Thanks for everyone's weighing in on this issue.
I can understand how codon usage would slow or speed translation to the point that secondary structure is altered, but the examples given in the paper did not support the statement that a single silent mutation can alter a protein's activity. The first study required the replacement of 16 consecutive codons to reduce the protein's activity by 20%. Another E. coli study required the change of 3 adjacent codons. What was interesting was that the mutations were all from rare codons to common codons suggesting that the pause in translation is the control mechanism most at risk. So, I will ask again, can you give me an example of a single nucleotide change that did not change the amino acid sequence but did result in a functional mutation?
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