Skip to main content
SpringerLink
Log in

NMR-Based Modeling and Refinement of Protein 3D Structures

  • Protocol
  • First Online:
Molecular Modeling of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1215))

Abstract

NMR is a well-established method to characterize the structure and dynamics of biomolecules in solution. High-quality structures can now be produced thanks to both experimental advances and computational developments that incorporate new NMR parameters and improved protocols and force fields in the structure calculation and refinement process. In this chapter, we give a short overview of the various types of NMR data that can provide structural information, and then focus on the structure calculation methodology itself. We discuss and illustrate with tutorial examples “classical” structure calculation, refinement, and structure validation approaches.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Wuthrich K (1986) Nmr of proteins and nucleic acids. Wiley, New York, NY

    Google Scholar 

  2. Neuhaus D, Williamson MP (2000) The nuclear overhauser effect in structural and conformational analysis. Wiley, New York, NY

    Google Scholar 

  3. Altona C (1996) Vicinal coupling constants and conformation of biomolecules. In Harris DMG, a K R (eds) Encyclopedia of nuclear magnetic resonance. Wiley, London. pp 4909–4922

    Google Scholar 

  4. Bax A, Kontaxis G, Tjandra N (2001) Dipolar couplings in macromolecular structure determination. Methods Enzymol 339:127–174

    Article  PubMed  CAS  Google Scholar 

  5. Bertini I, Luchinat C, Parigi G (2012) Towards mechanistic systems biology. Wiley-VCH Verlag GmbH, Weinheim, Germany. pp 154–171

    Google Scholar 

  6. Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci U S A 104:9615–9620

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  7. Shen Y et al (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A 105:4685–4690

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. Wishart DS et al (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res 36:W496–W502

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  9. Güntert P (1998) Structure calculation of biological macromolecules from NMR data. Q Rev Biophys 31:145–237

    Article  PubMed  Google Scholar 

  10. Linge JP, Williams MA, Spronk CAEM, Bonvin AMJJ, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50:496–506

    Article  PubMed  CAS  Google Scholar 

  11. Nederveen AJ et al (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59:662–672

    Article  PubMed  CAS  Google Scholar 

  12. Güntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378

    PubMed  Google Scholar 

  13. Brünger AT et al (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921

    Article  PubMed  Google Scholar 

  14. Brunger AT (2007) Version 1.2 of the Crystallography and NMR system. Nat Protoc 2:2728–2733

    Article  PubMed  CAS  Google Scholar 

  15. Doreleijers JF et al (2012) CING: an integrated residue-based structure validation program suite. J Biomol NMR 54:267–283

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  16. Luginbühl P, Szyperski T, Wüthrich K (1995) Statistical basis for the use of 13cα chemical shifts in protein structure determination. J Magn Res 109:92

    Google Scholar 

  17. Kuszewski J, Qin J, Gronenborn AM, Clore GM (1995) The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR. J Magn Reson B 106:92–96

    Article  PubMed  CAS  Google Scholar 

  18. 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  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  PubMed Central  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  21. Williamson MP, Kikuchi J, Asakura T (1995) Application of 1H NMR chemical shifts to measure the quality of protein structures. J Mol Biol 247:541–546

    PubMed  CAS  Google Scholar 

  22. Meiler J (2003) PROSHIFT: protein chemical shift prediction using artificial neural networks. J Biomol NMR 26:25–37

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  24. Karplus M (1963) Vicinal proton coupling in nuclear magnetic resonance. J Am Chem Soc 85:2870–2871

    Article  CAS  Google Scholar 

  25. Kim Y, Prestegard JH (1990) Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins 8:377–385

    Article  PubMed  CAS  Google Scholar 

  26. Torda AE, Brunne RM, Huber T, Kessler H, Van Gunsteren WF (1993) Structure refinement using time-averaged J-coupling constant restraints. J Biomol NMR 3:55–66

    Article  PubMed  CAS  Google Scholar 

  27. Wagner G, Wüthrich K (1982) Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance. J Mol Biol 160:343–361

    Article  PubMed  CAS  Google Scholar 

  28. Pervushin K et al (1998) NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci U S A 95:14147–14151

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  29. Cordier F, Rogowski M, Grzesiek S, Bax A (1999) Observation of through-hydrogen-bond 2hJHC' in a perdeuterated protein. J Magnet Res 140:510–512

    Article  CAS  Google Scholar 

  30. Bonvin AMJJ, Houben K, Guenneugues M, Kaptein R, Boelens R (2001) Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C“ scalar couplings (3hbJNC”). J Biomol NMR 21:221–233

    Article  PubMed  CAS  Google Scholar 

  31. Bax A (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 12:1–16

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  32. Bax A, Grishaev A (2005) Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr Opin Struct Biol 15:563–570

    Article  PubMed  CAS  Google Scholar 

  33. Prestegard JH, Bougault CM, Kishore AI (2004) Residual dipolar couplings in structure determination of biomolecules. Chem Rev 104:3519–3540

    Article  PubMed  CAS  Google Scholar 

  34. Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol 4:732–738

    Article  PubMed  CAS  Google Scholar 

  35. Fushman D, Varadan R, Assfalg M (2004) Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements. Prog Nucl Magn Reson Spectrosc 44:189–214

    Article  CAS  Google Scholar 

  36. Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM (1997) Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nat Struct Biol 4:443–449

    Article  PubMed  CAS  Google Scholar 

  37. Bertini I, Luchinat C, Parigi G, Pierattelli R (2005) NMR spectroscopy of paramagnetic metalloproteins. ChemBioChem 6:1536–1549

