Journal of Biomolecular NMR

, Volume 46, Issue 3, pp 217–225 | Cite as

Analysis of \( {}^{13}{\text{C}}^{{{\upalpha}}} \) and \( {}^{13}{\text{C}}^{{{\upbeta}}} \) chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach

  • Osvaldo A. Martin
  • Myriam E. Villegas
  • Jorge A. Vila
  • Harold A. Scheraga
Article

Abstract

Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the \( {}^{13}{\text{C}}^{{{\upalpha}}} \) and \( {}^{13}{\text{C}}^{{{\upbeta}}} \) chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed \( {}^{13}{\text{C}}^{{{\upalpha}}} \) chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed \( {}^{13}{\text{C}}^{{{\upalpha}}} \) chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced −SH \( {}^{13}{\text{C}}^{{{\upbeta}}} \), but not for the \( {}^{13}{\text{C}}^{{{\upalpha}}} \), chemical shifts, in good agreement with the observation of 375 \( {}^{13}{\text{C}}^{{{\upalpha}}} \) and 337 \( {}^{13}{\text{C}}^{{{\upbeta}}} \) resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of \( {}^{13}{\text{C}}^{{{\upalpha}}} \) and \( {}^{13}{\text{C}}^{{{\upbeta}}} \) chemical shifts of cysteines in cystines.

Keywords

13C chemical shift prediction Cysteine residue Protein structure validation X-ray and NMR structures Cysteine redox state 

Notes

Acknowledgments

This research was supported by grants from the National Institutes of Health (GM-14312 and GM-24893), and the National Science Foundation (MCB05-41633). Support was also received from CONICET, FONCyT-ANPCyT (PAV 22642/22672), and from the Universidad Nacional de San Luis (P-328501), Argentina. The research was conducted by using the resources of our 600-core Beowulf cluster at the Baker Laboratory of Chemistry and Chemical Biology, Cornell University.

Supplementary material

10858_2010_9396_MOESM1_ESM.pdf (693 kb)
Supplementary material 1 (PDF 693 kb)

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Osvaldo A. Martin
    • 1
  • Myriam E. Villegas
    • 1
  • Jorge A. Vila
    • 1
    • 2
  • Harold A. Scheraga
    • 2
  1. 1.Instituto de Matemática Aplicada San LuisUniversidad Nacional de San LuisSan LuisArgentina
  2. 2.Baker Laboratory of Chemistry and Chemical BiologyCornell UniversityIthacaUSA

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