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] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 PM
[NMR paper] NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.
NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.
Related Articles NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction.
BMC Bioinformatics. 2013 Mar 16;14(1):98
Authors: Dehof AK, Loew S, Lenhof HP, Hildebrandt A
Abstract
NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking...
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03-19-2013 01:22 PM
[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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01-21-2013 02:09 PM
[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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11-22-2012 11:49 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
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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
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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
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01-21-2012 06:26 PM
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: