Removing a binding site - (Mar/13/2012 )
I need to remove a binding site and I'm not exactly sure on how to choose the correct amino acid for a substitute. The binding occurs between a phenylalanine (via carbonyll oxygen) and the Mg ion in the chlorophyll.
the site is located at the end of the protein so it has minimal influence on the protein folding, but if possible I would like to keep as close to the native as possible.
I though using tyrosine or leucine would be OK, as they're similar somewhat. The major problem I'm having is there a way to check if the substitute amino acid will not again bind the chlorphyll (over than creating a set of mutant proteins and checking them in the lab)
I hope I've written in the right place and clearly enough,
Thanks for any advice!
I would not recommend changing the phenylalanine to tyrosine. They are nearly identical (except for tyrosine's -OH) and the binding may be retained. As you said, the AA is at the end of the protein so changes in conformation should be minimal. When you are trying to eliminate activity, drastic changes can be OK. Luecine or alanine should work for this. But if you find that you must keep an AA with an aromatic ring, then you can try tyrosine.
As for checking if it will bind. The only sure way is to make the mutation and check yourself. I am not aware of programs that can do this with any accuracy
thanks, for the reply. I think I will try with glycine first. Not sure why but I think it's a reasonable shot.
I would go for glycine too (and avoid Proline).
why avoid proline?
it's usually present in turns and alpha helices. avoid it since you want the protein to keep its original form.