Bombarda Elisa, Becker Torsten, Ullmann G Matthias
Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, 95447 Bayreuth, Germany.
J Am Chem Soc. 2006 Sep 20;128(37):12129-39. doi: 10.1021/ja0619657.
Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.
质子的结合与释放是蛋白质内部质子转移的基本步骤，而质子转移过程在生物化学催化和生物能量转导中至关重要。与水溶液相比，蛋白质中的局部电场会影响质子结合能。在膜蛋白中，膜电位也会影响局部静电作用，因此对蛋白质功能可能至关重要。在本文中，我们介绍了一种在存在膜电位的情况下计算膜蛋白可滴定位点质子化概率的方法。在连续介质静电学框架下，我们使用修正的泊松 - 玻尔兹曼方程来纳入膜电位的影响。我们的方法认为，在跨膜蛋白中，每个可滴定位点仅从膜的一侧可被质子接近，这取决于蛋白质的氢键模式。我们表明，从膜的不同侧接收质子的位点的质子化受膜电位的影响不同。此外，膜电位的影响与质子泵浦产生的pH梯度的影响相结合。我们的方法应用于细菌视紫红质，一种光激活质子泵。我们发现该蛋白的质子泵浦可能受Asp115调节，Asp115是一个尚未确定功能的保守残基。根据我们的计算，如果pH梯度或膜电位变得过大，Asp115与Asp85的相互作用会导致后者质子化。由于Asp85是光循环中的主要质子受体，Asp85质子化的细菌视紫红质分子无法泵浦质子。此外，我们估计了膜电位如何影响光循环中各个质子转移反应的能量学。除了从席夫碱到Asp85的初始质子转移外，大多数反应都受到影响。我们的计算为细菌视紫红质感知膜电位和pH梯度的机制以及这些参数如何调节质子泵浦提供了新的见解。
