Inter-peptide interaction and delocalization of amide I vibrational excitons in myoglobin and flavodoxin

The amide I vibrational normal-mode analyses of two globular proteins, myoglobin and flavodoxin, were carried out and the spatial delocalization and phase correlation of each normal mode was studied. The Hessian matrix in the restricted space constructed by the N peptides was obtained by using both ab initio quantum chemistry calculation results and empirical transition dipole coupling model. For both of the two proteins, the amide I normal modes are fairly delocalized and on average about 15% of the polypeptides in myoglobin and flavodoxin are participated in the formation of each amide I normal mode. The analysis of vibrational phase correlation of myoglobin reveals that the high-frequency amide I normal modes are mostly (symmetric) A-mode like, whereas the low-frequency ones are (antisymmetric) E-mode like. For flavodoxin, among the three distinct bands at 1653, 1636, and 1628 cm−1, the high-frequency modes are found to be fairly localized in the four α helices, the low-frequency modes around 1628 cm−1 are strictly localized in the five β sheets, and the midfrequency modes around 1636 cm−1 are delocalized in both the α helices and β sheets. Effects of the diagonal disorder on the amide I band of both proteins were studied. We found that the sharp peak at 1628 cm−1 in the resolution enhanced amide I infrared spectrum of flavodoxin is a direct signature that the through-space interactions between two different β sheets exist.