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Protein NMR Techniques pp 353–378Cite as

Automated NMR Structure Calculation With CYANA

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 278))

Abstract

This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columes from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY cross-peaks and the three-dimensional structure of the protein in solution can be calculated automatically with CYANA.

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References

  1. Moseley, H. N. B. and Montelione, G. T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol. 9, 635–642.

    Article  PubMed  CAS  Google Scholar 

  2. Solomon, I. (1955) Relaxation processes in a system of two spins. Phys. Rev. 99, 559–565.

    Article  CAS  Google Scholar 

  3. Macura, S. and Ernst, R. R. (1980) Elucidation of cross relaxation in liquids by 2D NMR spectroscopy. Mol. Phys. 41, 95–117.

    Article  CAS  Google Scholar 

  4. Neuhaus, D. and Williamson, M. P. (1989) The Nuclear Overhauser Effect in Structural and Conformational Analysis. VCH, Weinheim, Germany.

    Google Scholar 

  5. Herrmann, T., Güntert, P., and Wüthrich, 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  PubMed  CAS  Google Scholar 

  6. Gropp, W., Lusk, E., Doss, N., and Skjellum, A. (1996) A high-performance, portable implementation of the MPI message passing interface standard. Parallel Computing 22, 789–828.

    Article  Google Scholar 

  7. Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55.

    Article  PubMed  CAS  Google Scholar 

  8. Bartels, C., Xia, T. H., Billeter, M., Güntert, P., and Wüthrich, K. (1995) The program XEASY for computer-supported NMR-spectral analysis of biological macromolecules. J. Biomol. NMR 6, 1–10.

    Article  CAS  Google Scholar 

  9. Johnson, B. A. and Blevins, R. A. (1994) NMR View—a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614.

    Article  CAS  Google Scholar 

  10. Kraulis, P. J. (1989) ANSIG—a program for the assignment of protein H-1 2D NMR spectra by interactive computer graphics. J. Magn. Reson. 24, 627–633.

    Google Scholar 

  11. Helgstrand, M., Kraulis, P., Allard, P., and Härd, T. (2000) ANSIG for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra J. Biomol. NMR 18, 329–336.

    Article  PubMed  CAS  Google Scholar 

  12. Koradi, R., Billeter, M., Engeli, M., Güntert, P., and Wüthrich, K. (1998) Toward fully automatic peak picking and integration of biomolecular NMR spectra. J. Magn. Reson. 135, 288–297.

    Article  PubMed  CAS  Google Scholar 

  13. Herrmann, T., Güntert, P., and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J. Biomol. NMR 24, 171–189.

    Article  PubMed  CAS  Google Scholar 

  14. Doreleijers, J. F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J. L., et al. (2003) BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J. Biomol. NMR 26, 139–146.

    Article  PubMed  CAS  Google Scholar 

  15. Mumenthaler, C. and Braun, W. (1995) Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J. Mol. Biol. 254, 465–480.

    Article  PubMed  CAS  Google Scholar 

  16. Mumenthaler, C., Güntert, P., Braun, W., and Wüthrich, K. (1997) Automated procedure for combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR 10, 351–362.

    Article  PubMed  CAS  Google Scholar 

  17. Nilges, M., Macias, M., O’Donoghue, S. I., and Oschkinat, H. (1997) Automated NOESY interpretation with ambiguous distance constraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269, 408–4228

    Article  PubMed  CAS  Google Scholar 

  18. Nilges, M. and O’Donoghue, S. I. (1998) Ambiguous NOEs and automated NOE assignment. Prog. NMR Spectrosc. 32, 107–139.

    Article  CAS  Google Scholar 

  19. Linge, J. P., O’Donoghue, S. I., and Nilges, M. (2001) Automated assignment of ambiguous nuclear Overhauser effects with ARIA. Methods Enzymol. 339, 71–90.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  21. Nilges, M. (1993) A calculation strategy for the structure determination of symmetric dimers by 1H NMR. Proteins 17, 297–309.

    Article  PubMed  CAS  Google Scholar 

  22. Nilges, M. (1995) Calculation of protein structures with ambiguous distance restraints: automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J. Mol. Biol. 245, 645–660.

    Article  PubMed  CAS  Google Scholar 

  23. Güntert, P., Braun, W., and Wüthrich, K. (1991) Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517–530.

    Article  PubMed  Google Scholar 

  24. Güntert, P., Mumenthaler, C., and 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 

  25. Kirkpatrick, S., Gelatt, C. D., Jr., and Vecchi, M. P. (1983) Optimization by simulated annealing. Science 220, 671–680.

    Article  PubMed  CAS  Google Scholar 

  26. Katz, H., Walter, R., and Somorjay, R. L. (1979) Rotational dynamics of large molecules. Computers Chemistry 3, 25–32.

    Article  CAS  Google Scholar 

  27. Bae, D. S. and Haug, E. J. (1987) A recursive formulation for constrained mechanical system dynamics, part I: open loop systems. Mech. Struct. Mech. 15, 359–382.

    Google Scholar 

  28. Mazur, A. K. and Abagyan, R. A. (1989) New methodology for computer-aided modelling of biomolecular structure and dynamics (I): non-cyclic structures. J. Biomol. Struct. Dyn. 4, 815–832.

    Google Scholar 

  29. Mazur, A. K., Dorofeev, V. E., and Abagyan, R. A. (1991) Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comp. Phys. 92, 261–272.

    Article  CAS  Google Scholar 

  30. Jain, A., Vaidehi, N., and Rodriguez, G. (1993) A fast recursive algorithm for molecular dynamics simulation. J. Comp. Phys. 106, 258–268.

