Protein structure preference, tRNA copy number, and mRNA stem/loop content

From statistical analyses of protein sequences for humans and Escherichia coli we found that the messenger RNA segment of m-codons (for m=2 to 6) with average high tRNA copy number (TCN) (larger than ~10.5 for humans or ~1.95 for E. coli) preferably code for the (alpha) helix and that with low TCN (smaller than ~7.5 for humans or ~1.7 for E. coli) preferably code for coil. Between them there is an intermediate region without correlation to structure preference. For the (beta) strand the preference/ avoidance tendency is not obvious. All strong preference-modes of TCN for protein secondary structures have been deduced. The mutual interaction between two factors - protein secondary structural type and codon TCN - is tested by F distribution. A phenomenological model on the relation between structure preference and translational efficiency or accuracy is proposed. It is pointed out that the structure preference of codons is related to the distribution of mRNA stem/loop content in three TCN regions.