Skip to main content

Time-Resolved Serial Femtosecond Crystallography, Towards Molecular Movies of Biomolecules in Action

  • Chapter
  • First Online:
Book cover X-ray Free Electron Lasers

Abstract

Biological macromolecules, such as proteins, nucleic acids, and complexes thereof, are characterized by specific structural and dynamic features that are the basis of their respective biological activity, and define their dynamic personalities [29]. Understanding macromolecular activity thus requires studying structural changes over time and on various time-scales, such as equilibrium fluctuations and conformational changes orchestrating enzyme catalysis or enabling signal transduction. The first step in human vision, for instance, is the sub-picosecond time-scale photoisomerization of the retinal pigment in rhodopsin [73], which within microseconds leads to the conformational changes required for activation of transducin, the regulatory protein that initiates the signaling cascade beyond the macromolecular level.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 159.99
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

Institutional subscriptions

References

  1. Aquila, A., Hunter, M. S., Doak, R. B., Kirian, R. A., Fromme, P., White, T. A., et al. (2012). Time-resolved protein nanocrystallography using an X-ray free-electron laser. Optics Express, 20(3), 2706–2716. https://doi.org/10.1364/OE.20.002706.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Barends, T. R., Foucar, L., Ardevol, A., Nass, K., Aquila, A., Botha, S., et al. (2015). Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science, 350(6259), 445–450. https://doi.org/10.1126/science.aac5492.

    Article  CAS  PubMed  Google Scholar 

  3. Baxter, R. H., Ponomarenko, N., Srajer, V., Pahl, R., Moffat, K., & Norris, J. R. (2004). Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center. Proceedings of the National Academy of Sciences of the United States of America, 101(16), 5982–5987. https://doi.org/10.1073/pnas.0306840101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Beyerlein, K. R., Dierksmeyer, D., Mariani, V., Kuhn, M., Sarrou, I., Ottaviano, A., et al. (2017). Mix-and-diffuse serial synchrotron crystallography. IUCrJ, 4(Pt 6), 769–777. https://doi.org/10.1107/S2052252517013124.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Botha, S., Nass, K., Barends, T. R., 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, Biological crystallography, 71(Pt 2), 387–397. https://doi.org/10.1107/S1399004714026327.

    Article  CAS  PubMed  Google Scholar 

  6. Bourgeois, D., Vallone, B., Arcovito, A., Sciara, G., Schotte, F., Anfinrud, P. A., et al. (2006). Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography. Proceedings of the National Academy of Sciences of the United States of America, 103(13), 4924–4929. https://doi.org/10.1073/pnas.0508880103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bourgeois, D., Vallone, B., Schotte, F., Arcovito, A., Miele, A. E., Sciara, G., et al. (2003). Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography. Proceedings of the National Academy of Sciences of the United States of America, 100(15), 8704–8709. https://doi.org/10.1073/pnas.1430900100.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bourgeois, D., & Weik, M. (2009). Kinetic protein crystallography: A tool to watch proteins in action. Crystallography Reviews, 15(2), 87–118.

    Article  CAS  Google Scholar 

  9. Broichhagen, J., Frank, J. A., & Trauner, D. (2015). A roadmap to success in Photopharmacology. Accounts of Chemical Research, 48(7), 1947–1960. https://doi.org/10.1021/acs.accounts.5b00129.

    Article  CAS  PubMed  Google Scholar 

  10. Cammarata, M., Levantino, M., Schotte, F., Anfinrud, P. A., Ewald, F., Choi, J., et al. (2008). Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering. Nature Methods, 5(10), 881–886.

    Article  CAS  Google Scholar 

  11. Chapman, H. N., Fromme, P., Barty, A., White, T. A., Kirian, R. A., Aquila, A., et al. (2011). Femtosecond X-ray protein nanocrystallography. Nature, 470(7332), 73–77.

    Article  CAS  Google Scholar 

  12. Colletier, J. P., Bourgeois, D., Sanson, B., Fournier, D., Sussman, J. L., Silman, I., et al. (2008). Shoot-and-trap: Use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography. Proceedings of the National Academy of Sciences of the United States of America, 105(33), 11742–11747.

