Skip to main content
SpringerLink
Log in

Automated assignment of NMR chemical shifts based on a known structure and 4D spectra

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

Abstract

Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [1H,15N]-HSQC-NOESY-[1H,15N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73–82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign.

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
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14
Fig. 15
Fig. 16
Fig. 17
Fig. 18

Similar content being viewed by others

References

  • Berjanskii M, Wishart DS (2006) NMR: prediction of protein flexibility. Nat Protoc 1:683–688

    Article  Google Scholar 

  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535–542

    Article  Google Scholar 

  • Chao FA, Shi L, Masterson LR, Veglia G (2012) FLAMEnGO: a fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data. J Magn Reson 214:103–110

    Article  ADS  Google Scholar 

  • Chao FA, Kim JG, Xia YL, Milligan M, Rowe N, Veglia G (2014) FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances. J Magn Reson 245:17–23

    Article  ADS  Google Scholar 

  • Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836–6837

    Article  Google Scholar 

  • Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293

    Article  Google Scholar 

  • Exner TE, Frank A, Onila I, Moller HM (2012) Toward the quantum chemical calculation of NMR chemical shifts of proteins. 3. Conformational sampling and explicit solvents model. J Chem Theory Comput 8:4818–4827

    Article  Google Scholar 

  • Fesik SW, Shuker SB, Hajduk PJ, Meadows RP (1997) SAR by NMR: an NMR-based approach for drug discovery. Protein Eng 10:73

    Google Scholar 

  • Frank A, Onila I, Moller HM, Exner TE (2011) Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins. Proteins: struct. Funct Bioinf 79:2189–2202

    Article  Google Scholar 

  • Frank A, Moller HM, Exner TE (2012) Toward the quantum chemical calculation of NMR chemical shifts of proteins. 2. Level of theory, basis set, and solvents model dependence. J Chem Theory Comput 8:1480–1492

    Article  Google Scholar 

  • Garrett DS, Seok YJ, Liao DI, Peterkofsky A, Gronenborn AM, Clore GM (1997) Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. Biochemistry 36:2517–2530

    Article  Google Scholar 

  • Gobl C, Tjandra N (2012) Application of solution NMR spectroscopy to study protein dynamics. Entropy 14:581–598

    Article  ADS  MATH  Google Scholar 

  • Hajduk PJ (2006) SAR by NMR: putting the pieces together. Mol Interv 6:266–272

    Article  Google Scholar 

  • Han B, Liu YF, Ginzinger SW, Wishart DS (2011) SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR 50:43–57

    Article  Google Scholar 

  • He X, Wang B, Merz KM (2009) Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. J Phys Chem B 113:10380–10388

    Article  Google Scholar 

  • Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227

    Article  Google Scholar 

  • Hus JC, Prompers JJ, Bruschweiler R (2002) Assignment strategy for proteins with known structure. J Magn Reson 157:119–123

    Article  ADS  Google Scholar 

  • Jacob CR, Visscher L (2006) Calculation of nuclear magnetic resonance shieldings using frozen-density embedding. J Chem Phys 125:194104

    Article  ADS  Google Scholar 

  • Jang R, Gao X, Li M (2012) Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from N-15-NOESY. BMC Bioinf 13(Suppl 3):S4

    Article  Google Scholar 

  • Jung YS, Zweckstetter M (2004) Backbone assignment of proteins with known structure using residual dipolar couplings. J Biomol NMR 30:25–35

    Article  Google Scholar 

  • Jung YS, Sharma M, Zweckstetter M (2004) Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings. Angew Chem Int Ed Engl 43:3479–3481

    Article  Google Scholar 

  • Kay LE (2005) NMR studies of protein structure and dynamics. J Magn Reson 173:193–207

    Article  ADS  Google Scholar 

  • Keller RLJ (2004a) The computer aided resonance assignment tutorial. Cantina Verlag, Goldau

  • Keller RLJ (2004b) Optimizing the process of nuclear magnetic resonance spectrum analysis and computer aides resonance assignment. Ph.D., ETH Zürich

  • Kleckner IR, Foster MP (2011) An introduction to NMR-based approaches for measuring protein dynamics. Biochim Biophys Acta Proteins Proteomics 1814:942–968

    Article  Google Scholar 

  • Lee AM, Bettens RPA (2007) First principles NMR calculations by fragmentation. J Phys Chem A 111:5111–5115

    Article  Google Scholar 

  • Linge JP, Habeck M, Rieping W, Nilges M (2003) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19:315–316

