Efficient Proton Relay Orchestrated by Covalent Bond Switching of Active Amino Acids in Protein Channels

Abstract

Through systematic mutational simulations of the key site in a proton channel, we find that 13 of the 20 canonical amino acid residues are active for proton transfer through covalent bond switching, whereas the remaining 7 residues, whose side chains terminate in sp3 hybridized carbon-hydrogen covalent bonds, do not undergo such bond switching and are therefore inactive. All active residues have a negative electrostatic potential extremum at the proton accepting atom and lower energy barriers for proton relay orchestrated by bond switching, whereas the inactive residues have positive electrostatic potential extremum and significantly higher barriers for bond switching. We further find that the active residues tend to be distributed within the pore to mediate proton transfer, while the inactive residues are enriched in the periphery to stabilize the structure. This bond switching activity can also be observed in respiratory complex I. These findings establish a new classification criterion for amino acids based on their covalent bond switching activity, providing insights into how life utilizes the 20 types of amino acids.