Can any body suggest methods to analyse the biniding site for any molecule.i have already some molecules having interaction with microtubule but now I need to know the exact binding site on the tubulin.
Thanks Goutam for such a valuable suggestion.But I have the organic molecules not the protein which bind to the tubulin.
Saswat,
It is not a trivial thing to do and there are no universal techniques that would help you.
Goutam's suggestion would not work actually for most proteins, but definitely it won't work for tubulin. A better modification of the approach is Ala scanning mutagenesis (not deletion, but substituition of consequitive 5 amino acids with alanines). This will not work for tubulin either, as you will destroy the protein by most of the mutations. Do your drugs bind to tubulin dimers or to filaments (I guess the latter, right)? what are the functional effects?
Here is my best suggestion - it is labor demanding and challenging, (so you really have to think hard whether it worth doing at all) but at least something.
You would have to co-crystallize your drugs with tubulin in complex with one of its partners that prevent polymerization (see pdb.org). Alternatively, you have to soak crystals of tubulin with this other protein in solution containing your drugs with a hope that these will bind to the right side.
This won't work if your drugs: 1) stabilize filaments; 2) compete with tubulin binding partners for tubulin.
Alternatively, as a low resolution solution, you can monitor competition between your drugs and various tubulin binding partners. If they compete - there is a good chance they bind to the same region.
As you can see, there is not much.
You can do in silico predictions, docking. It's getting better and better, but this is still a prediction, not experimental proof.
Best.
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