The protein folding transition state: insights from kinetics and thermodynamics.
We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic definition of the transition state is based on the folding probability analysis method, and therefore on the selection of conformations with 0.4<P(fold)<0.6, while for the equilibrium characterization we consider conformations for which the evaluated values of several reaction coordinates correspond to the maximum of the free energy measured as a function of those reaction coordinates. Our results reveal a high degree of structural similarity between the ensembles determined by the two methods. However, the folding probability distribution of the conformations belonging to our definition of the equilibrium transition state (0.2<P(fold)<0.8) is broader than that displayed by the kinetic transition state.
Travasso
Rui D M
RD
Departamento de Física, Centro de Física Computacional, Universidade de Coimbra, Coimbra 3004-516, Portugal. rui@lca.uc.pt
Faísca
Patrícia F N
PF
Rey
Antonio
A
D007700:Kinetics; D009010:Monte Carlo Method; D044367:Phase Transition; D011336:Probability; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics