Quantum chemical study of the pKa control mechanism for the active center in bacteriorhodopsin and its M intermediate
Quantum chemical study of the pKa control mechanism for the active center in bacteriorhodopsin and its M intermediate
复制标题
细菌视紫红质及其M中间体活性中心pKa调控机制的量子化学研究
DOI：
10.1021/jp027688h
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发表时间：
2003
影响因子：
3.3
通讯作者：
M. Sakurai
中科院分区：
文献类型：
--
作者：
S. Nakajima;K. Ohno;and Yoshio Inoue;M. Sakurai
在本研究中，综合(MOZYME+DFT)方法(Ohno et al.化学。太棒了。让我们来吧。2001年，341,387。)用来解释视网膜席夫碱(RSB)和细菌视紫红质(BR)中Asp85的pKa是如何受到周围蛋白质基质的控制的，特别是涉及RSB的氢键网络。整个蛋白质分为两层。层1只包含氢键网络，并在理论的DFT级别进行处理。蛋白质的其余部分是使用一种名为MOZYME的线性缩放分子轨道方法计算的，该方法可以明确考虑蛋白质的三维结构。这里我们重点关注RSB和Asp85从基态到M中间体的pKa变化，因为它们是BR中质子转移机制的关键因素。这两种状态的三维结构都取自相应的X射线数据。计算结果成功地再现了RSB和Asp85在地面上形成两性离子的实验事实。
In this study, integrated (MOZYME + DFT) method (Ohno et al. Chem. Phys. Lett. 2001, 341, 387.) is applied to elucidate how the pKa's of retinal Schiff base (RSB) and Asp85 in bacteriorhodopisn (bR) are controlled by the surrounding protein matrix, especially a hydrogen bonding network involving RSB. The whole protein is divided into two layers. Layer 1 contains only the hydrogen bonding network and is treated at the DFT level of theory. The rest of the protein is calculated using a linear-scaling molecular orbital method called MOZYME that can explicitly take into account the protein three-dimensional structure. Here we focus our attention on the pKa changes of RSB and Asp85 on going from the ground state to the M intermediate, because they are key factors of the proton translocation mechanism in bR. The three-dimensional structures of both states are taken from corresponding X-ray data. The calculation successfully reproduces the experimental fact that RSB and Asp85 form the zwitterions in the ground st...