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Searching for Needles in Haystacks: Automation and the Task of Crystal Structure Determination

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Abstract

Chambers dictionary defines the expression look for a needle in a haystack as to undertake a hopeless search. Crystallographic investigations seem on many occasions to fit this definition closely. The use of synchrotron radiation sources with automated methods for beam delivery and sample changing has revolutionised the process of finding those crystals that have the properties required to elucidate a crystal structure.

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References

  1. Arndt UW, Wonnacott AJ (1977) The rotation method in crystallography. North Holland, Amsterdam

    Google Scholar 

  2. Ben-Shem A, Frolow F, Nelson N (2003) Crystal structure of plant photosystem I. Nature 426(6967):630–635

    Article  CAS  Google Scholar 

  3. Bourenkov GP, Popov AN (2006) A quantitative approach to data-collection strategies. Acta Crystallogr D Biol Crystallogr 62(Pt 1):58–64

    Article  Google Scholar 

  4. Bowler MW, Guijarro M, Petitdemange S, Baker I, Svensson O, Burghammer M, Mueller-Dieckmann C, Gordon EJ, Flot D, McSweeney SM, Leonard GA (2010) Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection. Acta Crystallogr D Biol Crystallogr 66(Pt 8):855–864

    Article  Google Scholar 

  5. Cherezov V, Hanson M, Griffith M, Hilgart M, Sanishvili R, Nagarajan V, Stepanov S, Fischetti R, Kuhn P, Stevens R (2009) Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 mm size x-ray synchrotron beam. J R Soc Interface 6(Suppl 5):S587–S597

    Article  CAS  Google Scholar 

  6. Cipriani F, Felisaz F, Launer L, Aksoy JS, Caserotto H, Cusack S, Dallery M, di Chiaro F, Guijarro M, Huet J, Larsen S, Lentini M, McCarthy J, McSweeney S, Ravelli R, Renier M, Taffut C, Thompson A, Leonard GA, Walsh MA (2006) Automation of sample mounting for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 62:1251–1259

    Article  CAS  Google Scholar 

  7. Cockburn JJ, Abrescia NG, Grimes JM, Sutton GC, Diprose JM, Benevides JM, Thomas GJ, Bamford JK, Bamford DH, Stuart DI (2004) Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432(7013):122–125

    Article  CAS  Google Scholar 

  8. Cohen AE, Ellis PJ, Miller MD, Deacon AM, Phizackerley RP (2002) An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot. J Appl Crystallogr 35(6):720–726

    Article  CAS  Google Scholar 

  9. Coureux PD, Wells AL, Ménétrey J, Yengo CM, Morris CA, Sweeney HL, Houdusse A (2003) A structural state of the myosin v motor without bound nucleotide. Nature 425(6956):419–423

    Article  CAS  Google Scholar 

  10. Cramer P, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292(5523):1863–1876

    Article  CAS  Google Scholar 

  11. Dauter Z (1999) Data-collection strategies. Acta Crystallogr D Biol Crystallogr 55(Pt 10):1703–1717

    Article  CAS  Google Scholar 

  12. Dawson RJ, Locher KP (2006) Structure of a bacterial multidrug ABC transporter. Nature 443(7108):180–185

    Article  CAS  Google Scholar 

  13. Delagenière S, Brenchereau P, Launer L, Ashton AW, Leal R, Veyrier S, Gabadinho J, Gordon EJ, Jones SD, Levik KE, McSweeney SM, Monaco S, Nanao M, Spruce D, Svensson O, Walsh MA, Leonard GA (2011) ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics 27(22):3186–3192

    Article  Google Scholar 

  14. Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280(5360):69–77

    Article  CAS  Google Scholar 

  15. Evans PR (1999) Some notes on choices in data collection. Acta Crystallogr D Biol Crystallogr 55(Pt 10):1771–1772

    Article  CAS  Google Scholar 

  16. Ferreira KN, Iverson TM, Maghlaoui K, Barber J, Iwata S (2004) Architecture of the photosynthetic oxygen-evolving center. Science 303(5665):1831–1838

    Article  CAS  Google Scholar 

  17. Grimes JM, Burroughs JN, Gouet P, Diprose JM, Malby R, Ziéntara S, Mertens PP, Stuart DI (1998) The atomic structure of the bluetongue virus core. Nature 395(6701):470–478

    Article  CAS  Google Scholar 

  18. Higuchi Y, Okamoto T, Yasuoka N (1996) The heterogeneity in a protein crystal revealed by synchrotron radiation. J Cryst Growth 168(1):99–105

    Article  CAS  Google Scholar 

  19. Incardona MF, Bourenkov GP, Levik K, Pieritz RA, Popov AN, Svensson O (2009) EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis. J Synchrotron Radiat 16(6):872–879

    Article  Google Scholar 

  20. Jacquamet L, Joly J, Bertoni A, Charrault P, Pirocchi M, Vernede X, Bouis F, Borel F, Périn JP, Denis T, Rechatin JL, Ferrer JL (2009) Upgrade of the CATS sample changer on FIPBM30A at the ESRF: towards a commercialized standard. J Synchrotron Radiat 16(1):14–21

