Skip to main content

2018 | OriginalPaper | Buchkapitel

2. Serial Femtosecond Crystallography (SFX): An Overview

verfasst von : Mark S. Hunter, Petra Fromme

Erschienen in: X-ray Free Electron Lasers

Verlag: Springer International Publishing

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

X-ray crystallography is a very powerful tool to determine structures of biological macromolecules at the atomic and molecular level and thereby enables insights into their function. Unfortunately, irradiating biological samples with X-rays is an inherently damaging and unavoidable process in conventional X-ray crystallography. The unique properties of X-ray free electron lasers (FELs), with pulse duration in the femtosecond range, allow data collection at time scales shorter than, or equivalent to, the time scales of the X-ray induced radiation damage pathways, offering a plausible way to diminish the ill effects of conventional radiation damage in biological structure determination. However, the high intensities of the X-ray FEL beam necessitated the development of novel techniques for sample preparation, characterization, introduction, data collection, and analysis. Serial femtosecond crystallography (SFX) represents a set of techniques developed to enable X-ray crystallography experiments at X-ray FELs, which encompasses multiple developments in sample introduction and data collection. This chapter summarizes the early experiments that demonstrated the SFX methods along with more recent developments and accomplishments that will be discussed in more detail in the following chapters of this book.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Literatur
10.
Zurück zum Zitat Botha, S., Nass, K., Barends, T. R. M., Kabsch, W., Latz, B., Dworkowski, F., et al. (2015). Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. Acta Crystallographica Section D, 71(2), 387–397. https://doi.org/10.1107/S1399004714026327.CrossRef Botha, S., Nass, K., Barends, T. R. M., Kabsch, W., Latz, B., Dworkowski, F., et al. (2015). Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. Acta Crystallographica Section D, 71(2), 387–397. https://​doi.​org/​10.​1107/​S139900471402632​7.CrossRef
13.
Zurück zum Zitat Caspar, D. L. D., Clarage, J., Salunke, D. M., & Clarage, M. (1988). Liquid-like movements in crystalline insulin. Nature, 332(6165), 659–662.CrossRefPubMed Caspar, D. L. D., Clarage, J., Salunke, D. M., & Clarage, M. (1988). Liquid-like movements in crystalline insulin. Nature, 332(6165), 659–662.CrossRefPubMed
14.
Zurück zum Zitat Chapman, H. N., Barty, A., Bogan, M. J., Boutet, S., Frank, M., Hau-Riege, S. P., et al. (2006). Femtosecond diffractive imaging with a soft-X-ray free-electron laser. Nature Physics, 2(12), 839–843.CrossRef Chapman, H. N., Barty, A., Bogan, M. J., Boutet, S., Frank, M., Hau-Riege, S. P., et al. (2006). Femtosecond diffractive imaging with a soft-X-ray free-electron laser. Nature Physics, 2(12), 839–843.CrossRef
16.
Zurück zum Zitat Chapman, H. N., Hau-Riege, S. P., Bogan, M. J., Bajt, S., Barty, A., Boutet, S., et al. (2007). Femtosecond time-delay X-ray holography. Nature, 448(7154), 676–679. CrossRefPubMed Chapman, H. N., Hau-Riege, S. P., Bogan, M. J., Bajt, S., Barty, A., Boutet, S., et al. (2007). Femtosecond time-delay X-ray holography. Nature, 448(7154), 676–679. CrossRefPubMed
17.
19.
21.
Zurück zum Zitat Colletier, J. P. (n.d.). Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nature Chemistry. Colletier, J. P. (n.d.). Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nature Chemistry.
24.
