Bacteriorhodopsin cytoplasmic surface structure

The exact location of the Schiff base and the Asp-96 carboxyl is yet to be found since the three-dimensional structure of bacteriorhodopsin is not known to atomic resolution. Electron microscopy of two-dimensional bacteriorhodopsin crystals indicates that the Schiff base is localized in the middle of the protein molecule, while Asp-96 is somewhere between the Schiff base and the cytoplasmic surface of the membrane [21]. It has also been shown that the protein regions separating the Schiff base from the outer and cytoplasmic membrane surfaces differ strongly in hydrophobicity, which is low in the former, and high in the latter case. Between the outer membrane surface and the Schiff base, there are four charged amino acids and no valine, leucine and isoleucine. At the same time, between the Schiff base and the cytoplasm, five leucines, valine and only one charged amino acid (Asp-96) seem to be localized [21]. Thus the dielectric... 

Fig. 3. Approximate structure of bacteriorhodopsin based on ref. [16]. Helices A through G span the lipid bilayer, and surround the retinal which is attached via Schiff-base linkage to Iys216 which is located near the middle of helix G. The retinal is shown as a -tmns. The two proton channels connecting the Schiff base to the extracellular and cytoplasmic surfaces are indicated as inclined dotted cylinders. In the former region the residues of interest (cf. the text) are arg82, asp85, and...

Integral membrane proteins. Membrane proteins are hard to crystallize178 and precise structures are known for only a few of them.179-181 A large fraction of all of the integral membrane proteins contain one or more membrane-spanning helices with loops of peptide chain between them. Folded domains in the cytoplasm or on the external membrane surface may also be present. The best-known structure of a transmembrane protein is that of the 248-residue bacteriorhodopsin. It consists of seven helical segments that span the plasma membrane (Fig. 23-45) and serves as a light-activated proton pump. Other proteins with similar structures act as hormone receptors in eukaryotic membranes. A seven-helix protein embedded in a membrane is depicted in Fig. 8-5 and also, in more detail, in Fig. 11-6. 

Initial protein structure studies indicated that bacteriorhodopsin is a 248-residue polypeptide. Its amino-terminal residue is on the membrane s outside surface, and its carboxyl residue projects into the cytoplasm. Careful analysis of bacteriorhodopsin s primary sequence revealed seven peptide segments with amino acid sequences typical of a-helices. Using electron microscopy and X-ray crystallography, researchers determined that bacteriorhodopsin possesses seven a-helices, which are roughly perpendicular to the membrane (Figure 11C). 

Figure 2.5 ILLustration of a structure determined from analysis of 2D crystals at 3 A resolution. Surface shaded views of (a) the cytoplasmic side and (b) the extracellular side of the bacteriorhodopsin trimer. Blue and red areas indicate positive and negative surface charges respectively. The arrow indicates the opening of the only proton channel that can be seen in this view. [Reproduced from Fujiyoshi, Y. (1999) Faseb J. 13 (suppl 2) S191-194]...

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