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Том 15   Выпуск 2   Год 2020
Петрова Т.Е., Лунин В.Ю.

Определение структуры биологических макромолекулярных частиц с использованием рентгеновских лазеров. Достижения и перспективы

Математическая биология и биоинформатика. 2020;15(2):195-234.

doi: 10.17537/2020.15.195.

Список литературы

  1. Lunin V.Y., Lunina N.L., Petrova T.E. Single Particle Study by X-Ray Diffraction: Crystallographic Approach. Mathematical Biology and Bioinformatics. 2019;14(S):t44–t60. doi: 10.17537/2019.14.t44
  2. Landau L.D., Lifshitz E.M. Mechanics, 3d edition. Butterworth-Heinemann; 1976. 224 p.
  3. Landau L.D., Lifshitz E.M. The Classical Theory of Fields, 4th edition. Butterworth-Heinemann; 1980. 402 p.
  4. Urzhumtsev A.G., Lunin V.Y. Introduction to crystallographic refinement of macromolecular atomic models. Crystallography Reviews. 2019;25:164–262. doi: 10.1080/0889311X.2019.1631817
  5. Blundell T.L., Johnson L.N. Protein crystallography. New York, San Francisco: Academic Press, 1976.
  6. Serdyuk I.N., Zaccai N.R., Zaccai J. Methods in Molecular Biophysics. Structure. Function. Dynamics. Cambridge University Press, 2007. ISBN-13: 978-0521815246. doi: 10.1017/CBO9780511811166
  7. Rupp B. Biomolecular Crystallography: Principles, Practice, and Applications to Structural Biology. New York: Garland Science, Taylor and Francis Group, 2010. P. xxi + 809.
  8. Urzhumtseva L., Klaholz B., Urzhumtsev A. On effective and optical resolutions of diffraction data sets. Acta Crystallographica D. 2013;69:1921–1934. doi: 10.1107/S0907444913016673
  9. Van Heel M., Schatz M. Fourier shell correlation threshold criteria. J. Struct. Biol. 2005;151:250–262. doi: 10.1016/j.jsb.2005.05.009
  10. Van Heel M., Schatz M. Reassessing the Revolution’s Resolutions. bioRxiv. 2017:224402. doi: 10.1101/224402
  11. Sobolev E., Zolotarev S., Giewekemeyer K., Bielecki J., Okamoto K., Reddy H.K.N, Andreasson J., Ayyer K., Barak I., Bari S. et al. Megahertz single-particle imaging at the European XFEL. Communications Physics. 2020;3:97. doi: 10.1038/s42005-020-0362-y
  12. Georgescu I. The first decade of XFELs. Nature Reviews Physics. 2020;2:345. doi: 10.1038/s42254-020-0204-6
  13. Margaritondo G., Ribič P.R. A simplified description of X-ray free-electron lasers. J. Synchrotron Radiation. 2011;18:101–108. doi: 10.1107/S090904951004896X
  14. Pellegrini C. The history of X-ray free-electron lasers. Eur. Phys. J. H. 2012;37:659–708. doi: 10.1140/epjh/e2012-20064-5
  15. White T.A., Mariani V., Brehm W., Yefanov O., Barty A, Beyerlein K.R., Chervinskii F., Galli L., Gati C., Nakane T. et al. Recent developments in CrystFEL. J. Appl. Cryst. 2016;49:680–689. doi: 10.1107/S1600576716004751
  16. Chapman H.N., Fromme P., Barty A., White T.A., Kirian R.A., Aquila A., Hunter M.S., Schulz J., DePonte D.P., Weierstall U. et al. Femtosecond X-ray protein nanocrystallography. Nature. 2011;470:73–77. doi: 10.1038/nature09750
  17. Boutet S., Lomb L., Williams G.J., Barends T.R., Aquila A., Doak R.B., Weierstall U., DePonte D.P., Steinbrener J., Shoeman R.L. et al. High-resolution protein structure determination by serial femtosecond crystallography. Science. 2012;337:362–364. doi: 10.1126/science.1217737
  18. Kern J., Alonso-Mori R., Hellmich J., Tran R., Hattne J., Laksmono H., Glöckner C., Echols N., Sierra R.G., Sellberg J. et al. Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proc Natl Acad Sci USA. 2012;109:9721–9726. doi: 10.1073/pnas.1204598109