Zurück zum Zitat DePonte, D. P., Weierstall, U., Schmidt, K., Warner, J., Starodub, D., Spence, J. C. H., & Doak, R. B. (2008). Gas dynamic virtual nozzle for generation of microscopic droplet streams. Journal of Physics D: Applied Physics, 41(19), 195505.CrossRef DePonte, D. P., Weierstall, U., Schmidt, K., Warner, J., Starodub, D., Spence, J. C. H., & Doak, R. B. (2008). Gas dynamic virtual nozzle for generation of microscopic droplet streams. Journal of Physics D: Applied Physics, 41(19), 195505.CrossRef
26.
Zurück zum Zitat Doucet, J., & Benoit, J. P. (1987). Molecular dynamics studied by analysis of the X-ray diffuse scattering from lysozyme crystals. Nature, 325(6105), 643–646.CrossRefPubMed Doucet, J., & Benoit, J. P. (1987). Molecular dynamics studied by analysis of the X-ray diffuse scattering from lysozyme crystals. Nature, 325(6105), 643–646.CrossRefPubMed
27.
Zurück zum Zitat Drenth, J. (2007). Principles of protein X-ray crystallography (3rd ed.). New York: Springer-Verlag. Drenth, J. (2007). Principles of protein X-ray crystallography (3rd ed.). New York: Springer-Verlag.
29.
Zurück zum Zitat Ekeberg, T., Svenda, M., Abergel, C., Maia, F. R. N. C., Seltzer, V., Claverie, J.-M., et al. (2015). Three-dimensional reconstruction of the Giant Mimivirus particle with an X-ray free-Electron laser. Physical Review Letters, 114(9), 098102.CrossRefPubMed Ekeberg, T., Svenda, M., Abergel, C., Maia, F. R. N. C., Seltzer, V., Claverie, J.-M., et al. (2015). Three-dimensional reconstruction of the Giant Mimivirus particle with an X-ray free-Electron laser. Physical Review Letters, 114(9), 098102.CrossRefPubMed
31.
Zurück zum Zitat Faure, P., Micu, A., Perahia, D., Doucet, J., Smith, J. C., & Benoit, J. P. (1994). Correlated intramolecular motions and diffuse x-ray scattering in lysozyme. Nature Structural & Molecular Biology, 1(2), 124–128.CrossRef Faure, P., Micu, A., Perahia, D., Doucet, J., Smith, J. C., & Benoit, J. P. (1994). Correlated intramolecular motions and diffuse x-ray scattering in lysozyme. Nature Structural & Molecular Biology, 1(2), 124–128.CrossRef
36.
Zurück zum Zitat Fukuda, Y., Tse, K. M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., et al. (2016). Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. Proceedings of the National Academy of Sciences, 113(11), 2928–2933. https://doi.org/10.1073/pnas.1517770113.CrossRef Fukuda, Y., Tse, K. M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., et al. (2016). Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. Proceedings of the National Academy of Sciences, 113(11), 2928–2933. https://​doi.​org/​10.​1073/​pnas.​1517770113.CrossRef
38.
Zurück zum Zitat Gañán-Calvo, A. M. (1998). Generation of steady liquid microthreads and Micron-sized Monodisperse sprays in gas streams. Physical Review Letters, 80(2), 285–288.CrossRef Gañán-Calvo, A. M. (1998). Generation of steady liquid microthreads and Micron-sized Monodisperse sprays in gas streams. Physical Review Letters, 80(2), 285–288.CrossRef
50.
Zurück zum Zitat Kam, Z., Koch, M. H. J., & Bordas, J. (1981). Fluctuation X-ray scattering from biological particles in frozen solution by using synchrotron radiation. Proceedings of the National Academy of Sciences of the United States of America, 78(6), 3559–3562.CrossRefPubMedPubMedCentral Kam, Z., Koch, M. H. J., & Bordas, J. (1981). Fluctuation X-ray scattering from biological particles in frozen solution by using synchrotron radiation. Proceedings of the National Academy of Sciences of the United States of America, 78(6), 3559–3562.CrossRefPubMedPubMedCentral
59.
