Of bits and bugs - on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat- protein structure

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Graebsch, Almut ^a,b   Roche, Stéphane ^a,b   Kostrewa, Dirk ^b   Söding, Johannes ^b   Niessing, Dierk ^a,b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DROSOPHILA PROTEIN;

ARTICLE; BACTERIUM; BIOINFORMATICS; COMPUTER MODEL; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DROSOPHILA; EUKARYOTE; NONHUMAN; NUCLEOTIDE REPEAT; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SENSITIVITY ANALYSIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY;

BACTERIA (MICROORGANISMS); DROSOPHILA MELANOGASTER; EUKARYOTA; PROKARYOTA;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; REPETITIVE SEQUENCES, AMINO ACID;

EID: 78149492329     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013402     Document Type: Article

References (50)

1. Chayen NE, Saridakis E (2008) Protein crystallization: from purified protein to diffraction-quality crystal. Nat Methods 5: 147-153.
2. Price WN, 2nd, Chen Y, Handelman SK, Neely H, Manor P, et al. (2009) Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol 27: 51-57.
3. Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, et al. (2005) Highthroughput limited proteolysis/mass spectrometry for protein domain elucidation. J Struct Funct Genomics 6: 129-134.
4. 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 U S A 102: 1901-1905.
5. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL, 2nd, et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6: 606-612.
6. Savchenko A, Yee A, Khachatryan A, Skarina T, Evdokimova E, et al. (2003) Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches. Proteins 50: 392-399.
7. Oldfield CJ, Ulrich EL, Cheng Y, Dunker AK, Markley JL (2005) Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins 59: 444-453.
8. Fischer D (2006) Servers for protein structure prediction. Curr Opin Struct Biol 16: 178-182.
9. Graebsch A, Roche S, Niessing D (2009) X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface. Proc Natl Acad Sci U S A 106: 18521-18526.
10. Khalili K, Del Valle L, Muralidharan V, Gault WJ, Darbinian N, et al. (2003) Pur-alpha is essential for postnatal brain development and developmentally coupled cellular proliferation as revealed by genetic inactivation in the mouse. Mol Cell Biol 23: 6857-6875.
11. Kanai Y, Dohmae N, Hirokawa N (2004) Kinesin transports RNA: isolation and characterization of an RNA-transporting granule. Neuron 43: 513-525.
12. White MK, Johnson EM, Khalili K (2009) Multiple roles for Puralpha in cellular and viral regulation. Cell Cycle 8: 1-7.
13. Bergemann AD, Ma ZW, Johnson EM (1992) Sequence of cDNA comprising the human pur gene and sequence-specific single-stranded-DNA-binding properties of the encoded protein. Mol Cell Biol 12: 5673-5682.
14. Biegert A, Söding J (2008) De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics 24: 807-814.
15. Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W374-378.
16. Gallia GL, Johnson EM, Khalili K (2000) Puralpha: a multifunctional singlestranded DNA- and RNA-binding protein. Nucleic Acids Res 28: 3197-3205.
17. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search progams. Nucleic Acids Res 25: 3389-3402.
18. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211-215.
19. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
20. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37: D205-210.
21. Biegert A, Mayer C, Remmert M, Söding J, Lupas AN (2006) The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res 34: W335-339.
22. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59.
23. Bahadur RP, Zacharias M (2008) The interface of protein-protein complexes: analysis of contacts and prediction of interactions. Cell Mol Life Sci 65: 1059-1072.
24. Hildebrand A, Remmert M, Biegert A, Söding J (2009) Fast and accurate automatic structure prediction with HHpred. Proteins 77(Suppl 9): 128-132.
25. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
26. Koehl P, Levitt M (2002) Sequence variations within protein families are linearly related to structural variations. J Mol Biol 323: 551-562.
27. Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12: 85-94.
28. Sadreyev RI, Tang M, Kim BH, Grishin NV (2007) COMPASS server for remote homology inference. Nucleic Acids Res 35: W653-658.
29. Battey JN, Kopp J, Bordoli L, Read RJ, Clarke ND, et al. (2007) Automated server predictions in CASP7. Proteins 69(Suppl 8): 68-82.
30. Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D (1999) A census of protein repeats. J Mol Biol 293: 151-160.
31. Bjorklund AK, Ekman D, Elofsson A (2006) Expansion of protein domain repeats. PLoS Comput Biol 2: e114.
32. Lunde BM, Moore C, Varani G (2007) RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 8: 479-490.
33. Doublie S (1997) Preparation of Selenomethionyl Proteins for Phase Determination. In: Charles W, Carter J, Sweet RM, eds. Meth Enzymol. pp 523-537.
34. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettingan PA, et al. (2007) ClustalW and ClustalX version 2.0. Bioinformatics 23: 2947-2948.
35. Kabsch W (2010) XDS. Acta Crystallogr D 66: 125-132.
36. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64: 112-122.
37. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60: 2126-2132.
38. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
39. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53: 240-255.
40. Terwilliger TC (2002) Automated structure solution, density modification and model building. Acta Crystallogr D 58: 1937-1940.
41. Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D 55: 191-205.
42. Collaborative Computational Project N (1994) The CCP4 Suite:Programs for Protein Crystallography. Acta Crystallogr D 50: 760-763.
43. Jones DT (1999) Protein secondary structure prediction based on positionspecific scoring matrices. J Mol Biol 292: 195-202.
44. Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
45. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
46. Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356: 83-85.
47. Melo F, Feytmans E (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277: 1141-1152.
48. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
49. Wong I, Lohman TM (1993) A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions. Proc Natl Acad SciUS A 90: 5428-5432.
50. Müller M, Richter K, Heuck A, Kremmer E, Buchner J, et al. (2009) Formation of She2p tetramers is required for mRNA binding, mRNP assembly, and localization 15: 2002-2012.