On Thu, Mar 3, 2016 at 11:02 AM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> Hello all,
> I apologise if this question has a trivial and obvious answer, but I'm
> trying to be extra sure and wrap my head around this.
> I performed an alanine scanning mutagenesis analysis of a system I have,
> mutating one residue to an alanine to determine the delta delta G.
> These are some of the relevant results:
>
> DELTA TOTAL -90.1156 5.6556
> 0.7998
> DELTA TOTAL -67.2848 4.8677
> 0.6884
> RESULT OF ALANINE SCANNING: DELTA DELTA G binding = -22.8307 +/-
> 2.4038
>
> The first is the GB calculation of the native system, the second is the
> alanine mutant, and the third is the summary. Why does it have a negative
> sign? Shouldn't the delta delta of the mutant be positive, given how less
> favourable the interaction is? Am I missing something here?
>
The alanine scanning results are reported as normal - mutant, which is the
opposite of what you may expect (hence the negative sign). Perhaps an
unfortunate choice, but you can always take the negative if it makes your
analyses easier.
>
> On an unrelated note, these are the results of two quasi-harmonic
> simulations on two related systems:
>
> DELTA S: -12.9349 -10.8184 -7.9907 -31.7440
> DELTA S: -13.1305 -11.3163 -11.0363 -35.4828
>
> Am I correct in assuming that the second has a more entropically
> unfavourable interaction because the entropy decreases by a larger amount
> upon complexation? Is that how I should interpret this data?
>
In principle, yes. In practice, the difference is too small to be
statistically meaningful.
HTH,
Jason
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Received on Thu Mar 03 2016 - 18:00:03 PST
