Dynamical frustration of protein's environment at the nanoseconds time scale

Research output: Contribution to journalArticlepeer-review

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 languageEnglish
Pages (from-to)139-144
Number of pages6
JournalJournal of Molecular Liquids
Volume145
Issue number3
Early online date25 Jun 2008
DOIs
Publication statusPublished - 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.2008.06.012

Keywords

  • dynamical frustration
  • protein folding
  • statistical complexity
  • computational mechanics
  • molecular dynamical system
  • phase space trajectory
  • protein's environment

Fingerprint

Dive into the research topics of 'Dynamical frustration of protein's environment at the nanoseconds time scale'. Together they form a unique fingerprint.

Cite this