[AMBER] Binding cooprativety and binding order of ligands

From: Sushil Mishra <smncbr.gmail.com>
Date: Thu, 25 Mar 2010 18:53:41 +0100

Hi all;
I wold like to ask is anyone one have some persona experience of checking
binding co-operativety and binding order. I have a protein which is a almost
circular (trimer). Three monomer units are arranged in way that they make a
circular str. There are total 6 binding sites. 3 ate the centre of each
monomer (intermonomeric) unit and 3 at the junctions of monomeric units
(intra-monomeric). All the 6 binding site are structurally similar that
means they have same aminoacids in same orientation at binding sites. There
are very slight (1-2 mino acids and they dont have any major interaction
with ligand) differences in amino acids betwee inter-monomeric and intra
monomeric binding pocket. All the six binding sites have same ligand (sugar)
in crystal structure.

I wold like to chack the binding cooprativiety and binding order of 6
ligands in the protein. If anyone of you have such experiences or know about
any publication of evaluationg binidng order in such type of problem then i
would be happy to know. from my experience it looks that they are
same.....but i want to show that there is no-cooprativety and all the ligand
have same BE no matters that order of binding. If anyone of u want any info
I will thank for discussion

Thanking u in advance !!

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Received on Thu Mar 25 2010 - 11:00:12 PDT
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