Bacteriorhodopsin molecules

Figure 12.S Schematic diagram of the bacteriorhodopsin molecule illustrating the relation between the proton channel and bound retinal in its tram form. A to E are the seven transmembrane helices. Retinal is covalently bound to a lysine residue. The relative positions of two Asp residues, which are important for proton transfer, are also shown. (Adapted from R. Henderson et al.,...

In reply to Dr. Hess I may add that, although energy is admittedly required to construct the bacteriorhodopsin molecules in the first place, the proteins are not assembled inside the membrane. They enter the membrane and form an equilibrium structure. On another point, ordering inside the membrane is analogous to crystallization. 

An essential feature of the above scheme is that there is practically no inward H -conducting pathway in the resting bacteriorhodopsin molecule. This pathway is organized only for a short period of time in the working protein at N and O stages. In these intermediates, no direct contact of the outward and the inward pathways is assumed. Such a mechanism excludes a passive H leak via bacteriorhodopsin, a property that seems to be important for this protein which can occupy up to 50% of the membrane in the halobacterial cell. 

The function of bacteriorhodopsin as a light-driven proton pump is well established from studies [14,70,83-85,323] of whole H. halobium cells, cell envelope vesicles prepared from the cells [78,324], and liposomes [17,18,135,191,325-327] as well as planar films [328-339] into which purple membrane was incorporated. In all of these cases light-dependent net translocation of protons across the membrane is observed, whose magnitude exceeds the number of bacteriorhodopsin molecules in the system by up to two orders of magnitude. 

Figure 10.16 Hydrophobicity plot for the bacteriorhodopsin molecule depicted in Figure 10.15. 

For a clarification of the above questions we have carried out calculations of spectroscopic transition energies and oscillator strengths for a model all-trans bacteriorhodopsin molecule. As required by the Resonance Raman data for both rhodopsin and bacteriorhodopsin we have assumed that in BR y the Schiff base nitrogen is fully protonated. This assumption constitutes the basis of models a. and c, but not of model where full protonation is claimed only for the bathophotoproducts, J525 bathorhodopsin. 

A continuous lipidic cubic phase is obtained by mixing a long-chain lipid such as monoolein with a small amount of water. The result is a highly viscous state where the lipids are packed in curved continuous bilayers extending in three dimensions and which are interpenetrated by communicating aqueous channels. Crystallization of incorporated proteins starts inside the lipid phase and growth is achieved by lateral diffusion of the protein molecules to the nucleation sites. This system has recently been used to obtain three-dimensional crystals 20 x 20 x 8 pm in size of the membrane protein bacteriorhodopsin, which diffracted to 2 A resolution using a microfocus beam at the European Synchrotron Radiation Facility. 

In 1990 the resolution was extended to 3 A, which confirmed the presence of the seven a helices (c). This structure also showed how these helices were connected by loop regions and where the retinal molecule was bound to bacteriorhodopsin. (Courtesy of R. Henderson.)... 

Like the photosynthetic reaction center and bacteriorhodopsin, the bacterial ion channel also has tilted transmembrane helices, two in each of the subunits of the homotetrameric molecule that has fourfold symmetry. These transmembrane helices line the central and inner parts of the channel but do not contribute to the remarkable 10,000-fold selectivity for K+ ions over Na+ ions. This crucial property of the channel is achieved through the narrow selectivity filter that is formed by loop regions from thefour subunits and lined by main-chain carbonyl oxygen atoms, to which dehydrated K ions bind. 

For targets that lack structural information, such as GPCRs or ion channels, a pharmacophore model or multiple pharmacophore models for different series of compounds can explain SAR and guide the synthesis of new analogs. Alternatively, homology models based on bacteriorhodopsin have been used to explain the interactions of small molecules with GPCRs. 

Roux, B. Nina, M. Pomes, R. Smith, J., Thermodynamic stability of water molecules in the Bacteriorhodopsin proton channel a molecular dynamics and free energy perturbation study, Biophys. J. 1996, 71, 670-681... 

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