Dear Rene

Ideally you must have more information about the proteins. Sequence will not be enough, and you will need structural information to carry out this analysis.

If you have only the structure of one of these proteins you can try to do homology modelling of the other ones in order to pinpoint what are the different residues positioned in the substrate-binding pocket. Using this information you can infer what's the contribution of every aminoacid to the global binding.

Best.

Paco

Dear Rene,

As Prof Enguita has suggested, you can determine the residues which are taking part in the protein-ligand interaction and how they are arranged in the binding pocket. By using the visualization tools and structure editing tools such as Pymol and Coot, you can superimpose both of them and determine the rmsd between the residues present in the active site and how they are contributing to the affinity. Additionally, you may also run the simulations.

Best Regards

Dear Enguita and Gary,

Thanks for your reply.

Both proteins have an pdb. However, from only one there is an crystalized structure.

From the literature we know the site of interactions. Having this info and yours I am still left puzzling. Is there a way to put this all into a publical appreciate?

René

OK Rene... let me know how can I help. If you have a PDB for both of the structures you can easily superimpose them as suggested by Archit, using Coot.

What's the other PDB ?.. is a NMR structure?

Send me a private e-mail with the info and I can look at your problem. (fenguita at fm.ul.pt).

Best. Paco

Dear Enguita,

I have a look at it tomorrow. In addition I ll send you a email.

Thanks,

René