corelation between codon and protein secondary structures

CCoburn 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 
expressed genes.

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