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

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.