Bacteriorhodopsin with lipid neighbors

Model of bacteriorhodopsin with lipid neighbors

If you are unfamiliar with bacteriorhodopsin, you should go to Tom Ebrey's tutorial and then return to this page. The model is viewed from the membrane plane, as a ribbon model in gray. The retinaldehyde is shown as an orange ball-and-stick model. The bacteriorhodopsin protein is surrounded by lipid and detergent molecules (white). Coordinates from the recent 1.55 angstrom resolution structure 1c3w.pdb (Luecke et al., 1).

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The protein is color-coded to show structure; helices are pink, coils white. The retinaldehyde is shown as a spacefilling purple structure; the lipid molecules are shown as wire-frame structures

Protein backbone in cyan, with lysine 216 and retinaldehyde highlighted in orange and white respectively.

Asp-96, Asp-85, Glu-204 (red) and Arg-82 (blue) are involved in the input and output channels for H⁺ conduction to the photactivated pumping mechanism at the retinaldehyde-lysine schiff's base (orange and white). The output pathway involves Asp-85 as immediate acceptor of a proton from the schiff's base (t_½ ~1 µs) after photoactivation changes the relative pKs. This induces a pK change at Glu-204, leading to release of a proton to the exterior. The pK change is probably mediated through Arg-82, but the mechanism is unsure. Other groups shown by mutagenesis studies to effect pKs in the output channel are Glu-194 and Arg-134 (shown as forming a salt bridge in the model), and Lys-129. Waters thought to be involved in the proton conduction are shown by their O-atoms as spacefilling models in cyan.

Protein colored by amino acid type, lipids colored CPK.

Protein backbone as ribbon; cross section through structure, showing important residues and waters (in yellow) (use Menu, and turn Slab Mode off to go back to full structure).

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(1) H.Luecke, B. Schobert, H.-T. Richter, J.-P. Cartailler and J.K. Lanyi (1999) Sructure of Bacteriorhodopsin at 1.55 Angstrom resolution. J.Mol.Biol. 291, 899