Conformational chaos and biomolecular instability in aqueous solution

Abstract

The glycine-rich tropoelastin tetrapeptide Ac-Gly-Leu-Gly-Gly-NMe has been modeled in aqueous solution by means of molecular dynamics simulations and the conformational motions have been characterized using nonlinear dynamics theory. Large amplitude fluctuations of the peptide backbone and H-bond patterns are detected. The end-to-end vector Ree undergoes anomalous diffusion with antipersistent fractional Brownian motion according to chaotic motions of molecules on fractal media. The vibrational picture of the intramolecular vectors shows a spatiotemporal self-similar disorder along the peptide chain on large scale observation demonstrating a high entropy state. The conformational chaos of the peptide is a consequence of the nonlinear effects of the attractive interactions between residues developed in aqueous solution due to water being a poor solvent. The viscous drag is high-lighted and is thought to be due to the percolation network of disordered H-bonded water molecules. The method of the reconstruction of the phase-space using the embedding theorem is presented and the invariant properties of the peptide are calculated. The existence of a low dimensional chaotic attractor according to dissipative systems has been demonstrated. The dynamical high entropy state of the peptide in solution is in agreement with the proposed mechanism of the transition-to-chaos for the elastin elasticity.