    Google Scholar 

  31. Kneller, G. R. and Hinsen, K. (1994) Generalized Euler equations for linked rigid bodies. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 50, 1559–1564.

    Article  Google Scholar 

  32. Mathiowetz, A. M., Jain, A., Karasawa, N., and Goddard, W. A., III. (1994) Protein simulations using techniques suitable for large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 20, 227–247.

    Article  PubMed  CAS  Google Scholar 

  33. Rice, L. M. and Brünger, A. T. (1994) Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19, 277–290.

    Article  PubMed  CAS  Google Scholar 

  34. Stein, E. G., Rice, L. M., and Brünger, A. T. (1997) Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124, 154–164.

    Article  PubMed  CAS  Google Scholar 

  35. Nilges, M., Clore, G. M., and Gronenborn, A. M. (1988) Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317–324.

    Article  PubMed  CAS  Google Scholar 

  36. Brünger, A. T. (1992) X-PLOR version 3.1: a system for X-ray crystallography and NMR. Yale University Press, New Haven, CT.

    Google Scholar 

  37. Enggist, E., Thöny-Meyer, L., Güntert, P., and Pervushin, K. (2002) NMR structure of the heme chaperone CcmE reveals a novel functional motif. Structure 10, 1551–1557.

    Article  PubMed  CAS  Google Scholar 

  38. Jee, J. G. and Güntert, P. (2003) Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J. Struct. Funct. Genomics 4, 179–189.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  40. Antuch, W., Güntert, P., and Wüthrich, K. (1996) Ancestral βγ-crystallin precursor structure in a yeast killer toxin, Nat. Struct. Biol. 3, 662–665

    Article  PubMed  CAS  Google Scholar 

  41. Calzolai, L., Lysek, D. A., Güntert, P., von Schroetter, C., Riek, R., Zahn, R., et al. (2000) NMR structures of three single-residue variants of the human prion protein. Proc. Natl. Acad. Sci. USA 97, 8340–8345.

    Article  PubMed  CAS  Google Scholar 

  42. Zahn, R., Güntert, P., von Schroetter, C., and Wüthrich, K. (2003) NMR structure of a human prion protein with two disulfide bridges. J. Mol. Biol. 326, 225–234.

    Article  PubMed  CAS  Google Scholar 

  43. Ellgaard, L., Riek, R., Herrmann, T., Güntert, P., Braun, D., Helenius, A., et al. (2001) NMR structure of the calreticulin P-domain. Proc. Natl. Acad. Sci. USA 98, 3133–3138.

    Article  PubMed  CAS  Google Scholar 

  44. Horst, R., Damberger, F., Luginbühl, P., Güntert, P., Peng, G., Nikonova, L., et al. (2001) NMR structure reveals intramolecular regulation mechanism for pheromone binding and release. Proc. Natl. Acad. Sci. USA 98, 14,374–14,379.

    Article  PubMed  CAS  Google Scholar 

  45. Lee, D., Damberger, F. D., Peng, G., Horst, R., Güntert, P., Nikonova, L., et al. (2002) NMR structure of the unliganded Bombyx mori pheromone-binding protein at physiological pH. FEBS Lett. 531, 314–318.

    Article  PubMed  CAS  Google Scholar 

  46. Miura, T., Klaus, W., Ross, A., Güntert, P., and Senn, H. (2002) The NMR structure of the class I human ubiquitin-conjugating enzyme 2b. J. Biomol. NMR 22, 89–92.

    Article  PubMed  CAS  Google Scholar 

  47. Hilge, M., Siegal, G., Vuister, G. W., Güntert, P., Gloor, S. M., and Abrahams, J. P. (2003) ATP-induced conformational changes of the nucleotide binding domain of Na,K-ATPase. Nat. Struct. Biol. 10, 10–18.

    Article  Google Scholar 

  48. Allen, M. P. and Tildesley, D. J. (1987) Computer Simulation of Liquids. Clarendon Press, Oxford, UK.

    Google Scholar 

  49. Abe, H., Braun, W., Noguti, T. and Go, N. (1984) Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles in proteins: general recurrent equations. Computers Chemistry 8, 239–247.

    Article  CAS  Google Scholar 

  50. Hockney, R. W. (1970) The potential calculation and some applications. Meth. Comput. Phys. 9, 136–211.

    Google Scholar 

  51. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690.

    Article  CAS  Google Scholar 

  52. Hare, B. J. and Wagner, G. (1999) Application of automated NOE assignment to three-dimensional structure refinement of a 28 kDa single-chain T cell receptor. J. Biomol. NMR 15, 103–113.

    Article  PubMed  CAS  Google Scholar 

  53. Ösapay, K. and Case, D. A. (1991) A new analysis of proton chemical shifts in proteins. J. Am. Chem. Soc. 113, 9436–9444.

    Article  Google Scholar 

  54. Sitkoff, D. and Case, D. A. (1997) Density functional calculations of proton chemical shifts in model peptides. J. Am. Chem. Soc. 119, 12,262–12,273.

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. RIKEN Genomic Sciences Center, Yokohama, Japan

    Peter Güntert

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  1. Peter Güntert
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Editor information

Editors and Affiliations

  1. Department of Biochemistry, University of Oxford, Oxford, UK

    A. Kristina Downing

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© 2004 Humana Press Inc., Totowa, NJ

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Güntert, P. (2004). Automated NMR Structure Calculation With CYANA. In: Downing, A.K. (eds) Protein NMR Techniques. Methods in Molecular Biology™, vol 278. Humana Press. https://doi.org/10.1385/1-59259-809-9:353

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  • DOI: https://doi.org/10.1385/1-59259-809-9:353

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-246-9

  • Online ISBN: 978-1-59259-809-0

  • eBook Packages: Springer Protocols

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