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

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.