Volume 102, Number 1, April 2013
|Number of page(s)||5|
|Published online||10 April 2013|
Nonequilibrium dynamics of an exactly solvable Ising-like model and protein translocation
1 Dipartimento di Scienza Applicata e Tecnologia, CNISM and Center for Computational Studies, Politecnico di Torino - Corso Duca degli Abruzzi 24, I-10129 Torino, Italy, EU
2 INFN, Sezione di Torino - Via Pietro Giuria 1, I-10125 Torino, Italy, EU
3 Human Genetics Foundation, HuGeF - Via Nizza 52, I-10126 Torino, Italy, EU
Received: 23 January 2013
Accepted: 13 March 2013
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free-energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model is then applied to the protein translocation phenomenon, taking inspiration from a recent experiment on the green fluorescent protein pulled by a molecular motor. The average translocation time is evaluated exactly, and the analysis of single trajectories shows that translocation proceeds through an intermediate state, similar to that observed in the experiment.
PACS: 05.50.+q – Lattice theory and statistics (Ising, Potts, etc.) / 87.15.Cc – Folding: thermodynamics, statistical mechanics, models, and pathways
© EPLA, 2013
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