Structure of archaerhodopsin-2 at 1.8 Å resolution

Abstract

Archaerhodopsin-2 (aR2), the sole protein found in the claret membrane ofHalorubrumsp. Aus-2, functions as a light-driven proton pump. In this study, structural analysis of aR2 was performed using a novel three-dimensional crystal prepared by the successive fusion of claret membranes. The crystal is made up of stacked membranes, in each of which aR2 trimers are arranged on a hexagonal lattice. This lattice structure resembles that found in the purple membrane ofH. salinarum, except that lipid molecules trapped within the trimeric structure are not distributed with perfect threefold symmetry. Nonetheless, diffraction data at 1.8 Å resolution provide accurate structural information about functionally important residues. It is shown that two glutamates in the proton-release channel form a paired structure that is maintained by a low-barrier hydrogen bond. Although the structure of the proton-release pathway is highly conserved among proton-pumping archaeal rhodopsins, aR2 possesses the following peculiar structural features: (i) the motional freedom of the tryptophan residue that makes contact with the C13 methyl group of retinal is restricted, affecting the formation/decay kinetics of the L state, and (ii) the N-terminal polypeptide folds into an Ω-loop, which may play a role in organizing the higher-order structure.

Disordered regions in transmembrane proteins

“…As expected, positively charged amino acids have a peak at +15Å where the negatively charged lipid head groups interact with positively charged amino acids, and according to the positive inside rule [58], the peak inside is higher than outside. Interestingly We have to note that a similar observation was described in the case of archaerhodopsin-2 (aR2), where disorder was observed for lipids filling the inter-trimer space and the side chains of arginine residues (Arg34 and Arg230) that can interact with negatively charged lipid head groups [59]. Moreover, it was shown that arginine and lysine are highly "disorder-promoting" amino acids [60], therefore the high frequencies of these amino acids close to the lipid head groups of the inside leaflet may promote disordered structure in loop regions.…”

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

“…2A and SI Appendix, Fig. S1), which is conserved among H + -pumping microbial rhodopsins (7,19,20) and is also found in the Cl − pump Nonlabens marinus rhodopsin 3 (NM-R3) (21,22). The hydrated cavity on the intracellular side contains Gln123 of the NDQ motif, as well as Asn61, which plays a role in the ion selectivity (7,23).…”

Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum

“…ARI and NpSRII, but also in the published structures of other proton pumps, such as XR (Luecke et al, 2008), PR (Ran et al, 2013) and the PR-like protein ESR (Gushchin et al, 2013). During the BR photocycle, the proton is first released from the proton-releasing group (PRG), composed of two or three water molecules and Tyr57 BR , Arg82 BR , Glu194 BR , Glu204 BR and other residues (Garczarek & Gerwert, 2005;Kouyama et al, 2014), and proton uptake subsequently occurs from the intracellular side. In contrast, the corresponding water cavity of ARI contains 14 water molecules and spans from the -ionone ring of the retinal to the solvent, whereas in BR the cavity on the outer side of PRG is closed.…”