Quantum Mechanical Studies of Proton Affinity of Amino Acid Residues in Protein Environments

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Protons play crucial roles in biomolecules. We studied the effects of nanoscale environment on proton affinity of amino acid residues using computer simulations based on quantum mechanics. The purpose of this study is to develop quantum mechanical analysis of structural information of proteins.In this study, we focused on the three environments:(1)the environment around isolated amino acid residues in solution, (2) the environment around amino acid residues working for proton pumping activity in cytochrome c oxidase, (3) the environment around amino acid residues working for amide-bond cleavage reaction in nylon-oligomer hydrolase. The present computer simulations based on quantum mechanics highlight the importance of physiological protein structures in terms of proton affinity.