Simulated annealing and molecular dynamics of an elastin-related tetrapeptide in aqueous solution

Abstract

For the first time a fully unrestrained simulated annealing of an aqueous solution is reported: a dilute solution of the elastinrelated tetrapeptide AcGlyLeuGlyGlyNMe has been heated to high temperature and cooled slowly to room temperature and pressure by using a heuristic molecular dynamics approach in the absence of fictitious potential. The peptide conformational patterns during the final equilibrium stages of the annealed states thus obtained have been characterized. The time constants τ T and τ P , which control the temperature and pressure relaxation, respectively, and thus the energy dissipation rate, have been varied and successful criteria fixed. The procedure is amenable, although attention must be paid to prevent vaporization of the system for particularly slow coolings at high temperature. The tetrapeptide in solution at ambient conditions is characterized by conformational disorder with large-amplitude motions giving rise to endless formation and breakage of γ- and β-turns, according to known experimental evidence. This dynamic, high-entropy behavior is in agreement with the mechanism proposed for the elasticity of elastin, of which the peptide represents a relevant block, and with the dynamic nonlinear behavior recently found by us for the isolated molecule.