title: On modeling the vibrational spectra of 14-s-cis retinal conformers in bacteriorhodopsin.
abstract: The vibrational properties of 13-cis, 14-s-trans and 13-cis, 14-s-cis protonated retinal Schiff base model compounds are explored with MNDO calculations. In particular, the effect of isomerization about the C14-C15 single bond on the vibrational properties of the deuterium in-plane rocking vibrations has been examined. Our MNDO calculations, using a variety of lysine models, lysine conformations and Schiff base charge environments, demonstrate that the C14-D and C15-D in-plane rocking vibrations in the 14,15-dideuterio retinal protonated Schiff base are strongly coupled in 13-cis, 14-s-cis molecules producing a splitting of ca. 80 cm-1 between the symmetric and antisymmetric rocking mode combinations but that these modes are only weakly coupled in 14-s-trans molecules. This analysis demonstrates that the 14,15-dideuterio labeling method developed earlier for determining C14-C15 conformation (S.P.A. Fodor, W. T. Pollard, R. Gebhard, E. M. M. van den Berg, J. Lugtenburg and R. A. Mathies, Proc. Natl. Acad. Sci. USA, 85, (1988) 2156-2160) is valid, and hence that the structure of the retinal chromophore in bacteriorhodopsin's L550 intermediate is 13-cis, 14-s-trans. The reasons for the misleading conclusions derived from MNDO calculations performed earlier by Schulten and Tavan are discussed.
authors.affiliation: Chemistry Department, University of California, Berkeley 94720, USA.
authors.forename: R A
authors.initials: RA
authors.lastname: Mathies
authors.forename: X Y
authors.initials: XY
authors.lastname: Li
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000378:metabolism; D008239:Lysine; D008968:Molecular Conformation; D011487:Protein Conformation; D012172:Retinaldehyde / Q000737:chemistry* / Q000378:metabolism; D012545:Schiff Bases; D013237:Stereoisomerism; D014732:Vibration
chemical_list: D012545:Schiff Bases; D001436:Bacteriorhodopsins; D008239:Lysine; D012172:Retinaldehyde