  19. Kupitz C., Basu S., Grotjohann I., Fromme R., Zatsepin N.A., Rendek K.N., Hunter M.S., Shoeman R.L., White T.A., Wang D. et al. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature. 2014;513:261–265. doi: 10.1038/nature13453
  20. Sierra R.G., Gati C., Laksmono H., Dao E.H., Gul S., Fuller F., Kern J., Chatterjee R., Ibrahim M., Brewster A.S. et al. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat. Methods. 2016;13:59–62. doi: 10.1038/nmeth.3667
  21. Liu W., Wacker D., Gati C., Han G.W., James D., Wang D., Nelson G., Weierstall U., Katritch V., Barty A. et al. Serial femtosecond crystallography of G protein-coupled receptors. Science. 2013;342:1521–1524. doi: 10.1126/science.1244142
  22. Kang Y., Zhou X.E., Gao X., He Y., Liu W., Ishchenko A., Barty A., White T.A., Yefanov O., Han G.W. et al. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature. 2015;523:561–567. doi: 10.1038/nature14656
  23. Johansson L.C., Arnlund D., White T.A., Katona G., DePonte D.P., Weierstall U., Doak R.B., Shoeman R.L., Lomb L., Malmerberg E. et al. Lipidic phase membrane protein serial femtosecond crystallography. Nat Methods. 2012;9:263–265. doi: 10.1038/nmeth.1867
  24. Johansson L.C., Arnlund D., Katona G., White T.A., Barty A., DePonte D.P., Shoeman R.L., Cecilia Wickstrand C., Sharma A., Williams G.J. et al. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat. Commun. 2013;4:2911. doi: 10.1038/ncomms3911
  25. Weierstall U., James D., Wang C., White T.A., Wang D., Liu W., Spence J.C.H., Doak R.B., Nelson G., Fromme P. et al. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat. Commun. 2014;5:3309. doi: 10.1038/ncomms4309
  26. Gati C., Oberthuer D., Yefanov O., Bunker R.D., Stellato F., Chiu E., Yeh S.M., Aquila A., Basu S., Bean R. et al. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. Proc. Natl. Acad. Sci. USA. 2017;114:2247–2252. doi: 10.1073/pnas.1609243114
  27. Grünbein M.L., Bielecki J., Gorel A., Stricker M., Bean R., Cammarata M., Dörner K., Fröhlich L., Hartmann E., Hauf S. et al. Megahertz data collection from protein microcrystals at an X-ray free-electron laser. Nat. Commun. 2018;9:3487. doi: 10.1038/s41467-018-05953-4
  28. Wiedorn M.O., Oberthür D., Bean R., Schubert R., Werner N., Abbey B., Aepfelbacher M., Adriano L., Allahgholi A., Al-Qudami N. et al. Megahertz serial crystallography. Nat. Commun. 2018;9:4025. doi: 10.1038/s41467-018-06156-7
  29. Gisriel C., Coe J., Letrun R., Yefanov O.M., Luna-Chavez C., Stander N.E., Lisova S., Mariani V., Kuhn M., Aplin S. et al. Membrane protein megahertz crystallography at the European XFEL. Nat. Commun. 2019;10:5021. doi: 10.1038/s41467-019-12955-3
  30. Glownia J.M., Cryan J., Andreasson J., Belkacem A., Berrah N., Blaga C., Bostedt C., Bozek J., DiMauro L., Fang L. et al. Time-resolved pump-probe experiments at the LCLS. Opt. Express. 2010;18:17620–17630. doi: 10.1364/OE.18.017620
  31. Aquila A., Hunter M.S., Doak R.B., Kirian R.A., Fromme P., White T.A., Andreasson J., Arnlund D., Bajt S., Barends T.R.M. et al. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt. Express. 2012;20:2706–2716. doi: 10.1364/OE.20.002706
  32. Tenboer J., Basu S., Nadia Zatsepin N., Pande K., Milathianaki D., Frank M., Hunter M., Boutet S., Williams G.J., Koglin J.E. et al. Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science. 2014;346:1242–1246. doi: 10.1126/science.1259357
  33. Barends T.R., Foucar L. , Ardevol A., Nass K., Aquila A., Botha S., Doak R.B., Falahati K., Hartmann E., Hilpert M. et al. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science. 2015;350:445–450. doi: 10.1126/science.aac5492
