧性和静电相互作用在塑造质子转移能量分布方面都起着重要作用。对光循环前半段假定跃迁能量学的详细分析集中在两个因素上，这两个因素决定了在质子泵浦循环中活性位点特定构型出现的可能性。首先，质子转移的限速屏障必须与光循环的动力学一致。其次，活性位点构型必须与高效的整体泵浦循环兼容。
