Extracting and Searching for Structural Information: A Multiresolution Approach

  • Natalia Jiménez-Lozano
  • Mónica Chagoyen
  • Pedro Antonio de Alarcón
  • José María Carazo
Part of the Principles and Practice book series (PRINCIPLES)

Abstract

Nowadays, the scientific community is aware of the importance of the structure of proteins in order to understand the functional events in which they are involved. Indeed, a wide range of diseases are induced by modifications in their structural properties, leading to a loss of protein function (e.g. muscular dystrophy). Thus, protein structure elucidation can provide crucial information about its biochemical function. The two most widely spread methods of protein structure determination, at high resolution, are X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR).

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References

  1. Acehan D, Jiang X, Morgan DG, Heuser JE, Wang X, Akey CW (2002) Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding, and activation. Mol Cell 9: 423–32PubMedCrossRefGoogle Scholar
  2. Agrawal RK, Linde J, Sengupta J, Nierhaus KH, Frank J (2001) Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation. J Mol Biol 311: 777–87PubMedCrossRefGoogle Scholar
  3. Alberts B (1998) Three-dimensional fold of the human AQP1 water channel determined at 4 A resolution by electron crystallography of two-dimensional crystals embedded in ice. Cell 92: 291–4PubMedCrossRefGoogle Scholar
  4. Auer M (2000) Three-dimensional electron cryo-microscopy as a powerful structural tool in molecular medicine. J Mol Med 78: 191–202PubMedCrossRefGoogle Scholar
  5. Baker TS, Olson NH, Fuller SD (1999) Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev 63: 862–922PubMedGoogle Scholar
  6. Bârcena M, Ruiz T, Donate LE, Brown SE, Dixon NE, Radermacher M, Carazo JM (2001) The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. EMBO J 20: 1462–8PubMedCrossRefGoogle Scholar
  7. Baumeister W (2002) Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr Opin Struct Biol 12: 679–84PubMedCrossRefGoogle Scholar
  8. Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B (1992) The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys. J 63: 751–759. http://ndbserver.rutgers.edu/ Google Scholar
  9. Bernal RA, Hafenstein S, Olson NH, Bowman VD, Chipman PR, Baker TS, Fane BA, Rossmann MG (2003) Structural studies of bacteriophage alpha3 assembly. J Mol Biol 325: 11–24PubMedCrossRefGoogle Scholar
  10. Bottcher B, Bertsche I, Reuter R, Graber P (2000) Direct visualisation of conformational changes in EF(0)F(1) by electron microscopy. J Mol Biol 296: 449–57PubMedCrossRefGoogle Scholar
  11. Carazo JM, Stelzer EH (1999) The Biolmage Database Project: organizing multidimensional biological images in an object-relational database. J Struct Biol 125: 97–102PubMedCrossRefGoogle Scholar
  12. Carrascosa JL, Llorca O, Valpuesta JM (2001) Structural comparison of prokaryotic and eukaryotic chaperonins. Micron 32: 43–50PubMedCrossRefGoogle Scholar
  13. de-Alarcón PA, Pascual-Montano A, Carazo JM (2002) Spin images and neural networks for efficient content-based retrieval in 3D object databases. Lecture notes on computer science 2383: 225–234CrossRefGoogle Scholar
  14. de-Alarcón PA, Pascual-Montano A, Gupta A, Carazo JM (2002) Modeling shape and topology of low-resolution density maps of biological macromolecules. Biophysical Journal 83: 619–632PubMedCrossRefGoogle Scholar
  15. Edelsbrunner H, Liang J, Woodward C (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 7: 1884–1897PubMedCrossRefGoogle Scholar
  16. Edelsbrunner H, Mücke EP (1994) Three-dimensional alpha shapes. ACM Tr. On Graphics 13: 43–72Google Scholar
  17. Eidhammer I, Jonassen I, Taylor W (2000) Structure Comparison and Structure Patterns. Journal of Computational Biology 7: 685–716PubMedCrossRefGoogle Scholar
  18. Ferlenghi I, Gowen B, de Haas F, Mancini EJ, Garoff H, Sjoberg M, Fuller SD (1998) The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike. J Mol Biol 283: 71–81PubMedCrossRefGoogle Scholar
  19. Hatch V, Zhi G, Smith L, Stull JT, Craig R, Lehman W (2001) Myosin light chain kinase binding to a unique site on F-actin revealed by three-dimensional image reconstruction. J Cell Biol 154: 611–7PubMedCrossRefGoogle Scholar
  20. Hawkes P.W and Kasper E (1996) Principles of electron optics. Academic Press, vol 3, LondonGoogle Scholar
  21. Henrick and Thornton (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23:358–61. PQS:http://www.pqs.ebi.ac.uk/Google Scholar
  22. Hubbard SJ, Gross KH, Argos P (1994) Intramolecular cavities in globular proteins. Protein Engineering 7: 613–626PubMedCrossRefGoogle Scholar
  23. Hubbard SJ, Argos P (1995) Detection of internal cavities in globular proteins. Protein Eng 8: 1011–5PubMedCrossRefGoogle Scholar
  24. Jones S, Thornton JM (1996) Principles of protein-protein interaction. Proc. Natl. Acad. Sci. USA 93: 13–20Google Scholar
  25. Jones S, Thornton JM (1997) Analysis of protein-protein interaction sites using surface patches. J Mol Biol 272 (1): 121–32PubMedCrossRefGoogle Scholar
  26. Rawat UB, Zavialov AV, Sengupta J, Valle M, Grassuci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J (2003). A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421: 87–90PubMedCrossRefGoogle Scholar
