Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis.
p53 is mutated in roughly 50% of all human tumors, predominantly in the DNA-binding domain codons. Structural, biochemical, and functional studies have reported that the different p53 mutants possess a broad range of behaviors that include the elimination of the tumor-suppression function of wild-type protein, the acquisition of dominant-negative function over the wild-type form, and the establishment of gain-of-function activities. The contribution of each of these types of mutations to tumor progression, grade of malignancy, and response to anticancer treatments has been so far analyzed only for a few "hot-spots." In an attempt to identify new approaches to systematically characterize the complete spectrum of p53 mutations, we applied recurrence quantification analysis (RQA), a non-linear signal analysis technique, to p53 primary structure. Moving from the study of the p53 hydrophobicity pattern, which revealed important similarities with the singular deterministic structuring of prions, we could statistically discriminate, on a pure amino acid sequence basis, between experimentally characterized DNA-contact defective and conformational p53 mutants with a very high percentage of success. This result indicates that RQA is a mathematical tool particularly advantageous for the development of a database of p53 mutations that integrates epidemiological data with structural and functional categorizations.
Porrello
Alessandro
A
Department of Experimental Oncology, Regina Elena Cancer Institute, Via delle Messi d'Oro, Rome, Italy. porrello@ifo.it
Soddu
Silvia
S
Zbilut
Joseph P
JP
Crescenzi
Marco
M
Giuliani
Alessandro
A
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D019295:Computational Biology / Q000379:methods*; D016002:Discriminant Analysis; D057927:Hydrophobic and Hydrophilic Interactions; D008962:Models, Theoretical; D009154:Mutation; D011110:Polymorphism, Genetic; D011328:Prions / Q000737:chemistry; D011392:Proline / Q000032:analysis; D017434:Protein Structure, Tertiary; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry / Q000235:genetics*
D011328:Prions; D016159:Tumor Suppressor Protein p53; D011392:Proline