We have a peptide, made by the chemistry department, that they say should bind to the alpha V beta 6 integrin. How would I go about seeing where exactly the peptide will bind to the integrin? This is not my area so could do with some help
My feeling is that you should find someone who has expertise in ligand docking. You should search for literature to see if there are studies regarding other lignads and the sites where they bind to Integrins, maybe you can find something close to your subject. A nice software should be GOLD (from ccdc) or Autodock (which is free).
Hi James, most alphaV integrins bind to RGD sequences in adhesion proteins.
If the peptide has an RGD sequence, then there is a good chance it will inhibit most aV containing integrins.
I think that a good place to start is to see if this peptide inhibits cell adhesion to fibronectin, vitronectin or gelatin. Most cancer cell lines either express aVb3 or avb5, or both. I'm not familiar with a cell line that only has avb6.
You can contact me if you want nauseating details about doing cell adhesion assays in the presence of an inhibitor. Or take a look at some of my pubs.
My group has been working on integrin alpha-v-beta-6 recognition for several years and we have found that specific recognition to this integrin over other alpha-v integrins is a real challenge. We have shown that specfic avb6 recognition utilises peptides with a RGDLXXL motif in a turn-helix conformation. Problem is that many of these peptides will bind other alpha-v integrins because they all possess RGD. The pubmed reference above is from my group and we have published several papers on peptide specificity.
Please feel free to contact me if you want to discuss anything further.