title: A local-mode model for understanding the dependence of the extended amide III vibrations on protein secondary structure.
abstract: The extended amide III region in vibrational spectra of polypeptides and proteins is particularly sensitive to changes in secondary structure. To investigate this structural sensitivity, we have performed density-functional calculations on the small model compound N-acetyl-l-alanine-N-methylamide, which are analyzed using the recently developed analysis in terms of localized modes [J. Chem. Phys. 2009, 130, 084106]. We find that the local modes obtained for different backbone conformations are actually rather similar. To probe the secondary structure sensitivity, we investigate the dependence of the local-mode frequencies and coupling constants on the torsional angles phi and psi. This enables us to set up a local-mode model of the extended amide III region for better understanding its structural sensitivity.
authors.affiliation: ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Weymuth
authors.forename: Christoph R
authors.initials: CR
authors.lastname: Jacob
authors.forename: Markus
authors.initials: M
authors.lastname: Reiher
mesh_terms: D000577:Amides / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D014732:Vibration
chemical_list: D000577:Amides; D011506:Proteins