Hi Niko,
I was a bit curious about this, so I had a dig around. It seems that the
random-coil shifts (and secondary-structure shifts) are coming from the DANGLE
code, which is using random-coil shifts from J. Biomol. NMR 18, 43-48 (2000).
These were measured in 8 M urea at pH 2, so I suspect the low pH accounts for the
big discrepancies for Glu and Asp (I also see similar differences). For the
proline Cb, it looks as if it is the random-coil shift for the cis geometry (34.8
ppm) that is being used rather than that for the trans (32.22 ppm); I guess this
means there could be a bug somewhere, since both the cis and trans values are
present in the reference table.
Cheers
John
On 08/01/2019 05:20, Niko Loening wrote:
> Can somebody explain to me what values are used as the baseline for
> calculating the secondary chemical shifts for Cb's in the Secondary Structure
> Chart? The references in the documentation only refer to Ca/Co/N/HN/Ha
> chemical shifts. I've got a suspicion that the values that CCPN has, at least
> for proline, are incorrect.
>
> In my case, I've got a (mostly) disordered protein with proline Cb shifts
> between 32.0 and 32.1 for the five prolines. These values are very close to
> the random coil chemical shift values reported by Wishart (J. Bionmr, 5 (1995)
> 67-81) and also very close to the BMRB average value (31.9 ppm). However, the
> secondary chemical shift reported by CCPN analysis is a whopping -2.7 for
> these residues. Other Cb shifts are not wildly off, so its not a referencing
> problem on my part, and I'm very sure these prolines are in the trans
> conformation based on their Cb and Cg shifts.
>
> In fact, when I use CCPN to generate a set of predicted random coil chemical
> shifts (Data Analysis -> Measurement Lists -> Make Random Coil Chemical Shift
> List) I find that the resulting list seems to have some rather different
> values for the following residues compared to the results published by Wishart
> in 1995.
>
> Asp (Co, Ca, and Cb) Glu (Cb and maybe Co) Gly (Co) Pro (Co and Cb)
>
> There also might be deviations for Cys, Phe, Tyr, and Thr but my protein
> doesn't have those amino acids so I couldn't check them easily. Of course,
> things have progressed in the 20 years since Wishart published his results so
> CCPN might be using newer data or a more sophisticated algorithm. But, based
> on what I'm seeing, I still think there are some mistakes in CCPN's data.
>
> So, what algorithm is CCPN using to predict random coil chemical shifts? Is
> there a way to correct this?
>
> Thanks,
>
> Niko Loening
>
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