I see a flexible loop opening from a protein after removal of the ligands from the active site (Molecular Dynamics simulations). I expect that the reinsertion of the same ligand molecules in the active site would close the loop again because of the considerable interaction present between the loop residues and the ligand molecules (from the crystal structure).
Loop opening is very easy one, while I feel the closing event is bit tedious. Any comment on this would be appreciated.
Hi,
what are you looking is a "rare event" in MD. Binding mechanism is a very challenging task in MD. You have to go through enhanced MD simulations, such metadynamics, amd, etc ...
have look to:
http://iopscience.iop.org/0034-4885/71/12/126601
http://pubs.acs.org/doi/abs/10.1021/ja806846q
hope it helps
and
Entropy is "on your side" with loop opening and "against you" for loop closing.
You can force the loop to close using steered MD and then allow for equilibration. Just to model the complex, not to simulate the natural process.
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