Skip to main content
Log in

CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

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

Abstract

UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

References

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

    Article  Google Scholar 

  • Dutta SK, Serrano P, Proudfoot A, Geralt M, Pedrini B, Herrmann T, Wüthrich K (2015) APSY-NMR for protein backbone assignment in high-throughput structural biology. J Biomol NMR 61:47–53. doi:10.1007/s10858-014-9881-8

    Article  Google Scholar 

  • Fadel V, Bettendorff P, Herrmann T, de Azevedo WF Jr, Oliveira EB, Yamane T, Wüthrich K (2005) Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus. Toxicon 46:759–767. doi:10.1016/j.toxicon.2005.07.018

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Guerry P, Herrmann T (2012) Comprehensive automation for NMR structure determination of proteins. Methods Mol Biol 831:429–451. doi:10.1007/978-1-61779-480-3_22

    Article  Google Scholar 

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

    Article  Google Scholar 

  • 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  Google Scholar 

  • Herrmann T, Güntert P, Wüthrich K (2002a) 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 

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

    Article  Google Scholar 

  • Jaudzems K, Pedrini B, Geralt M, Serrano P, Wüthrich K (2015) J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from streptococcus pneumoniae TIGR4. J Biomol NMR 61:65–72. doi:10.1007/s10858-014-9886-3

    Article  Google Scholar 

  • Knight MJ, Webber AL, Pell AJ, Guerry P, Barbet-Massin E, Bertini I, Felli IC, Gonnelli L, Pierattelli R, Emsley L, Lesage A, Herrmann T, Pintacuda G (2011) Fast resonance assignment and fold determination of human superoxide dismutase by high-resolution proton-detected solid-state mas nmr spectroscopy. Angew Chem Int Edit 50:11697–11701

    Article  Google Scholar 

  • Knight MJ, Pell AJ, Bertini I, Felli IC, Gonnelli L, Pierattelli R, Herrmann T, Emsley L, Pintacuda G (2012) Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR. Proc Natl Acad Sci USA 109:11095–11100

    Article  ADS  Google Scholar 

  • Koradi R, Billeter M, Güntert P (2000) Point-centered domain decomposition for parallel molecular dynamics simulation. Comput Phys Commun 124:139–147

    Article  ADS  MATH  Google Scholar 

  • Lee W, Kim JH, Westler WM, Markley JL (2011) PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinformatics 27:1727–1728

    Article  Google Scholar 

  • Luginbuhl P, Güntert P, Billeter M, Wüthrich K (1996) The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 8:136–146

    Article  Google Scholar 

  • Manolikas T, Herrmann T, Meier BH (2008) Protein structure determination from C-13 spin-diffusion solid-state NMR spectroscopy. J Am Chem Soc 130:3959–3966

    Article  Google Scholar 

  • Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL (2013) Recommendations of the wwPDB NMR validation task force. Structure 21:1563–1570

    Article  Google Scholar 

  • ODonoghue SI, King GF, Nilges M (1996) Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: the case of leucine zippers. J Biomol NMR 8:193–206

    Google Scholar 

  • Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66:27–85

    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 

  • Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HRA, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AMJJ (2009) CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods 6:625–626

    Article  Google Scholar 

  • Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He YF, Herrmann T, Huang YPJ, Jaravine V, Jonker HRA, Kennedy MA, Lange OF, Liu GH, Malliavin TE, Mani R, Mao BC, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, de Vries S, Vuister GW, Wu B, Yang YH, Bonvin AMJJ (2012) Blind testing of routine fully automated determination of protein structures from NMR data. Structure 20:227–236

    Article  Google Scholar 

  • Serrano P, Pedrini B, Mohanty B, Geralt M, Herrmann T, Wüthrich K (2012) The J-UNIO protocol for automated protein structure determination by NMR in solution. J Biomol NMR 53:341–354

    Article  Google Scholar 

  • 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  Google Scholar 

  • Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, Jaravine V, Güntert P, Schwalbe H, Vranken WF, Doreleijers JF, Vriend G, Vuister GW, Franke D, Kikhney A, Svergun DI, Fogh RH, Ionides J, Laue ED, Spronk C, Jurksa S, Verlato M, Badoer S, Dal Pra S, Mazzucato M, Frizziero E, Bonvin AMJJ (2012) WeNMR: Structural biology on the grid J Grid Comput 10:743–767 doi: 10.1007/s10723-012-9246-z

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

    Article  Google Scholar 

  • Zhang ZY, Porter J, Tripsianes K, Lange OF (2014) Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta. J Biomol NMR 59:135–145

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Torsten Herrmann.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guerry, P., Duong, V.D. & Herrmann, T. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO. J Biomol NMR 62, 473–480 (2015). https://doi.org/10.1007/s10858-015-9934-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-015-9934-7

Keywords

Navigation