I have a DNA sequence for an enzyme available in Human. I took the sequence and generated a set of codon optimized sequences using random codon optimization for expression in E.coli. Now what are the possibilities that the proteins generated by individual codon optimized sequences differ from each other? What can be the levels of differences?
In practice the aminoacid sequences will be the same. Perhaps the resulting products may exhibit different folding states owing to their different rates of translation, but that's about it.
In theory there might be cases -depending on the details of your procedure and the aminoacid sequence of the protein- where codon-optimizing the DNA sequence might introduce transcriptional terminators, thereby yielding a truncated protein (although these are usually removed by the SsrA system). By the same token, it would in theory be possible to introduce a more efficient RBS close to a Met codon, yielding an alternative initiation site and, again, a shorter protein.
Hope it helps!
If you have a codon usage issue you can try the Rosetta system. See here:
https://www.embl.de/pepcore/pepcore_services/protein_expression/ecoli/optimisation_expression_levels/
*But as already mentioned by Alejandro Martin there are many options to reach higher expression levels (stronger promoter, stronger RBS, selection of E. coli strains, toxicity issues and use of pLys plasmid, induction conditions - temperature, salt addition and much more).
Yoram
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