Folding kinetics of an entangled protein
Fig 2
Folding thermodynamics of the non-entangled SH3 domain.
Probability of native contact formation in the transition state ensemble at the folding temperature for the non-entangled SH3 domain. The inset shows the dimensionless free energy profile F(Q) as a function of the fraction of native contacts Q at the folding temperature. The shaded area in the inset highlights the interval of Q values used to define the transition state ensemble. (a) Energy function with 12/6 Lennard-Jones potential. (b) Energy function with 12/10 Lennard-Jones potential. The similarity of the two contact maps can be quantified by computing correlation coefficients between the respective contact formation probabilities. Pearson’s linear correlation coefficient: r = 0.981; Spearman’s rank correlation coefficient: r = 0.985; in both cases p–value < 10−77.