Computing the transition state populations in simple protein models

S. Banu Ozkan, Ken A. Dill, Ivet Bahar

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


We describe the master equation method for computing the kinetics of protein folding. We illustrate the method using a simple Go model. Presently most models of two-state fast-folding protein folding kinetics invoke the classical idea of a transition state to explain why there is a single exponential decay in time. However, if proteins fold via funnel-shaped energy landscapes, as predicted by many theoretical studies, then it raises the question of what is the transition state. Is it a specific structure, or a small ensemble of structures, as is expected from classical transition state theory? Or is it more like the denatured states of proteins, a very broad ensemble? The answer that is usually obtained depends on the assumptions made about the transition state. The present method is a rigorous way to find transition states, without assumptions or approximations, even for very nonclassical shapes of energy landscapes. We illustrate the method here, showing how the transition states in two-state protein folding can be very broad ensembles.

Original languageEnglish (US)
Pages (from-to)35-46
Number of pages12
Issue number1
StatePublished - Jan 2003
Externally publishedYes


  • Go model
  • Kinetics of protein folding
  • Master equation method
  • Transition state
  • Two-state fast-folding

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry


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