Jump to main content
Jump to site search
PLANNED MAINTENANCE Close the message box

Scheduled maintenance work on Wednesday 22nd May 2019 from 11:00 AM to 1:00 PM (GMT).

During this time our website performance may be temporarily affected. We apologise for any inconvenience this might cause and thank you for your patience.

Issue 38, 2011
Previous Article Next Article

Diffusion models of protein folding

Author affiliations


In theory and in the analysis of experiments, protein folding is often described as diffusion along a single coordinate. We explore here the application of a one-dimensional diffusion model to interpret simulations of protein folding, where the parameters of a model that “best” describes the simulation trajectories are determined using a Bayesian analysis. We discuss the requirements for such a model to be a good approximation to the global dynamics, and several methods for testing its accuracy. For example, one test considers the effect of an added bias potential on the fitted free energies and diffusion coefficients. Such a bias may also be used to extend our approach to determining parameters for the model to systems that would not normally explore the full coordinate range on accessible time scales. Alternatively, the propagators predicted from the model at different “lag” times may be compared with observations from simulation. We then present some applications of the model to protein folding, including Kramers-like turnover in folding rates of coarse-grained models, the effect of non-native interactions on folding, and the effect of the chosen coordinate on the observed position-dependence of the diffusion coefficients. Lastly, we consider how our results are useful for the interpretation of experiments, and how this type of Bayesian analysis may eventually be applied directly to analyse experimental data.

Graphical abstract: Diffusion models of protein folding

Back to tab navigation

Publication details

The article was received on 12 May 2011, accepted on 13 Jul 2011 and first published on 15 Aug 2011

Article type: Perspective
DOI: 10.1039/C1CP21541H
Phys. Chem. Chem. Phys., 2011,13, 16902-16911

  •   Request permissions

    Diffusion models of protein folding

    R. B. Best and G. Hummer, Phys. Chem. Chem. Phys., 2011, 13, 16902
    DOI: 10.1039/C1CP21541H

Search articles by author