[gmx-users] binding affinity

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 12 13:26:31 CET 2010

leila karami wrote:
> Hi
> I want to compare DNA-binding affinity of PRH protein by mutation of 
> some aminoacids.
> I think KD (dissociation constant) is related to binding affinity.
> I dont know how do I obtain KD (dissociation constant) by MD simulation 
> and gromacs (what command).

There isn't any one, single command that will do this for you.

> If there is another way, please guide me.

What you are asking to do is potentially very difficult.  To obtain Kd, you 
would need to calculate the binding free energy of your complex, which would 
require a thermodynamic cycle.  Unfortunately, given the very highly-charged 
nature of DNA, the results may or may not be reliable.  Decoupling a species 
with a net charge leads to very large error bars, from what I've read.

You could potentially use the free energy code to do the "mutations" and obtain 
values of delta(deltaG) relative to the WT, but that assumes you can actually 
accomplish what I outlined in the above paragraph.

You can try g_lie, which gives an estimate of the free energy, but I don't know 
how reliable it is, having never used it, especially for a large and complex 
"ligand" such as DNA.


> Any help will highly appreciated!


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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