    Article  CAS  Google Scholar 

  13. Conrad, C. E., Basu, S., James, D., Wang, D., Schaffer, A., Roy-Chowdhury, S., et al. (2015). A novel inert crystal delivery medium for serial femtosecond crystallography. IUCrJ, 2(4), 421–430. https://doi.org/10.1107/S2052252515009811.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Coquelle, N., Brewster, A. S., Kapp, U., Shilova, A., Weinhausen, B., Burghammer, M., et al. (2015). Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. Acta Crystallographica Section D, 71(5), 1184–1196. https://doi.org/10.1107/S1399004715004514.

    Article  CAS  Google Scholar 

  15. Coquelle, N., Sliwa, M., Woodhouse, J., SchirĂ², G., Adam, V., Aquila, A., et al. (2018). Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nature Chemistry, 10, 31–37. https://doi.org/10.1038/nchem.2853.

    Article  CAS  PubMed  Google Scholar 

  16. Danailov, M. B., Bencivenga, F., Capotondi, F., Casolari, F., Cinquegrana, P., Demidovich, A., et al. (2014). Towards jitter-free pump-probe measurements at seeded free electron laser facilities. Optics Express, 22(11), 12869–12879. https://doi.org/10.1364/oe.22.012869.

    Article  CAS  PubMed  Google Scholar 

  17. Duan, C., Adam, V., Byrdin, M., Ridard, J., Kieffer-Jaquinod, S., Morlot, C., et al. (2013). Structural evidence for a two-regime photobleaching mechanism in a reversibly switchable fluorescent protein. Journal of the American Chemical Society, 135(42), 15841–15850. https://doi.org/10.1021/ja406860e.

    Article  CAS  PubMed  Google Scholar 

  18. Efremov, R., Gordeliy, V. I., Heberle, J., & BĂ¼ldt, G. (2006). Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics. Biophysical Journal, 91(4), 1441–1451. https://doi.org/10.1529/biophysj.106.083345.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Fermi, G., Perutz, M. F., Dickinson, L. C., & Chien, J. C. W. (1982). Structure of human deoxy cobalt haemoglobin. Journal of Molecular Biology, 155(4), 495–505. https://doi.org/10.1016/0022-2836(82)90483-1.

    Article  CAS  PubMed  Google Scholar 

  20. Fuller, F. D., Gul, S., Chatterjee, R., Burgie, E. S., Young, I. D., Lebrette, H., et al. (2017). Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature Methods, 14(4), 443–449. https://doi.org/10.1038/nmeth.4195.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Garman, E. F., & Weik, M. (2017). Radiation damage in macromolecular crystallography. Methods in Molecular Biology, 1607, 467–489. https://doi.org/10.1007/978-1-4939-7000-1_20.

    Article  CAS  PubMed  Google Scholar 

  22. Gati, C., Bourenkov, G., Klinge, M., Rehders, D., Stellato, F., Oberthur, D., et al. (2014). Serial crystallography on in vivo grown microcrystals using synchrotron radiation. IUCrJ, 1(Pt 2), 87–94. https://doi.org/10.1107/S2052252513033939.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Genick, U. K., Borgstahl, G. E., Ng, K., Ren, Z., Pradervand, C., Burke, P. M., et al. (1997). Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science, 275(5305), 1471–1475.

    Article  CAS  Google Scholar 

  24. Gerwert, K., Hess, B., Michel, H., & Buchanan, S. (1988). FTIR studies on crystals of photosynthetic reaction centers. FEBS Letters, 232(2), 303–307. https://doi.org/10.1016/0014-5793(88)80758-0.

    Article  CAS  Google Scholar 

  25. Glownia, J. M., Cryan, J., Andreasson, J., Belkacem, A., Berrah, N., Blaga, C. I., et al. (2010). Time-resolved pump-probe experiments at the LCLS. Optics Express, 18(17), 17620–17630. https://doi.org/10.1364/oe.18.017620.

