Dear Dr. Roitberg,
Sorry for the confusion.
The protein has ~40 residues, and the experimental shift values for the 40 N
(of amide group) are roughly from 115 to 125. The predicted values are
roughly from 110 to 120. In average, shifts program under-estimate the N
shift values by 5. The correlation between simulation and experiment is
strong.
Doing the simulation in explicit is impossible ( can't reach meaningful time
scale and sample enough conformational space.), which is why I chose
implicit solvent model.
The under-estimation mentioned above makes me a little nervous. I am a
totally layman on NMR thing, really in need of a reasonable explanation.
I jumped into a wet lab after graduate study, which is really good because I
can finally test my simulation with benchwork. But one thing bad is that I
can't find someone to talk about the theoretical thing. :(
Thanks,
Mingfeng
On 5/3/07, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
>
>
> Dear Mingfeng,
> N (of Amide) chemical shifts should be around 120, but some range of
> maybe 20 to 30. Do you mean that your N shifts from the program are
> around 25 ? That would make them 5 times smaller then experiment.
>
> Please clarify.
> We can N shifts around 120 for amide N using the same setup. As
> mentioned H-amide chemical shifts are much harder. Doing the simulation
> in real water does not help either, because shifts does not really look
> at the waters when doing the calculation, so you are still missing the
> effect of charges.
>
> Cheers
> Adrian
>
>
> Mingfeng Yang wrote:
> > Emmm. I am gotta reply to myself.
> >
> > I guess the under-estimate of backbone N chemical shift must due to the
> > fact that N-H can't form hydrogen bond with water in implicit solvent.
> > Am I
> > right?
> >
> > Anyway, it's pretty exciting to see that simulation can reproduce
> > experimental values so well.
> >
> >
>
> >> I took an ensemble average of the chemical shift values of N, CA, CB
> >> which were calculated by Dr. Case's SHIFTS program, and compared with
> >> the corresponding chemical shifts determined by solution state NMR.
> >>
> but the N chemical shifts
> >> are smaller than experimental values by 5.
> >>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>
> ============================================================================
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Received on Sun May 06 2007 - 06:07:25 PDT