  34. Pande K., Hutchison C.D.M., Groenhof G., Aquila A., Robinson J.S., Tenboer J., Basu S., Boutet S., DePonte D.P., Liang M. et al. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science. 2016;352:725–729. doi: 10.1126/science.aad5081
  35. Kubo M., Nango E., Tono K., Kimura T., Owada S., Song C., Mafuné F., Miyajima K., Takeda Y., Kohno J.Y. et al. Nanosecond pump–probe device for time-resolved serial femtosecond crystallography developed at SACLA. J. Synchrotron Radiat. 2017;24:1086–1091. doi: 10.1107/S160057751701030X
  36. Pandey S., Bean R., Sato T., Poudyal I., Bielecki J., Villarreal J.C., Yefanov O., Mariani V., White T.A., Kupitz C. et al. Time-resolved serial femtosecond crystallography at the European XFEL. Nat. Methods. 2020;17:73–78. doi: 10.1126/science.aad5081
  37. Lunin V.Y., Lunina N.L., Petrova T.E. The biological crystallography without crystals. Mathematical Biology and Bioinformatics. 2017. 12:55–72. doi: 10.17537/2017.12.55
  38. Neutze R., Wouts R., van der Spoel D., Weckert E., Hajdu J. Potential for biomolecular imaging with femtosecond X-ray pulses. Nature. 2000;406:752–757. doi: 10.1038/35021099
  39. Cryan J.P., Glownia J.M., Andreasson J., Belkacem A., Berrah N., Blaga C.I., Bostedt C., Bozek J., Buth C., DiMauro L.F. et al. Auger electron angular distribution of double core-hole states in the molecular reference frame. Phys. Rev. Lett. 2010;105:083004. doi: 10.1103/PhysRevLett.105.083004
  40. Chapman H.N., Yefanov O.M., Ayyer K., White T.A., Barty A., Morgan A., Mariani V., Oberthuer D., Pande K. Continuous diffraction of molecules and disordered molecular crystals. J. Appl. Crystallogr. 2017;50:1084–1103. doi: 10.1107/S160057671700749X
  41. Hau-Riege S.P., London R.A., Szoke A. Dynamics of biological molecules irradiated by short x-ray pulses. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 2004;69:051906. doi: 10.1103/PhysRevE.69.051906
  42. Lorenz U., Kabachnik N.M., Weckert E., Vartanyants I.A. Impact of ultrafast electronic damage in single particle x-ray imaging experiments. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 2012;86:051911. doi: 10.1103/PhysRevE.86.051911
  43. Ziaja B., Jurek Z., Medvedev N., Saxena V., Son S.-K., Santra R. Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser. Photonics. 2015;2:256–269. doi: 10.3390/photonics2010256
  44. Kai T., Moribayashi K. Effects of electron-impact ionization on the damage to biomolecules irradiated by XFEL. Journal of Physics: Conference Series. 2009;163:012035. doi: 10.1088/1742-6596/163/1/012035
  45. Ziaja B., de Castro Antonio R.B., Weckert E., Moeller T. Modelling dynamics of samples exposed to free-electron-laser radiation with Boltzmann equations. Eur. Phys. J. 2006;40:465–480. doi: 10.1140/epjd/e2006-00240-x
  46. Fortmann-Grote C., Buzmakov A., Jurek Z., Loh N.D., Samoylova L., Santra R., Schneidmiller E.A., Tschentscher T., Yakubov S., Yoon C.H. et al. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser. IUCrJ. 2017;4:560–568. doi: 10.1107/S2052252517009496
  47. Caleman C., Bergh M., Scott H.A., Spence J.C., Chapman H.N., Tîmneanu N. Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses. J. Mod. Opt. 2011;58:1486–1497. doi: 10.1080/09500340.2011.597519
  48. Hau-Riege S.P. Nonequilibrium electron dynamics in materials driven by high-intensity x-ray pulses. Phys. Rev. E. 2013;87:053102. doi: 10.1103/PhysRevE.87.053102
