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HandWiki. Protein Chemical Shift Re-referencing. Encyclopedia. Available online: https://encyclopedia.pub/entry/29191 (accessed on 21 September 2026).
HandWiki. Protein Chemical Shift Re-referencing. Encyclopedia. Available at: https://encyclopedia.pub/entry/29191. Accessed September 21, 2026.
HandWiki. "Protein Chemical Shift Re-referencing" Encyclopedia, https://encyclopedia.pub/entry/29191 (accessed September 21, 2026).
HandWiki. (2022, October 14). Protein Chemical Shift Re-referencing. In Encyclopedia. https://encyclopedia.pub/entry/29191
HandWiki. "Protein Chemical Shift Re-referencing." Encyclopedia. Web. 14 October, 2022.
Protein Chemical Shift Re-referencing
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The content is sourced from: https://handwiki.org/wiki/Biology:Protein_chemical_shift_re-referencing

Protein chemical shift re-referencing is a post-assignment process of adjusting the assigned NMR chemical shifts to match IUPAC and BMRB recommended standards in protein chemical shift referencing. In NMR chemical shifts are normally referenced to an internal standard that is dissolved in the NMR sample. These internal standards include tetramethylsilane (TMS), 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS) and trimethylsilyl propionate (TSP). For protein NMR spectroscopy the recommended standard is DSS, which is insensitive to pH variations (unlike TSP). Furthermore, the DSS 1H signal may be used to indirectly reference 13C and 15N shifts using a simple ratio calculation . Unfortunately, many biomolecular NMR spectroscopy labs use non-standard methods for determining the 1H, 13C or 15N “zero-point” chemical shift position. This lack of standardization makes it difficult to compare chemical shifts for the same protein between different laboratories. It also makes it difficult to use chemical shifts to properly identify or assign secondary structures or to improve their 3D structures via chemical shift refinement. Chemical shift re-referencing offers a means to correct these referencing errors and to standardize the reporting of protein chemical shifts across laboratories.

trimethylsilyl biomolecular chemical shift

References

  1. Wishart, DS; Bigam CG; Yao J; Abildgaard F et al. (1995). "1H, 13C and 15N chemical shift referencing in biomolecular NMR". Journal of Biomolecular NMR 6 (2): 135–40. doi:10.1007/bf00211777. PMID 8589602.  https://dx.doi.org/10.1007%2Fbf00211777
  2. Zhang, H; Neal, S.; Wishart, D.S. (Mar 2003). "RefDB: A database of uniformly referenced protein chemical shifts". J. Biomol. NMR 25 (3): 173–195. doi:10.1023/A:1022836027055. PMID 12652131.  https://dx.doi.org/10.1023%2FA%3A1022836027055
  3. Wishart, DS; Case DA (2001). Use of chemical shifts in macromolecular structure determination. 338. 3–34. doi:10.1016/s0076-6879(02)38214-4. ISBN 9780121822392.  https://dx.doi.org/10.1016%2Fs0076-6879%2802%2938214-4
  4. Wang, L; Markley JL (2009). "Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing". Journal of Biomolecular NMR 44 (2): 95–99. doi:10.1007/s10858-009-9324-0. PMID 19436955.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2782637
  5. Wishart, DS (Feb 2011). "Interpreting protein chemical shift data". Progress in Nuclear Magnetic Resonance Spectroscopy 58 (1–2): 62–87. doi:10.1016/j.pnmrs.2010.07.004. PMID 21241884.  https://dx.doi.org/10.1016%2Fj.pnmrs.2010.07.004
  6. Ginzinger, SW; Gerick F; Coles M; Heun V (2007). "CheckShift: automatic correction of inconsistent chemical shift referencing". Journal of Biomolecular NMR 39 (3): 223–227. doi:10.1007/s10858-007-9191-5. PMID 17899394.  https://dx.doi.org/10.1007%2Fs10858-007-9191-5
  7. Ginzinger, SW; Skocibusić M; Heun V (2009). "CheckShift improved: fast chemical shift reference correction with high accuracy". Journal of Biomolecular NMR 44 (4): 207–211. doi:10.1007/s10858-009-9330-2. PMID 19575298.  https://dx.doi.org/10.1007%2Fs10858-009-9330-2
  8. Moseley, NH; Sahota G; Montelione TG (Jul 2004). "Assignment validation software suite for the evaluation and presentation of the protein resonance assignment data". Journal of Biomolecular NMR 28 (4): 341–355. doi:10.1023/B:JNMR.0000015420.44364.06. PMID 14872126.  https://dx.doi.org/10.1023%2FB%3AJNMR.0000015420.44364.06
  9. Wang, L; Eghbalnia HR; Bahrami A; Markley JL (May 2005). "Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications". Journal of Biomolecular NMR 32 (1): 13–22. doi:10.1007/s10858-005-1717-0. PMID 16041479.  https://dx.doi.org/10.1007%2Fs10858-005-1717-0
  10. Wang, Y; Wishart DS (2005). "A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins". Journal of Biomolecular NMR 31 (2): 143–148. doi:10.1007/s10858-004-7441-3. PMID 15772753.  https://dx.doi.org/10.1007%2Fs10858-004-7441-3
  11. Wang, B; Wang Y (2010). "A probabilistic approach for validating protein NMR chemical shift assignments". Journal of Biomolecular NMR 47 (2): 85–99. doi:10.1007/s10858-010-9407-y. PMID 20446018.  https://dx.doi.org/10.1007%2Fs10858-010-9407-y
  12. Neal, S; Nip AM; Zhang H; Wishart DS (Jul 2003). "Rapid and accurate calculation of protein 1H 13C and 15N chemical shifts". Journal of Biomolecular NMR 26 (3): 215–240. doi:10.1023/A:1023812930288. PMID 12766419.  https://dx.doi.org/10.1023%2FA%3A1023812930288
  13. McGuffin, LJ; Bryson K; Jones DT (2000). "The PSIPRED protein structure prediction server". Bioinformatics 16 (4): 404–405. doi:10.1093/bioinformatics/16.4.404. PMID 10869041.  https://dx.doi.org/10.1093%2Fbioinformatics%2F16.4.404
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