Journal of Biomolecular NMR

, Volume 44, Issue 4, pp 185–194 | Cite as

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Article

Abstract

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1Hα and 13C′ chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Keywords

Protein secondary structure CSI GFT NMR Protein folding 3D structure 

Supplementary material

10858_2009_9327_MOESM1_ESM.doc (886 kb)
(DOC 855 kb)

References

  1. Atreya HS, Szyperski T (2004) G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignments. Proc Natl Acad Sci USA 101:9642–9647CrossRefADSGoogle Scholar
  2. Atreya HS, Szyperski T (2005) Rapid NMR data collection. Methods Enzymol 394:78–108CrossRefGoogle Scholar
  3. Atreya HS, Sahu SC, Chary KVR, Govil G (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J Biomol NMR 17:125–136CrossRefGoogle Scholar
  4. Atreya HS, Eletsky A, Szyperski T (2005) Resonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in highly resolved G2FT NMR experiments. J Am Chem Soc 127:4554–4555CrossRefGoogle Scholar
  5. Atreya HS, Garcia E, Shen Y, Szyperski T (2007) J-GFT NMR for precise measurement of mutually correlated spin–spin couplings. J Am Chem Soc 129:680–692CrossRefGoogle Scholar
  6. Baran MC, Huang YJ, Moseley HNB, Montelione G (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3555CrossRefGoogle Scholar
  7. Barnwal RP, Chary KVR (2008) An efficient method for secondary structure determination in polypeptides by NMR. Curr Sci 94:1302–1306Google Scholar
  8. Barnwal RP, Jobby MK, Sharma Y, Chary KVR (2006) NMR assignment of M-crystallin: a novel Ca(+2) binding protein of the βγ-crystallin superfamily from methanosarcina acetivorans. J Biomol NMR 36(Suppl. 5):32–32CrossRefGoogle Scholar
  9. Barnwal RP, Rout AK, Chary KV, Atreya HS (2007) Rapid measurement of 3J(HN-Hα) and 3J(N-Hβ) coupling constants in polypeptides. J Biomol NMR 39:259–263CrossRefGoogle Scholar
  10. Bartels C, Xia TH, Billeter M, Guntert P, Wuthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10CrossRefGoogle Scholar
  11. Carolina PI, Miguel AAN (2008) K2D2: estimation of protein secondary structure from circular dichroism spectra. BMC Struct Biol 8(25):1–5Google Scholar
  12. Cavanagh C, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2007) Protein NMR spectroscopy. Elsevier Academic Press, San DiegoGoogle Scholar
  13. Choy WY, Sanctuary BC, Zhu G (1997) Using neural network predicted secondary structure information in automatic protein NMR assignment. J Chem Inf Comput Sci 37:1086–1094Google Scholar
  14. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302CrossRefGoogle Scholar
  15. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  16. Dyson HJ, Wright PE (2004) Unfolded proteins and protein folding studied by NMR. Chem Rev 104:3607–3622CrossRefGoogle Scholar
  17. Eletski A, Atreya HS, Liu G, Szyperski T (2005) Probing structure and functional dynamics of (large) proteins with aromatic rings: L-GFT-TROSY (4, 3)D HCCH NMR spectroscopy. J Am Chem Soc 127:14578–14579CrossRefGoogle Scholar
  18. Güntert P (2003) Automated NMR protein structure calculation. Prog NMR Spectrosc 43:105–125CrossRefGoogle Scholar
  19. Kabsch W, Sander C (1983) A dictionary of protein secondary structure. Biopolymers 22:2577–2637CrossRefGoogle Scholar
  20. Kim S, Szyperski T (2003) GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc 125:1385–1393CrossRefGoogle Scholar
  21. Metzler WJ et al (1993) Characterization of the three-dimensional solution structure of human profillin: 1H, 13C, and 15N NMR assignments and global folding pattern. Biochemistry 32:13818–13829CrossRefGoogle Scholar
  22. Mielke SP, Krishnan VV (2005) Estimation of protein secondary structure content directly from NMR spectra using an improved empirical correlation with average chemical shift. J Struct Func Genom 6:281–285CrossRefGoogle Scholar
  23. Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski TS (2000) Protein NMR spectroscopy in structural genomics. Nat Struct Mol Biol 7:982–985CrossRefGoogle Scholar
  24. Mount DW (2004) Bioinformatics sequence and genome analysis. CSHL Press, USAGoogle Scholar
  25. Page R, Peti W, Wilson IA, Stevens RC, Wüthrich K (2005) NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc Natl Acad Sci USA 102:1901–1905CrossRefADSGoogle Scholar
  26. Pardi A, Billeter M, Wüthrich K (1984) Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHNHα, in a globular protein. Use of 3JHNHα for identification of helical secondary structure. J Mol Biol 180:741–751CrossRefGoogle Scholar
  27. Schwarzinger S, Kroon GJA, Foss TR, Chung J, Wright PE, Dyson HJ (2001) Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc 123:2970–2978CrossRefGoogle Scholar
  28. Shen Y, Atreya HS, Liu G, Szyperski T (2005) G-matrix Fourier transform NOESY based protocol for high-quality protein structure determination. J Am Chem Soc 127:9085–9099CrossRefGoogle Scholar
  29. Swain M, Atreya HS (2008) A method to selectively observe a desired linear combination of chemical shifts in GFT projection NMR spectroscopy. Open Magn Reson J 1:96–104Google Scholar
  30. Szyperski T, Atreya HS (2006) Principles and applications of GFT projection NMR spectroscopy. Magn Reson Chem 44:S51–S60CrossRefGoogle Scholar
  31. Torizawa T, Shimizu M, Taoka M, Miyano H, Kainosho M (2004) Efficient production of isotopically labeled proteins by cell-free synthesis: a practical protocol. J Biomol NMR 30:311–325CrossRefGoogle Scholar
  32. Wang Y, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852–861CrossRefGoogle Scholar
  33. Wishart DS, Sykes BD (1994) Chemical shifts as a tool for structure determination. Methods Enzymol 239:363–392CrossRefGoogle Scholar
  34. Wolfgang P, Loma JS, Christina R, Harald S (2001) Chemical shifts in denatured proteins: resonance assignments for denatured ubiquitin and comparisons with other denatured proteins. J Biomol NMR 19:153–165CrossRefGoogle Scholar
  35. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New YorkGoogle Scholar
  36. Yee A et al (2002) An NMR approach to structural proteomics. Proc Natl Acad Sci USA 99:1825–1830CrossRefADSGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.NMR Research CentreIndian Institute of ScienceBangaloreIndia
  2. 2.Solid State and Structural Chemistry UnitIndian Institute of ScienceBangaloreIndia

Personalised recommendations