Fig. 8: Cancer variants in TP53 could modify the population-shift mechanism induced by S-nitrosylation.

A The green cartoon shows the AlphaFold model of the tumor protein 53 (p53). We show, as a reference, the location of the DNA from the X-ray structure of the p53 tetramer (PDB entry 3KZ8) as a grey transparent cartoon. We used AlphaFill to include the missing zinc atom (grey sphere) in the DNA-binding domain of p53. The stick and ball representation highlight the S-nitrosylated site C124 (SNO, orange), proximal C135 and C141 (proxy, blue), and K120 (dark green), a key residue for interaction with DNA located in the DNA-binding loop L1. B We analyzed the coarse-grained models of the variants of p53 in the proximity of the SNO site and proximal cysteines and compared them to the wild-type (WT) p53. The heatmaps summarized the values calculated for the SNO site C124 and proximal C135 and C141 (left and right heatmap, respectively). Each heatmap shows the distance between the two sulfur groups of the two cysteines (Sγ-Sγ distance, second column) and the predicted pK_a of the SNO site and proximal cysteines (third and fourth column, respectively). We then classified each variant (first column of the heatmaps) on its effects on the structural mechanisms of S-nitrosylation. We classified the variants as i) stabilizing (decreased pK_a of the SNO site and shorter Sγ-Sγ distance respect to WT), ii) neutral (similar pK_a of the SNO site and similar Sγ-Sγ distance between variant and WT) and iii) destabilizing (increased pK_a of the SNO site and longer Sγ-Sγ distance respect to WT, and cases with a large increase of pK_a of the SNO site). Stabilizing variants are highlighted in red, while blue indicates the destabilizing ones. Grey tiles indicate unknown/uncertain classification. We observed several variants of p53 that are classified as stabilizing for the SNO site C124 and proximal C135 (V122A, Q136L, T140I, T140A, N235H, Y236F) and C141 (S116F, S116P, Q136E, Q136K, T140S, P142L, N235H, N235M, N235T, V272M). These variants could make the protein environment more favorable to the population-shift mechanism or S-nitrosylation. On the other hand, we observed few variants that could have destabilizing effects and impair the structural mechanisms (V274I, V274C, N235K for proximal C135 and V274I, V274C for proximal C141). C The cartoon representations show the structural ensemble from CABSFlex of the stabilizing variant N235H. The stick and ball representations highlight the S-nitrosylation site C124 (SNO, orange), proximal C135 and C141 (proxy, blue), K120 and H235 (dark green). We observed that N235H favors shorter distances between the SNO site C124 and the proximal C141, Cβ-Sγ-Sγ-Cβ dihedral values around −90 degrees, and lower pK_a of C124. These effects suggest that N253H could enhance the S-nitrosylation of C124 and the population-shift mechanism for disulfide-bridge formation.