Zurück zum Zitat Landau, E. M., & Rosenbusch, J. P. (1996). Lipidic cubic phases: A novel concept for the crystallization of membrane proteins. Proceedings of the National Academy of Sciences, 93(25), 14532–14535.CrossRef Landau, E. M., & Rosenbusch, J. P. (1996). Lipidic cubic phases: A novel concept for the crystallization of membrane proteins. Proceedings of the National Academy of Sciences, 93(25), 14532–14535.CrossRef
63.
Zurück zum Zitat Lomb, L., Barends, T. R. M., Kassemeyer, S., Aquila, A., Epp, S. W., Erk, B., et al. (2011). Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Physical Review B, 84(21), 214111.CrossRef Lomb, L., Barends, T. R. M., Kassemeyer, S., Aquila, A., Epp, S. W., Erk, B., et al. (2011). Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Physical Review B, 84(21), 214111.CrossRef
65.
Zurück zum Zitat Malkin, A. J., Kuznetsov, Y. G., Land, T. A., DeYoreo, J. J., & McPherson, A. (1995). Mechanisms of growth for protein and virus crystals. Nature Structural & Molecular Biology, 2(11), 956–959.CrossRef Malkin, A. J., Kuznetsov, Y. G., Land, T. A., DeYoreo, J. J., & McPherson, A. (1995). Mechanisms of growth for protein and virus crystals. Nature Structural & Molecular Biology, 2(11), 956–959.CrossRef
66.
Zurück zum Zitat Marchesini, S., He, H., Chapman, H. N., Hau-Riege, S. P., Noy, A., Howells, M. R., et al. (2003). X-ray image reconstruction from a diffraction pattern alone. Physical Review B, 68(14), 140101.CrossRef Marchesini, S., He, H., Chapman, H. N., Hau-Riege, S. P., Noy, A., Howells, M. R., et al. (2003). X-ray image reconstruction from a diffraction pattern alone. Physical Review B, 68(14), 140101.CrossRef
69.
71.
Zurück zum Zitat Nass, K., Meinhart, A., Barends, T., Foucar, L., Gorel, A., Aquila, A., et al. (2016a). Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data. IUCrJ, 3, 1–12.CrossRef Nass, K., Meinhart, A., Barends, T., Foucar, L., Gorel, A., Aquila, A., et al. (2016a). Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data. IUCrJ, 3, 1–12.CrossRef
84.
Zurück zum Zitat Rossmann, M. G. (1990). The molecular replacement method. Acta Crystallographica. Section A, 46(Pt 2), 73–82. Rossmann, M. G. (1990). The molecular replacement method. Acta Crystallographica. Section A, 46(Pt 2), 73–82.
85.
Zurück zum Zitat Rupp, B. (2013). Macromolecular crystallography: Overview. In G. C. K. Roberts (Ed.), Encyclopedia of biophysics (pp. 1346–1353). Berlin, Heidelberg: Springer Berlin Heidelberg.CrossRef Rupp, B. (2013). Macromolecular crystallography: Overview. In G. C. K. Roberts (Ed.), Encyclopedia of biophysics (pp. 1346–1353). Berlin, Heidelberg: Springer Berlin Heidelberg.CrossRef
90.
Zurück zum Zitat Seibert, M. M., Ekeberg, T., Maia, F. R. N. C., Svenda, M., Andreasson, J., Jonsson, O., et al. (2011). Single mimivirus particles intercepted and imaged with an X-ray laser. Nature, 470(7332), 78–81.CrossRefPubMedPubMedCentral Seibert, M. M., Ekeberg, T., Maia, F. R. N. C., Svenda, M., Andreasson, J., Jonsson, O., et al. (2011). Single mimivirus particles intercepted and imaged with an X-ray laser. Nature, 470(7332), 78–81.CrossRefPubMedPubMedCentral
99.
Zurück zum Zitat Stevens, R. C., Cherezov, V., Katritch, V., Abagyan, R., Kuhn, P., Rosen, H., & Wuthrich, K. (2013). The GPCR network: A large-scale collaboration to determine human GPCR structure and function. Nature Reviews. Drug Discovery, 12(1), 25–34.CrossRefPubMed Stevens, R. C., Cherezov, V., Katritch, V., Abagyan, R., Kuhn, P., Rosen, H., & Wuthrich, K. (2013). The GPCR network: A large-scale collaboration to determine human GPCR structure and function. Nature Reviews. Drug Discovery, 12(1), 25–34.CrossRefPubMed
100.
