Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
Angew Chem Int Ed Engl. 2017 Jul 24;56(31):9151-9154. doi: 10.1002/anie.201705512. Epub 2017 Jun 30.
Neutron diffraction analysis studies reported an isolated hydronium ion (H O ) in the interior of d-xylose isomerase (XI) and phycocyanobilin-ferredoxin oxidoreductase (PcyA). H O forms hydrogen bonds (H-bonds) with two histidine side-chains and a backbone carbonyl group in PcyA, whereas H O forms H-bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabilization of H O by the protein environment. QM/MM calculations indicated that H O was unstable in the PcyA crystal structure, releasing a proton to an H-bond partner His88, producing H O and protonated His88. On the other hand, H O was stable in the XI crystal structure. H-bond partners of isolated H O would be practically limited to acidic residues such as aspartic and glutamic acids in the protein environment.
中子衍射分析研究报道在 d-木糖异构酶 (XI) 和藻蓝胆素-铁氧还蛋白氧化还原酶 (PcyA) 的内部存在孤立的水合氢离子 (H3O+)。H3O+ 与 PcyA 中的两个组氨酸侧链和一个骨架羰基形成氢键 (H-bonds)，而 H3O+ 与 XI 中的三个酸性残基形成氢键。使用量子力学/分子力学 (QM/MM) 方法，我们分析了蛋白质环境对 H3O+ 的稳定作用。QM/MM 计算表明，H3O+ 在 PcyA 晶体结构中不稳定，会向氢键供体 His88 释放质子，生成 H3O+ 和质子化的 His88。另一方面，H3O+ 在 XI 晶体结构中稳定。孤立的 H3O+ 的氢键供体在蛋白质环境中实际上将仅限于酸性残基，如天冬氨酸和谷氨酸。
