Thr94 and Wat2b effect protonation of the retinal chromophore in rhodopsin
Thr94 and Wat2b effect protonation of the retinal chromophore in rhodopsin
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DOI：
10.1002/anie.200351034
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发表时间：
2003-01-01
影响因子：
16.6
通讯作者：
Hafner, J
中科院分区：
文献类型：
--
作者：
Buss, V;Sugihara, M;Hafner, J
视紫质中质子化的视网膜希夫碱的非凡稳定性（估计表观 pKa 可能高于 16）[1] 以及光吸收后去质子化的速度作为达到信号状态的结构先决条件 [2] 一直是许多研究的主题。已经提出了各种结合位点模型，包括 Glu 113 作为反离子，以及水桥接和稳定离子对。 [3]最近获得的第一个蛋白质 X 射线结构 [4, 5] 提供了研究原子细节结合位点的机会，并开始了解自然界根据特定中间体的需要切换发色团质子化状态的机制。我们将从头开始的量子力学应用于蛋白质，发现结合口袋中离子对的特殊排列足以建立一个能量平台，从该能量平台可以可逆地获得两种状态，即附着在希夫碱或羧酸根离子上的质子。平台的微调是通过 Thr94 和水分子 (Wat2b) 实现的，我们建议水分子与 Glu113 一起形成视紫红质中发色团的复杂抗衡离子。为了对结合位点进行建模，考虑了以下组件：与 Lys296 连接的完整视网膜发色团、抗衡离子 Glu113、Thr94（通过氢键与 Glu113 连接）和水分子。起始几何结构取自蛋白质数据库 (PDB) [4] 中的视紫红质坐标 1F88 以及更新的 X 射线结构 [5]，该结构将两个水分子（Wat2a 和 Wat2b）定位在靠近结合位点的位置。必要时，参与肽键合的氨基酸原子被氢饱和。此外，这些原子是在几何优化和分子动力学 (MD) 过程中唯一保持固定的原子
Both the extraordinary stability of the protonated retinal Schiff base in rhodopsin, with an estimated apparent pKa possibly higher than 16,[1] and the swiftness of deprotonation following light absorption as a structural pre-requisite for reaching the signaling state [2] have been the subject of much study. Various models of the binding site, involving Glu 113 as the counterion, and water bridging and stabilizing the ion pair, have been proposed.[3] The first X-ray structures of the protein which have become available recently [4, 5] offer the opportunity to study the binding site in atomic detail and start to understand the mechanism which nature has developed to switch the protonation state of the chromophore according to the need of the particular intermediate. We have applied abinitio quantum-mechanics to the protein and find that the peculiar arrangement of the ion pair in the binding pocket is sufficient to establish an energy plateau from which both states, the proton attached either to the Schiff base or to the carboxylate ion, are reversibly accessible. Fine tuning of the plateau is achieved by Thr94 and a water molecule (Wat2b) which we propose form together with Glu113 the complex counterion of the chromophore in rhodopsin.For modeling the binding site the following components have been considered: the complete retinal chromophore linked to Lys296, the counterion Glu113, Thr94 (which connects by a hydrogen bond to Glu113), and a water molecule. The starting geometry was taken from the rhodopsin coordinates laid down as 1F88 in the protein data bank (PDB)[4] and from a more recent X-ray structure [5] which locates two water molecules (Wat2a and Wat2b) close to the binding site. The atoms of the amino acids involved in peptide bonding were saturated with hydrogen where necessary. Also, these atoms were the only ones which were kept fixed during geometry optimization and the molecular dynamics (MD)