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Serial Millisecond Crystallography of Membrane Proteins

  • Kathrin Jaeger
  • Florian Dworkowski
  • Przemyslaw Nogly
  • Christopher Milne
  • Meitian Wang
  • Joerg Standfuss
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 922)

Abstract

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a powerful method to determine high-resolution structures of pharmaceutically relevant membrane proteins. Recently, the technology has been adapted to carry out serial millisecond crystallography (SMX) at synchrotron sources, where beamtime is more abundant. In an injector-based approach, crystals grown in lipidic cubic phase (LCP) or embedded in viscous medium are delivered directly into the unattenuated beam of a microfocus beamline. Pilot experiments show the application of microjet-based SMX for solving the structure of a membrane protein and compatibility of the method with de novo phasing. Planned synchrotron upgrades, faster detectors and software developments will go hand-in-hand with developments at free-electron lasers to provide a powerful methodology for solving structures from microcrystals at room temperature, ligand screening or crystal optimization for time-resolved studies with minimal or no radiation damage.

Keywords

Serial crystallography High viscosity injector LCP injector Synchrotron Membrane proteins 

Notes

Acknowledgments

The work was financially supported by A Co-fund PSI Fellowship (to P.N.) and the SNSF project grant 31003A_141235 and 31003A_159558 (toJ.S.).