    Article  Google Scholar 

  • Luan T, Jaravine V, Yee A, Arrowsmith CH, Orekhov VY (2005) Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition. J Biomol NMR 33:1–14

    Article  Google Scholar 

  • Mittermaier A, Kay LE (2006) Review—New tools provide new insights in NMR studies of protein dynamics. Science 312:224–228

    Article  ADS  Google Scholar 

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

    Article  Google Scholar 

  • Oldfield E (2002) Chemical shifts in amino acids, peptides, and proteins: from quantum chemistry to drug design. Annu Rev Phys Chem 53:349–378

    Article  ADS  Google Scholar 

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

    Article  Google Scholar 

  • Pristovsek P, Ruterjans H, Jerala R (2002) Semiautomatic sequence-specific assignment of proteins based on the tertiary structure—the program st2nmr. J Comput Chem 23:335–340

    Article  Google Scholar 

  • Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M (2007) ARIA2: automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23:381–382

    Article  Google Scholar 

  • Shen Y, Bax A (2010) SPARTA plus: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48:13–22

    Article  Google Scholar 

  • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274:1531–1534

    Article  ADS  Google Scholar 

  • Sprangers R, Kay LE (2007a) Probing supramolecular structure from measurement of methyl H-1-C-13 residual dipolar couplings. J Am Chem Soc 129:12668–12669

    Article  Google Scholar 

  • Sprangers R, Kay LE (2007b) Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445:618–622

    Article  Google Scholar 

  • Stratmann D, van Heijenoort C, Guittet E (2009) NOEnet-Use of NOE networks for NMR resonance assignment of proteins with known 3D structure. Bioinformatics 25:474–481

    Article  Google Scholar 

  • Stratmann D, Guittet E, van Heijenoort C (2010) Robust structure-based resonance assignment for functional protein studies by NMR. J Biomol NMR 46:157–173

    Article  Google Scholar 

  • Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL (2008) BioMagResBank. Nucl Acids Res 36:D402–D408

    Article  Google Scholar 

  • Venditti V, Fawzi NL, Clore GM (2011) Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy. J Biomol NMR 51:319–328

    Article  Google Scholar 

  • Vijaykumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 a resolution. J Mol Biol 194:531–544

    Article  Google Scholar 

  • Vogeli B, Segawa TF, Leitz D, Sobol A, Choutko A, Trzesniak D, van Gunsteren W, Riek R (2009) Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups. J Am Chem Soc 131:17215–17225

    Article  Google Scholar 

  • Walker CA, Hinderhofer M, Witte DJ, Boos W, Moller HM (2008) Solution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis. J Biomol NMR 42:69–76

    Article  Google Scholar 

  • Wishart DS, Watson MS, Boyko RF, Sykes BD (1997) Automated H-1 and C-13 chemical shift prediction using the BioMagResBank. J Biomol NMR 10:329–336

    Article  Google Scholar 

  • Xu XP, Case DA (2001) Automated prediction of (15)N, (13)C(alpha), (13)C(beta) and (13)C ‘ chemical shifts in proteins using a density functional database. J Biomol NMR 21:321–333

    Article  Google Scholar 

  • Xu YQ, Matthews S (2013) MAP-XSII: an improved program for the automatic assignment of methyl resonances in large proteins. J Biomol NMR 55:179–187

    Article  Google Scholar 

  • Xu YQ, Liu MH, Simpson PJ, Isaacson R, Cota E, Marchant J, Yang DW, Zhang XD, Freemont P, Matthews S (2009) Automated assignment in selectively methyl-labeled proteins. J Am Chem Soc 131:9480–9481

    Article  Google Scholar 

Download references

Acknowledgments

We thank Dr. Remco Sprangers for providing the 4D spectra of Ubiquitin and Prof. G. Marius Clore for the chemical shifts of the amide groups of enzyme I. This work was supported by the German Research Foundation (DFG) [EX15/17-1 to T.E.E.].

Author information

Authors and Affiliations

  1. Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany

    Matthias Trautwein, Kai Fredriksson & Thomas E. Exner

  2. Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam OT Golm, Germany

    Heiko M. Möller

Authors
  1. Matthias Trautwein
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kai Fredriksson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Heiko M. Möller
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Thomas E. Exner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Thomas E. Exner.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 67 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Trautwein, M., Fredriksson, K., Möller, H.M. et al. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra. J Biomol NMR 65, 217–236 (2016). https://doi.org/10.1007/s10858-016-0050-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-016-0050-0

Keywords

Search

Navigation