Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins
Fig 4
Average IDP contact maps and time-dependent secondary structure formation of each residue.
(A, B) Pairwise contact occupancies were determined from MD simulations (without outlier trajectories, S2 Fig, S4 and S5 Tables) for (A) p53TAD and (B) Pup. Darker/lighter shades of blue denote contacts that are more frequently/rarely formed according to legend (vertical bar). Self-contacts, first-neighbor contacts (between residues i,i+1), and second-neighbor contacts (between residues i,i+2) are not shown since they are present in most snapshots. (C, D) secondary structure of each residue in MD simulations are predicted using the DSSP algorithm with α-helices shown in red and β-strands in blue. (E, F) In the residue clusters at the bottom, pairwise contacts with occupancies > 0.2 are depicted as an edge connecting two nodes (residues) with edge widths proportional to the pairwise contact occupancies. Labels A1–A5 denote dominant clusters in p53TAD and B1–B8 in Pup. Examples of transiently formed subclusters are indicated by dashed lines (A1.1, A1.2, and A1.3 in p53TAD and B1.1 and B1.2 in Pup).