Understanding normal modes of proteins

Abstract

In order to obtain accurate normal modes of proteins, which is a prerequisite for detailed analyses in a variety of vibrational spectroscopic techniques, reliable conformation-dependent force fields are required. We discuss the use of empirical polypeptide force fields for this purpose, since they have generally been quite successful in reproducing spectra of synthetic polypeptides. Although their limitations are motivating our development of a spectroscopically determined force field (SDFF), empirical force fields can still provide important insights into the normal modes of proteins. We illustrate this by calculations on deoxymyoglobin. Together with ab initio dipole derivatives, amide I and amide II IR band profiles have been computed. These, together with the eigenvectors, show how helix irregularity and force constant variation can influence the delocalization of displacements in the mode, and the shape and breadth of observed bands. The influence of rigid peptide group geometry on the low-frequency density-of-states is also examined.