Proteorhodopsin Activation Is Modulated by Dynamic Changes in Internal Hydration

Proteorhodopsin, a member of the microbial rhodopsin family, is a seven-transmembrane α-helical protein that functions as a light-driven proton pump. Understanding the proton-pumping mechanism of proteorhodopsin requires intimate knowledge of the proton transfer pathway via complex hydrogen-bonding networks formed by amino acid residues and internal water molecules. Here we conducted a series of microsecond time scale molecular dynamics simulations on both the dark state and the initial photoactivated state of blue proteorhodopsin to reveal the structural basis for proton transfer with respect to protein internal hydration. A complex series of dynamic hydrogen-bonding networks involving water molecules exists, facilitated by water channels and hydration sites within proteorhodopsin. High levels of hydration were discovered at each proton transfer sitethe retinal binding pocket and proton uptake and release sitesunderscoring the critical participation of water molecules in the proton-pumping mechanism. Water-bridged interactions and local water channels were also observed and can potentially mediate long-distance proton transfer between each site. The most significant phenomenon is after isomerization of retinal, an increase in water flux occurs that connects the proton release group, a conserved arginine residue, and the retinal binding pocket. Our results provide a detailed description of the internal hydration of the early photointermediates in the proteorhodopsin photocycle under alkaline pH conditions. These results lay the fundamental groundwork for understanding the intimate role that hydration plays in the structure–function relationship underlying the proteorhodopsin proton-pumping mechanism, as well as providing context for the relationship of hydration in proteorhodopsin to other microbial retinal proteins