    Article  CAS  PubMed  Google Scholar 

  26. Grotjohann, T., Testa, I., Reuss, M., Brakemann, T., Eggeling, C., Hell, S. W., et al. (2012). rsEGFP2 enables fast RESOLFT nanoscopy of living cells. eLife, 1, e00248. https://doi.org/10.7554/eLife.00248.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Harmand, M., Coffee, R., Bionta, M. R., Chollet, M., French, D., Zhu, D., et al. (2013). Achieving few-femtosecond time-sorting at hard X-ray free-electron lasers. Nature Photonics, 7, 215. https://doi.org/10.1038/nphoton.2013.11.

    Article  CAS  Google Scholar 

  28. Hekstra, D. R., White, K. I., Socolich, M. A., Henning, R. W., Srajer, V., & Ranganathan, R. (2016). Electric-field-stimulated protein mechanics. Nature, 540(7633), 400–405. https://doi.org/10.1038/nature20571.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Henzler-Wildman, K., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450(7172), 964–972.

    Article  CAS  Google Scholar 

  30. Heymann, M., Opthalage, A., Wierman, J. L., Akella, S., Szebenyi, D. M., Gruner, S. M., et al. (2014). Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction. IUCrJ, 1(Pt 5), 349–360. https://doi.org/10.1107/S2052252514016960.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., et al. (2014). Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Nature Methods, 11(7), 734–736. https://doi.org/10.1038/nmeth.2962.

    Article  CAS  PubMed  Google Scholar 

  32. Huang, C. Y., Olieric, V., Ma, P., Panepucci, E., Diederichs, K., Wang, M., et al. (2015). In meso in situ serial X-ray crystallography of soluble and membrane proteins. Acta crystallographica Section D, Biological crystallography, 71(Pt 6), 1238–1256. https://doi.org/10.1107/S1399004715005210.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hutchison, C. D. M., Kaucikas, M., Tenboer, J., Kupitz, C., Moffat, K., Schmidt, M., et al. (2016). Photocycle populations with femtosecond excitation of crystalline photoactive yellow protein. Chemical Physics Letters, 654, 63–71. https://doi.org/10.1016/j.cplett.2016.04.087.

    Article  CAS  Google Scholar 

  34. Ihee, H., Rajagopal, S., Srajer, V., Pahl, R., Anderson, S., Schmidt, M., et al. (2005). Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. Proceedings of the National Academy of Sciences of the United States of America, 102(20), 7145–7150 Epub 2005 May 7143.

    Article  CAS  Google Scholar 

  35. Jaeger, K., Dworkowski, F., Nogly, P., Milne, C., Wang, M., & Standfuss, J. (2016). Serial millisecond crystallography of membrane proteins. Advances in Experimental Medicine and Biology, 922, 137–149. https://doi.org/10.1007/978-3-319-35072-1_10.

    Article  CAS  PubMed  Google Scholar 

  36. Jung, Y. O., Lee, J. H., Kim, J., Schmidt, M., Moffat, K., Srajer, V., et al. (2013). Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nature Chemistry, 5(3), 212–220. https://doi.org/10.1038/nchem.1565.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R. J., Echols, N., et al. (2013). Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science, 340(6131), 491–495. https://doi.org/10.1126/science.1234273.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., et al. (2014). Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications, 5, 4371. https://doi.org/10.1038/ncomms5371.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Knapp, J. E., Pahl, R., Srajer, V., & Royer Jr., W. E. (2006). Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin. Proceedings of the National Academy of Sciences of the United States of America, 103(20), 7649–7654. https://doi.org/10.1073/pnas.0509411103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Kok, B., Forbush, B., & McGloin, M. (1970). Cooperation of charges in photosynthetic O2 evolution-I. A linear four step mechanism. Photochemistry and Photobiology, 11(6), 457–475.

    Article  CAS  Google Scholar 

  41. Kort, R., Ravelli, R. B., Schotte, F., Bourgeois, D., Crielaard, W., Hellingwerf, K. J., et al. (2003). Characterization of photocycle intermediates in crystalline photoactive yellow protein. Photochemistry and Photobiology, 78(2), 131–137. https://doi.org/10.1562/0031-8655(2003)0780131copiic2.0.co2.

