A dynamical approach to protein folding

A Torcini, R Livi, A Politi

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22 Citations (Scopus)

Abstract

In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the native configuration. The results reported in this paper have been obtained for a two-dimensional toy-model of aminoacid sequences, whose native configurations were previously determined by Monte Carlo techniques. The somewhat controversial scenario emerging from the comparison among different thermodynamical indicators is definitely better resolved with the help of a truly dynamical description. In particular, we are able to identify the metastable states visited during the folding process by monitoring the temporal evolution of the `long-range' potential energy. Moreover, the resulting dynamical scenario is consistent with the picture arising from a reconstruction of the energy landscape in the vicinity of the global minimum. This suggests that the introduction of efficient `static' indicators too should properly account for the complex `orography' of the landscape.

Original languageEnglish
Pages (from-to)181-203
Number of pages23
JournalJournal of Biological Physics
Volume27
Issue number2
Publication statusPublished - 2001

Keywords

  • dynamical simulations
  • off lattice models
  • proteins
  • off-lattice model
  • sequences
  • kinetics
  • thermodynamics
  • equilibrium

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