Dear All,<br> I have an disaccharide bound to a C-type lectin. The
sequence of disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH of
beta-galactose coordinate to the Ca2+ at the active site. FRET
experiments have shown that if the disaccharide linkage is changed to
beta-galactose1-3beta-GlcNAc then the binding affinity drops to 20 fold.
I have
attached both disaccharides in the figure. The left side residue is galactose
and right side residue is N-Acetylgalactoseamine. . <br>
In order to do a free energy perturbation and find the relative free
energy of binding for these two ligands, I have to slowly change the
linkage from beta1-4 to beta1-3. If you look at the models of both
disaccharides from the figure, to convert the beta 1-4 linked
disaccharide to beta 1-3 linked disaccharide, I have to make the the C1
atom of Galactose attached to O4 of N-Acetylgalactoseamine as H atom and
rest of the galactose residue to dummy atoms. On the other hand I have
to grow the residue from H attached to O3 of N-acetylgalactoseamine to a
galactose. The number of atoms involved is 21 atoms. Further the
constraints I have is that the sugar should be bound in right
conformation at the active site. So may be I need distance restraints.<br>
Does my approach make any sense? I have seen some papers by others where
they add a fragment or delete a fragment between two ligands. But in my
case the difference is the linkage between two residues.<br><br>Thanks
for your time in advance.<br>
<br>Regards<br>Sai Ramadugu<br>