    Article  CAS  PubMed  Google Scholar 

  42. Kostov, K. S., & Moffat, K. (2011). Cluster analysis of time-dependent crystallographic data: Direct identification of time-independent structural intermediates. Biophysical Journal, 100(2), 440–449. https://doi.org/10.1016/j.bpj.2010.10.053.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Kovacsova, G., Grunbein, M. L., Kloos, M., Barends, T. R. M., Schlesinger, R., Heberle, J., et al. (2017). Viscous hydrophilic injection matrices for serial crystallography. IUCrJ, 4(Pt 4), 400–410. https://doi.org/10.1107/S2052252517005140.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kubelka, J. (2009). Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics. Photochemical & Photobiological Sciences, 8(4), 499–512. https://doi.org/10.1039/b819929a.

    Article  CAS  Google Scholar 

  45. Kupitz, C., Basu, S., Grotjohann, I., Fromme, R., Zatsepin, N. A., Rendek, K. N., et al. (2014). Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature, 513(7517), 261–265. https://doi.org/10.1038/nature13453.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Kupitz, C., Olmos, J. L., Holl, M., Tremblay, L., Pande, K., Pandey, S., et al. (2017). Structural enzymology using X-ray free electron lasers. Structural Dynamics, 4(4), 044003. https://doi.org/10.1063/1.4972069.

    Article  CAS  PubMed  Google Scholar 

  47. Levantino, M., Schiro, G., Lemke, H. T., Cottone, G., Glownia, J. M., Zhu, D., et al. (2015). Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser. Nature Communications, 6, 6772. https://doi.org/10.1038/ncomms7772.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Lincoln, C. N., Fitzpatrick, A. E., & van Thor, J. J. (2012). Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein. Physical Chemistry Chemical Physics, 14(45), 15752–15764. https://doi.org/10.1039/c2cp41718a.

    Article  CAS  PubMed  Google Scholar 

  49. Liu, W., Wacker, D., Gati, C., Han, G. W., James, D., Wang, D., et al. (2013). Serial femtosecond crystallography of G protein-coupled receptors. Science, 342(6165), 1521–1524. https://doi.org/10.1126/science.1244142.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Löhl, F., Arsov, V., Felber, M., Hacker, K., Jalmuzna, W., Lorbeer, B., et al. (2010). Electron bunch timing with femtosecond precision in a superconducting free-electron laser. Physical Review Letters, 104(14), 144801.

    Article  Google Scholar 

  51. Martin-Garcia, J. M., Conrad, C. E., Nelson, G., Stander, N., Zatsepin, N. A., Zook, J., et al. (2017). Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. IUCrJ, 4(Pt 4), 439–454. https://doi.org/10.1107/S205225251700570X.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Meents, A., Wiedorn, M. O., Srajer, V., Henning, R., Sarrou, I., Bergtholdt, J., et al. (2017). Pink-beam serial crystallography. Nature Communications, 8(1), 1281. https://doi.org/10.1038/s41467-017-01417-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Miller, R. J. D. (1994). Energetics and dynamics of deterministic protein motion. Accounts of Chemical Research, 27(5), 145–150. https://doi.org/10.1021/ar00041a005.

    Article  CAS  Google Scholar 

  54. Moffat, K. (1989). Time-resolved macromolecular crystallography. Annual Review of Biophysics and Biophysical Chemistry, 18, 309–332. https://doi.org/10.1146/annurev.bb.18.060189.001521.

    Article  CAS  PubMed  Google Scholar 

  55. Mozzarelli, A., & Rossi, G. L. (1996). Protein function in the crystal. Annual Review of Biophysics and Biomolecular Structure, 25, 343–365.

    Article  CAS  Google Scholar 

  56. Nango, E., Royant, A., Kubo, M., Nakane, T., Wickstrand, C., Kimura, T., et al. (2016). A three-dimensional movie of structural changes in bacteriorhodopsin. Science, 354(6319), 1552–1557. https://doi.org/10.1126/science.aah3497.

