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Non‐random usage of ‘degenerate’ codons is related to protein three‐dimensional structure
Author(s) -
Adzhubei Alexei A.,
Adzhubeib Ivan A.,
Krasheninnikov Igor A.,
Neidle Stephen
Publication year - 1996
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(96)01287-2
Subject(s) - codon usage bias , genetics , coding region , gene , biology , silent mutation , exon , sequence (biology) , stop codon , protein secondary structure , synonymous substitution , protein structure , nucleotide , computational biology , biochemistry , mutation , genome , missense mutation
We report an analysis of a novel sequence‐structure database of mammalian proteins incorporating nucleotide sequences of the exon regions of their genes together with protein sequence and structural information. We find that synonymous codon families (i.e. coding the same residue) have non‐random codon distribution frequencies between protein secondary structure types. Their structural preferences are related to the third, ‘silent’ nucleotide position in a codon. We also find that some synonymous codons show very different or even opposite structural preferences at the N‐ or C‐termini of structure fragments, relative to those observed for their amino acid residues.