Analysis of the distributed computing approach applied to the folding of a small beta peptide

  • Paci E
  • Cavalli A
  • Vendruscolo M
 et al. 
  • 1


    Mendeley users who have this article in their library.
  • N/A


    Citations of this article.


In the recently proposed distributed computing approach to protein folding a very large number of short independent simulations is performed. Using this method, folding events on a time scale orders of magnitude shorter than the experimental one have been reported. However, it has also been observed that the folding process is not an elementary kinetic step and that the presence of initial lag phases can bias short simulations toward atypical pathways. We study here a 20-residue three-stranded antiparallel beta-sheet peptide whose equilibrium properties can be characterized by atomistic molecular dynamics simulations. We found that the folding rate of this peptide is estimated correctly by the distributed computing approach when trajectories > approximately 1/100 of the equilibrium folding time are considered. We also found that the fastest folding events occur through high-energy pathways, which are unlikely under equilibrium conditions. These very fast folding pathways do not relax within the equilibrium denatured state that is stabilized by the transient presence of both native and non-native interactions, and they are characterized by the nearly simultaneous formation of the two beta-hairpins and a very small number of non-native contacts

Author-supplied keywords

  • Computer Simulation
  • Models,Molecular
  • Molecular Dynamics Simulation
  • Peptides
  • Protein Denaturation
  • Protein Folding
  • Protein Structure,Secondary
  • Research Support,Non-U.S.Gov't
  • Solvents
  • Stochastic Processes
  • Time
  • Time Factors
  • analysis
  • chemical synthesis
  • chemistry

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

  • PMID: 12815104


  • E Paci

  • A Cavalli

  • M Vendruscolo

  • A Caflisch

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free