Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (α-helix, β-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different ma...

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Bibliographic Details
Published in:Gene 1999-09, Vol.238 (1), p.23-31
Main Authors: Chiusano, Maria Luisa, D'Onofrio, Giuseppe, Alvarez-Valin, Fernando, Jabbari, Kamel, Colonna, Giovanni, Bernardi, Giorgio
Format: Article
Language:English
Subjects:
Animals
Base Composition
Codon
Evolution
Genomes
Mammals
Mutation
Mutational bias
nucleotides
Protein Structure, Secondary
Selection-protein structure
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Summary:We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (α-helix, β-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be α-helix, β-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.
ISSN:0378-1119
1879-0038
DOI:10.1016/S0378-1119(99)00258-9