Kinetics of the Wako-Saito-Munoz-Eaton Model of Protein Folding

Abstract

We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach, for which we prove that (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the infinite time limit, and (iii) the folding rate is an upper bound of the exact one. The kinetics is compared to the exact one for a small peptide and to Monte Carlo simulations for a longer protein, then rates are studied for a real protein and a model structure.

arXiv comment4 pages, 4 figures

References in corpus (4)

• Cluster Variation Method in Statistical Physics and Probabilistic Graphical Models
• Exact Solution of the Munoz-Eaton Model for Protein Folding
• Analytical solution of 1D lattice gas model with infinite number of multiatom interactions
• Exactness of the cluster variation method and factorization of the equilibrium probability for the Wako-Saito-Munoz-Eaton model of protein folding

Cited by in corpus (14)

• An Ising-Like model for protein mechanical unfolding
• Mechanical unfolding and refolding pathways of ubiquitin
• Downhill versus two-state protein folding in a statistical mechanical model
• Rate Determining Factors in Protein Model Structures
• Protein mechanical unfolding: a model with binary variables
• Rigorous results on the local equilibrium kinetics of a protein folding model
• Analysis of the Equilibrium and Kinetics of the Ankyrin Repeat Protein Myotrophin
• Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model
• A simplified exactly solvable model for beta-amyloid aggregation
• Pathways of mechanical unfolding of FnIII_{10}: low force intermediates
• Multi-Dimensional Theory of Protein Folding
• Large Deviations in Renewal Models of Statistical Mechanics
• An exactly solvable model for a beta-hairpin with random interactions
• Transfer matrix solution of the Wako-Saitô-Muñoz-Eaton model augmented by arbitrary short range interactions