A local-mode model for understanding the dependence of the extended amide III vibrations on protein secondary structure.
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.
Weymuth
Thomas
T
ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
Jacob
Christoph R
CR
Reiher
Markus
M
D000577:Amides / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D014732:Vibration
D000577:Amides; D011506:Proteins