On Tue, Feb 5, 2013 at 10:07 AM, BERGY <nucleic81.gmail.com> wrote:
> ---------- Forwarded message ----------
> From: BERGY <nucleic81.gmail.com>
> Date: Tue, Feb 5, 2013 at 8:31 PM
> Subject:
> To: AMBER Mailing List <amber.ambermd.org>, Rashmi Panigrahi <
> rashmi.panigrahi19.gmail.com>
>
>
> Hi all i carried out MMPBSA alanine scan using amber12 MMPBSA.py.
> I found that the criticall residues mutated gave me a Negative value
> instead of positive value.
> Then i went and rea some papers and many said Dela-Delat G = DelatG(Mutant)
> minus DeltaG Native.
> and the value will be positive.
>
> SO i did the tutorial on alanine scanning
> it just addded more to my confusion
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section3.htm
>
> i am pasting the values given in tutorial page first (only PB given)
> NATIVE: DELTA G binding = -89.9575 +/-
> 8.2480 1.1664
> MUTANT: DELTA G binding = -87.8385 +/-
> 8.0665 1.1408
>
> and the so the
> RESULT OF ALANINE SCANNING: (I21A MUTANT:) DELTA DELTA G binding =
> 2.1190 +/- 11.5368
>
> Its coming positve which means: Mutant(-87.8) minus Native(-89.9) =
> 2.1190)
>
> Here comes the problem.
> Whne i repaetd the tutorial
> i got the opposite
> My result for RAS_RAF is
> NATIVE: DELTA TOTAL -28.3249
> 8.3093 1.1751
> MUTANT:DELTA TOTAL -25.8148
> 8.3300 1.1780
>
> RESULT OF ALANINE SCANNING: (I21A) DELTA DELTA G binding = -2.5100
> +/- 0.8185
>
> Here the results say that
> Its coming negative which means ( native(-28.3) minus Mutant(-25.8)=
> -2.5).
>
> I feel somewhere down the line the A-B has got interchanged to B-A...
> Can some one explain which is correct. Please not that i understand that i
> used amber12 and the tutorial might have been done in old mmpbsa. but even
> then its the difference in value that matters. I think the
>
> This paper
> http://depts.washington.edu/bakerpg/papers/FriApr3012:42:182004.pdf
> says Positive values mean that replacement by alanine is predicted to
> destabilize the complex;
> ans it uses native minus mutant.
>
>
> In this paper,
> http://peds.oxfordjournals.org/content/24/1-2/197.full
> they say Mutant minus native ????
>
> which is correct. i guess in the end i shwed just see the delta G values
> individually for native n mutant
>
It is simply a convention, and not a particularly important one, either.
Compare the free energies of binding: whichever has a lower free energy of
binding is more stable. So if the alanine mutant has a lower binding free
energy than the native structure, then that mutation is stabilizing. The
order that you subtract them is rather arbitrary. If you do NATIVE -
MUTANT, then positive values means that MUTANT is smaller than NATIVE;
smaller values are stabilizing, so the MUTANT is more stable. If you do
MUTANT - NATIVE, then positive values mean exactly the opposite -- NATIVE
is smaller than MUTANT, so the NATIVE state is more stable.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 05 2013 - 07:30:05 PST
