All residues have van der waals interactions. Polar ones may also have
stronger electrostatics.
On Mar 9, 2016 3:26 AM, "Zhang Marc" <marczhang_md.zoho.com> wrote:
> 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 &
> lt;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.
>
> >
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> >
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> >
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> > The ligand binding free energy was calculated using MMGBSA.
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> >
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> >
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> >
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> > The energy was decomposed onto residues in the binding pocket for
>
> > identifying residues important for ligand-protein interactions.
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> >
>
> >
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> >
>
> > 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:
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> >
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> >
>
> >
>
> > Resides van der Waals Electrostatic Polar Solvation
>
> > Non-Polar Solvation TOTAL
>
> >
>
> > Thr119 -1.21 -2.37 0.27
>
> > -0.93 -4.23
>
> >
>
> >
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> >
>
> > But Threonine is a polar residue and it is seldomly contributes to
>
> > hydrophobic interactions, as I was taught during biochemistry course.
>
> >
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> >
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> >
>
> > 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 - 03:30:21 PST
