Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy

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Abstract
Much progress has been made in our understanding of water molecule reactions on surfaces1, proton solvation in gas-phase water clusters2,3 and proton transfer through liquids4. Compared with our advanced understanding of these physico-chemical systems, much less is known about individual water molecules and their cooperative behaviour in heterogeneous proteins during enzymatic reactions. Here we use time-resolved Fourier transform infrared5 spectroscopy (trFTIR) and in situ H218O/H216O exchange FTIR to determine how the membrane protein bacteriorhodopsin6 uses the interplay among strongly hydrogen-bonded water molecules, a water molecule with a dangling hydroxyl group and a protonated water cluster7 to transfer protons. The precise arrangement of water molecules in the protein matrix results in a controlled Grotthuss proton transfer, in contrast to the random proton migration that occurs in liquid water. Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids.