title: On Nature's Strategy for Assigning Genetic Code Multiplicity.
abstract: Genetic code redundancy would yield, on the average, the assignment of three codons for each of the natural amino acids. The fact that this number is observed only for incorporating Ile and to stop RNA translation still waits for an overall explanation. Through a Structural Bioinformatics approach, the wealth of information stored in the Protein Data Bank has been used here to look for unambiguous clues to decipher the rationale of standard genetic code (SGC) in assigning from one to six different codons for amino acid translation. Leu and Arg, both protected from translational errors by six codons, offer the clearest clue by appearing as the most abundant amino acids in protein-protein and protein-nucleic acid interfaces. Other SGC hidden messages have been sought by analyzing, in a protein structure framework, the roles of over- and under-protected amino acids.
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Simone
authors: S
authors: Gardini
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Sara
authors: S
authors: Cheli
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Silvia
authors: S
authors: Baroni
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Gabriele
authors: G
authors: Di Lascio
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Guido
authors: G
authors: Mangiavacchi
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Nicholas
authors: N
authors: Micheletti
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Carmen Luigia
authors: CL
authors: Monaco
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Lorenzo
authors: L
authors: Savini
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Davide
authors: D
authors: Alocci
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Stefano
authors: S
authors: Mangani
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
authors: Neri
authors: N
authors: Niccolai
mesh_terms: D003062:Codon / Q000235:genetics; D019295:Computational Biology; D030562:Databases, Protein; D005815:Genetic Code / Q000235:genetics*; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D003062:Codon; D011506:Proteins