Amide I infrared spectral features characteristic of some untypical conformations appearing in the structures suggested for amyloids.
Amide I infrared (IR) spectral features are studied, by using the density functional theoretical method, for two untypical (but possibly rather prevalent) structures inspired from those recently suggested for amyloids: a structure consisting of loop regions in the (alpha L, alpha R) conformation stacked to form an alpha-sheet, and a structure involving some main-chain peptide groups (of any residues) and some side-chain amide groups of glutamine and asparagine residues closely located with each other. The amide I vibrational (off-diagonal) coupling constants are examined by extracting them from the calculated Cartesian-based force constants with the average partial vector method and by comparing them with those estimated on the basis of the transition dipole coupling mechanism. It is suggested that the amide I IR band characteristic of the alpha-sheet conformation in dry environment (without hydrogen bonding to solvent water molecules) is located in a high-frequency region (approximately >1670 cm(-1), somewhat higher than that of alpha-helix), because of the dependence of the diagonal (uncoupled) frequency and the off-diagonal coupling constant on the Phi and Psi dihedral angles. It is also shown that the amide I vibrations of the closely located peptide and amide groups are strongly coupled through-space with each other, and in the presence of this type of strong vibrational coupling, a noticeable change in the IR intensity upon (13)C=O substitution may occur even for a mode that arises mainly from an unsubstituted group and is not much shifted in frequency. The meaning of these results in the interpretation of observed amide I spectral profiles, especially the possible usefulness of IR spectroscopic measurements for detecting those untypical structures in the process of amyloid formation, is also discussed.
Torii
Hajime
H
Department of Chemistry, School of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan. torii@ed.shizuoka.ac.jp
D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D000682:Amyloid / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared / Q000379:methods*; D014867:Water / Q000737:chemistry
D000577:Amides; D000682:Amyloid; D012997:Solvents; D014867:Water