Skip to main content
SpringerLink
Log in

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to Hδ21 and Hε21, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Abbreviations

NOE:

Nuclear Overhauser effect

NOESY:

Nuclear Overhauser enhancement spectroscopy

UACSB:

Unbiased artificial chemical shift database

References

  • Berenden HJC, van der Spoerl D, van Dunen R (1995) GROMACS: a message-passing parallel dynamics impmementation. Comp Phys Comm 91:43–56

    Article  ADS  Google Scholar 

  • Bundi A, Wuthrich K (1979) 1H-nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 18:285–297

    Article  Google Scholar 

  • Gronwald W, Kalbitzer HR (2004) Automated structure determination of proteins by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 44:33–96

    Article  Google Scholar 

  • Harsch T, Dasch C, Donaubauer H, Baskaran K, Kremer W, Kalbitzer HR (2013) Stereospecific assignment of the asparagine and glutamine side chain amide protons in random-coil peptides by combination of molecular dynamic simulations with relaxation matrix calculations. Appl Magn Reson 44(1–2):319–331

    Article  Google Scholar 

  • Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435–447

    Article  Google Scholar 

  • Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wüthrich K (1998) Recommendations for the presentation of nmr structures of proteins and nucleic acids. Pure Appl Chem 70:117–142

    Article  Google Scholar 

  • McIntosh LP, Brun E, Kay LE (1997) Stereospecific assignment of the NH2 resonances from the primary amides of asparagine and glutamine side chains in isotopically labeled proteins. J Biomol NMR 9:306–312

    Article  Google Scholar 

  • Nasser, A. (2006) Optimierung der Zuordnung mehrdeutiger NOESY-NMR-Signale unter Anwendung einer Datenbank nichtredundanter Proteinstrukturen. Doctoral thesis, University of Regensburg.

  • Neal S, Nip AM, Zhang H, Wishart DS (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR 26:215–240

    Article  Google Scholar 

  • Osapay K, Case DA (1991) A new analysis of proton chemical shifts in proteins. J Am Chem Soc 113(25):9436–9444

    Article  Google Scholar 

  • Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O et al (2011) Scikit-learn: machine learning in Python. J Machine Learn Res 12:2825–2830

    MathSciNet  MATH  Google Scholar 

  • Schölkopf B, Smola AJ (2002) Learning with kernels support vector machines, regularization, optimization, and beyond. Adaptive computation and machine learning. MIT Press, Cambridge

    Google Scholar 

  • Sillitoe, I., Cuff, Alison L. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res 41:D490–D498

    Article  Google Scholar 

  • Silverman BW (1998) Density estimation for statistics and data analysis. Chapman & Hall, London

    MATH  Google Scholar 

  • Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidi YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Wenger RK, Yao H, Markley JL (2007) BioMagResBank. Nucl Acids Res 36:D402–D408

    Article  Google Scholar 

  • Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285(4):1735–1747

    Article  Google Scholar 

  • Wüthrich K (1986) NMR of Proteins and Nucleic Acids. Wiley, New York

    Google Scholar 

Download references

Acknowledgements

This work has been supported by the DFG (FOR1979 and KA 647), the Humboldt Society, the Fonds of the Chemical Industry (VCI), and the Human Frontier Science Program Organization (HFSPO).

Author information

Authors and Affiliations

  1. Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany

    Tobias Harsch, Philipp Schneider, Bärbel Kieninger, Harald Donaubauer & Hans Robert Kalbitzer

Authors
  1. Tobias Harsch
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Philipp Schneider
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bärbel Kieninger
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Harald Donaubauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hans Robert Kalbitzer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hans Robert Kalbitzer.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Harsch, T., Schneider, P., Kieninger, B. et al. Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis. J Biomol NMR 67, 157–164 (2017). https://doi.org/10.1007/s10858-017-0093-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-017-0093-x

Keywords

Search

Navigation