The investigation of the electronic structure of periodic and non-periodic collagen models

Abstract

Collagen is a protein which is not periodic, but its sequence still has some well defined regularities. We have performed model investigation for the electronic structure of this protein which is one of the few native polypeptides which does not possess a nearly random sequence (intermediate case between periodic polypeptides and polypeptides with random sequences). The total electron density of states has been determined for model polypeptide chains of the type I collagen triple helix, with priodic and aperiodic amino sequences. Calculations have been performed using the negative factor counting technique in its ab initio Hartree—Fock matrix block form. The well-known sequence regularities of collagen have been taken into account, in order to simplify the model calculations. Beside glycine, proline, hydroxyproline and alanine, only the next two most frequently occurring amino acid residues (glutamine and arginine) have been incorporated in the sequences. The conformation of the polypeptide chain was that occurring in the collagen triple helix. It has been taken from previous empirical potential energy calculations of collagen-like model triple helices by Némethy and Scheraga. The density of state histograms for the periodic polypeptide chains show only very narrow peaks in both the valence and conduction bands attributable to the sequence regularities, while the aperiodic chains exhibit both narrow peaks and broader allowed regions in both bands. In other words, the electronic structure of the aperiodic model chains investigated falls between those for periodic and completely random polypeptides. The results are discussed in terms of the general regularities of the collagen sequence.