Dynamics of proton transfer in bacteriorhodopsin.
Dynamics of proton transfer in bacteriorhodopsin.
复制标题
细菌视紫红质中质子转移的动力学。
DOI：
10.1021/ja036115v
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发表时间：
2004
影响因子：
15
通讯作者：
Krauss,Morris
中科院分区：
文献类型：
--
作者：
Lee,Yong-Sok;Krauss,Morris
细菌视紫红质从细胞质到细胞外侧的质子转移是从细胞质区域中质子化的 asp96 向去质子化的席夫碱开始的。这发生在从光循环后期 M 状态到 N 状态的转变中。为了研究这种质子转移过程，根据细菌视紫红质 E204Q 突变体晶体结构构建了量子力学/分子力学 (QM/MM) 模型。三个残基，asp96、asp85 和 thr89，以及大部分视网膜发色团和 lys216 的希夫碱链接经过量子力学处理，并通过连接原子氢连接到剩余的经典蛋白质。 M态的结构转变导致希夫碱和asp96之间形成水通道。由于该通道的一部分排列有疏水残基，因此对疏水通道中质子转移的机制存在疑问。使用 CHARMM/GAMESS 方法的从头算动力学用于模拟质子通过部分疏水通道的转移。一旦足够的水分子被添加到通道中以形成从 asp96 到席夫碱的单水链，无论 asp85 的质子化状态如何，转移都会以快速（小于皮秒）的一致事件发生。质子从 asp96 到最近的水的动态转移启动了强键合水链的组织，有利于质子转移到席夫碱氮。
Proton transfer in bacteriorhodopsin from the cytoplasm to the extracellular side is initiated from protonated asp96 in the cytoplasmic region toward the deprotonated Schiff base. This occurs in the transition from the photocycle late M state to the N state. To investigate this proton-transfer process, a quantum mechanics/molecular mechanics (QM/MM) model is constructed from the bacteriorhodopsin E204Q mutant crystal structure. Three residues, asp96, asp85, and thr89, as well as most of the retinal chromophore and the Schiff base link of lys216 are treated quantum mechanically and connected to the remaining classical protein through linker atom hydrogens. Structural transformation in the M state results in the formation of a water channel between the Schiff base and asp96. Since a part of this channel is lined with hydrophobic residues, there has been a question on the mechanism of proton transfer in a hydrophobic channel. Ab initio dynamics using the CHARMM/GAMESS methodology is used to simulate the transfer of the proton through a partially hydrophobic channel. Once sufficient water molecules are added to the channel to allow the formation of a single chain of waters from asp96 to the Schiff base, the transfer occurs as a fast (less than a picosecond) concerted event irrespective of the protonation state of asp85. Dynamic transfer of the proton from asp96 to the nearest water initiates the organization of a strongly bonded water chain conducive to the transfer of the proton to the Schiff base nitrogen.