Kinetics of the Wako-Saitô-Muñoz-Eaton model of protein folding.
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 equilibration 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.
Zamparo
Marco
M
Dipartimento di Fisica and CNISM, Politecnico di Torino, corso Duca degli Abruzzi 24, Torino, Italy. marco.zamparo@polito.it
Pelizzola
Alessandro
A
D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
D011506:Proteins