Comparison of the protein–protein interfaces in the p53–DNA crystal structures: Towards elucidation of the biological interface

Abstract

p53, the tumor suppressor protein, functions as a dimer of dimers. However, how the tetramer binds to the DNA is still an open question. In the crystal structure, three copies of the p53 monomers (containing chains A, B, and C) were crystallized with the DNAconsensus element. Although the structure provides crucial data on the p53-DNA contacts, the active oligomeric state is unclear because the two dimeric (A-B and B-C) interfaces present in the crystal cannot both exist in the tetramer. Here, we address the question of which of these two dimeric interfaces may be more biologically relevant. We analyze the sequence and structural properties of the p53-p53 dimeric interfaces and carry out extensive molecular dynamics simulations of the crystal structures of the human and mouse p53 dimers. We find that the A-B interface residues are more conserved than those of the B-C. Molecular dynamics simulations show that the A-B interface can provide a stable DNA-binding motif in the dimeric state, unlike B-C. Our results indicate that the interface between chains A-B in the p53-DNA complex constitutes a better candidate for a stable biological interface, whereas the B-C interface is more likely to be due to crystal packing. Thus, they have significant implications toward our understanding of DNA binding by p53 as well as p53-mediated interactions with other proteins. p53 dimeric interface ͉ p53 tetramer ͉ hot spots ͉ cancer ͉ gene regulation

Cooperative Fluctuations Point to the Dimerization Interface of P53 Core Domain

“…Ma et al (20) obtained that, helix 1 residues of monomer B (R181, C182) forms hydrogen bonding with several residues in monomer A (V172, R174, R175, G244) and S185 of monomer B also interacts with T211 of monomer A. These findings map into our suggested dimerization interface region.…”

“…In their experimental work, Jiao et al (43) reported observations of dynamic interactions of p53 with DNA including continuous association/dissociation and sliding. Ma et al (20) proposed models for p53 dimer binding to DNA including one that is a sliding mechanism. However, no distinction was made in any of these models between the monomers A, B, or C with respect to their interactions with the DNA.…”

“…Previous studies performed, both molecular dynamics (20) and NMR spectroscopy (36,37), pointed out the importance of H1 helix in dimerization. Ma et al (20) obtained that, helix 1 residues of monomer B (R181, C182) forms hydrogen bonding with several residues in monomer A (V172, R174, R175, G244) and S185 of monomer B also interacts with T211 of monomer A.…”

Structural Basis for p53 Binding-induced DNA Bending

“…These specific ways of association between p53 and DNA and between p53 monomers are supported by several experiments (24 -27). Alternatively, p53 core domain dimerization interface in a crystal structure was also examined to explore their biological relevance (28). Overall, there are little experimental data with respect to the association between the p53 dimers.…”

Dimerization of the core domain of the p53 family: A computational study

“…The DBD of p53 has been well characterized structurally by x-ray crystallography 2,48,49 NMR 42 and computational studies. [50][51][52][53][54][55][56][57] The core domain consists of a central β-sandwich that serves as a basic scaffold, and the DNA binding surface is composed of two large loops L2 and L3 that are held together by a zinc ion and a loop-sheet-helix motif (Fig. 1).…”