PROTEIN-STRUCTURE AND THE SEQUENTIAL STRUCTURE OF MESSENGER-RNA - ALPHA-HELIX AND BETA-SHEET SIGNALS AT THE NUCLEOTIDE LEVEL

A direct comparison of experimentally determined protein structures an d their corresponding protein coding mRNA sequences has been performed , We examine whether real world data support the hypothesis that clust ers of rare codons correlate with the location of structural units in the resulting protein, The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate o f the ribosome, and may thus in vivo have a catalyzing effect on the f olding of the polypeptide chain, A complete search for GenBank nucleot ide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, ami no acid sequence, and secondary structure assignment, By neural networ k analysis, we found strong signals in mRNA sequence regions surroundi ng helices and sheets, These signals do not originate from the cluster ing of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sh eets, No correlation between the positioning of rare codons and the lo cation of structural units was found, The mRNA signals were also compa red with conserved nucleotide features of 16S-like ribosomal RNA seque nces and related to mechanisms for maintaining the correct reading fra me by the ribosome. (C) 1996 Wiley-Liss, Inc.