Towards In Situ Dynamics of DNA-bound Full-Length p53 Tetramer

p53 is the most important tumor suppressor in humans as well as the most frequently mutated gene found in human cancers with ~50% of all human tumors bearing p53 missense mutations that leave p53 inactive. Restoring the p53 activity proved to lead to tumor regression even in advanced tumors in mouse models - and thus, is among the most attractive potential strategies for novel cancer therapy. Full-length p53 (fl-p53) consists of 393 residues and multiple domains; some folded and some disordered. Using crystal structures of folded domains and integrative molecular modelling techniques for disordered domains, we generated the first wild-type fl-p53 tetramer model bound to DNA. When solvated, the system size nears 500K atoms challenging extensive sampling. Using Anton2 supercomputer for microsecond-timescale simulations in explicit solvent and the rigorous Markov state model (MSM) framework, we elucidated the conformational landscape of wild-type p53 as well as two of the p53 hot-spot cancer mutants, Y220C and G245S, in a physiological DNA-bound, full-length tetramer context. In the simulated timescale, DNA-bound fl-p53 tetramer bent DNA and formed a compact complex with interactions between the N-terminal and DNA-binding domains (DBDs), and the C-terminal domains (CTDs) with DNA. WT fl-p53 tetramer also sampled a unique quaternary DBD organization not accessed by the cancer mutants. Free energy landscapes indicated differential dynamics for inner and outer p53 DBDs due to the dimer-dimer interface. The dynamics of the druggable L1/S3 pocket is also closely monitored. Ultimately the MSMs identified an underexplored loop 6 (L6) cryptic pocket and captured the effect of p53 tetramerization and cancer mutations.