References

  1. Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ et al (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58(11):1948–1954CrossRefPubMedGoogle Scholar
  2. Axford D, Foadi J, Hu N-J, Choudhury HG, Iwata S et al (2015) Structure determination of an integral membrane protein at room temperature from crystals in situ. Acta Crystallogr D Biol Crystallogr 71(6):1228–1237CrossRefPubMedPubMedCentralGoogle Scholar
  3. Barends TR, Foucar L, Botha S, Doak RB, Shoeman RL et al (2014) De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505:244–247CrossRefPubMedGoogle Scholar
  4. Barends T, White TA, Barty A, Foucar L, Messerschmidt M et al (2015) Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data. J Synchrotron Radiat 22(3):644–652CrossRefPubMedGoogle Scholar
  5. Barty A, Kirian RA, Maia FR, Hantke M, Yoon CH et al (2014) Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J Appl Crystallogr 47(3):1118–1131CrossRefPubMedPubMedCentralGoogle Scholar
  6. Botha S, Nass K, Barends TR, Kabsch W, Latz B et al (2015) Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. Acta Crystallogr D Biol Crystallogr 71(2):387–397CrossRefPubMedGoogle Scholar
  7. Boutet S, Lomb L, Williams GJ, Barends TR, Aquila A et al (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science 337:362–364CrossRefPubMedPubMedCentralGoogle Scholar
  8. Brehm W, Diederichs K (2014) Breaking the indexing ambiguity in serial crystallography. Acta Crystallogr D Biol Crystallogr 70(1):101–109CrossRefPubMedGoogle Scholar
  9. Caffrey M (2015) A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun 71(1):3–18CrossRefGoogle Scholar
  10. Caffrey M, Cherezov V (2009) Crystallizing membrane proteins using lipidic mesophases. Nat Protoc 4(5):706–731CrossRefPubMedPubMedCentralGoogle Scholar
  11. Caffrey M, Li D, Howe N, Shah ST (2014) ‘Hit and run’ serial femtosecond crystallography of a membrane kinase in the lipid cubic phase. Philos Trans R Soc Lond Ser B 369:20130621CrossRefGoogle Scholar
  12. Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581–586CrossRefPubMedPubMedCentralGoogle Scholar
  13. Chapman HN, Fromme P, Barty A, White TA, Kirian RA et al (2011) Femtosecond X-ray protein nanocrystallography. Nature 470:73–77 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Cherezov V (2011) Lipidic cubic phase technologies for membrane protein structural studies. Curr Opin Struct Biol 21(4):559–566CrossRefPubMedPubMedCentralGoogle Scholar
  15. Cherezov V, Hanson MA, Griffith MT, Hilgart MC, Sanishvili R et al (2009) Rastering strategy for screening and centring of microcrystal samples of human membrane proteins with a sub-10 microm size X-ray synchrotron beam. J R Soc Interface 6: S587–S597CrossRefPubMedPubMedCentralGoogle Scholar
  16. Coquelle N, Brewster AS, Kapp U, Shilova A, Weinhausen B et al (2015) Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. Acta Crystallogr D Biol Crystallogr 71(5):1184–1196CrossRefPubMedPubMedCentralGoogle Scholar
  17. Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ (2013) Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 69(9):1066–1069CrossRefPubMedPubMedCentralGoogle Scholar
  18. DePonte DP, Weierstall U, Schmidt K, Warner J, Starodub D et al (2008) Gas dynamic virtual nozzle for generation of microscopic droplet streams. J Phys D Appl Phys 41(19):195505CrossRefGoogle Scholar
  19. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(12):2126–2132CrossRefPubMedGoogle Scholar
  20. Garman EF (2010) Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr D Biol Crystallogr 66(4):339–351CrossRefPubMedPubMedCentralGoogle Scholar
  21. Garman EF, Schneider TR (1997) Macromolecular cryocrystallography. J Appl Crystallogr 30:211–237CrossRefGoogle Scholar
  22. Ginn HM, Brewster AS, Hattne J, Evans G, Wagner A et al (2015) A revised partiality model and post-refinement algorithm for X-ray free-electron laser data. Acta Crystallogr D Biol Crystallogr 71(6):1400–1410CrossRefPubMedPubMedCentralGoogle Scholar
  23. Graber T, Anderson S, Brewer H, Chen YS, Cho HS et al (2011) BioCARS: a synchrotron resource for time-resolved X-ray science. J Synchrotron Radiat 18(4):658–670CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hettel R (2014) DLSR design and plans: an international overview. J Synchrotron Radiat 21(5):843–855CrossRefPubMedGoogle Scholar
  25. Heymann M, Opthalage A, Wierman JL, Akella S, Szebenyi DM et al (2014) Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction. IUCrJ 1(5):349–360CrossRefPubMedPubMedCentralGoogle Scholar
  26. Hirata K, Shinzawa-Itoh K, Yano N, Takemura S, Kato K et al (2014) Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Nat Methods 11(7):734–736CrossRefPubMedGoogle Scholar
  27. Huang C-Y, Olieric V, Ma P, Panepucci E, Diederichs K et al (2015) In meso in situ serial X-ray crystallography of soluble and membrane proteins. Acta Crystallogr D Biol Crystallogr 71(6):1399–0047 CrossRefGoogle Scholar
  28. Johansson LC, Arnlund D, White TA, Katona G, Deponte DP et al (2012) Lipidic phase membrane protein serial femtosecond crystallography. Nat Methods 9(3):263–265CrossRefPubMedPubMedCentralGoogle Scholar
  29. Johansson LC, Arnlund D, Katona G, White TA, Barty A et al (2013) Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun 4:2911CrossRefPubMedPubMedCentralGoogle Scholar
  30. Johnson I, Bergamaschi A, Buitenhuis J, Dinapoli R, Greiffenberg D et al (2012) Capturing dynamics with Eiger, a fast-framing X-ray detector. J Synchrotron Radiat 19(6):1001–1005CrossRefPubMedPubMedCentralGoogle Scholar
  31. Johnson I, Bergamaschia A, Billich H, Cartier S, Dinapoli R, Greiffenberg D, Guizar-Sicairos M, Henrich B, Jungmann J, Mezza D, Mozzanica A, Schmitt B, Shi X, Tinti G (2014) Eiger: a single-photon counting x784 ray detector. J Instrum 9Google Scholar
  32. Joosten RP, Joosten K, Murshudov GN, Perrakis A (2012) PDB_REDO: constructive validation, more than just looking for errors. Acta Crystallogr D Biol Crystallogr 68(4):484–496CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kabsch W (2014) Processing of X-ray snapshots from crystals in random orientations. Acta Crystallogr D Biol Crystallogr 70(8):2204–2216CrossRefPubMedPubMedCentralGoogle Scholar
