Targeting the Conformational Transitions of MDM2 and MDMX. PART II: Insights into Key Residues Affecting p53 Recognition.

MDM2 and MDMX are oncogenic proteins that regulate the activity and stability of p53, a tumour suppressor protein involved in more than 50% of human cancers. MDM2 is an E3 ubiquitin ligase enzyme that, upon binding to p53, leads the tumour suppressor protein to the proteasomal degradation. Being MDM2 also a gene target of the transcriptional activity of p53, this module of protein-protein interaction constitutes an example of negative feedback loop where the induced expression of MDM2 gene by p53, in turn, downregulates the activity of p53. The availability of structural information of the N-terminal domain of MDM2 in complex with p53-derived peptides and inhibitors, and the very recent disclosure of the crystal structure of the N-terminal domain of MDMX bound to a p53 peptide, offer an unprecedented opportunity to get insight into the molecular basis of p53 recognition and the identification of discriminating features affecting the binding of the tumour suppressor protein to MDM2 and MDMX. In this second part of the study, we have carried out four molecular dynamic simulations (MDs) of 60ns each in order to identify key residues affecting the recognition of p53 on an energetical basis. In particular, we focused our attention both on the p53 binding site and to structural motifs of MDM2 and MDMX more remotely localized from the binding cleft. In order to accomplish this task ,we have applied Linear Discriminant Analyses (LDA) to a pool of representative conformations generated during the four simulations.