Folding kinetics of an entangled protein
Fig 7
Examples of exponential fits to the contact formation probabilities for the entangled RD1 protein.
Two examples of native contact formation probabilities as a function of time, averaged over the 52 refolding trajectories that fold to the RD1 protein native structure at T = 0.9Tf through the fast channel, and of the corresponding exponential fits. Time is measured in MD steps. Both the average time series and the corresponding block averages (see the Exponential fit of contact formation curves subsection for details) are plotted (see legend). The block averages are fit to the exponential function reported in the legend and the resulting fits are shown in the plots. The fit parameters are A, the saturation value of the contact formation probability in the folded state, B, the gain of the former quantity in going from the unfolded to the final folded state, and k, the contact folding rate (See Exponential fit of contact formation curves section for details). Top row: native contact between V6 and E25; one of the “trap-avoiding” N-terminal thread contacts framed in red in Fig 6 and in the left panel of Fig 8. Bottom row: native contact between K23 and I37; one of the “first-entangling” contacts framed in magenta in Fig 6 and in the left panel of Fig 8.