| Title |
Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications
|
|---|---|
| Published in |
Journal of Biomolecular NMR, May 2005
|
| DOI | 10.1007/s10858-005-1717-0 |
| Pubmed ID | |
| Authors |
Liya Wang, Hamid R. Eghbalnia, Arash Bahrami, John L. Markley |
| Abstract |
Statistical analysis reveals that the set of differences between the secondary shifts of the alpha- and beta-carbons for residues i of a protein (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) provides the means to detect and correct referencing errors for 1H and 13C nuclei within a given dataset. In a correctly referenced protein dataset, linear regression plots of Deltadelta13C(alpha)i, Deltadelta13C(beta)i, or Deltadelta1H(alpha)i vs. (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) pass through the origin from two directions, the helix-to-coil and strand-to-coil directions. Thus, linear analysis of chemical shifts (LACS) can be used to detect referencing errors and to recalibrate the 1H and 13C chemical shift scales if needed. The analysis requires only that the signals be identified with distinct residue types (intra-residue spin systems). LACS allows errors in calibration to be detected and corrected in advance of sequence-specific assignments and secondary structure determinations. Signals that do not fit the linear model (outliers) deserve scrutiny since they could represent errors in identifying signals with a particular residue, or interesting features such as a cis-peptide bond. LACS provides the basis for the automated detection of such features and for testing reassignment hypotheses. Early detection and correction of errors in referencing and spin system identifications can improve the speed and accuracy of chemical shift assignments and secondary structure determinations. We have used LACS to create a database of offset-corrected chemical shifts corresponding to nearly 1800 BMRB entries: 300 with and 1500 without corresponding three-dimensional (3D) structures. This database can serve as a resource for future analysis of the effects of amino acid sequence and protein secondary and tertiary structure on NMR chemical shifts. |
Mendeley readers
The data shown below were compiled from readership statistics for 44 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Russia | 1 | 2% |
| Belgium | 1 | 2% |
| Unknown | 42 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 12 | 27% |
| Researcher | 11 | 25% |
| Student > Bachelor | 4 | 9% |
| Professor > Associate Professor | 3 | 7% |
| Student > Master | 3 | 7% |
| Other | 6 | 14% |
| Unknown | 5 | 11% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 13 | 30% |
| Chemistry | 13 | 30% |
| Biochemistry, Genetics and Molecular Biology | 9 | 20% |
| Environmental Science | 1 | 2% |
| Pharmacology, Toxicology and Pharmaceutical Science | 1 | 2% |
| Other | 1 | 2% |
| Unknown | 6 | 14% |
Attention Score in Context
This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 April 2014.
All research outputs
#7,454,951
of 22,790,780 outputs
Outputs from Journal of Biomolecular NMR
#132
of 614 outputs
Outputs of similar age
#20,340
of 58,099 outputs
Outputs of similar age from Journal of Biomolecular NMR
#3
of 10 outputs
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