    Article  PubMed  CAS  Google Scholar 

  38. Banci L et al (2004) Paramagnetism-based restraints for Xplor-NIH. J Biomol NMR 28:249–261

    Article  PubMed  CAS  Google Scholar 

  39. Bertini I, Luchinat C, Parigi G (2002) Paramagnetic constraints: an aid for quick solution structure determination of paramagnetic metalloproteins. Concepts Magn Reson 14:259–286

    Article  CAS  Google Scholar 

  40. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magnet Res 160:65–73

    Article  CAS  Google Scholar 

  41. Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298

    Article  PubMed  Google Scholar 

  42. Hus JC, Marion D, Blackledge M (2000) De novo determination of protein structure by NMR using orientational and long-range order restraints. J Mol Biol 298:927–936

    Article  PubMed  CAS  Google Scholar 

  43. Case DA et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  44. van der Spoel D et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718

    Article  Google Scholar 

  45. Krieger E, Koraimann G, Vriend G (2002) Increasing the precision of comparative models with YASARA NOVA–a self-parameterizing force field. Proteins 47:393–402

    Article  PubMed  CAS  Google Scholar 

  46. Montelione GT et al (2013) Recommendations of the wwPDB NMR validation task force. Structure 21(9):1563–1570

    Article  PubMed  CAS  Google Scholar 

  47. Kirchner DK, Güntert P (2011) Objective identification of residue ranges for the superposition of protein structures. BMC Bioinformatics 12:170

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  48. Mao B, Guan R, Montelione GT (2011) Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure 19:757–766

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  49. Vuister GW, Fogh RH, Hendrickx PMS, Doreleijers JF, Gutmanas A (2013) An overview of tools for the validation of protein NMR structures. J Biomol NMR 58(4):259–285

    Article  PubMed  Google Scholar 

  50. Spronk C, Nabuurs SB, Krieger E (2004) Validation of protein structures derived by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 45:315–337

    Article  CAS  Google Scholar 

  51. van der Schot G et al (2013) Improving 3D structure prediction from chemical shift data. J Biomol NMR 57:27–35

    Article  PubMed  Google Scholar 

  52. Rosato A et al (2009) CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods 6:625–626

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  53. Rosato A et al (2012) Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20:227–236

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  54. Vranken WF et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696

    Article  PubMed  CAS  Google Scholar 

  55. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  56. Cheung M-S, Maguire ML, Stevens TJ, Broadhurst RW (2010) DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure. J Magn Reson 202:223–233

    Article  PubMed  CAS  Google Scholar 

  57. Wishart DS, Sykes BD (1994) Chemical shifts as a tool for structure determination. Methods Enzymol 239:363–392

    Article  PubMed  CAS  Google Scholar 

  58. Berjanskii MV, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970–14971

    Article  PubMed  CAS  Google Scholar 

  59. Wassenaar TA, et al (2012) WeNMR: structural biology on the grid. J Grid Comp 10:743–767

    Google Scholar 

  60. Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665–1674

    Article  PubMed  CAS  Google Scholar 

  61. Guerry P, Herrmann T (2012) Comprehensive automation for NMR structure determination of proteins. Methods Mol Biol 831:429–451

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  63. Raman S et al (2010) Accurate automated protein NMR structure determination using unassigned NOESY data. J Am Chem Soc 132:202–207

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  64. Linge JP, O'Donoghue SI, Nilges M (2001) Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol 339:71–90

    Article  PubMed  CAS  Google Scholar 

  65. Seavey BR, Farr EA, Westler WM, Markley JL (1991) A relational database for sequence-specific protein NMR data. J Biomol NMR 1:217–236

    Article  PubMed  CAS  Google Scholar 

  66. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795

    Article  PubMed  CAS  Google Scholar 

  67. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52–56

    Article  PubMed  CAS  Google Scholar 

  68. Laskowski RA, Rullmann J, MacArthur MW (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486

    Article  PubMed  CAS  Google Scholar 

  69. Herráez A (2006) Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 34:255–261

    Article  PubMed  Google Scholar 

  70. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14(51–5):29–32

    Google Scholar 

  71. Moseley HNB, Sahota G, Montelione GT (2004) Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 28:341–355

    Article  PubMed  CAS  Google Scholar 

  72. Wang L, Eghbalnia HR, Bahrami A, Markley JL (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. J Biomol NMR 32:13–22

    Article  PubMed  Google Scholar 

  73. 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. J Biomol NMR 44:95–99

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  74. Wang B, Wang Y, Wishart DS (2010) A probabilistic approach for validating protein NMR chemical shift assignments. J Biomol NMR 47:85–99

    Article  PubMed  CAS  Google Scholar 

  75. Ginzinger SW, Gerick F, Coles M, Heun V (2007) CheckShift: automatic correction of inconsistent chemical shift referencing. J Biomol NMR 39:223–227

    Article  PubMed  CAS  Google Scholar 

  76. Rieping W, Vranken WF (2010) Validation of archived chemical shifts through atomic coordinates. Proteins 78:2482–2489

    PubMed  CAS  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Structural Biology, VIB Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium

    Wim F. Vranken

  2. Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK

    Geerten W. Vuister

  3. Faculty of Science—Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands

    Alexandre M. J. J. Bonvin

Authors
  1. Wim F. Vranken
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Geerten W. Vuister
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alexandre M. J. J. Bonvin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alexandre M. J. J. Bonvin .

Editor information

Editors and Affiliations

  1. University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom

    Andreas Kukol

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Vranken, W.F., Vuister, G.W., Bonvin, A.M.J.J. (2015). NMR-Based Modeling and Refinement of Protein 3D Structures. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_16

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-1465-4_16

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1464-7

  • Online ISBN: 978-1-4939-1465-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation