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

Area of Science:

• Molecular Biology
• Biophysics
• Computational Biology

Background:

• The p53 protein is a critical human tumor suppressor, frequently inactivated by mutations in ~50% of cancers.
• Restoring p53 activity is a highly sought-after cancer therapy strategy, showing promise in preclinical models.
• Full-length p53 (fl-p53) is a multi-domain protein whose structure and dynamics in a physiological context are complex.

Purpose of the Study:

• To generate the first atomic model of the wild-type full-length p53 tetramer bound to DNA.
• To investigate the conformational landscape and dynamics of wild-type and mutant p53 using advanced computational simulations.
• To understand how p53 tetramerization and cancer mutations affect its DNA-binding and overall structure.

Main Methods:

• Integrative molecular modeling combining crystal structures and disordered domain modeling.
• Microsecond-timescale molecular dynamics simulations on the Anton2 supercomputer in explicit solvent.
• Markov state modeling (MSM) to analyze the conformational landscape and identify key dynamic features.
• Analysis of DNA bending, protein-protein interactions, and druggable pocket dynamics.

Main Results:

• A detailed model of the DNA-bound wild-type fl-p53 tetramer was generated, revealing DNA bending and compact complex formation.
• Differential dynamics were observed between inner and outer p53 DNA-binding domains (DBDs) due to the dimer-dimer interface.
• Wild-type p53 tetramer adopted a unique quaternary DBD organization not seen in the analyzed cancer mutants (Y220C, G245S).
• An underexplored cryptic pocket in loop 6 (L6) was identified, and the impact of tetramerization and mutations on its dynamics was captured.

Conclusions:

• The study provides unprecedented insights into the structural dynamics of the full-length p53 tetramer bound to DNA.
• Cancer mutations and tetramerization significantly alter p53's conformational landscape and dynamics, particularly affecting DBD organization and cryptic pocket accessibility.
• These findings lay the groundwork for developing novel therapeutic strategies targeting p53 reactivation in cancer.