[jakeb]

Let's say that you were to prepare two .5% solutions of a peptide. If you were to prepare one solution using 95% purity peptide and another solution using 98% purity peptide, the 95% purity solution would contain additional .0002% of impure peptides compared to the solution made with 98%.

To me, it seems very unlikely that this small increase would significantly alter the solution's biological activity, but I have been told that I'm not understanding it correctly. I'm curious to hear views from more people. Thanks very much!

[Extracted]

If the difference is 3%, and the impurity has no biological activity, you should see a difference of 3%.

[fledarmus]

I'm not sure exactly how your math worked. If you are trying to prepare a 0.5% solution, and the material that you started with was only 98% pure, then the solution you end up with should actually be a 0.49% solution of peptide with 0.01% impurity. If it was 95% pure, you get a 0.475% solution, with 0.025% added impurity. I see a difference of 0.015%, rather than 0.0002%. Am I missing something in your description?

[Babcock_Hall]

When dealing with enzymes, a 1% impurity can either be nothing to worry about or can completely mess things up.  If you mutate a key residue in an enzyme that knocks activity down by four orders of magnitude, but you have a 1% impurity of wild-type enzyme, your estimate of the effect of the mutation on rate will be in error by 100-fold.  The same impurity in a crystallization experiment would probably have no discernible effect.

I can think of two kinds of impurities in commercial peptides, namely small molecules left over from the process of making/cleaving/deprotecting it, and other peptides (for example shorter peptides created when the coupling of one amino acid did not go to 100% completion.  Small molecules can fluoresce, and this problem made one batch of peptide we bought near worthless in fluorescence-based titrations.  The other peptides might or might not have the same biological activity as the desired peptide.