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Abstract

Identification of proton-conducting pathways in a protein is a key to understanding the mechanisms of biomolecular proton transfer. Starting from a known protein structure, proton pathways are modeled here as hydrogen bonded networks of proton conducting groups, including proton-exchanging groups of amino acid sidechains and bound water molecules. The energy minimized static structure is often found to be inadequate to detect suitable proton transfer paths leading, e.g., from the protein surface to the active site buried inside the protein. A general method is developed to study the effect of sidechain rotations and change in internal hydration of the protein on the formation of dynamic connections in the networked path. Application to cytochrome P450cam shows that cooperative rotation of amino acids and motion of water molecules connects the protein surface to the molecular oxygen at the active site. Our observations emphasize the intrinsic dynamical nature of proton pathways.