Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains

Netaly Khazanov, Yaakov Levy

Research output: Contribution to journalArticlepeer-review

59 Scopus citations

Abstract

The p53 protein is a homotetrameric transcription factor whose monomers comprise several domains. Although its organization with and without DNA was elucidated recently, characterizing the p53-DNA complex at the atomic level remains challenging because of its many disordered regions. Here we use computational models to predict the wiring of the four chains composing p53 and study its sliding dynamics along DNA in different oligomeric states. We find that helical sliding along the major groove is the most feasible DNA search mechanism for a large range of salt concentrations. Tighter packing of the tetrameric core domain is associated with a greater nonspecific affinity for DNA and the slowest linear diffusion dynamics along DNA. C-tails facilitate linear diffusion but restrict the association of two primary dimers into a tetramer. This restriction can disappear at higher salt concentrations, which decrease the affinity of C-tails for DNA, or upon interaction of the C-tail with other DNA segments. Our results support evidence for the positive regulation of p53 function by the C-tails and suggest that posttranslational charge modifications may alter the affinity of the tails for DNA. Conversely, the N-termini have little effect on sliding characteristics. Changes in the electrostatic potentials of the core domain via missense mutations corresponding to cancer development can also affect sliding by p53. Our study provides molecular insight into the role of various p53 domains during DNA search and indicates that the complex interdomain and protein-DNA cross-talks in which p53 engages may be related to its repertoire of cellular functions.

Original languageEnglish
Pages (from-to)335-355
Number of pages21
JournalJournal of Molecular Biology
Volume408
Issue number2
DOIs
StatePublished - 29 Apr 2011
Externally publishedYes

Bibliographical note

Funding Information:
To illustrate the sliding of full-length and CTetCD models of p53 along DNA, we present snapshots from the simulations ( ). The snapshots illustrate that full-length and truncated p53 follow a helical 1D path along the DNA (as shown elsewhere for the sliding of other DNA binding proteins Fig. 3 46,48 ) both with and without the secondary interface. The C-tails, which are mostly positively charged (each C-tail includes nine positively charged residues and four negatively charged residues), engage in strong electrostatic interactions with the negatively charged phosphate groups of the DNA molecule. During sliding, the Tet domain is oriented parallel with the DNA, and the positioning of the Tet domain is supported by the interactions of the C-tails with the DNA ( Fig. 3a and c ). When the primary dimers of the core domain freely diffuse along the DNA (under the constraints imposed by the linkers, which may limit the diffusion of the core domain), the C-tails interact with the intervening DNA and further restrict the relative motion of the dimers ( Fig. 3b and d ). Formation of the secondary interface in this case will not occur solely by a linear diffusion of the dimers but will require the dissociation of the C-tails. Importantly, the N-termini (mostly negatively charged) in full-length p53 do not interact with the C-tails (mostly positively charged) but are exposed to the solvent. While the N-termini may affect the affinity of p53 for DNA, they seem not to affect the interaction of the core domain and C-tails with DNA. We therefore continued our study by focusing on the truncated CTetCD model of p53 to decipher potential cross-talks between the core domain, the Tet domain, and the C-tails.

Funding

To illustrate the sliding of full-length and CTetCD models of p53 along DNA, we present snapshots from the simulations ( ). The snapshots illustrate that full-length and truncated p53 follow a helical 1D path along the DNA (as shown elsewhere for the sliding of other DNA binding proteins Fig. 3 46,48 ) both with and without the secondary interface. The C-tails, which are mostly positively charged (each C-tail includes nine positively charged residues and four negatively charged residues), engage in strong electrostatic interactions with the negatively charged phosphate groups of the DNA molecule. During sliding, the Tet domain is oriented parallel with the DNA, and the positioning of the Tet domain is supported by the interactions of the C-tails with the DNA ( Fig. 3a and c ). When the primary dimers of the core domain freely diffuse along the DNA (under the constraints imposed by the linkers, which may limit the diffusion of the core domain), the C-tails interact with the intervening DNA and further restrict the relative motion of the dimers ( Fig. 3b and d ). Formation of the secondary interface in this case will not occur solely by a linear diffusion of the dimers but will require the dissociation of the C-tails. Importantly, the N-termini (mostly negatively charged) in full-length p53 do not interact with the C-tails (mostly positively charged) but are exposed to the solvent. While the N-termini may affect the affinity of p53 for DNA, they seem not to affect the interaction of the core domain and C-tails with DNA. We therefore continued our study by focusing on the truncated CTetCD model of p53 to decipher potential cross-talks between the core domain, the Tet domain, and the C-tails.

FundersFunder number
Federal German Ministry for Education and Research
Kimmelman Center for Macromolecular Assemblies
Minerva Foundation

    Keywords

    • coarse-grained model
    • nonspecific protein-DNA interactions
    • p53
    • sliding

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