Assigning protonation patterns in water networks in bacteriorhodopsin based on computed IR spectra

Abstract

Car-Parrinello simulations were used to study two types of protonated hydrogen-bonded networks inside the proton pump bacteriorhodopsin (see picture). The computed infrared spectra exhibit complementary absorption continua, a finding that could possibly open the door to time-resolved spectroscopic probes of proton transport on the molecular level.