molecular docking simulation: multiple ligand simultaneous docking

A MLSD multiple ligand simultaneous docking example:
docking of substrates FAD and PO4 simultaneously to E. coli PNP

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine nucleosides. E. coli PNP has been tested for cancer suicide gene therapy. The hexameric PNP has six homo-monomers arranged in an alternative up/down fashion around the central disc, with three of the active sites near the top and the other three near the bottom. The dimer subunit of PNP contains two deeply buried active sites, one near the top and the other near the bottom. We used substrates 2-fluoroadenosine (FAD) and phosphate (PO4) as ligands, and the dimer subunit of PNP as host for multi-ligand docking validations (PDB ID 1PK9).

Docking with LGA algorithm found a few distinct conformational clusters. The lowest energy found was -14.2 kcal/mol with the conformational cluster where both FAD and PO4 docked to the same active site near the top of PNP dimer (the movie only shows a monomer for viewing effect). The docked structure aligned very well with the crystal structure binding modes. FAD and PO4 contributed a binding energy of -8.0 kcal/mol and -6.2 kcal/mol respectively. The interaction of FAD and PO4 accounted for an energy of -0.6 kcal/mol. Alternatively, both FAD and PO4 occupied the active site near the bottom with a mean binding energy of -11.2 kcal/mol, showing the asymmetry of the two active sites. Interestingly, the most populated conformational cluster had a mean energy of -13.6 kcal/mol, in which FAD and PO4 bound to separate active sites: PO4 in the site near the top and FAD near the bottom. In a reverse manner, PO4 docked in the active site near the bottom while FAD near the top. The mean energy of this conformation cluster was -11.4 kcal/mol due to higher binding energy of PO4 in site near the bottom. Analysis of the difference of binding energy and binding sites for PO4 suggests that the binding site near the top is preferred for PO4, with a difference of energy of -2.4 kcal/mol. The docking results are completely consistent with the proposed random ping-pong bi-bi binding mechanism of E. coli PNP, with the lowest energy cluster being the catalytically competent complex and others being binding intermediates during the enzymatic cycle (the movie snapshots showing either FAD or PO4 in the monomer binding site are actual intermediates; in these cases, the other substrates bind to the other active site).

Category:

Science & Technology

Tags:

• computational
• chemistry

[sanosss1]

I don't understand the point of doing MD simulation and keeping receptor rigid...Why is the receptor rigid????