1. The Influence of Configurational Dependent Diffusion on Fast Protein Folding Dynamics Jin Wang, SUNY at Stony Brook
1. Diffusion coefficients versus Q and compactness Z : Diffusion coefficient D (left axis) and average number of nonbonded contacts ( Z ) (right axis) as a function of reaction coordinate Q (number of native spatial contacts) for low- and high hydrophobicity cases (decrease in Q).
2. Free energy and folding times versus reaction coordinate Q: Free energy F(Q) and F(Q) - kTln(D(Q)/D0) profiles (controlling the kinetic first passage time with Q-dependent diffusion relative to constant diffusion) as a function of reaction coordinate Q. The effect of configurational dependent diffusion is to shift the thermodynamic transition state and increase the effective free energy barrier height for folding kinetics.