PROTEIN SECONDARY STRUCTURAL TYPES ARE DIFFERENTIALLY CODED ON MESSENGER-RNA

Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. Th e fractional frequency values of the individual codons as they occur i n mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were cla ssified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation b etween codon usage in mRNA and topological features of the encoded pro teins. Alpha helices on proteins tend to be preferentially coded by tr anslationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid cod ing for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic asp ects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is pre sented relating the observation to the reported kinetic data on the fo rmation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selecti on for codons in non-highly expressed genes is compatible with existin g theories that mutation pressure may well dominate codon selection in non-highly expressed genes.