Folding kinetics of an entangled protein
Fig 6
Intermediate state ensemble contact maps for the entangled RD1 protein.
Probability of native contact formation for the entangled RD1 protein in the longer-lived IT ensemble (above diagonal) and the short-lived IE− ensemble (below diagonal). Both intermediate state ensembles are detected at T = 0.9Tf in Fig 5. The red arrows mark the location of the native contacts involving the first 6 N-terminal residues, which are likely to be formed in IE− whereas they are less likely to be formed in IT. Among the former ones, the “trap-avoiding” native contacts framed in red are those whose formation probabilities differ most in the two ensembles (see the Ensemble definition and pathway classification subsection for details). The shaded area framed in blue contains 28 out of the 30 natively entangled contacts, with G′ < −0.75. The native contacts framed in magenta are the “first-entangling” ones more likely to be formed in IE− (see the Ensemble definition and pathway classification subsection for details).