Zurück zum Zitat Stevenson, H. P., DePonte, D. P., Makhov, A. M., Conway, J. F., Zeldin, O. B., Boutet, S., & Cohen, A. E. (2014a). Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647). https://doi.org/10.1098/rstb.2013.0322.CrossRef Stevenson, H. P., DePonte, D. P., Makhov, A. M., Conway, J. F., Zeldin, O. B., Boutet, S., & Cohen, A. E. (2014a). Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647). https://​doi.​org/​10.​1098/​rstb.​2013.​0322.CrossRef
101.
Zurück zum Zitat Stevenson, H. P., Makhov, A. M., Calero, M., Edwards, A. L., Zeldin, O. B., Mathews, I. I., et al. (2014b). Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proceedings of the National Academy of Sciences, 111(23), 8470–8475. https://doi.org/10.1073/pnas.1400240111.CrossRef Stevenson, H. P., Makhov, A. M., Calero, M., Edwards, A. L., Zeldin, O. B., Mathews, I. I., et al. (2014b). Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proceedings of the National Academy of Sciences, 111(23), 8470–8475. https://​doi.​org/​10.​1073/​pnas.​1400240111.CrossRef
102.
Zurück zum Zitat Strüder, L., Epp, S., Rolles, D., Hartmann, R., Holl, P., Lutz, G., et al. (2010). Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 614(3), 483–496. https://doi.org/10.1016/j.nima.2009.12.053.CrossRef Strüder, L., Epp, S., Rolles, D., Hartmann, R., Holl, P., Lutz, G., et al. (2010). Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 614(3), 483–496. https://​doi.​org/​10.​1016/​j.​nima.​2009.​12.​053.CrossRef
110.
Zurück zum Zitat Van Benschoten, A. H., Liu, L., Gonzalez, A., Brewster, A. S., Sauter, N. K., Fraser, J. S., & Wall, M. E. (2016). Measuring and modeling diffuse scattering in protein X-ray crystallography. Proceedings of the National Academy of Sciences, 113(15), 4069–4074. https://doi.org/10.1073/pnas.1524048113.CrossRef Van Benschoten, A. H., Liu, L., Gonzalez, A., Brewster, A. S., Sauter, N. K., Fraser, J. S., & Wall, M. E. (2016). Measuring and modeling diffuse scattering in protein X-ray crystallography. Proceedings of the National Academy of Sciences, 113(15), 4069–4074. https://​doi.​org/​10.​1073/​pnas.​1524048113.CrossRef
111.
Zurück zum Zitat Wall, M. E., Ealick, S. E., & Gruner, S. M. (1997). Three-dimensional diffuse x-ray scattering from crystals of staphylococcal nuclease. Proceedings of the National Academy of Sciences, 94(12), 6180–6184. CrossRef Wall, M. E., Ealick, S. E., & Gruner, S. M. (1997). Three-dimensional diffuse x-ray scattering from crystals of staphylococcal nuclease. Proceedings of the National Academy of Sciences, 94(12), 6180–6184. CrossRef
113.
119.
Zurück zum Zitat Woolfson, M. M. (1997). An introduction to X-ray crystallography (2nd ed.). Cambridge: Cambridge University Press.CrossRef Woolfson, M. M. (1997). An introduction to X-ray crystallography (2nd ed.). Cambridge: Cambridge University Press.CrossRef
129.
Zurück zum Zitat Zhu, D., Feng, Y., Stoupin, S., Terentyev, S. A., Lemke, H. T., Fritz, D. M., et al. (2014). Performance of a beam-multiplexing diamond crystal monochromator at the Linac coherent light source. Review of Scientific Instruments, 85(6), 063106. https://doi.org/10.1063/1.4880724.CrossRef Zhu, D., Feng, Y., Stoupin, S., Terentyev, S. A., Lemke, H. T., Fritz, D. M., et al. (2014). Performance of a beam-multiplexing diamond crystal monochromator at the Linac coherent light source. Review of Scientific Instruments, 85(6), 063106. https://​doi.​org/​10.​1063/​1.​4880724.CrossRef
Metadaten
Titel
Serial Femtosecond Crystallography (SFX): An Overview
verfasst von
Mark S. Hunter
Petra Fromme
Copyright-Jahr
2018
DOI
https://doi.org/10.1007/978-3-030-00551-1_2

Neuer Inhalt