Aromatic Aminoacids - (Nov/07/2008 )

How to know weather the protein of our intrest contains aromatic aminoacids or not. Does IPTG has any affect on protein structure.

Dear Sandy21,
I guess your protein has been described previously, then if you have its theorical sequence you have to look for: W (tryptophan), Y (tyrosine) and F (phenylalanine), which are the aromatic aa. There is a web page very useful:

http://www.expasy.org/tools/protparam.html

In this page you can see the aa composition of your protein. Another reference is the extinction coefficient of the protein, the higher it is, the bigger content in aromatic aa. There are proteins with a very low content in aromatic aa that does not have nearly any absorption at 280 nm, but if you load it in a SDS-PAGE you can see a terrific comassie band, in this webpage you can find also information about the extinction coefficient.
Regarding IPTG, it should not have any effect on the protein structure. You add IPTG to the cultures to induce the expression of your heterologous gene and the corresponding protein is not in contact with the inductor.