    Article  CAS  PubMed  Google Scholar 

  57. Neutze, R., Wouts, R., van der Spoel, D., Weckert, E., & Hajdu, J. (2000). Potential for biomolecular imaging with femtosecond X-ray pulses. Nature, 406(6797), 752–757.

    Article  CAS  Google Scholar 

  58. Ng, K., Getzoff, E. D., & Moffat, K. (1995). Optical studies of a bacterial photoreceptor protein, photoactive yellow protein, in single crystals. Biochemistry, 34(3), 879–890. https://doi.org/10.1021/bi00003a022.

    Article  CAS  PubMed  Google Scholar 

  59. Nogly, P., James, D., Wang, D., White, T. A., Zatsepin, N., Shilova, A., et al. (2015). Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. IUCrJ, 2(Pt 2), 168–176. https://doi.org/10.1107/S2052252514026487.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Nogly, P., Panneels, V., Nelson, G., Gati, C., Kimura, T., Milne, C., et al. (2016). Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nature Communications, 7, 12314. https://doi.org/10.1038/ncomms12314.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Oghbaey, S., Sarracini, A., Ginn, H. M., Pare-Labrosse, O., Kuo, A., Marx, A., et al. (2016). Fixed target combined with spectral mapping: Approaching 100% hit rates for serial crystallography. Acta crystallographica Section D, Structural Biology, 72(Pt 8), 944–955. https://doi.org/10.1107/S2059798316010834.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Owen, R. L., Axford, D., Sherrell, D. A., Kuo, A., Ernst, O. P., Schulz, E. C., et al. (2017). Low-dose fixed-target serial synchrotron crystallography. Acta Crystallographica Section D, 73(4), 373–378. https://doi.org/10.1107/S2059798317002996.

    Article  CAS  Google Scholar 

  63. Pande, K., Hutchison, C. D., Groenhof, G., Aquila, A., Robinson, J. S., Tenboer, J., et al. (2016). Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science, 352(6286), 725–729. https://doi.org/10.1126/science.aad5081.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Rajagopal, S., Kostov, K. S., & Moffat, K. (2004). Analytical trapping: Extraction of time-independent structures from time-dependent crystallographic data. Journal of Structural Biology, 147(3), 211–222. https://doi.org/10.1016/j.jsb.2004.04.007.

    Article  CAS  PubMed  Google Scholar 

  65. Roedig, P., Ginn, H. M., Pakendorf, T., Sutton, G., Harlos, K., Walter, T. S., et al. (2017). High-speed fixed-target serial virus crystallography. Nature Methods, 14(8), 805–810. https://doi.org/10.1038/nmeth.4335.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Sauter, N. K., Echols, N., Adams, P. D., Zwart, P. H., Kern, J., Brewster, A. S., et al. (2016). No observable conformational changes in PSII. Nature, 533(7603), E1–E2.

    Article  CAS  Google Scholar 

  67. Schiro, G., Woodhouse, J., Weik, M., Schlichting, I., & Shoeman, R. L. (2017). Simple and efficient system for photoconverting light-sensitive proteins in serial crystallography experiments. Journal of Applied Crystallography, 50(3), 932–939. https://doi.org/10.1107/S1600576717006264.

    Article  CAS  Google Scholar 

  68. Schlichting, I., Almo, S. C., Rapp, G., Wilson, K., Petratos, K., Lentfer, A., et al. (1990). Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis. Nature, 345(6273), 309–315.

    Article  CAS  Google Scholar 

  69. Schlichting, I., Berendzen, J., Chu, K., Stock, A. M., Maves, S. A., Benson, D. E., et al. (2000). The catalytic pathway of cytochrome p450cam at atomic resolution. Science, 287(5458), 1615–1622.

