Molecular vibrations and normal modes in L-prolyl-glycyl-glycine using Wilson GF matrix method.

Collagen is one of the most important proteins containing mostly proline hydroxyproline and glycine. In collagen, approximately 33 percent of the amino acid residues are glycine and they occur at every third position, whereas remaining percentage is constituted by mainly proline or hydroxyproline and some part by alanine etc. having no definite positional placement in the chain. Thus, a study of conformation of proline and glycine containing dipeptides and tripeptides is important for understanding the conformation of collagen as a sequence of its constituent amino acids. In the present communication, we have studied spectral features of L-proline, L-prolyl-glycine (PG), L-prolyl-alanine (PA), L-glycylglycine (GG), Collagen and L-prolyl-glycyl-glycine (PGG). We have carried out detailed normal mode analysis of only PGG, because interpretation of spectra of other proline and glycine containing peptides can be treated as derivatives of this molecule. Urey-Bradley force field, which involves non-bonded interactions in the gem and cis configurations is used for calculation of normal modes. The "best-fit" set of constants are generated for PGG.

Vibrational dynamics and heat capacity in polyglycine II.

The earlier works on the vibrational dynamics of polyglycine II (PG II) suffer from several infirmities, which not only suppress the dynamical nature of normal modes, but also lead to several incorrect assignments and interactive constants of the potential field. In this study, we have re-examined the phonon dispersion profiles of PG II using Higgs method for evaluation of phase-related normal modes and have attempted to remove the infirmities, as far as possible. The Wilson's GF matrix method combined with the Urey-Bradley force field has been used for normal mode analysis. This potential field leads to correct assignments of Raman, infrared and inelastic neutron scattering frequencies. Characteristic features of the dispersion curve (v versus delta/pi plot), such as repulsion and regions of high density-of-states have been interpreted. In addition, the heat capacity as a function of temperature has been obtained via density-of-states. It agrees well with the experimental data and is being reported for the first time.