Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.

Journal of Biomolecular NMR
Jorge A VilaHarold A Scheraga

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...Continue Reading

References

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Sep 10, 2008·Journal of Computational Chemistry·Jorge A VilaHarold A Scheraga
Jul 4, 2009·Accounts of Chemical Research·Jorge A Vila, Harold A Scheraga
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jorge A VilaHarold A Scheraga

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Citations

Dec 18, 2012·Journal of Biomolecular NMR·Jianyang ZengBruce Randall Donald
Oct 2, 2013·Proceedings of the National Academy of Sciences of the United States of America·Osvaldo A MartinJorge A Vila
Apr 13, 2012·Bioinformatics·Osvaldo A MartinHarold A Scheraga
May 7, 2011·Annual Review of Biophysics·Harold A Scheraga
Jul 30, 2014·Journal of Computational Chemistry·Pablo G GarayJorge A Vila
Feb 16, 2011·Biophysical Journal·Mahmoud MoradiChristopher Roland
Jan 10, 2014·Journal of Computational Chemistry·Jorge A VilaHarold A Scheraga
Sep 26, 2013·Current Opinion in Structural Biology·Antonio RosatoGaetano T Montelione
Jan 14, 2014·Journal of Chemical Theory and Computation·Chris Vanessa SumowskiChristian Ochsenfeld
Jan 22, 2011·Journal of Medical Microbiology·Maya KitaokaStefan Pukatzki

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Methods Mentioned

BETA
nuclear magnetic resonance
NMR
X-ray

Software Mentioned

CYANA
Gaussian
OPALp
PROCHECK

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