THE RELATIONSHIP BETWEEN SYNONYMOUS CODON USAGE AND PROTEIN-STRUCTURE

The hypothesis that synonymous codon usage is related to protein three -dimensional structure is examined by investigating the correlation be tween synonymous codon usage and protein secondary structure. All exce pt two codons in E, coli show the same secondary structural preference for alpha-helix, beta-strand or coil as that of amino acids to be enc oded by the respective codons, while 17 codons show secondary structur al bias in mammalian proteins. The results indicate that there is no s ignificant correlation between synonymous codon usage and protein seco ndary structure in E, coli, but there is a correlation in mammals. It could be deduced that synonymous codons carry much less structural inf ormation in prokaryotes than in eukaryotes due to their divergent evol utionary mechanism. (C) 1998 Federation of European Biochemical Societ ies.