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
########################################################################
To unsubscribe from the CCPNMR list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPNMR&A=1
|