Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization

Abstract

Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.

Photoactivation of Cell-Free Expressed Archaerhodopsin-3 in a Model Cell Membrane

“…Archaerhodopsin proteins (Arch) are among a class of transmembrane receptor proteins called photoreceptors that react to light [ 14 , 15 ]. Upon illumination with green light, Arch will undergo deprotonation of a Schiff base, resulting in proton pumping [ 16 , 17 , 18 , 19 ]. In this way, Arch actively transports protons through the membrane and out of the cell [ 14 , 18 , 19 ].…”

“…Upon illumination with green light, Arch will undergo deprotonation of a Schiff base, resulting in proton pumping [ 16 , 17 , 18 , 19 ]. In this way, Arch actively transports protons through the membrane and out of the cell [ 14 , 18 , 19 ]. In vivo, the resulting proton gradient enables ATP synthases to produce ATP [ 18 , 20 ].…”

“…In this way, Arch actively transports protons through the membrane and out of the cell [ 14 , 18 , 19 ]. In vivo, the resulting proton gradient enables ATP synthases to produce ATP [ 18 , 20 ]. Photoreceptors typically consist of seven transmembrane helices and the chromophore retinal [ 16 , 18 , 21 ].…”

“…In vivo, the resulting proton gradient enables ATP synthases to produce ATP [ 18 , 20 ]. Photoreceptors typically consist of seven transmembrane helices and the chromophore retinal [ 16 , 18 , 21 ]. The structure of Arch corresponds to G protein-coupled receptors that include rhodopsin.…”

“…Besides being photo active, Arch-3 fluorescence is also voltage sensitive [ 16 , 23 ], and it is often used in optogenetics as a voltage sensor [ 16 , 17 ]. To our knowledge, an electrophysiological characterization of Arch-3 has not yet been reported in the literature [ 18 ].…”