title: The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins.
abstract: Dynamic molecular interaction networks underlie biological phenomena. Among the many genes which are involved, p53 plays a central role in networks controlling cellular life and death. It not only operates as a tumor suppressor, but also helps regulate hundreds of genes in response to various types of stress. To accomplish these functions as a guardian of the genome, p53 interacts extensively with both nucleic acids and proteins. This paper examines the physical interfaces of the p53 protein with cellular proteins. Previously, in the analysis of the structures of protein-protein complexes, we have observed that amino acids Trp, Met and Phe are important for protein-protein interactions in general. Here we show that these residues are critical for the many functions of p53. Several clusters of the Trp/Met/Phe residues are involved in the p53 protein-protein interactions. Phe19/Trp23 in the TA1 region extensively binds to the transcriptional factors and the MDM2 protein. Trp53/Phe54 in the TA2 region is crucial for transactivation and DNA replication. Met243 in the core domain interacts with 53BP1, 53BP2 and Rad 51 proteins. Met384/Phe385 in the C-terminal region interacts with the S100B protein and the Bromodomain of the CBP protein. Thus, these residues may assist in elucidating the p53 interactions when structural data are not available.
authors.affiliation: Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, 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: Ozlem
authors.initials: O
authors.lastname: Keskin
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: D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000378:metabolism; D004261:DNA Replication; D006801:Humans; D008715:Methionine / Q000737:chemistry*; D008958:Models, Molecular; D010649:Phenylalanine / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000378:metabolism; D015533:Transcriptional Activation; D014364:Tryptophan / Q000737:chemistry*; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D016159:Tumor Suppressor Protein p53; D010649:Phenylalanine; D014364:Tryptophan; D004247:DNA; D008715:Methionine