  34. Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ et al (2013) Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science 340:491–495CrossRefPubMedPubMedCentralGoogle Scholar
  35. Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N et al (2014) Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun 5:4371CrossRefPubMedPubMedCentralGoogle Scholar
  36. Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JC et al (2010) Femtosecond protein nanocrystallography-data analysis methods. Opt Express 18:5713–5723CrossRefPubMedPubMedCentralGoogle Scholar
  37. Landau EM, Rosenbusch JP (1996) Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A 93:14532–14535CrossRefPubMedPubMedCentralGoogle Scholar
  38. Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3(7):1171–1179CrossRefPubMedPubMedCentralGoogle Scholar
  39. Liu H, Spence JC (2014) The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm. IUCrJ 1(6):393–401CrossRefPubMedPubMedCentralGoogle Scholar
  40. Liu W, Wacker D, Gati C, Han GW, James D et al (2013) Serial femtosecond crystallography of G protein-coupled receptors. Science 342:1521–1524CrossRefPubMedPubMedCentralGoogle Scholar
  41. Liu W, Ishchenko A, Cherezov V (2014) Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nat Protoc 9:2123–2134CrossRefPubMedPubMedCentralGoogle Scholar
  42. Lomb L, Barends TR, Kassemeyer S, Aquila A, Epp SW et al (2011) Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B Condens Matter Mater Phys 84(21):214111 CrossRefPubMedPubMedCentralGoogle Scholar
  43. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40(4):658–674CrossRefPubMedPubMedCentralGoogle Scholar
  44. Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67(4):355–367CrossRefPubMedPubMedCentralGoogle Scholar
  45. Nass K, Foucar L, Barends TR, Hartmann E, Botha s et al (2015) Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. J Synchrotron Radiat 22(2):225–238CrossRefPubMedGoogle Scholar
  46. Neutze R, Wouts R, van der Spoel D, Weckert E, Hajdu J (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406:752–757CrossRefPubMedGoogle Scholar
  47. Nogly P, James D, Wang D, White T, Zatsepin N et al (2015) Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. IUCrJ 2(2):168–176 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Owen RL, Axford D, Nettleship JE, Owens RJ, Robinson JI et al (2012) Outrunning free radicals in room-temperature macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 68(7):810–818CrossRefPubMedPubMedCentralGoogle Scholar
  49. Park J, Joti Y, Ishikawa T, Song C (2013) Monte Carlo study for optimal conditions in single-shot imaging with femtosecond x-ray laser pulses. Appl Phys Lett 103(26):264101CrossRefGoogle Scholar
  50. Redecke L, Nass K, DePonte DP, White TA, Rehders D et al (2013) Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 339:227–230CrossRefPubMedGoogle Scholar
  51. Royant A, Nollert P, Edman K, Neutze R, Landau EM et al (2001) X-ray structure of sensory rhodopsin II at 2.1-A resolution. Proc Natl Acad Sci U S A 98:10131–10136CrossRefPubMedPubMedCentralGoogle Scholar
  52. Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N (2013) New Python-based methods for data processing. Acta Crystallogr D Biol Crystallogr 69(7):1274–1282CrossRefPubMedPubMedCentralGoogle Scholar
  53. Schotte F, Lim M, Jackson TA, Smirnov AV, Soman J et al (2003) Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science 300:1944–1947CrossRefPubMedGoogle Scholar
  54. Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N et al (2012) Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proc Natl Acad Sci U S A 109:19256–19261CrossRefPubMedPubMedCentralGoogle Scholar
  55. Stellato F, Oberthur D, Liang M, Bean R, Gati C et al (2014) Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCrJ 1(4):204–212CrossRefPubMedPubMedCentralGoogle Scholar
  56. Sugahara M, Mizohata E, Nango E, Suzuki M, Tanaka T et al (2015) Grease matrix as a versatile carrier of proteins for serial crystallography. Nat Methods 12:61–63CrossRefPubMedGoogle Scholar
  57. Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS et al (2015) Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. Elife 4:e05421CrossRefPubMedCentralGoogle Scholar
  58. Vonrhein C, Blanc E, Roversi P, Bricogne G (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364:215–230PubMedGoogle Scholar
  59. Weierstall U, Spence JC, Doak RB (2012) Injector for scattering measurements on fully solvated biospecies. Rev Sci Instrum 83(3):35108CrossRefGoogle Scholar
  60. Weierstall U, James D, Wang C, White TA, Wang D et al (2014) Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat Commun 5:3309CrossRefPubMedPubMedCentralGoogle Scholar
  61. Weik M, Colletier JP (2010) Temperature-dependent macromolecular X-ray crystallography. Acta Crystallogr D Biol Crystallogr 66(4):437–446 CrossRefPubMedPubMedCentralGoogle Scholar
  62. White SH (2004) The progress of membrane protein structure determination. Protein Sci 13(7):1948–1949CrossRefPubMedPubMedCentralGoogle Scholar
  63. White TA (2014) Post-refinement method for snapshot serial crystallography. Philos Trans R Soc Lond Ser B 369:20130330CrossRefGoogle Scholar
  64. White TA, Kirian RA, Martin AV, Aquila A, Nass K et al (2012) CrystFEL: a software suite for snapshot serial crystallography. J Appl Crystallogr 45(2):335–341CrossRefGoogle Scholar
  65. Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug-target network. Nat Biotechnol 25:1119–1126CrossRefGoogle Scholar
  66. Zhang H, Unal H, Gati C, Han GW, Liu W et al (2015) Structure of the Angiotensin receptor revealed by serial femtosecond crystallography. Cell 161:833–844 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Kathrin Jaeger
    • 1
  • Florian Dworkowski
    • 2
  • Przemyslaw Nogly
    • 1
  • Christopher Milne
    • 2
  • Meitian Wang
    • 2
  • Joerg Standfuss
    • 1
  1. 1.Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligen PSISwitzerland
  2. 2.Swiss Light SourcePaul Scherrer InstituteVilligen PSISwitzerland

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