    Article  CAS  Google Scholar 

  70. Schlichting, I., & Miao, J. (2012). Emerging opportunities in structural biology with X-ray free-electron lasers. Current Opinion in Structural Biology, 22(5), 613–626. https://doi.org/10.1016/j.sbi.2012.07.015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Schmidt, M. (2013). Mix and inject: Reaction initiation by diffusion for time-resolved macromolecular crystallography. Advances in Condensed Matter Physics, 2013, 10. https://doi.org/10.1155/2013/167276.

    Article  CAS  Google Scholar 

  72. Schmidt, M., Rajagopal, S., Ren, Z., & Moffat, K. (2003). Application of singular value decomposition to the analysis of time-resolved macromolecular X-ray data. Biophysical Journal, 84(3), 2112–2129. https://doi.org/10.1016/S0006-3495(03)75018-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Schoenlein, R. W., Peteanu, L. A., Mathies, R. A., & Shank, C. V. (1991). The first step in vision: Femtosecond isomerization of rhodopsin. Science, 254(5030), 412–415.

    Article  CAS  Google Scholar 

  74. Schotte, F., Cho, H. S., Kaila, V. R., Kamikubo, H., Dashdorj, N., Henry, E. R., et al. (2012). Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proceedings of the National Academy of Sciences of the United States of America, 109(47), 19256–19261. https://doi.org/10.1073/pnas.1210938109.

    Article  PubMed  PubMed Central  Google Scholar 

  75. Schotte, F., Lim, M., Jackson, T. A., Smirnov, A. V., Soman, J., Olson, J. S., et al. (2003). Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science, 300(5627), 1944–1947. https://doi.org/10.1126/science.1078797.

    Article  CAS  PubMed  Google Scholar 

  76. Schubert, R., Kapis, S., Gicquel, Y., Bourenkov, G., Schneider, T. R., Heymann, M., et al. (2016). A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution. IUCrJ, 3(6), 393–401. https://doi.org/10.1107/S2052252516016304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., et al. (2017). A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase. Science Advances, 3(7), e1603042. https://doi.org/10.1126/sciadv.1603042.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Sierra, R. G., Laksmono, H., Kern, J., Tran, R., Hattne, J., Alonso-Mori, R., et al. (2012). Nanoflow electrospinning serial femtosecond crystallography. Acta crystallographica Section D, Biological crystallography, 68(Pt 11), 1584–1587. https://doi.org/10.1107/S0907444912038152.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Å rajer, V., T-y, T., Ursby, T., Pradervand, C., Ren, Z., Adachi, S.-i., et al. (1996). Photolysis of the carbon monoxide complex of myoglobin: Nanosecond time-resolved crystallography. Science, 274(5293), 1726.

    Article  Google Scholar 

  80. Stagno, J. R., Liu, Y., Bhandari, Y. R., Conrad, C. E., Panja, S., Swain, M., et al. (2017). Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature, 541(7636), 242–246. https://doi.org/10.1038/nature20599.

    Article  CAS  PubMed  Google Scholar 

  81. Stellato, F., Oberthur, D., Liang, M., Bean, R., Gati, C., Yefanov, O., et al. (2014). Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCrJ, 1(Pt 4), 204–212. https://doi.org/10.1107/S2052252514010070.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Suga, M., Akita, F., Hirata, K., Ueno, G., Murakami, H., Nakajima, Y., et al. (2015). Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. Nature, 517(7532), 99–103. https://doi.org/10.1038/nature13991.

    Article  CAS  PubMed  Google Scholar 

  83. Suga, M., Akita, F., Sugahara, M., Kubo, M., Nakajima, Y., Nakane, T., et al. (2017). Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. Nature, 543(7643), 131–135. https://doi.org/10.1038/nature21400.

    Article  CAS  PubMed  Google Scholar 

  84. Sugahara, M., Mizohata, E., Nango, E., Suzuki, M., Tanaka, T., Masuda, T., et al. (2015). Grease matrix as a versatile carrier of proteins for serial crystallography. Nature Methods, 12(1), 61–63. https://doi.org/10.1038/nmeth.3172.

