SM&FT 2006

 

Wako-Saito-Munoz-Eaton model of protein folding

 

 

 

Alessandro Pelizzola

 

 

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 long 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 then studied for a real protein and a model structure. Applications to pulling phenomena are also addressed.