title: Vibrational coupling between helices influences the amide I infrared absorption of proteins: application to bacteriorhodopsin and rhodopsin.
abstract: The amide I spectrum of multimers of helical protein segments was simulated using transition dipole coupling (TDC) for long-range interactions between individual amide oscillators and DFT data from dipeptides (la Cour Jansen et al. J. Chem. Phys.2006, 125, 44312) for nearest neighbor interactions. Vibrational coupling between amide groups on different helices shift the helix absorption to higher wavenumbers. This effect is small for helix dimers (1 cm(-1)) at 10 Å distance and only moderately affected by changes in the relative orientation between the helices. However, the effect becomes considerable when several helices are bundled in membrane proteins. Particular examples are the 7-helix membrane proteins bacteriorhodopsin (BR) and rhodopsin, where the upshift is 4.3 and 5.3 cm(-1), respectively, due to interhelical coupling within a BR monomer. A further upshift of 4.0 cm(-1) occurs when BR monomers associate to trimers. We propose that interhelical vibrational coupling explains the experimentally observed unusually high wavenumber of the amide I band of BR.
authors.affiliation: Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm, Sweden.
authors.forename: Eeva-Liisa
authors.initials: EL
authors.lastname: Karjalainen
authors.forename: Andreas
authors.initials: A
authors.lastname: Barth
mesh_terms: D000577:Amides / Q000737:chemistry*; D001436:Bacteriorhodopsins / Q000737:chemistry*; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012243:Rhodopsin / Q000737:chemistry*; D017550:Spectroscopy, Fourier Transform Infrared; D014732:Vibration
chemical_list: D000577:Amides; D001436:Bacteriorhodopsins; D012243:Rhodopsin