Advertisement

Effective Techniques for Protein Structure Mining

  • Stefan J. SuhrerEmail author
  • Markus Gruber
  • Markus Wiederstein
  • Manfred J. Sippl
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 857)

Abstract

Retrieval and characterization of protein structure relationships are instrumental in a wide range of tasks in structural biology. The classification of protein structures (COPS) is a web service that provides efficient access to structure and sequence similarities for all currently available protein structures. Here, we focus on the application of COPS to the problem of template selection in homology modeling.

Key words

Protein structure space Protein structure comparison Template selection Structure alignment Structure similarity search Classification Homology modeling Ligand binding 

Notes

Acknowledgments

This work was supported by FWF Austria grant number P21294-B12.

References

  1. 1.
    Suhrer SJ, Wiederstein M, Gruber M, et al. (2009) COPS-a novel workbench for explorations in fold space. Nucleic Acids Res 37:W539–W544PubMedCrossRefGoogle Scholar
  2. 2.
    Suhrer SJ, Wiederstein M, Sippl MJ (2007) QSCOP – SCOP quantified by structural relationships. Bioinformatics 23:513–514PubMedCrossRefGoogle Scholar
  3. 3.
    Suhrer SJ, Gruber M, Sippl MJ (2007) QSCOP-BLAST–fast retrieval of quantified structural information for protein sequences of unknown structure. Nucleic Acids Res 35:W411–W415PubMedCrossRefGoogle Scholar
  4. 4.
    Choi WS, Jeong BC, Joo YJ, et al. (2010) Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nat Struct Mol Biol 17:1175–1181PubMedCrossRefGoogle Scholar
  5. 5.
    Norambuena T, Melo F (2010) The Protein-DNA Interface database. BMC Bioinformatics 11:262PubMedCrossRefGoogle Scholar
  6. 6.
    Berman HM, Westbrook J, Feng Z, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242PubMedCrossRefGoogle Scholar
  7. 7.
    Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823–826PubMedGoogle Scholar
  8. 8.
    Sippl MJ, Wiederstein M (2008) A note on difficult structure alignment problems. Bioinformatics 24:426–427PubMedCrossRefGoogle Scholar
  9. 9.
    Sippl MJ, Suhrer SJ, Gruber M, et al. (2008) A discrete view on fold space. Bioinformatics 24:870–871PubMedCrossRefGoogle Scholar
  10. 10.
    Riedl SJ, Li W, Chao Y, et al. (2005) Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 434:926–933PubMedCrossRefGoogle Scholar
  11. 11.
    Cozzetto D, Kryshtafovych A, Fidelis K, et al. (2009) Evaluation of template-based models in CASP8 with standard measures. Proteins 77 Suppl 9:18–28PubMedCrossRefGoogle Scholar
  12. 12.
    Frank K, Gruber M, Sippl MJ (2010) COPS Benchmark: interactive analysis of database search methods. Bioinformatics 26:574–575PubMedCrossRefGoogle Scholar
  13. 13.
    Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951–960PubMedCrossRefGoogle Scholar
  14. 14.
    JCSG (2008) Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification (1591455) from Methanococcus jannaschii at 1.75Å resolution. To be publishedGoogle Scholar
  15. 15.
    Kuzin A, Xu JGX, Neely H, et al. (2007) Crystal structure of the protein O27018 from Methanobacterium thermoautotrophicum. To be publishedGoogle Scholar
  16. 16.
    Ito K, Arai R, Fusatomi E, et al. (2006) Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD. Protein Sci 15:1187–1192PubMedCrossRefGoogle Scholar
  17. 17.
    Kim Y, Joachimiak A, Brunzelle J, et al. (2003) Crystal Structure Analysis of Thermotoga maritima protein TM1620 (APC4843). To be PublishedGoogle Scholar
  18. 18.
    Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277PubMedCrossRefGoogle Scholar
  19. 19.
    JCSG (2007) Crystal structure of Putative carboxymuconolactone decarboxylase (YP-555818.1) from Burkholderia xenovorans LB400 at 1.65Å resolutionGoogle Scholar
  20. 20.
    Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39:309–338PubMedCrossRefGoogle Scholar
  21. 21.
    Pál C, Papp B, Lercher MJ (2006) An integrated view of protein evolution. Nat Rev Genet 7:337–348PubMedCrossRefGoogle Scholar
  22. 22.
    Andreeva A, Murzin AG (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16:399–408PubMedCrossRefGoogle Scholar
  23. 23.
    Chothia C, Gough J (2009) Genomic and structural aspects of protein evolution. Biochem J 419:15–28PubMedCrossRefGoogle Scholar
  24. 24.
    Worth CL, Gong S, Blundell TL (2009) Structural and functional constraints in the evolution of protein families. Nat Rev Mol Cell Biol 10:709–720PubMedGoogle Scholar
  25. 25.
    Yan N, Chai J, Lee ES, et al. (2005) Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans. Nature 437:831–837PubMedCrossRefGoogle Scholar
