Finding the protein structural information contained in codon usages
As life first appeared on this planet, we can assume that the primitive genetic code was both smaller and simpler than that seen today. Most likely it only contained a handful of amino acids, each one with its own unique properties. As evolution progressed additional amino acids were including in code, turning the originally coarse grained scheme into a sensitive system. My research asks why this increase in complexity stopped at just 20 amino acids when there are 64 codons? Why are there not64 amino acids for 64 codons, one for each, thereby allowing for even greater control and variation in the protein product? Why does degeneracy still exists within the genetic code? My hypothesis and work is based on the combined theory of codon optimality and cotranslational folding, that the choice of codon directly affects the translation efficiency of the ribosome.  Consequently, different codons give the nascent polypeptide chain varying amounts of time to explore the
fold-space and as such the choice of codon directly affects the final structure of protein.