    Article  CAS  PubMed  Google Scholar 

  85. Sugahara, M., Nakane, T., Masuda, T., Suzuki, M., Inoue, S., Song, C., et al. (2017). Hydroxyethyl cellulose matrix applied to serial crystallography. Scientific Reports, 7(1), 703. https://doi.org/10.1038/s41598-017-00761-0.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Sugahara, M., Song, C., Suzuki, M., Masuda, T., Inoue, S., Nakane, T., et al. (2016). Oil-free hyaluronic acid matrix for serial femtosecond crystallography. Scientific Reports, 6, 24484. https://doi.org/10.1038/srep24484.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Tenboer, J., Basu, S., Zatsepin, N., Pande, K., Milathianaki, D., Frank, M., et al. (2014). Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science, 346(6214), 1242–1246. https://doi.org/10.1126/science.1259357.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Terwilliger, T. C., & Berendzen, J. (1995). Difference refinement: Obtaining differences between two related structures. Acta Crystallographica. Section D, Biological Crystallography, 51(Pt 5), 609–618.

    Article  CAS  Google Scholar 

  89. Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., et al. (2017). Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate. Nature Communications, 8(1), 1585. https://doi.org/10.1038/s41467-017-01702-1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Umena, Y., Kawakami, K., Shen, J.-R., & Kamiya, N. (2011). Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature, 473, 55. https://doi.org/10.1038/nature09913.

    Article  CAS  PubMed  Google Scholar 

  91. Ursby, T., & Bourgeois, D. (1997). Improved estimation of structure-factor difference amplitudes from poorly accurate data. Acta Crystallogr. Sect. A, 53(5), 564–575. https://doi.org/10.1107/S0108767397004522.

    Article  Google Scholar 

  92. Weierstall, U., James, D., Wang, C., White, T. A., Wang, D., Liu, W., et al. (2014). Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nature Communications, 5, 3309. https://doi.org/10.1038/ncomms4309.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Weierstall, U., Spence, J. C., & Doak, R. B. (2012). Injector for scattering measurements on fully solvated biospecies. The Review of Scientific Instruments, 83(3), 035108. https://doi.org/10.1063/1.3693040.

    Article  CAS  PubMed  Google Scholar 

  94. Weinert, T., Olieric, N., Cheng, R., Brunle, S., James, D., Ozerov, D., et al. (2017). Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nature Communications, 8(1), 542. https://doi.org/10.1038/s41467-017-00630-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Wickstrand, C., Dods, R., Royant, A., & Neutze, R. (2015). Bacteriorhodopsin: Would the real structural intermediates please stand up? Biochimica et Biophysica Acta, 1850(3), 536–553. https://doi.org/10.1016/j.bbagen.2014.05.021.

    Article  CAS  PubMed  Google Scholar 

  96. Wohri, A. B., Katona, G., Johansson, L. C., Fritz, E., Malmerberg, E., Andersson, M., et al. (2010). Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction. Science, 328(5978), 630–633.

    Article  Google Scholar 

  97. Yano, J., Kern, J., Irrgang, K. D., Latimer, M. J., Bergmann, U., Glatzel, P., et al. (2005). X-ray damage to the Mn4Ca complex in single crystals of photosystem II: A case study for metalloprotein crystallography. Proceedings of the National Academy of Sciences of the United States of America, 102(34), 12047–12052.

    Article  CAS  Google Scholar 

  98. Yeremenko, S., van Stokkum, I. H. M., Moffat, K., & Hellingwerf, K. J. (2006). Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy. Biophysical Journal, 90(11), 4224–4235. https://doi.org/10.1529/biophysj.105.074765.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Young, I. D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F. D., Koroidov, S., et al. (2016). Structure of photosystem II and substrate binding at room temperature. Nature, 540(7633), 453–457.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Martin Weik .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Colletier, JP., SchirĂ², G., Weik, M. (2018). Time-Resolved Serial Femtosecond Crystallography, Towards Molecular Movies of Biomolecules in Action. In: Boutet, S., Fromme, P., Hunter, M. (eds) X-ray Free Electron Lasers. Springer, Cham. https://doi.org/10.1007/978-3-030-00551-1_11

Download citation

Publish with us

Policies and ethics