Abstract Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of 13C NMR data of RNAs. Our procedure uses five 13C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the 13C calibration and detect errors or inconsistencies in RNA 13C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structureâ??13C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable 13C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structureâ??chemical shift relationships with this improved list of 13C chemical shift data. This is demonstrated by a clear relationship between ribose 13C shifts and the sugar pucker, which can be used to predict a C2â?²- or C3â?²-endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.
Content Type Journal Article
Category Article
Pages 1-12
DOI 10.1007/s10858-011-9600-7
Authors
Thomas Aeschbacher, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
Mario Schubert, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
SHIFTX2: Chemical Shift Prediction
SHIFTX2 website
SHIFTX2 is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain...
gwnmr
NMR software
0
01-10-2012 06:13 PM
[NMR Geek blog] Chemical Shift Referencing Calculator
Chemical Shift Referencing Calculator
Below is the protocol I follow for chemical shift referencing (direct for 1H, and indirect for 13C and 15N). Actually I always have to look back and forth for referencing, so thought why not make a small script and put it on web so that the access becomes handy. !!! The referencing should be done
Full story can be found on the NMR geek blog
New way to correct misreferenced chemical shifts
A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins.
Wang Y, Wishart DS.
J Biomol NMR. 2005 Feb;31(2):143-8.
http://pronmr.com/yunjunwang_files/yjw_pssi.jpg
Abstract:
Chemical shift of protons?
Can someone give me the answers to the chemical shift of the protons in this compound: CH3CH2OCH2CH(CH3)COOH? Of if you can explain how to get the chemical shift it would be quite helpful as the info online does not really help me.
Tim Mrudande
NMR Questions and Answers
1
01-16-2005 08:23 AM
HNMR chemical shift characteristic?
Hi, I'm trying to justify why that specific proton has such chemical shift characteristic.The molecule I'm working with is cyclopentadiene. I know that two protons attached on one of five carbon has 2.89ppm and the proton attached to the next carbon has 6.46ppm and the one on next carbon has 6.57ppm. I can't seem to justify the reason for that pattern.Another molecule is anisole. The methiyl group attached to the ester oxygen has 3.79ppm and the proton attached to carbon that is at ortho position with oxygen has 6.88ppm and the next proton(meta position) is 7.29ppm and the next one (para...
Filumena M
NMR Questions and Answers
1
01-09-2005 01:40 AM
what is/ how do you calculate the chemical shift in an NMR?
I have read the technical definitions but I still do not understand what the chemical shift means and how you calculate it given an NMR peak. If someone could kind of dumb it down for me but still give me the important things to know/ how it helps you determine the structure of a molecule with the NMR I would appreciate it.
A procedure to validate and correct the 13C chemical shift calibration of RNA datasets
Linear Mode
