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Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

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Artificial Neural Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1260))

Abstract

Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from 1H, 15N, and 13C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

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References

  1. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New York

    Google Scholar 

  2. Englander SW, Wand AJ (1987) Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins. Biochemistry 26:5953–5958

    Article  CAS  PubMed  Google Scholar 

  3. Oh BH, Westler WM, Darba P et al (1988) Protein 13C spin systems by a single two-dimensional nuclear magnetic resonance experiment. Science 240:908–911

    Article  CAS  PubMed  Google Scholar 

  4. Ikura M, Kay LE, Bax A (1990) A novel approach for sequential assignment of 1H, 13C, and 15N spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29:4659–4667

    Article  CAS  PubMed  Google Scholar 

  5. Wagner G (1993) Prospects for NMR of large proteins. J Biomol NMR 3:375–385

    Article  CAS  PubMed  Google Scholar 

  6. Saito H (1986) Conformation-dependent C13 chemical shifts—a new means of conformational characterization as obtained by high resolution solid state C13 NMR. Magn Reson Chem 24:835–852

    Article  CAS  Google Scholar 

  7. Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311–333

    Article  CAS  PubMed  Google Scholar 

  8. Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and Ca and Cb 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490–5492

    Article  CAS  Google Scholar 

  9. Haigh CW, Mallion RB (1979) Ring current theories in nuclear magnetic resonance. Prog Nucl Magn Reson Spectrosc 13:303–344

    Article  CAS  Google Scholar 

  10. Avbelj F, Kocjan D, Baldwin RL (2004) Protein chemical shifts arising from alpha-helices and beta-sheets depend on solvent exposure. Proc Natl Acad Sci U S A 101:17394–17397

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. de Dios AC, Pearson JG, Oldfield E (1993) Secondary and tertiary structural effects on protein NMR chemical shifts—an ab initio approach. Science 260:1491–1496

    Article  PubMed  Google Scholar 

  12. Case DA (1998) The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 8:624–630

    Article  CAS  PubMed  Google Scholar 

  13. Vila JA, Aramini JM, Rossi P et al (2008) Quantum chemical C-13(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci U S A 105:14389–14394

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Kohlhoff KJ, Robustelli P, Cavalli A et al (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131:13894–13895

    Article  CAS  PubMed  Google Scholar 

  15. Asakura T, Taoka K, Demura M et al (1995) The relationship between amide proton chemical shifts and secondary structure in proteins. J Biomol NMR 6:227–236

    Article  CAS  PubMed  Google Scholar 

  16. Bax A, Grzesiek S (1993) Methodological advances in protein NMR. Acc Chem Res 26:131–138

    Article  CAS  Google Scholar 

  17. Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34:93–158

    Article  CAS  Google Scholar 

  18. Salzmann M, Wider G, Pervushin K et al (1999) TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins. J Am Chem Soc 121:844–848

    Article  CAS  Google Scholar 

  19. Wagner G, Pardi A, Wuthrich K (1983) Hydrogen-bond length and H-1-NMR chemical-shifts in proteins. J Am Chem Soc 105:5948–5949

    Article  CAS  Google Scholar 

  20. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302

    Article  CAS  PubMed  Google Scholar 

  21. Berman HM, Kleywegt GJ, Nakamura H et al (2012) The Protein Data Bank at 40: reflecting on the past to prepare for the future. Structure 20:391–396

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Markley JL, Ulrich EL, Berman HM et al (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40:153–155

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Wishart DS (2011) Interpreting protein chemical shift data. Prog Nucl Magn Reson Spectrosc 58:62–87

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56:227–241

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. 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  CAS  PubMed Central  PubMed  Google Scholar 

  27. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202

    Article  CAS  PubMed  Google Scholar 

  28. Rost B, Sander C (1993) Prediction of protein secondary structure at better than 70 percent accuracy. J Mol Biol 232:584–599

    Article  CAS  PubMed  Google Scholar 

  29. Ramirez BE, Voloshin ON, Camerini-Otero RD et al (2000) Solution structure of DinI provides insight into its mode of RecA inactivation. Protein Sci 9:2161–2169

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Maltsev AS, Ying JF, Bax A (2012) Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein alpha-synuclein. J Biomol NMR 54:181–191

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  32. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637

    Article  CAS  PubMed  Google Scholar 

  33. Schwieters CD, Kuszewski JJ, Tjandra N et al (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73

    Article  CAS  PubMed  Google Scholar 

  34. 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  CAS  PubMed  Google Scholar 

  35. Markley JL, Bax A, Arata Y et al (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids (Reprinted from Pure and Applied Chemistry, vol 70, pp. 117–142, 1998). J Mol Biol 280:933–952

    Article  CAS  PubMed  Google Scholar 

  36. Wang LY, Eghbalnia HR, Bahrami A et al (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 

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Acknowledgments

This work was funded by the Intramural Research Program of the NIDDK, NIH.

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Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA

    Yang Shen & Ad Bax

Authors
  1. Yang Shen
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  2. Ad Bax
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Corresponding authors

Correspondence to Yang Shen or Ad Bax .

Editor information

Editors and Affiliations

  1. Chemistry Department, Oxford University, UK, and University of Victoria, Victoria, British Columbia, Canada

    Hugh Cartwright

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Shen, Y., Bax, A. (2015). Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N . In: Cartwright, H. (eds) Artificial Neural Networks. Methods in Molecular Biology, vol 1260. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2239-0_2

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  • DOI: https://doi.org/10.1007/978-1-4939-2239-0_2

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-2238-3

  • Online ISBN: 978-1-4939-2239-0

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