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The Existence of an Isolated Hydronium Ion in the Interior of Proteins.

ABSTRACT: Neutron diffraction analysis studies reported an isolated hydronium ion (H3 O+ ) in the interior of d-xylose isomerase (XI) and phycocyanobilin-ferredoxin oxidoreductase (PcyA). H3 O+ forms hydrogen bonds (H-bonds) with two histidine side-chains and a backbone carbonyl group in PcyA, whereas H3 O+ forms H-bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabilization of H3 O+ by the protein environment. QM/MM calculations indicated that H3 O+ was unstable in the PcyA crystal structure, releasing a proton to an H-bond partner His88, producing H2 O and protonated His88. On the other hand, H3 O+ was stable in the XI crystal structure. H-bond partners of isolated H3 O+ would be practically limited to acidic residues such as aspartic and glutamic acids in the protein environment.

SUBMITTER: Ikeda T

PROVIDER: S-EPMC5575531 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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The Existence of an Isolated Hydronium Ion in the Interior of Proteins.

Ikeda Takuya T Saito Keisuke K Hasegawa Ryo R Ishikita Hiroshi H

Angewandte Chemie (International ed. in English) 20170630 31

Neutron diffraction analysis studies reported an isolated hydronium ion (H3 O+ ) in the interior of d-xylose isomerase (XI) and phycocyanobilin-ferredoxin oxidoreductase (PcyA). H3 O+ forms hydrogen bonds (H-bonds) with two histidine side-chains and a backbone carbonyl group in PcyA, whereas H3 O+ forms H-bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabiliza ...[more]

PMID: 28613440

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