Conformational non-linear dynamical behavior of the peptide Boc-Gly-Leu-Gly-Gly-NMe

Abstract

The conformational motion of a peptide has been investigated by means of molecular dynamics simulations and has been characterized in the time and the frequency domains. The tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe has been considered as a model for some repetitive amino acid sequences of glycine-rich regions of elastin, which could play a key role in the entropic elasticity mechanism. The classical tools of dynamical analysis (time series, spectral density, time correlation functions, delay maps) have been used and new methods, introducing the idea of travelling trajectory packets and trajectories in the frequency space, have been developed. In vacuo, non-ergodic, essentially quasiperiodic motion has been revealed and solitons have been observed according to the non-linear dynamical behavior of systems with small anharmonic perturbation. This particularly concerns the dynamics of the end-to-end distance, a global variable very sensitive to the whole conformational flexibility of the model molecule. The dynamical picture has been joined with the experimentally observed conformational disorder and with the amplitude instability of KAM theory for non-linear systems: a transition is hypothesized from quasiperiodic (solitons) to ergodic motion (Hamiltonian chaos) for the peptide in solution and the entropic mechanism of elastin elasticity is interpreted from a new and unitary dynamical point of view.