Journal of biomolecular NMR (2012). Thomas Aeschbacher, Mario Schubert, Frédéric H-T Allain et al.
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 (13)C NMR data of RNAs. Our procedure uses five (13)C 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 (13)C calibration and detect errors or inconsistencies in RNA (13)C 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 structure-(13)C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable (13)C 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 structure-chemical shift relationships with this improved list of (13)C chemical shift data. This is demonstrated by a clear relationship between ribose (13)C shifts and the sugar pucker, which can be used to predict a C2'- or C3'-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.
[NMR paper] A procedure to validate and correct the (13)C chemical shift calibration of RNA datasets.
From Mendeley Biomolecular NMR group:
A procedure to validate and correct the (13)C chemical shift calibration of RNA datasets.
Journal of biomolecular NMR (2012). Thomas Aeschbacher, Mario Schubert, Frédéric H-T Allain et al.
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....
nmrlearner
Journal club
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10-12-2012 09:58 AM
[NMR paper] A procedure to validate and correct the (13)C chemical shift calibration of RNA datasets.
From Mendeley Biomolecular NMR group:
A procedure to validate and correct the (13)C chemical shift calibration of RNA datasets.
Journal of biomolecular NMR (2012). Thomas Aeschbacher, Mario Schubert, Frédéric H-T Allain et al.
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....
nmrlearner
Journal club
0
08-24-2012 08:01 PM
A procedure to validate and correct the 13C chemical shift calibration of RNA datasets
A procedure to validate and correct the 13C chemical shift calibration of RNA datasets
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...
nmrlearner
Journal club
0
01-21-2012 06:26 PM
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...
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:
nmrlearner
NMR software
0
07-03-2005 12:02 AM
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
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.