(2010) The Scottish Structural Proteomics Facility : targets, methods and outputs. Journal of Structural and Functional Genomics, Vol.11 (No.2). pp. 167-180. ISSN 1345-711X

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Abstract

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.

Item Type:	Submitted Journal Article
Subjects:	Q Science > QP Physiology Q Science > QH Natural history > QH301 Biology
Divisions:	Faculty of Science > Chemistry
Library of Congress Subject Headings (LCSH):	Proteomics, Proteins -- Structure, Molecular biology -- Research
Journal or Publication Title:	Journal of Structural and Functional Genomics
Publisher:	Springer Netherlands
ISSN:	1345-711X
Date:	June 2010
Volume:	Vol.11
Number:	No.2
Page Range:	pp. 167-180
Identification Number:	10.1007/s10969-010-9090-y
Status:	Peer Reviewed
Access rights to Published version:	Open Access
Funder:	Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Scottish Funding Council (SFC), European Union (EU)
Grant number:	SSPF (SFC), SULSA (SFC), BB/S/B14450 (BBSRC), Aeropath (EU)
References:	1. Banci L, Bertini I, Cusack S, de Jong RN, Heinemann U, Jones EY, Kozielski F, Maskos K, Messerschmidt A, Owens R, Perrakis A, Poterszman A, Schneider G, Siebold C, Silman I, Sixma T, Stewart-Jones G, Sussman JL, Thierry JC, Moras D (2006) First steps towards effective methods in exploiting highthroughput technologies for the determination of human protein structures of high biomedical value. Acta Crystallogr D Biol Crystallogr 62(Pt 10):1208–1217 2. Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD (2009) SGC—structural biology and human health: a new approach to publishing structural biology results. PLoS One 4(10):e7675 3. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340(4):783–795 4. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3): 567–580 5. Li X, Romero P, Rani M, Dunker AK, Obradovic Z (1999) Predicting protein disorder for N-, C-, and internal regions. Genome Inform Ser Workshop Genome Inform 10:30–40 6. Yang ZR, Thomson R, McNeil P, Esnouf RM (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21(16):3369–3376 7. Canaves JM, Page R, Wilson IA, Stevens RC (2004) Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol 344(4):977–991 8. Overton IM, van Niekerk CA, Carter LG, Dawson A, Martin DM, Cameron S, McMahon SA, White MF, Hunter WN, Naismith JH, Barton GJ (2008) TarO: a target optimisation system for structural biology. Nucleic Acids Res 36(Web Server issue):W190– W196 9. Overton IM, Barton GJ (2006) A normalised scale for structural genomics target ranking: the OB-score. FEBS Lett 580(16):4005– 4009 10. Overton IM, Padovani G, Girolami MA, Barton GJ (2008) Par- Crys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics 24(7):901– 907 11. Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O (2001) The comprehensive microbial resource. Nucleic Acids Res 29(1):123–125 12. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E (2007) Ensembl 2007. Nucleic Acids Res 35(Database issue):D610– D6177 13. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402 14. Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12(2):85–94 15. Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide protein data bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35(Database issue):D301–D303 16. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LS (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32(Database issue):D115–D119 17. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths- Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) The Pfam protein families database. Nucleic Acids Res 32(Database issue):D138– D141 18. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32(Database issue):D258–D261 19. Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554–571 20. Forsyth RA, Haselbeck RJ, Ohlsen KL, Yamamoto RT, Xu H, Trawick JD, Wall D, Wang L, Brown-Driver V, Froelich JM, Kedar GC, King K, McCarthy M, Malone C, Misiner B, Robbins D, Tan Z, Zhu ZY, Carr G, Mosca DA, Zamudio C, Foulkes JG, Zyskind JW (2002) A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43(6):1387–1400 21. Ji Y, Zhang B, Van SF, Horn WP, Woodnutt G, Burnham MK, Rosenberg M (2001) Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293(5538):2266–2269 22. Liu H, Naismith JH (2009) A simple and efficient expression and purification system using two newly constructed vectors. Protein Expr Purif 63(2):102–111 23. Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41(1):207– 234 24. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227(5259): 680–685 25. Guerrero SA, Hecht HJ, Hofmann B, Biebl H, Singh M (2001) Production of selenomethionine-labelled proteins using simplified culture conditions and generally applicable host/vector systems. Appl Microbiol Biotechnol 56(5–6):718–723 26. Kapust RB, Tozser J, Fox JD, Anderson DE, Cherry S, Copeland TD, Waugh DS (2001) Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng 14(12):993–1000 27. Rupp B (2003) Maximum-likelihood crystallization. J Struct Biol 142(1):162–169 28. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. In: Methods in enzymology. Academic Press, New York, pp 307–326 29. Leslie AGW (1992) Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 ? ESF-EAMCB newsletter on protein crystallography, no. 26 30. Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62(Pt 1):72–82 31. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell contants. J Appl Crystallogr 26:795–800 32. Schneider TR, Sheldrick GM (2002) Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 58(Pt 10 Pt 2):1772–1779 33. Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55(Pt 4):849–861 34. Terwilliger TC (2000) Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 56(Pt 8):965–972 35. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58(Pt 11):1948–1954 36. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse- Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54(Pt 5): 905–921 37. Collaborative Computational Project N (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50(Pt 5):760–763 38. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126–2132 39. McRee DE (1999) XtalView/Xfit—a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125(2–3):156–165 40. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53(Pt 3):240–255 41. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, 3rd, Snoeyink J, Richardson JS, Richardson DC (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35(Web Server issue):W375–W383 42. Dumon-Seignovert L, Cariot G, Vuillard L (2004) The toxicity of recombinant proteins in Escherichia coli: a comparison of overexpression in BL21(DE3), C41(DE3), and C43(DE3). Protein Expr Purif 37(1):203–206 43. Miroux B, Walker JE (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol 260(3):289–298 44. Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A (2007) XtalPred: a web server for prediction of protein crystallizability. Bioinformatics 23(24):3403–3405 45. Schmelz S, Kadi N, McMahon SA, Song L, Oves-Costales D, Oke M, Liu H, Johnson KA, Carter LG, Botting CH, White MF, Challis GL, Naismith JH (2009) AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis. Nat Chem Biol 5(3):174–182 46. Seetharamappa J, Oke M, Liu H, McMahon SA, Johnson KA, Carter L, Dorward M, Zawadzki M, Overton IM, van Niekirk CA, Graham S, Botting CH, Taylor GL, White MF, Barton GJ, Coote PJ, Naismith JH (2007) Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/ tyrosine/phenylalanine pyridoxal-50-phosphate-dependent aminotransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 5):452–456 47. Seetharamappa J, Oke M, Liu H, McMahon SA, Johnson KA, Carter L, Dorward M, Zawadzki M, Overton IM, van Niekirk CA, Graham S, Botting CH, Taylor GL, White MF, Barton GJ, Coote PJ, Naismith JH (2007) Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 6):488–491 48. Liu H, Rudolf J, Johnson KA, McMahon SA, Oke M, Carter L, McRobbie AM, Brown SE, Naismith JH, White MF (2008) Structure of the DNA repair helicase XPD. Cell 133(5):801–812 49. Richards JD, Johnson KA, Liu H, McRobbie AM, McMahon S, Oke M, Carter L, Naismith JH, White MF (2008) Structure of the DNA repair helicase hel308 reveals DNA binding and autoinhibitory domains. J Biol Chem 283(8):5118–5126 50. McRobbie AM, Carter LG, Kerou M, Liu H, McMahon SA, Johnson KA, Oke M, Naismith JH, White MF (2009) Structural and functional characterisation of a conserved archaeal RadA paralog with antirecombinase activity. J Mol Biol 389(4):661–673 51. Williams GJ, Johnson K, Rudolf J, McMahon SA, Carter L, Oke M, Liu H, Taylor GL, White MF, Naismith JH (2006) Structure of the heterotrimeric PCNA from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 62(Pt 10):944–948 52. Haring M, Peng X, Brugger K, Rachel R, Stetter KO, Garrett RA, Prangishvili D (2004) Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323(2):233–242 53. Peng X, Blum H, She Q, Mallok S, Brugger K, Garrett RA, Zillig W, Prangishvili D (2001) Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291(2):226–234 54. Oke M, Ching RT, Carter LG, Johnson KA, Liu H, McMahon SA, White MF, Bloch C Jr, Botting CH, Walsh MA, Latiff AA, Kennedy MW, Cooper A, Naismith JH (2008) Unusual chromophore and cross-links in ranasmurfin: a blue protein from the foam nests of a tropical frog. Angew Chem Int Ed Engl 47(41):7853–7856 55. Marsden RL, Orengo CA (2008) Target selection for structural genomics: an overview. Methods Mol Biol 426:3–25 56. Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ (2007) The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol 370(5): 870–886 57. McMahon SA, Roberts GA, Johnson KA, Cooper LP, Liu H, White JH, Carter LG, Sanghvi B, Oke M, Walkinshaw MD, Blakely GW, Naismith JH, Dryden DT (2009) Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. Nucleic Acids Res 37(15):4887– 4897 58. Sheikh MA, Potter JA, Johnson KA, Sim RB, Boyd EF, Taylor GL (2008) Crystal structure of VC1805, a conserved hypothetical protein from a Vibrio cholerae pathogenicity island, reveals homology to human p32. Proteins 71(3):1563–1571 59. Fairhead M, Johnson KA, Kowatz T, McMahon SA, Carter LG, Oke M, Liu H, Naismith JH, van der Walle CF (2008) Crystal structure and silica condensing activities of silicatein alphacathepsin L chimeras. Chem Commun (Camb) 15:1765–1767
URI:	http://wrap.warwick.ac.uk/id/eprint/3294

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