  26. 26.
    Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6:197–208PubMedCrossRefGoogle Scholar
  27. 27.
    Bordoli L, Kiefer F, Arnold K, et al. (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4:1–13PubMedCrossRefGoogle Scholar
  28. 28.
    Wlodawer A, Minor W, Dauter Z, et al. (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275:1–21PubMedCrossRefGoogle Scholar
  29. 29.
    Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355–362PubMedCrossRefGoogle Scholar
  30. 30.
    Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410PubMedCrossRefGoogle Scholar
  31. 31.
    Weichenberger CX, Byzia P, Sippl MJ (2008) Visualization of unfavorable interactions in protein folds. Bioinformatics 24:1206–1207PubMedCrossRefGoogle Scholar
  32. 32.
    Ginzinger SW, Weichenberger CX, Sippl MJ (2010) Detection of unrealistic molecular environments in protein structures based on expected electron densities. J Biomol NMR 47:33–40PubMedCrossRefGoogle Scholar
  33. 33.
    Laskowski RA, MacArthur MW, Moss DS, et al. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  34. 34.
    Chen VB, Arendall WB, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21PubMedCrossRefGoogle Scholar
  35. 35.
    Hooft RW, Vriend G, Sander C, et al. (1996) Errors in protein structures. Nature 381:272PubMedCrossRefGoogle Scholar
  36. 36.
    Davidson AR (2008) A folding space odyssey. Proc Natl Acad Sci U S A 105:2759–2760PubMedCrossRefGoogle Scholar
  37. 37.
    Sippl MJ (2009) Fold space unlimited. Curr Opin Struct Biol 19:312–320PubMedCrossRefGoogle Scholar
  38. 38.
    Dalal S, Balasubramanian S, Regan L (1997) Protein alchemy: changing beta-sheet into alpha-helix. Nat Struct Biol 4:548–552PubMedCrossRefGoogle Scholar
  39. 39.
    He Y, Chen Y, Alexander P, et al. (2008) NMR structures of two designed proteins with high sequence identity but different fold and function. Proc Natl Acad Sci U S A 105:14412–14417PubMedCrossRefGoogle Scholar
  40. 40.
    Roessler CG, Hall BM, Anderson WJ, et al. (2008) Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proc Natl Acad Sci U S A 105:2343–2348PubMedCrossRefGoogle Scholar
  41. 41.
    Murzin AG (2008) Metamorphic Proteins. Science 320:1725–1726PubMedCrossRefGoogle Scholar
  42. 42.
    Gambin Y, Schug A, Lemke EA, et al. (2009) Direct single-molecule observation of a protein living in two opposed native structures. Proc Natl Acad Sci U S A 106:10153–10158PubMedCrossRefGoogle Scholar
  43. 43.
    Bryan PN, Orban J (2010) Proteins that switch folds. Curr Opin Struct Biol 20:482–488PubMedCrossRefGoogle Scholar
  44. 44.
    Tuinstra RL, Peterson FC, Kutlesa S, et al. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state. Proc Natl Acad Sci U S A 105:5057–5062PubMedCrossRefGoogle Scholar
  45. 45.
    Ginalski K (2006) Comparative modeling for protein structure prediction. Curr Opin Struct Biol 16:172–177PubMedCrossRefGoogle Scholar
  46. 46.
    Kosloff M, Kolodny R (2008) Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 71:891–902PubMedCrossRefGoogle Scholar
  47. 47.
    Zhang H, Neal S, Wishart DS (2003) RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR 25:173–195PubMedCrossRefGoogle Scholar
  48. 48.
    Schwieters CD, Kuszewski JJ, Tjandra N, et al. (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73PubMedCrossRefGoogle Scholar
  49. 49.
    Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647–1651PubMedCrossRefGoogle Scholar
  50. 50.
    Wang Y, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852–861PubMedCrossRefGoogle Scholar
  51. 51.
    Berjanskii MV, Neal S, Wishart DS (2006) PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res 34:W63–W69PubMedCrossRefGoogle Scholar
  52. 52.
    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 44:213–223PubMedCrossRefGoogle Scholar
  53. 53.
    Oldfield E (1995) Chemical shifts and three-dimensional protein structures. J Biomol NMR 5:217–225PubMedCrossRefGoogle Scholar
  54. 54.
    Ginzinger SW, Fischer J (2006) SimShift: identifying structural similarities from NMR chemical shifts. Bioinformatics 22:460–465PubMedCrossRefGoogle Scholar
  55. 55.
    Ginzinger SW, Coles M (2009) SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database. J Biomol NMR 43:179–185PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media,LLC 2011

Authors and Affiliations

  • Stefan J. Suhrer
    • 1
    Email author
  • Markus Gruber
    • 1
  • Markus Wiederstein
    • 1
  • Manfred J. Sippl
    • 1
  1. 1.Center of Applied Molecular Engineering, Division of BioinformaticsUniversity of SalzburgSalzburgAustria

Personalised recommendations