Abstract
A 21-residue peptide in explicit water has been simulated using classical molecular dynamics. The system's trajectory has been analysed with a novel approach that quantifies the process of how atom's environment trajectories are explored. The approach is based on the measure of Statistical Complexity that extracts complete dynamical information from the signal. The introduced characteristic quantifies the system's dynamics at the nanoseconds time scale. It has been found that the peptide exhibits nanoseconds long periods that significantly differ in the rates of the exploration of the dynamically allowed configurations of the environment. During these periods the rates remain the same but different from other periods and from the rate for water. Periods of dynamical frustration are detected when only limited routes in the space of possible trajectories of the surrounding atoms are realised.
| Original language | English |
|---|---|
| Pages (from-to) | 139-144 |
| Number of pages | 6 |
| Journal | Journal of Molecular Liquids |
| Volume | 145 |
| Issue number | 3 |
| Early online date | 25 Jun 2008 |
| DOIs | |
| Publication status | Published - 15 May 2009 |
Bibliographical note
NOTICE: this is the author’s version of a work that was accepted for publication in Journal of molecular liquids. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published Nerukh, D, 'Dynamical frustration of protein's environment at the nanoseconds time scale', Journal of molecular liquids, vol 145, no. 3, (2009) DOI http://dx.doi.org/10.1016/j.molliq.2008.06.012Keywords
- dynamical frustration
- protein folding
- statistical complexity
- computational mechanics
- molecular dynamical system
- phase space trajectory
- protein's environment