P53 is a major tumor suppressor that is mutated and inactivated in ~50% of all human cancers. Thus, reactivation of mutant p53 using small molecules has been a long sought-after anticancer therapeutic strategy. Full structural characterization of the full-length oligomeric p53 is challenging because of its complex architecture and multiple highly flexible regions. To explore p53 structural dynamics, here we developed a series of atomistic integrative models with available crystal structures of the full-length p53 (fl-p53) tetramer bound to three different DNA sequences: a p21 response element, a puma response element and a nonspecific DNA sequence. Explicitly solvated, all-atom molecular dynamics simulations of the three complexes (totaling nearly 1 μs of aggregate simulation time) yield final structures consistent with electron microscopy maps and, for the first time, show the direct interactions of the p53 C-terminal with DNA. Through a collective principal component analysis, we identify sequence-dependent differential quaternary binding modes of the p53 tetramer interfacing with DNA. Additionally, L1 loop dynamics of fl-p53 in the presence of DNA is revealed, and druggable pockets of p53 are identified via solvent mapping to aid future drug discovery studies.
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Structural assessment of the full-length wild-type tumor suppressor protein p53 by mass spectrometry-guided computational modeling
Scientific Reports Open Access 25 May 2023
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We thank Mikel Valle for kindly providing the three-dimensional cryo-EM maps in 2011 Melero et al. article, and Steffen Lindert, Rob Swift, Clarisse Ricci, Lane Votapka, Jacob Durrant and Elizabeth Villa for helpful discussions. This work was supported by the University of California Cancer Research Coordinating Committee award and NIH Innovator award DP2-007237. Computing time on Stampede and Comet supercomputers was provided through the NSF XSEDE supercomputer resources grant RAC CHE060073N (to REA). Additional support from the National Biomedical Computation Resource NIH P41 GM103426 is acknowledged.
ÖD, PUI and REA designed research; ÖD designed the model; PUI performed the simulations; ÖD and PUI analyzed data; ÖD, PUI, and REA wrote the paper.
REA is a co-founder of Actavalon Inc., a company developing p53 reactivation compounds for anticancer therapeutics.
Supplementary Information accompanies this paper on the Oncogene website
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Demir, Ö., Ieong, P. & Amaro, R. Full-length p53 tetramer bound to DNA and its quaternary dynamics. Oncogene 36, 1451–1460 (2017). https://doi.org/10.1038/onc.2016.321
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