Proton channel, bacteriorhodopsin

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.,...

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... 

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...

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]...

Proton transfer is closely linked to the structure of the reaction-center protein. Since protons are present in the external aqueous medium, the (reduced) quinone molecules are buried inside the interior ofthe reaction-center protein, therefore protonation would seem to require some kind of channel for the passage of water molecules. However, at least until recently (see below), there was no evidence for the presence of channels large enough to accommodate water molecules. An alternative mechanism might involve a chain of ionizable amino acids which extends from the surface of the protein to the interior where the reduced quinone is located, forming a pathway along which protons may be transported. Such a mechanism has been likened to a bucket brigade or relay station and shown to exist in such proteins as bacteriorhodopsin, ATP synthase and cytochrome oxidase. 

The scarcity of free proton in the cytoplasmic space of bacteria, eukaryotic cells or the mitochondrial matrix imposes a time limitation on the rate at which a free proton can diffuse towards the enzyme s active sites, so that the system appears to be rate-limited by the availability of free protons. However, the measured rates stUl seem to exceed the predicted values, for a review see Ref. [26], indicating that the protein s surface participates in channeling the proton to the orifice of the protonconducting channels. This case was first demonstrated with bacteriorhodopsin, a membranal protein which utilizes the energy of a photon, absorbed by its chromo-phore, to drive protons from the cytoplasmic space of the bacteria to the external space. 

There is a strong resemblance between the mechanism of ion motion next to the protein and the proton-collecting antenna reported for bacteriorhodopsin [78, 79] or cytochrome c oxidase [2]. These domains consist of a cluster of carboxylates that function as proton binding sites. The protonation on any carboxylate of the cluster leads to rapid proton exchange reactions that finally deliver the proton to the immediate vicinity of the proton-conducting channel of the protein. 

Checovee, S., et al., Mechanism of proton entry into the cytoplasmic section of the proton-conducting channel of bacteriorhodopsin, Biochemistry, 1997, 36, 13919-13928. 

The experimental structure of bR determined at atomic resolution from cryoelectron microscopy and X-ray crystallography revealed a channel containing the Schiff base of the retinal chromophore (27, 28). Site-directed mutagenesis and vibrational spectroscopy experiments have enabled the identification of polar residues in the channel involved in the proton transfer pathway (29-32). Recent work on bacteriorhodopsin has concentrated on hydration and conformational thermodynamics. 

The third alternative is proton exchange along hydrogen-bonded water molecules (33-35). In bacteriorhodopsin, for example, a recent structural model at 3.5-A resolution strongly suggests that water molecules form a narrow channel and are involved in proton delivery to the chromophore (36). The remainder of this review will discuss chains of hydrogen-bonded water molecules as potential proton translocators and describe some initial tests of the concept. 

Bacteriorhodopsin is an integral bacterial membrane protein. As seen in Figure 10.15, the linear polypeptide chain of bacteriorhodopsin folds back and forth several times in the membrane to provide a channel through which protons move. Figure 10.16 shows that a plot of the hydrophobic tendency of amino acids in the protein parallels the regions embedded in the membrane. Thus, hydrophobic regions of the protein are embedded in the protein and hydrophilic regions are at the surfaces. 

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