Proton conduction through proteins: an overview of theoretical principles and applications.

Publisher Summary This chapter provides an overview of theoretical principles and applications of proton conduction through proteins. The proton currents in biological systems involve only a small percentage of the atoms composing the system and the bonds in the proton conductors are constantly being broken by the reorientation of the conducting groups. These two aspects of the biological proton transport make its detection exceedingly difficult. Two studied proton transport systems are the membrane protein bacteriorhodopsin, which functions as a light-driven proton pump in Halobacterium halobium, and the proteolipid of ATPase, which functions as a passive proton conductor. The constituents of a biological proton conductor are most likely the molecules of bound water or the polar amino acid side groups of the protein. The molecular dynamics calculations on the ion channel in gramicidin indicate that a linear water channel may be the conducting pathway in ion channels as well. The observables that are suitable to elucidate the structure and function of biological proton conductors are summarized in the chapter.