  27. Kozubek M, Skalnikova M, Matula P, Bartova E, Rauch J, Neuhaus F, Eipel H, Hausmann M (2002) Automated microaxial tomography of cell nuclei after specific labelling by fluorescence in situ hybridization. Micron 33: 655–65PubMedCrossRefGoogle Scholar
  28. Larsen TA, Olson AJ, Goodsell DS (1998) Morphology of protein-protein interfaces. Structure 6: 421–7PubMedCrossRefGoogle Scholar
  29. Laskowski R A (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29:221–222. http://www.biochem.ucl.ac.uk/bsm/pdbsum/ Google Scholar
  30. Li H, DeRosier DJ, Nicholson WV, Nogales E, Downing KH (2002) Microtubule structure at 8A resolution. Structure (Camb) 10: 1317–28CrossRefGoogle Scholar
  31. Liang J, Edelsbrunner H, Fu P, Sudharkar PV, Subramaniam S (1998) Analytic shape computation of macromolecules I: molecular area and volume through alpha shape. Proteins: Structure, Function, and Genetics 33: 1–17Google Scholar
  32. Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramanian S (1998a) Analytical Shape Computation of Macromolecules: II. Inaccessible cavities in proteins. Proteins 33: 1829Google Scholar
  33. Liang J, Edelsbrunner H, Woodward C (1998b) Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Sci 7: 1884–97Google Scholar
  34. Llorca 0, Martin-Benito J, Gómez-Puertas P, Ritco-Vonsovici M, Willison KR, Carrascosa JL, Valpuesta JM (2001) Analysis of the interaction between the eukaryotic chaperonin CCT and its substrates actin and tubulin. J Struct Biol 135: 205–18PubMedCrossRefGoogle Scholar
  35. Llorca O, Martin-Benito J, Gómez-Puertas P, Ritco-Vonsovici M, Willison KR, Carrascosa JL, Valpuesta JM (2001) Analysis of the interaction between the eukaryotic chaperonin CCT and its substrates actin and tubulin J Struct Biol 135: 205–18Google Scholar
  36. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 30: 264–7PubMedCrossRefGoogle Scholar
  37. Lowe J, Li H, Downing KH, Nogales E (2001) Refined structure of alpha beta-tubulin at 3.5 A resolution. J Mol Biol 313: 1045–57PubMedCrossRefGoogle Scholar
  38. McEwen BF, Marko M (2001) The emergence of electron tomography as an important tool for investigating cellular ultrastructure. J Histochem Cytochem 49: 553–64PubMedCrossRefGoogle Scholar
  39. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536–540. http://scop.mrc-lmb.cam.ac.uk/scop Google Scholar
  40. Ochoa WF, Kalko SG, Mateu MG, Gomes P, Andreu D, Domingo E, Fita I, Verdaguer N (2000) A multiply substituted G-H loop from foot- and-mouth disease virus in complex with a neutralizing antibody: a role for water molecules. J Gen Virol 81: 1495–505PubMedGoogle Scholar
  41. Orlova EV, Papakosta M, Booy FP, van Heel M, Dolly JO (2003) Voltage-gated K(+) Channel from Mammalian Brain: 3D Structure at 18Â of the Complete (alpha)(4)(beta)(4) Complex. J Mol Biol 326: 1005–12PubMedCrossRefGoogle Scholar
  42. Pascual-Montano A, Donate LE, Valle M, Bârcena M, Pascual-Marqui RD, Carazo JM (2001) A novel neural network technique for analysis and classification of EM single-particle images. J Struct Biol 133: 233–45PubMedCrossRefGoogle Scholar
  43. Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA (2003) The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res 31: 452–5PubMedCrossRefGoogle Scholar
  44. Ren G, Cheng A, Reddy V, Melnyk P, Mitra AK (2000) Three-dimensional fold of the human AQP 1 water channel determined at 4 A resolution by electron crystallography of two-dimensional crystals embedded in ice. J Mol Biol 301: 369–87PubMedCrossRefGoogle Scholar
  45. Sander C and Schneider R (1991) Database of homology derived protein structures and the structural meaning of sequence alignment. Proteins 9:56–68. http://www.cmbi.kun.nl/gv/hssp/Google Scholar
  46. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. J Cell 107: 373–86Google Scholar
  47. Stark H (2002) Three-dimensional electron cryomicroscopy of ribosomes. Curr Protein Pept Sci 3: 79–91PubMedCrossRefGoogle Scholar
  48. Stark H, Dube P, Luhrmann R, Kastner B (2001) Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature 409: 539–42PubMedCrossRefGoogle Scholar
  49. Subramaniam S, Henderson R (1999) Electron crystallography of bacteriorhodopsin with millisecond time resolution. J Struct Biol 128: 19–25PubMedCrossRefGoogle Scholar
  50. Tagari M, Newman R, Chagoyen M, Carazo JM, Henrick K (2002) New electron microscopy database and deposition system. Trends Biochem Sci 27: 589PubMedCrossRefGoogle Scholar
  51. Thouvenin E, Hewat E (2000) When two into one won’t go: fitting in the presence of steric hindrance and partial occupancy. Acta Crystallogr D Biol Crystallogr 56: 1350–7PubMedCrossRefGoogle Scholar
  52. Wang DN, Kuhlbrandt W (1991) High-resolution electron crystallography of light-harvesting chlorophyll a/b-protein complex in three different media. J Mol Biol 217: 691–699PubMedCrossRefGoogle Scholar
  53. Zhang W, Mukhopadhyay S, Pletnev SV, Baker TS, Kuhn RJ, Rossmann MG (2002) Placement of the structural proteins in Sindbis virus. J Virol 76: 11645–58PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Natalia Jiménez-Lozano
  • Mónica Chagoyen
  • Pedro Antonio de Alarcón
  • José María Carazo

There are no affiliations available

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