title: Orientation of the protonated retinal Schiff base group in bacteriorhodopsin from absorption linear dichroism.
abstract: Linear dichroism experiments are performed on light-adapted bacteriorhodopsin (BR568) films containing native retinal (A1) and its 3,4-dehydroretinal (A2) analogue to measure the angle between the chromophore transition dipole moment and the membrane normal. QCFF/pi calculations show that the angle between the transition moment and the long axis of the polyene is changed by 3.4 degrees when the C3-C4 bond is unsaturated. The difference vector between the two transition moments points in the same direction as the Schiff base (N----H) bond for the all-trans BR568 chromophore. Because the plane of the chromophore is perpendicular to the membrane plane, a comparison of the transition moment orientations in the A1- and A2-pigments enables us to determine the orientation of the N----H bond with respect to the absolute chromophore (N----C5 vector) orientation. The angles of the transition moments are 70.3 degrees +/- 0.4 degrees and 67.8 degrees +/- 0.4 degrees for the A1- and A2-pigments, respectively. The fact that the change in the transition moment angle (2.5 degrees) is close to the predicted 3.4 degrees supports the idea that the chromophore plane is nearly perpendicular to the membrane plane. The decreased transition moment angle in the A2-analogue requires that the N----H bond and the N----C5 vector point toward the same membrane surface. Available results indicate that the N----C5 vector points toward the exterior in BR568. With this assignment, we conclude that the N----H bond points toward the exterior surface and its most likely counterion Asp-212. This information makes possible the construction of a computer graphics model for the active site in BR568.
authors.affiliation: Department of Chemistry, University of California, Berkeley 94720.
authors.forename: S W
authors.initials: SW
authors.lastname: Lin
authors.forename: R A
authors.initials: RA
authors.lastname: Mathies
mesh_terms: D001436:Bacteriorhodopsins / Q000378:metabolism*; D006217:Halobacterium / Q000378:metabolism; D008027:Light; D008961:Models, Structural; D011487:Protein Conformation; D012172:Retinaldehyde / Q000378:metabolism*; D012176:Retinoids / Q000378:metabolism*; D012545:Schiff Bases; D013053:Spectrophotometry / Q000379:methods
chemical_list: D012176:Retinoids; D012545:Schiff Bases; D001436:Bacteriorhodopsins; D012172:Retinaldehyde