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The Existence of an Isolated Hydronium Ion in the Interior of Proteins
Author(s) -
Ikeda Takuya,
Saito Keisuke,
Hasegawa Ryo,
Ishikita Hiroshi
Publication year - 2017
Publication title -
angewandte chemie international edition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.831
H-Index - 550
eISSN - 1521-3773
pISSN - 1433-7851
DOI - 10.1002/anie.201705512
Subject(s) - hydrogen bond , chemistry , protonation , crystallography , oxidoreductase , histidine , crystal structure , hydronium , isomerase , neutron diffraction , protein crystallization , stereochemistry , ion , molecule , organic chemistry , enzyme , crystallization
Neutron diffraction analysis studies reported an isolated hydronium ion (H 3 O + ) in the interior of d ‐xylose isomerase (XI) and phycocyanobilin‐ferredoxin oxidoreductase (PcyA). H 3 O + forms hydrogen bonds (H‐bonds) with two histidine side‐chains and a backbone carbonyl group in PcyA, whereas H 3 O + forms H‐bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabilization of H 3 O + by the protein environment. QM/MM calculations indicated that H 3 O + was unstable in the PcyA crystal structure, releasing a proton to an H‐bond partner His88, producing H 2 O and protonated His88. On the other hand, H 3 O + was stable in the XI crystal structure. H‐bond partners of isolated H 3 O + would be practically limited to acidic residues such as aspartic and glutamic acids in the protein environment.