Figure 1.

Folding pattern of p53 (A) Evolution of secondary structures of the p53 peptides as a function of simulation time Colour code: purple, α-helix; red, π-helix; yellow, β-sheet; green, isolated bridge; cyan, turn; white, random coil. (B) Hydrogen bond statistics of the secondary structures averaged over 100 ns of simulations; the lifetime of hydrogen bonds in 5 ns windows is shown as: Space ( ) for 0-5%, dot (.) for 5-20%, dash (-) for 20-40%, o for 40-60%, x for 60-80%, star (*) for 80-95% and at (@) for 95 – 100%. (C) Cluster analysis of secondary structures in terms of RMSD as a function of simulation time; a representative structure (N-terminus in blue, C-terminus in red) from each cluster is shown with % of population; colour code of the plot: red is helix, yellow is β-Sheet and green is random structure. Conserved residues F19, W23 and L26 are shown as sticks. (D) Snapshot of the putative nucleation conformation of p53during the folding simulation; nucleation residue L22 and hydrogen bond between D21 side chain and backbone of W23 are shown. Hydrogen Bonds are shown as red dotted lines.

Mavinahalli et al. BMC Genomics 2010 11(Suppl 1):S5   doi:10.1186/1471-2164-11-S1-S5