Career-Path Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Biochemistry. 2011 Nov 15;50(45):9836-44. doi: 10.1021/bi201366j. Epub 2011 Oct 20.
The crystal structure of photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed a remarkably short H-bond between redox-active tyrosine Y(Z) and D1-His190 (2.46 Å donor-acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [Y(Z)O···H···N(ε)-His-N(δ)H···O═Asn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y(Z) and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y(Z) and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved.
通过对 1.9Å分辨率的光合作用系统 II（PSII）晶体结构的分析，发现氧化还原活性酪氨酸 Y(Z)与 D1-His190（供体-受体距离 2.46Å）之间存在着非常短的氢键。利用包含 PSII 蛋白环境的大规模量子力学/分子力学（QM/MM）计算，我们能够在晶体结构的原始几何形状中再现中性 [Y(Z)O···H···N(ε)-His-N(δ)H···O=Asn]状态下这种非常短的氢键，但在氧化状态下则不能，这表明观察到的晶体结构是中性状态。除了 Y(Z)和 D1-His190 的适当氧化还原/质子化状态外，我们还发现，一群水分子的存在在缩短 Y(Z)和 D1-His190 之间的距离方面起着关键作用。水分子簇的取向通过高度极化的 PSII 蛋白环境得到能量稳定，其中氧释放复合物（OEC）的 Ca 离子和 OEC 配体 D1-Glu189 也参与其中。
