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Automated Structure Determination from NMR Spectra

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Structural Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1261))

Abstract

Three-dimensional structures of proteins in solution can be calculated on the basis of conformational restraints derived from NMR measurements. This chapter gives an overview of the computational methods for NMR protein structure analysis highlighting recent automated methods for the assignment of NMR spectra, the collection of conformational restraints, and the structure calculation.

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References

  1. Moseley HNB, Montelione GT (1999) Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol 9:635–642

    Article  CAS  PubMed  Google Scholar 

  2. Schmidt E (2014) Institute of biophysical chemistry. Goethe University, Frankfurt am Main

    Google Scholar 

  3. Güntert P (2011) In: Lian LY, Roberts GCK (eds). Protein NMR spectroscopy: principal techniques and applications. Wiley, Chichester, UK. pp 159–192

    Google Scholar 

  4. Schmidt E, Gath J, Habenstein B et al (2013) Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J Biomol NMR 56:243–254

    Article  CAS  PubMed  Google Scholar 

  5. Billeter M, Wagner G, Wüthrich K (2008) Solution NMR structure determination of proteins revisited. J Biomol NMR 42:155–158

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Güntert P (2003) Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 43:105–125

    Article  Google Scholar 

  8. Malmodin D, Billeter M (2005) High-throughput analysis of protein NMR spectra. Prog Nucl Magn Reson Spectrosc 46:109–129

    Article  CAS  Google Scholar 

  9. Muskett FW (2011) In: Lian LY, Roberts GCK (eds). Protein NMR spectroscopy: practical techniques and applications. Wiley, Chichester, UK. pp 5–21

    Google Scholar 

  10. Garrett DS, Powers R, Gronenborn AM, Clore GM (1991) A common sense approach to peak picking two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J Magn Reson 95:214–220

    CAS  Google Scholar 

  11. Pons JL, Malliavin TE, Delsuc MA (1996) Gifa V. 4: a complete package for NMR data set processing. J Biomol NMR 8:445–452

    Article  CAS  PubMed  Google Scholar 

  12. Koradi R, Billeter M, Engeli M et al (1998) Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J Magn Reson 135:288–297

    Article  CAS  PubMed  Google Scholar 

  13. Herrmann T, Güntert P, 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  CAS  PubMed  Google Scholar 

  14. Goddard TD, Kneller DG (2001) Sparky 3. University of California, San Francisco

    Google Scholar 

  15. Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313–352

    CAS  PubMed  Google Scholar 

  16. Johnson BA, Blevins RA (1994) NMR view—a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614

    Article  CAS  PubMed  Google Scholar 

  17. Neidig KP, Geyer M, Gorler A et al (1995) Aurelia, a program for computer-aided analysis of multidimensional NMR spectra. J Biomol NMR 6:255–270

    Article  CAS  PubMed  Google Scholar 

  18. Vranken WF, Boucher W, Stevens TJ et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696

    Article  CAS  PubMed  Google Scholar 

  19. Bartels C, Xia TH, Billeter M et al (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10

    Article  CAS  PubMed  Google Scholar 

  20. Wüthrich K, Wider G, Wagner G, Braun W (1982) Sequential resonance assignments as a basis for determination of spatial protein structures by high-resolution proton nuclear magnetic resonance. J Mol Biol 155:311–319

    Article  PubMed  Google Scholar 

  21. Guerry P, Herrmann T (2011) Advances in automated NMR protein structure determination. Q Rev Biophys 44:257–309

    Article  CAS  PubMed  Google Scholar 

  22. Zimmerman DE, Kulikowski CA, Huang YP et al (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610

    Article  CAS  PubMed  Google Scholar 

  23. Zimmerman D, Kulikowski C, Wang LZ et al (1994) Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence. J Biomol NMR 4:241–256

    Article  CAS  PubMed  Google Scholar 

  24. Bahrami A, Assadi AH, Markley JL, Eghbalnia HR (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol 5:e1000307

    Article  PubMed Central  PubMed  Google Scholar 

  25. Bahrami A, Tonelli M, Sahu SC, Singarapu KK et al (2012) Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR. PLoS One 7:e33173

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Volk J, Herrmann T, Wüthrich K (2008) Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J Biomol NMR 41:127–138

    Article  CAS  PubMed  Google Scholar 

  27. Hiller S, Fiorito F, Wüthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci U S A 102:10876–10881

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  28. Jung YS, Zweckstetter M (2004) Mars—robust automatic backbone assignment of proteins. J Biomol NMR 30:11–23

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  30. Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT—a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139–149

    Article  CAS  Google Scholar 

  31. Bartels C, Billeter M, Güntert P, Wüthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207–213

    Article  CAS  PubMed  Google Scholar 

  32. Fiorito F, Hiller S, Wider G, Wüthrich K (2006) Automated resonance assignment of proteins: 6D APSY-NMR. J Biomol NMR 35:27–37

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  33. Hiller S, Wider G, Wüthrich K (2008) APSY-NMR with proteins: practical aspects and backbone assignment. J Biomol NMR 42:179–195

    Article  CAS  PubMed  Google Scholar 

  34. Malmodin D, Papavoine CHM, Billeter M (2003) Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR 27:69–79

    Article  CAS  PubMed  Google Scholar 

  35. López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128:13112–13122

    Article  PubMed  Google Scholar 

  36. Ikeya T, Takeda M, Yoshida H et al (2009) Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. J Biomol NMR 44:261–272

    Article  CAS  PubMed  Google Scholar 

  37. Scott A, López-Méndez B, Güntert P (2006) Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. Magn Reson Chem 44:S83–S88

