Skip to main content
SpringerLink
Log in
Book cover

The Next Generation in Membrane Protein Structure Determination pp 137–149Cite as

Serial Millisecond Crystallography of Membrane Proteins

  • Chapter

Part of the book series: Advances in Experimental Medicine and Biology ((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.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • 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):1948–1954

    Article  CAS  PubMed  Google Scholar 

  • 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):1228–1237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 505:244–247

    Article  CAS  PubMed  Google Scholar 

  • 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):644–652

    Article  CAS  PubMed  Google Scholar 

  • 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):1118–1131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):387–397

    Article  CAS  PubMed  Google Scholar 

  • Boutet S, Lomb L, Williams GJ, Barends TR, Aquila A et al (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science 337:362–364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brehm W, Diederichs K (2014) Breaking the indexing ambiguity in serial crystallography. Acta Crystallogr D Biol Crystallogr 70(1):101–109

    Article  CAS  PubMed  Google Scholar 

  • 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):3–18

    Article  CAS  Google Scholar 

  • Caffrey M, Cherezov V (2009) Crystallizing membrane proteins using lipidic mesophases. Nat Protoc 4(5):706–731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 369:20130621

    Article  Google Scholar 

  • Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581–586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chapman HN, Fromme P, Barty A, White TA, Kirian RA et al (2011) Femtosecond X-ray protein nanocrystallography. Nature 470:73–77

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cherezov V (2011) Lipidic cubic phase technologies for membrane protein structural studies. Curr Opin Struct Biol 21(4):559–566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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–S597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):1184–1196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):1066–1069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):195505

    Article  CAS  Google Scholar 

  • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(12):2126–2132

    Article  CAS  PubMed  Google Scholar 

  • Garman EF (2010) Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr D Biol Crystallogr 66(4):339–351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garman EF, Schneider TR (1997) Macromolecular cryocrystallography. J Appl Crystallogr 30:211–237

    Article  Google Scholar 

  • 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):1400–1410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):658–670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hettel R (2014) DLSR design and plans: an international overview. J Synchrotron Radiat 21(5):843–855

    Article  PubMed  Google Scholar 

  • 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):349–360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):734–736

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Johansson LC, Arnlund D, White TA, Katona G, Deponte DP et al (2012) Lipidic phase membrane protein serial femtosecond crystallography. Nat Methods 9(3):263–265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 4:2911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):1001–1005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 9

    Google Scholar 

  • 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):484–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kabsch W (2014) Processing of X-ray snapshots from crystals in random orientations. Acta Crystallogr D Biol Crystallogr 70(8):2204–2216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 340:491–495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 5:4371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JC et al (2010) Femtosecond protein nanocrystallography-data analysis methods. Opt Express 18:5713–5723

    Article  PubMed  PubMed Central  Google Scholar 

  • Landau EM, Rosenbusch JP (1996) Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A 93:14532–14535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):1171–1179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H, Spence JC (2014) The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm. IUCrJ 1(6):393–401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu W, Wacker D, Gati C, Han GW, James D et al (2013) Serial femtosecond crystallography of G protein-coupled receptors. Science 342:1521–1524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu W, Ishchenko A, Cherezov V (2014) Preparation of microcrystals in lipidic cubic phase for serial femtosecond crystallography. Nat Protoc 9:2123–2134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40(4):658–674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):355–367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):225–238

    Article  CAS  PubMed  Google Scholar 

  • Neutze R, Wouts R, van der Spoel D, Weckert E, Hajdu J (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406:752–757

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):810–818

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):264101

    Article  CAS  Google Scholar 

  • 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 339:227–230

    Article  CAS  PubMed  Google Scholar 

  • 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 98:10131–10136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N (2013) New Python-based methods for data processing. Acta Crystallogr D Biol Crystallogr 69(7):1274–1282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 300:1944–1947

    Article  CAS  PubMed  Google Scholar 

  • 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 109:19256–19261

    Article  PubMed  PubMed Central  Google Scholar 

  • Stellato F, Oberthur D, Liang M, Bean R, Gati C et al (2014) Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCrJ 1(4):204–212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 12:61–63

    Article  CAS  PubMed  Google Scholar 

  • 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:e05421

    Article  PubMed Central  Google Scholar 

  • Vonrhein C, Blanc E, Roversi P, Bricogne G (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364:215–230

    PubMed  CAS  Google Scholar 

  • Weierstall U, Spence JC, Doak RB (2012) Injector for scattering measurements on fully solvated biospecies. Rev Sci Instrum 83(3):35108

    Article  CAS  Google Scholar 

  • 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 5:3309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weik M, Colletier JP (2010) Temperature-dependent macromolecular X-ray crystallography. Acta Crystallogr D Biol Crystallogr 66(4):437–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White SH (2004) The progress of membrane protein structure determination. Protein Sci 13(7):1948–1949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White TA (2014) Post-refinement method for snapshot serial crystallography. Philos Trans R Soc Lond Ser B 369:20130330

    Article  Google Scholar 

  • 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):335–341

    Article  CAS  Google Scholar 

  • Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug-target network. Nat Biotechnol 25:1119–1126

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

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.).

Author information

Authors and Affiliations

  1. Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland

    Kathrin Jaeger, Przemyslaw Nogly & Joerg Standfuss

  2. Swiss Light Source, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland

    Florian Dworkowski, Christopher Milne & Meitian Wang

Authors
  1. Kathrin Jaeger
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Florian Dworkowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Przemyslaw Nogly
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Christopher Milne
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Meitian Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Joerg Standfuss
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joerg Standfuss .

Editor information

Editors and Affiliations

  1. Membrane Protein Laboratory, Diamond Light Source/Imperial College London, Harwell Campus, Didcot, Oxfordshire, UK

    Isabel Moraes

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Jaeger, K., Dworkowski, F., Nogly, P., Milne, C., Wang, M., Standfuss, J. (2016). Serial Millisecond Crystallography of Membrane Proteins. In: Moraes, I. (eds) The Next Generation in Membrane Protein Structure Determination. Advances in Experimental Medicine and Biology, vol 922. Springer, Cham. https://doi.org/10.1007/978-3-319-35072-1_10

Download citation

Publish with us

Policies and ethics

Search

Navigation