Folding kinetics of an entangled protein
Fig 3
Folding thermodynamics of the entangled RD1 protein at the folding transition temperature.
Contour plot of the dimensionless free energy surface in the (Q, 〈G′〉) plane for the entangled RD1 protein. The free energy is evaluated as the negative of the log-scale histogram of data collected from 8 long equilibrium trajectories at T = Tf. Histogram negative log-counts are smoothed using KDE (see the Ensemble definition and pathway classification subsection for details) and shifted in order for their minimum to be 0. Contour levels correspond to approximately 0.4 in log-histogram units. The bottom horizontal inset shows the dimensionless free energy profile F(Q) obtained using the WHAM method (see the Weighted histogram method subsection). The left vertical inset shows the dimensionless free energy profile F(〈G′〉) after the projection onto the entanglement indicator.