MOLECULAR MODELING OF SOLVATION OF (PRO PRO GLY)10 & RELATED COLLAGEN MIMETICS

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We are investigating the contribution of bound waters to the stability in aqueous solution of the triple-helical conformation of (Pro-Pro-Gly)10 ((PPG)10), a simple mimic of the collagen triple helix. An understanding of the factors stabilizing this molecule may contribute to the design of intelligent polymers and biomaterials. We previously constructed a model for bound waters in (PPG)10 in which bridging hydrogen bonds are formed between each bound water and a pair of backbone carbonyls on different polypeptide chains. The waters forming the bridges are in sterically crowded positions, leading to unusual behavior, such as a large increase in the melting temperature of (PPG)10 when water is replaced by deuterium oxide. We are now testing the validity of this model further by using molecular dynamics (MD) simulations of (PPG)10 in a bath of explicit water molecules, to study the formation of the aforementioned water bridges starting with waters in arbitrary locations. We will monitor the dynamic behavior, percent occupancy, and lifetime over the timespan of a long simulation. We have seen several solvation phenomena, including both our model (at less than 100% occupancy) and the types of hydration displayed in a recently published crystal structure of (PPG)10. We are also investigating solvation effects on the relative stability of triple-helical structures composed of (Gly-Pro-Ala)10, (Gly-Ala-Pro)10, and (Pro-Pro-[Beta-alanine])10. MidasPlus and the facilities of the UCSF Computer Graphics Laboratory have been used for modeling these collagen mimetics into starting conformations for calculations, for observing the structures resulting from calculations.