MOLECULAR MODELLING OF CONFORMATIONS OF NON TRIPLE HELICAL REGIONS OF COLLAGEN

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We have investigated the deviation from the triple-helical polyproline-II (ppII) conformation of a proline-poor sequence within collagen. This segment, GTPGPQGIAGQRGVV, referred to as P15, acts as a cell adhesion peptide: It binds to receptors on cells and promotes differentiation of these cells. Small peptides derived from P15 act in a similar fashion. There are numerous practical applications of research relating to these peptides, since the ability to induce cell binding and differentiation is relevant to wound healing, tissue repair, and the design of medical and dental prostheses. Our ultimate goal is to design, for biomedical applications, a non-peptide compound that mimics the structure and biological activity of the active core of P15 and the P15-derived peptide s. This core appears to be the sequence Isoleucine-Alanine. We have examined ways in which a beta-bend could fit into a native collagen molecule. In particular, we have examined how a bend at the central GIAG could fit into collagen without disrupting the conformations of the flanking regions of the same strand. We have found, using graphical modelling and molecular mechanics, that a bend at GIAG, surrounded by two different types of extended conformations, has the same end-to-end distance as an all-pp-II P15 sequence, with an insignificant difference in energy from the pp-II conformation. The most extended conformation for the QRGVV sequence was found to be that with phi and psi backbone torsion angles of approximately -170 and 165 degrees, respectively, while for GTPGPQ the most extended conformation was found to be that with phi and psi approximately equal to -85 and 85 degrees, because of the kinks in the chain introduced by the proline residues. This demonstrates that the combination of the three modelled non-pp-II conformations can fit into the relevant strand of collagen without disrupting the pp-II conformation of the strand found beyond the termini of p15. MidasPlus and the facilities of the UCSF Computer Graphics laboratory have been used for graphical modelling and visualization of the molecular geometry, for preparing P15 in the starting structures for the theoretical calculations, and for monitoring the structures after these calculations.