title: 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 DNA-consensus 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.
authors.affiliation: Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD 21702, USA. mab@ncifcrf.gov
authors.forename: Buyong
authors.initials: B
authors.lastname: Ma
authors.forename: Yongping
authors.initials: Y
authors.lastname: Pan
authors.forename: K
authors.initials: K
authors.lastname: Gunasekaran
authors.forename: R Babu
authors.initials: RB
authors.lastname: Venkataraghavan
authors.forename: Arnold J
authors.initials: AJ
authors.lastname: Levine
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D020816:Amino Acid Motifs; D003198:Computer Simulation; D003461:Crystallography; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D017434:Protein Structure, Tertiary; D012984:Software; D013997:Time Factors; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry* / Q000378:metabolism
chemical_list: D016159:Tumor Suppressor Protein p53; D004247:DNA
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