FEP/binding free energy difference WT vs Mut

From: Luis Cunha (luis.cunha_at_mssm.edu)
Date: Fri Feb 13 2009 - 16:43:27 CST

Dear NAMD users,
I need your advice. I use NAMD to study ligand binding to my protein,
but so far I've only been interested in conformation changes, not
energies. I need advice with the following problem:
I have an xray structure of a protein (actually a domain of the
protein)/DNA complex. In this complex, an arginine makes a Hbond with
a specific DNA base. We've found patients with a specific genetic
disease who have a mutation (Arg to Cys) of this very arginine.
Obviously this mutation has profound effects in the way the protein
interacts with the DNA, hence it causes a disease. I'm hypothesizing
that the Hbond removal in the mutant severely affects the binding
capacity. An assay is being developed by someone else to test this in
vitro. Meanwhile, I would like to estimate the difference in the
binding energy between the mutant and wild type proteins.

Please let me know if I got this correctly: What I need is a
thermodynamic cycle:

        deltaG1
WT-DNA ---------> WT + DNA
       | deltaG4 | deltaG2
       | |
MUT-DNA --------> MUT + DNA
        DeltaG3

And the deltadeltaG (the difference in free energy of binding between
the mutant and the wild type) that I'm interested in would be given
by subtracting deltaG4 from DeltaG2. These 2 deltaGs would be
calculated in two alchemical FEP/MD experiments.

1) If this concept is correct, should I do the simulation in solvated
systems, with PBC, PME?
2) since the positive charge of the arginine disappears, I guess I
need a ion to appear in lambda=1?
3) is it possible to evaluate the individual contributions to the
free energy difference? (electrostatic, VdW)

thank you in advance to any help provided,

Luis

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