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Dynamics and Molecular Mechanisms of p53 Transcriptional Activation

Tavina L. Offutt, Pek U. Ieong, Özlem Demir, Rommie E. Amaro
Biochemistry 2018 v.57 no.46 pp. 6528-6537
DNA, DNA damage, DNA-binding domains, apoptosis, asymmetry, cell cycle checkpoints, crystal structure, drug resistance, genome, genomics, humans, hypoxia, models, molecular dynamics, mutants, neoplasms, site-directed mutagenesis, transcription factors, transcriptional activation
The “guardian of the genome”, p53, functions as a tumor suppressor that responds to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Mutation of p53 disrupts its tumor suppressor function, leading to various types of human cancers. One particular mutant, R175H, is a structural mutant that inactivates the DNA damage response pathway and acquires oncogenic functions that promotes both cancer and drug resistance. Our current work aims to understand how p53 wild-type function is disrupted due to the R175H mutation. We use a series of atomistic integrative models built previously from crystal structures of the full-length p53 tetramer bound to DNA and model the R175H mutant using in silico site-directed mutagenesis. Explicitly solvated all-atom molecular dynamics (MD) simulations on wild-type and the R175H mutant p53 reveal insights into how wild-type p53 searches and recognizes DNA, and how this mechanism is disrupted as a result of the R175H mutation. Specifically, our work reveals the optimal quaternary DNA binding mode of the DNA binding domain and shows how this binding mode is altered via symmetry loss as a result of the R175H mutation, indicating a recognition mechanism that is reminiscent of the asymmetry seen in wild type p53 binding to nonspecific genomic elements. Altogether our work sheds new light into the hitherto unseen molecular mechanisms governing transcription factor, DNA recognition.