Folding kinetics of an entangled protein
Fig 5
Folding pathways of the entangled RD1 protein below the folding transition temperature.
Log-scale histogram contour plot in the (Q, 〈G′〉) plane from 100 refolding trajectories for the RD1 protein at T = 0.9Tf. 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 and the colour scale are the same as in Fig 3. Letters refer to the unfolded (U), folded (F), trap intermediate (IT), entangled intermediate with negative chirality (IE−) states, and to the positive chirality configurations populated during refolding (IE+). Representative snapshots for each state are shown with the same colour as in the upper left panel of Fig 1. In IT, the non-correct threading of the N-terminal portion (in blue) through the loop (in red) which eventually becomes entangled in the folded state F is apparent. The arrows show the different transitions observed: fast folding from U to F through IE−, possible disentanglement from IE− to U, trapping from U to IT, folding by threading from IT to F, backtracking from IT to U.