Dear all,
I want to calculate the binding free energy between ATP , UTP etc. and RNA polymerase, DNA and RNA using MMPBSA method. In crystal structure, the catalytic active center has two Mg2+, one is bound to beta and gamma position of triphosphate of ATP, the other is coordinated by the hydroxyl of tyrosine and 2' oxygen of nucleotide. But after explicit MD simulation, the Mg 2+ coordinated shifts to another place far away from the original position in crystal structure.
In the course of binding energy calculation, ligand is ATP and one magnesium ion which is bound to beta and gamma position of triphosphate of ATP, and receptor is RNA polymerase, DNA and RNA. whether will this influence the binding energy calculation?
Another question is whether should I exclude the magnesium ion in the course of binding energy calculation. Would you like to give some suggestions about binding energy calculation of this system? Thanks for your help.
Best wishes,
Yours sincerely
Duan Baogen
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Received on Tue Nov 20 2012 - 18:30:01 PST
