Lipid patches in membrane protein oligomers: Crystal structure of the bacteriorhodopsin-lipid complex

Abstract

Heterogenous nucleation on small molecule crystals causes a monoclinic crystal form of bacteriorhodopsin (BR) in which trimers of this membrane protein pack differently than in native purple membranes. Analysis of single crystals by nano-electrospray ionization-mass spectrometry demonstrated a preservation of the purple membrane lipid composition in these BR crystals. The 2.9-Å x-ray structure shows a lipid-mediated stabilization of BR trimers where the glycolipid S-TGA-1 binds into the central compartment of BR trimers. The BR trimer͞lipid complex provides an example of local membrane thinning as the lipid head-group boundary of the central lipid patch is shifted by 5 Å toward the membrane center. Nonbiased electron density maps reveal structural differences to previously reported BR structures, especially for the cytosolic EF loop and the proton exit pathway. The terminal proton release complex now comprises an E194-E204 dyad as a diffuse proton buffer.

Mechanism of a proton pump analyzed with computer simulations

“…When both the Zundel ion and the negatively charged E194/E204 pair were treated with QM, the proton was attracted by E194/E204 and remained shared by E194/E204 for the entire length of the simulations [41]. This geometry with E194/E204 sharing a proton gives an IR spectrum in reasonable qualitative agreement with experiments [41], bringing support to the initial proposal [87,88] that the E194/E204 dyad, probably in association with water molecules, may act as the extracellular proton release group. E194/E204 may also be important for controlling the mechanical stability of the extracellular region of bacteriorhodopsin [89].…”

Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics

“…In what follows, we compare the structure of each TM helix and that of the x-ray structure (49) (Fig. S2 B).…”

Role of trimer–trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy

“…To obtain the amount of W12I bR whose the molar extinction coefficient is unknown, the change in its absorption at 350 nm caused by complete photobleaching was compared with that of WT bR because the absorption at 350 nm is proportional to the amount of retinal oxime produced by photobleaching. Figure 1A shows a schematic of the bR lattice assembly constructed from the PDB (1BRR) structure of bR trimers (Essen et al, 1998). The positions of W12 and F135 are highlighted by the white and light-blue spheres, respectively.…”

“…Numerous membrane proteins interact with each other or other components in two-dimensional membrane environments, e.g., self-assembly into oligomers or crystals (Essen et al, 1998;Persike et al, 2001;van Huizen et al, 1999;Colom et al, 2012), receptor-mediated protein-protein interactions for signal transduction (Szidonya et al, 2008), and the membrane localization of proteins via association with lipid rafts (Simons and Ikonen, 1997). Thus, elucidating the intermolecular packing of membrane proteins is essential for understanding the structure-function relationship and the general principle of membrane protein assembly.…”