    Article  CAS  Google Scholar 

  21. Leslie AGW, Powell HR (2007) Processing diffraction data with mosflm. In: Read RJ, Sussman JL (eds) Evolving methods for macromolecular crystallography, vol 245, NATO Science series. Springer, Dordrecht, pp 41–51

    Chapter  Google Scholar 

  22. Leslie AGW, Powell HR, Winter G, Svensson O, Spruce D, McSweeney S, Love D, Kinder S, Duke E, Nave C (2002) Automation of the collection and processing of X-ray diffraction data – a generic approach. Acta Crystallogr D Biol Crystallogr 58(11):1924–1928

    Article  CAS  Google Scholar 

  23. Ohana J, Jacquamet L, Joly J, Bertoni A, Taunier P, Michel L, Charrault P, Pirocchi M, Carpentier P, Borel F, Kahn R, Ferrer JL (2004) CATS: a Cryogenic Automated Transfer System installed on the beamline FIP at ESRF. J Appl Crystallogr 37(1):72–77

    Article  CAS  Google Scholar 

  24. Owen RL, Rudiño-Piñera E, Garman EF (2006) Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc Natl Acad Sci USA 103(13):4912–4917

    Article  CAS  Google Scholar 

  25. Popov AN, Bourenkov GP (2011) Features and development of BEST. Acta Crystallogr A 67(a1):C45

    Google Scholar 

  26. Ravelli RB, Garman EF (2006) Radiation damage in macromolecular cryocrystallography. Curr Opin Struct Biol 16(5):624–629

    Article  CAS  Google Scholar 

  27. Sauter NK, Grosse-Kunstleve RW, Adams PD (2004) Robust indexing for automatic data collection. J Appl Crystallogr 37(Pt 3):399–409

    Article  CAS  Google Scholar 

  28. Selmer M, Dunham CM, Murphy FV, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V (2006) Structure of the 70s ribosome complexed with mRNA and tRNA. Science 313(5795):1935–1942

    Article  CAS  Google Scholar 

  29. Snell G, Cork C, Nordmeyer R, Cornell E, Meigs G, Yegian D, Jaklevic J, Jin J, Stevens RC, Earnest T (2004) Automated sample mounting and alignment system for biological crystallography at a synchrotron source. Structure 12(4):537–545

    Article  CAS  Google Scholar 

  30. Soltis SM, Cohen AE, Deacon A, Eriksson T, González A, McPhillips S, Chui H, Dunten P, Hollenbeck M, Mathews I, Miller M, Moorhead P, Phizackerley RP, Smith C, Song J, van dem Bedem H, Ellis P, Kuhn P, McPhillips T, Sauter N, Sharp K, Tsyba I, Wolf G (2008) New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection. Acta Crystallogr D Biol Crystallogr 64(Pt 12):1210–1221

    Article  Google Scholar 

  31. Song J, Mathew D, Jacob S, Corbett L, Moorhead P, Soltis S (2007) Diffraction-based automated crystal centering. J Synchrotron Radiat 14(2):191–195

    Article  CAS  Google Scholar 

  32. Sung BJ, Hwang KY, Jeon YH, Lee JI, Heo YS, Kim JH, Moon J, Yoon JM, Hyun YL, Kim E, Eum SJ, Park SY, Lee JO, Lee TG, Ro S, Cho JM (2003) Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules. Nature 425(6953):98–102

    Article  CAS  Google Scholar 

  33. Ueno G, Hirose R, Ida K, Kumasaka T, Yamamoto M (2004) Sample management system for a vast amount of frozen crystals at SPring-8. J Appl Crystallogr 37(6):867–873

    Article  CAS  Google Scholar 

  34. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AG, Tate CG, Schertler GF (2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454(7203):486–491

    Article  CAS  Google Scholar 

  35. Williams PA, Cosme J, Ward A, Angove HC, MatakVinković D, Jhoti H (2003) Crystal structure of human cytochrome p450 2c9 with bound warfarin. Nature 424(6947):464–468

    Article  CAS  Google Scholar 

  36. Williams PA, Cosme J, Vinkovic DM, Ward A, Angove HC, Day PJ, Vonrhein C, Tickle IJ, Jhoti H (2004) Crystal structures of human cytochrome p450 3a4 bound to metyrapone and progesterone. Science 305(5684):683–686

    Article  CAS  Google Scholar 

  37. Zouni A, Witt HT, Kern J, Fromme P, Krauss N, Saenger W, Orth P (2001) Crystal structure of photosystem II from synechococcus elongatus at 3.8 Å resolution. Nature 409(6821):739–743

    Article  CAS  Google Scholar 

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Acknowledgments

The work described in this paper represents the efforts of many staff members at the ESRF and the EMBL synchrotron groups over more than a decade. Without their countless hours of toil none of the results from the ESRF would have been possible.

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Correspondence to Seán McSweeney .

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McSweeney, S. (2013). Searching for Needles in Haystacks: Automation and the Task of Crystal Structure Determination. In: Read, R., Urzhumtsev, A., Lunin, V. (eds) Advancing Methods for Biomolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6232-9_5

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