ArticleJournal of biomolecular NMR2010
Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.
Article in Journal of biomolecular NMR, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 14 citations in OpenAlex.
- Article
- Factors affecting the computation of the 13C shielding in disaccharides.Journal of computational chemistry · 2014Article
- Are accurate computations of the 13C' shielding feasible at the DFT level of theory?Journal of computational chemistry · 2014Article
- Physics-based method to validate and repair flaws in protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
- Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.Journal of biomolecular NMR · 2013Article
- HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts.Journal of biomolecular NMR · 2013Article
- CheShift-2: graphic validation of protein structures.Bioinformatics (Oxford, England) · 2012Article
- A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides.Biophysical journal · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed (13)C(alpha) chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical (13)C(alpha) chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed (13)C(alpha) chemical shifts, Delta(ca,i), for the individual residues along the sequence. This indicates that the Delta(ca,i)-values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.
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