Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain

Abstract

Most p53 mutations associated with cancer are located in its DNA binding domain (DBD). Many structures (X‐ray and NMR) of this domain are available in the protein data bank (PDB) and a vast conformational heterogeneity characterizes the various free and complexed states. The major difference between the apo and the holo‐complexed states appears to lie in the L1 loop. In particular, the conformations of this loop appear to depend intimately on the sequence of DNA to which it binds. This conclusion builds upon recent observations that implicate the tetramerization and the C‐terminal domains (respectively TD and Cter) in DNA binding specificity. Detailed PCA analysis of the most recent collection of DBD structures from the PDB have been carried out. In contrast to recommendations that small molecules/drugs stabilize the flexible L1 loop to rescue mutant p53, our study highlights a need to retain the flexibility of the p53 DNA binding surface (DBS). It is the adaptability of this region that enables p53 to engage in the diverse interactions responsible for its functionality. Proteins 2016; 84:1443–1461. © 2016 Wiley Periodicals, Inc.

Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance

“…Low modes are recognize by long dynamics in proteins 76,77 . Further, PCA reduces the motion in a trajectory 78–80 where A set of variables z1, z2…, zp, transformed, called principal components (PCs) are generated. Free Energy Landscape (FEL) 81,82 is applied to calculate the energies of macromolecule conformations sets.…”

Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance

“…PCA is carried with long time dynamics by recognizing low modes in proteins [ 28 , 29 ]. PCA reduces and simplifies the complicated movement in long trajectory generated during MD simulation [ [30] , [31] , [32] ]. A transformed set of variables z1, z2…, zp called principal components (PCs) were generated during PCA.…”

NMR Hydrogen Exchange and Relaxation Reveal Positions Stabilized by p53 Rescue Mutants N239Y and N235K

“…Further evidence of increased stability in the DNA binding interface comes from the increase rigidity observed in S 2 values of N239Y in the latter half of L2, which spans residue 183-194 ( Figure 6 ). Principle component analyses of residue positions in multiple p53 DBD crystal structures have shown this part of L2 to be highly flexible (45). S 2 calculations of WT show that this flexibility is confirmed to be present in WT (32) and N235K but not N239Y ( Figure 6 ).…”

“…L1 has been shown to be involved in dynamic DNA binding (37). Principle component analysis (45), molecular dynamics (46, 47), and NMR studies (37) of p53 DBD have shown L1(113-123) to be highly flexible. This flexibility is observed in WT (32) and N235K ( Figure 6 ).…”