Fig 1.
Domain structures of A) p53, and B) CREB-binding protein (CBP).
Also shown in A) include: the sequence of p53-TAD (in bold fonts with phosphorylation sites marked in red), known cancer mutants (in light fonts below the sequence; three additional mutants, P60L/S/Q, are not shown), and its key interaction partners to be studied. Both TAD sub-domains, TAD1 (1–40) and TAD2 (41–61), contain short helices (pα1, pα2) that form upon specific binding to various targets. Four separate CBP domains (colored in grey) can interact with p53-TAD. Abbreviations: TAD: transactivation domain (1–61); P-rich: proline rich region; DBD: DNA-binding domain (102–292); TD: tetramerization domain (325–356); NRD: negative regulatory domain; TAZ1 (340–439) & TAZ2 (1764–1855): cysteine-histidine-rich regions; KIX (586–572), NCBD: nuclear receptor coactivator binding domain (2059–2117).
Fig 2.
A) Averaged residue helicity profiles calculated using different 80-ns segments of the control and folding RE-GA simulations of wild-type p53-TAD.
B) Probability distributions between termini and D21-K/N24 calculated from the last 80-ns of RE-GA simulations of the wild-type p53-TAD and two cancer-associated mutants. The inter-residue distances were calculated as the distances between corresponding CA atoms.
Fig 3.
Probabilities of long-range contacts calculated from the last 80-ns segments of the folding (upper half) and control (lower half) RE-GA simulations.
Contours are drawn from 0.06 with an equidistant increment of 0.04. Residues are considered to be in contact if the minimal heavy atom distance is no greater than 4.2 Å. The correlation efficient of two contacts is 0.91 and the RMSD is 0.016.
Fig 4.
A) Comparison of the average residue helicity profile with the secondary Hα chemical shifts for the wild-type p53-TAD[38].
The uncertainties of the average residue helicities were estimated as the difference between values calculated from the folding and control RE-GA runs (see Fig 2A). The reference random coil values were taken from statistics of the BMRB database[50]. B) Back-calculated RDC profiles in comparison with the experimental one[39]. Note that the calculated profiles were globally scaled to best reproduce the experimental values.
Fig 5.
Comparison of theoretical (red traces) and experimental (black bars) PRE effects induced by four site-specific spin labels.
The theoretical profiles were calculated from the last 80-ns of the folding simulation of wild-type p53-TAD. The experimental profiles were extracted from the Supplementary Materials of Stancik et al. (2008) [43]. The correlation coefficient between the theoretical and experimental profiles is 0.5.
Fig 6.
Residue helicity profiles for the wild-type p53-TAD and five cancer mutants, derived from the last 80-ns segments of the RE-GA simulations.
Estimated uncertainties are similar for all profiles and only shown for the wild-type for clarity.
Fig 7.
Distributions of helical substates of the wild-type p53-TAD and five cancer mutants, calculated from the last 80-ns of folding RE-GA simulations.
Contours are drawn 0.001, 0.002, 0.004, 0.008, 0.012, 0.024 and 0.048.
Fig 8.
Average contact probabilities derived from RE-GA simulations of the wild-type p53-TAD (black contours), K24N (red; lower half), and N29K/N30D (violet; upper half).