Hi Jason
Thanks a lot for your explanation.
The non-polar interaction I refereed is the value of van der waals component.
The result show van der waals= -1.21 that could be difficult to understand, as Threonine is a polar residue.
I do not know how it contributes to the van der waals interaction.
Cheers
Marc​
---- On Wed, 09 Mar 2016 03:44:13 +0100 Jason Swails <jason.swails.gmail.com>wrote ----
On Tue, Mar 8, 2016 at 12:08 PM, Zhang Marc <marczhang_md.zoho.com> wrote:
>
>
> Dear experts in Amber users group
>
>
>
> I performed a 20 ns MD simulations of a ligand-protein complex system.
>
>
>
> The ligand binding free energy was calculated using MMGBSA.
>
>
>
> The energy was decomposed onto residues in the binding pocket for
> identifying residues important for ligand-protein interactions.
>
>
>
> Now I have difficulties to interpret the decomposition result, as it
> suggested Threonine 119 is critical for both polar &amp; non-polar
> interactions.
>
>
>
> Here is the part of the result:
>
>
>
> Resides van der Waals Electrostatic Polar Solvation
> Non-Polar Solvation TOTAL
>
> Thr119 -1.21 -2.37 0.27
> -0.93 -4.23
>
>
>
> But Threonine is a polar residue and it is seldomly contributes to
> hydrophobic interactions, as I was taught during biochemistry course.
>
>
>
> Could you please help me figure out where the problem is?
>
The nonpolar solvation free energy term is a very simple SASA based term.
Basically, you take your solvent accessible surface area, multiply it by a
constant, and that gives you the "nonpolar" part of solvation.
It's unclear here whether these results are the *binding* results (i.e.,
the bound - unbound energies), or if they are the bound or unbound values.
But assuming this is the binding free energy, what a negative non-polar
solvation energy here means is that the surface area exposed to solvent for
this threonine in the bound state is smaller than that in the unbound
state. If this is near the ligand, that makes sense. In the unbound state
it's interacting with solvent (large SASA). In the bound state, it's
interacting with the ligand (small SASA).
HTH,
Jason
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Received on Wed Mar 09 2016 - 00:30:05 PST
