[gmx-users] Effect of a single mutation in a protein

[Justin Lemkul]

On 3/27/14, 2:32 PM, Pappu Kumar wrote:
> Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha
> atoms of one trajectory and then projected the other trajectory on it.
>

Sounds reasonable.

> I obtained the ATP parameters from a paper. Like all simulations, MD has some
> limitations. So I don't want to highlight the things which may not be correct.
>

OK, I thought you were trying to indicate something else.  Presumably the ATP 
parameters are pretty good; it's a standard molecule in just about every force 
field.

> There is no unfolding. Also the gibbs energy surface projected on PC1 and PC2
> looks quite different than RMSD vs. Rg surface calculated by g_sham (also the
> lowest energy structures.)
>

Without significant conformational changes, I still don't see how RMSD or Rg are 
relevant metrics for what you're seeing.

> Can I calculate del del G by TI? I am not sure how to define the reaction
> coordinates. Is it a good idea to do umbrella sampling between two states to
> determine the free energy?
>

The ddG of what?  Folding?  Ligand binding?  Umbrella sampling isn't the best 
approach here, but doing an alchemical transformation between the WT and mutant 
might be possible.  You'll have to define very clearly what you're trying to 
achieve.

-Justin

> On Thursday, 27 March 2014 8:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 3/26/14, 2:24 PM, Pappu Kumar wrote:
>  > I have already used g_hbond. I am not sure how accurate is the H-bond
> lifetime calculation. Also the trajectory snapshots need to be saved quite
> often. Could you tell me how to interpret output from g_hbond -ac :
>  >
>
> There should be references provided in the g_hbond output when calculating
> lifetimes.  At the very least, they're in the manual.  So you can determine for
> yourself how reliable the outcome is.
>
>  > @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
>  > @ s1 legend "Ac(t)"
>  > @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
>  > @ s3 legend "-dAc\sfs\v{}\z{}/dt"
>  >
>
> Plotting these data sets in XmGrace will clear things up.
>
>  > Could you tell me how to  project the configurations of the mutant simulation
> on WT PC1? Are you aware of any paper where I can read more about it? Can I
> compare the PC1 vs PC2 in case of WT and mutant?
>  >
>
> See g_anaeig -h, as well as previous discussions in the list archive on doing this.
>
>  >
>  > I am trying to find out how such mutation buried inside the protein away from
> the ligand binding pocket can influence the function of the protein. I actually
> see some changes in the positon of the bound ATP in the mutant compared to the
> WT. But I am not sure how reliable it is due to the inaccuracies in
> parameterization.
>  >
>
> Well, if your parametrization is inaccurate and you know it is, what use are the
> simulations?  Or are you just wondering if there is a possibility of
> inaccuracies?  Either way, that's something that should be sorted out long
> before doing any real simulations :)
>
>
>  >
>  > I also calculated the Gibbs free energy landscape by g_sham using Rg and
> RMSD. The value varies from 0-6.5 kJ/mol in both cases but the regions with ~0
> kJ/mol has changed.
>
>  >
>
> Do the proteins unfold?  If not, I doubt Rg vs. RMSD is a very sensitive metric
> of anything.  You can, of course, map back the locations of the energy minima to
> see if there are any interesting differences there, but such a plot (Rg vs.
> RMSD) is probably only useful in protein (un)folding simulations.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================