Model calculations on the amide-I infrared bands of globular proteins

Abstract

Model calculations are performed on the amide-I infrared (ir) bands of globular proteins by assigning one oscillator with a transition dipole to each peptide group. Coupling between these oscillators is introduced through the transition dipole coupling mechanism. As examples of application of the model, the ir spectra in the amide-I region of eight representative proteins, viz., carbonmonoxy myoglobin, ribonuclease A, α-lactalbumin, lysozyme, flavodoxin, carboxypeptidase A, concanavalin A, and β-trypsin are calculated. Good agreement is obtained between the calculated and observed amide-I band envelopes. Some structure-spectrum correlations are discussed on the basis of the model calculations. The presence of bands with significant ir intensities for myoglobin in the region below 1640 cm−1 is consistent with its x-ray structure having no β sheet. Analysis of the contributions of β sheets to the amide-I band envelopes shows that parallel, antiparallel, and mixed parallel/antiparallel β sheets give rise to strong ir bands at a similar position in the wave number region below 1650 cm−1, and that no band in the region above 1650 cm−1 can be regarded as a reliable marker of antiparallel β sheets. The contributions of non-α-non-β parts spread over a wide wave number region. The differences in the amide-I band envelopes between α-lactalbumin and lysozyme originate most probably from the structural differences between the α-helical parts near the N termini of these proteins.