corelation between codon and protein secondary structures
CCoburn at pofvax.pnb.sunysb.edu
Wed Jan 7 18:58:10 EST 1998
Some work on this problem has been done. A fairly recent reference (with
abstract) is given below.
Thanaraj TA. Argos P.
Protein secondary structural types are differentially coded on messenger
Protein Science. Vol 5(10) (pp 1973-1983), 1996.
Tricodon regions on messenger RNAs corresponding to a set of proteins from
Escherichia coli were scrutinized for their translation speed. The fractional
frequency values of the individual codons as they occur in mRNAs of highly
expressed genes from Escherichia coli were taken as an indicative measure of
the translation speed. The tricodons were classified 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 between codon usage in mRNA and topological
features of the encoded proteins. Alpha helices on proteins tend to be
preferentially coded by translationally fast mRNA regions while the slow
segments often code for beta strands and coil regions. Fast regions
correspondingly avoid coding for beta strands and coil regions while the slow
regions similarly move away from encoding alpha helices.
Structural and mechanistic aspects of the ribosome peptide channel support the
relevance of sequence fragment translation and subsequent conformation. A
discussion is presented relating the observation to the reported kinetic data
on the formation and stabilization of protein secondary structural types
during protein folding. The observed absence of such strong positive selection
for codons in non highly expressed genes is compatible with existing theories
that mutation pressure may well dominate codon selection in non highly
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