    Article  CAS  PubMed  Google Scholar 

  38. Ikeya T, Jee J-G, Shigemitsu Y et al (2011) Exclusively NOESY-based automated NMR assignment and structure determination of proteins. J Biomol NMR 50:137–146

    Article  CAS  PubMed  Google Scholar 

  39. Schmidt E, Güntert P (2012) A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 134:12817–12829

    Article  CAS  PubMed  Google Scholar 

  40. Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J 38:129–143

    Article  PubMed  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. Schmucki R, Yokoyama S, Güntert P (2009) Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm. J Biomol NMR 43:97–109

    Article  CAS  PubMed  Google Scholar 

  43. Ulrich EL, Akutsu H, Doreleijers JF et al (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  44. Levitt MH (2008) Spin dynamics: basics of nuclear magnetic resonance. Wiley, New York

    Google Scholar 

  45. Duggan BM, Legge GB, Dyson HJ, Wright PE (2001) SANE (structure assisted NOE evaluation): an automated model-based approach for NOE assignment. J Biomol NMR 19:321–329

    Article  CAS  PubMed  Google Scholar 

  46. Güntert P, Berndt KD, Wüthrich K (1993) The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J Biomol NMR 3:601–606

    Article  Google Scholar 

  47. Meadow RP, Olejniczak ET, Fesik SW (1994) A computer-based protocol for semiautomated assignments and 3D structure determination of proteins. J Biomol NMR 4:79–96

    Google Scholar 

  48. Mumenthaler C, 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  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  50. Habeck M, Rieping W, Linge JP, Nilges M (2004) NOE assignment with ARIA 2.0: the nuts and bolts. Methods Mol Biol 278:379–402

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  53. Nilges M, Macias MJ, ODonoghue SI, Oschkinat H (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol 269:408–422

    Article  CAS  PubMed  Google Scholar 

  54. Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 62:587–603

    Article  CAS  PubMed  Google Scholar 

  55. Gronwald W, Moussa S, Elsner R et al (2002) Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR 23:271–287

    Article  CAS  PubMed  Google Scholar 

  56. Herrmann T, Güntert P, 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  CAS  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  58. Kuszewski J, Schwieters CD, Garrett DS et al (2004) Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments. J Am Chem Soc 126:6258–6273

    Article  CAS  PubMed  Google Scholar 

  59. Hung LH, Samudrala R (2006) An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. J Biomol NMR 36:189–198

    Article  CAS  PubMed  Google Scholar 

  60. Jee J, 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  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  62. Güntert P, Braun W, 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 

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

    Article  CAS  PubMed  Google Scholar 

  64. Brünger AT, Adams PD, Clore GM (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr Sect D Biol Crystallogr 54:905–921

    Article  Google Scholar 

  65. Brünger AT (1992) X-PLOR, Version 3.1. A system for X-ray crystallography and NMR. Yale University Press, New Haven

    Google Scholar 

  66. Williamson MP, Craven CJ (2009) Automated protein structure calculation from NMR data. J Biomol NMR 43:131–143

    Article  CAS  PubMed  Google Scholar 

  67. Moseley HNB, Sperling LJ, Rienstra CM (2010) Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of beta 1 immunoglobulin binding domain of protein G (GB1). J Biomol NMR 48:123–128

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  68. Li KB, Sanctuary BC (1997) Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. J Chem Inf Comput Sci 37:467–477

    Article  CAS  PubMed  Google Scholar 

  69. Li KB, Sanctuary BC (1997) Automated resonance assignment of proteins using heteronuclear 3D NMR. 1. Backbone spin systems extraction and creation of polypeptides. J Chem Inf Comput Sci 37:359–366

    Article  CAS  Google Scholar 

  70. Leutner M, Gschwind RM, Liermann J et al (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J Biomol NMR 11:31–43

    Article  CAS  PubMed  Google Scholar 

  71. Coggins BE, Zhou P (2003) PACES: Protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93–111

    Article  CAS  PubMed  Google Scholar 

  72. Güntert P, Salzmann M, Braun D, Wüthrich K (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR 18:129–137

    Article  PubMed  Google Scholar 

  73. Fiorito F, Herrmann T, Damberger FF, Wüthrich K (2008) Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY. J Biomol NMR 42:23–33

    Article  CAS  PubMed  Google Scholar 

  74. Hitchens TK, Lukin JA, Zhan YP et al (2003) MONTE: an automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR 25:1–9

    Article  CAS  PubMed  Google Scholar 

  75. Atreya HS, Sahu SC, Chary KVR, Govil G (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J Biomol NMR 17:125–136

    Article  CAS  PubMed  Google Scholar 

  76. Grishaev A, Llinás M (2002) Protein structure elucidation from NMR proton densities. Proc Natl Acad Sci U S A 99:6713–6718

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  77. Lukin JA, Gove AP, Talukdar SN, Ho C (1997) Automated probabilistic method for assigning backbone resonances of (C-13, N-15)-labeled proteins. J Biomol NMR 9:151–166

    Article  CAS  PubMed  Google Scholar 

  78. Hu KN, Qiang W, Tycko R (2011) A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers. J Biomol NMR 50:267–276

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Schmidt, E., Güntert, P. (2015). Automated Structure Determination from NMR Spectra. In: Owens, R. (eds) Structural Proteomics. Methods in Molecular Biology, vol 1261. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2230-7_16

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  • DOI: https://doi.org/10.1007/978-1-4939-2230-7_16

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  • Print ISBN: 978-1-4939-2229-1

  • Online ISBN: 978-1-4939-2230-7

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