  49. Akça B., Erzeneoğlu S. The Mass Attenuation Coefficients, Electronic, Atomic, and Molecular Cross-Sections, Effective Atomic Numbers, and Electron Densities for Compounds of Some Biomedically Important Elements at 59.5 keV. Science and Technology of Nuclear Installations. 2014:901465. doi: 10.1155/2014/901465
  50. Zeldin O.B., Gerstel M., Garman E.F. RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography. J. Appl. Cryst. 2013;46:1225–1230. doi: 10.1107/S0021889813011461
  51. Bury C.S., Brooks-Bartlett C., Walsh S.P., Garman E.F. Estimate your dose: RADDOSE-3D. Protein Sci. 2018;27:217–228. doi: 10.1002/pro.3302
  52. Dickerson J.L., McCubbin P.T.N., Garman E.F. RADDOSE-XFEL: femtosecond time-resolved dose estimates for macromolecular X-ray free-electron laser experiments. J. Appl. Cryst. 2020;53:549–560. doi: 10.1107/S1600576720000643
  53. Owen R.L., Rudino-Pinera E., Garman E.F. Experimental determination of the radiation dose limit for cryocooled protein crystals. Proc. Natl. Acad. Sci. USA. 2006;103:4912–4917. doi: 10.1073/pnas.0600973103
  54. de la Mora E., Coquelle N., Bury C.S., Rosenthal M., Holton J.M., Carmichael I., Garman E.F., Burghammer M., Colletier J.P., Weik M. Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Proc. Natl. Acad. Sci. USA. 2020;117:4142–4151. doi: 10.1073/pnas.1821522117
  55. Huang B., Bates M., Zhuang, X. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 2009;78:993–1016. doi: 10.1146/annurev.biochem.77.061906.092014
  56. Rodriguez J.A., Xu R., Chen C.-C., Huang Z., Jiang H., Chen A.L., Raines K.S., Pryor A. Jr, Nam D., Wiegart L. et al. Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells. IUCrJ. 2015;2:575–583. doi: 10.1107/S205225251501235X
  57. Howells M.R., Beetz T., Chapman H.N., Cui C., Holton J.M., Jacobsen C.J., Kirz J., Lima E., Marchesini S., Miao H. et al. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. J. Electron Spectrosc. Relat. Phenom. 2009;170:4–12. doi: 10.1016/j.elspec.2008.10.008
  58. Kimura T., Joti Y., Shibuya A., Song C., Kim S., Tono K., Yabashi M., Tamakoshi M., Moriya T., Oshima T. et al. Imaging live cell in micro-liquid enclosure by X-ray laser diffraction. Nat. Commun. 2014;5:3052. doi: 10.1038/ncomms4052
  59. Borek D., Cymborowski M., Machius M., Minor W., Otwinowski Z. Diffraction data analysis in the presence of radiation damage. Acta Crystallogr D. 2010;66:426–436. doi: 10.1107/S0907444909040177
  60. Warkentin M.A., Atakisi H., Hopkins J.B., Walko D., Thorn R.E. Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams. IUCrJ. 2017;4:785–794. doi: 10.1107/S2052252517013495
  61. Lomb L., Barends T.R.M., Kassemeyer S., Aquila A., Epp S.W., Erk B., Foucar L., Hartmann R., Rudek B., Rolles D. et al. Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys. Rev. B. Condens. Matter Mater. Phys. 2011;84:214111. doi: 10.1103/PhysRevB.84.214111
  62. Young L., Kanter E.P., Krässig B., Li Y., March A.M., Pratt S.T., Santra R., Southworth S.H., Rohringer N., Dimauro L.F. et al. Femtosecond electronic response of atoms to ultra-intense X-rays. Nature. 2010;466:56–61. doi: 10.1038/nature09177
  63. Erk B., Rolles D., Foucar L., Rudek B., Epp S.W., Cryle M., Bostedt C., Schorb S., Bozek J., Rouzee A. et al. Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. Phys. Rev. Lett. 2013;110:053003. doi: 10.1103/PhysRevLett.110.053003
  64. Fukuzawa H., Son S.K., Motomura K., Mondal S., Nagaya K., Wada S., Liu X.J., Feifel R., Tachibana T., Ito Y. et al. Deep inner-shell multiphoton ionization by intense X-ray free-electron laser pulses. Phys. Rev. Lett. 2013;110:173005. doi: 10.1103/PhysRevLett.110.173005
  65. Rudenko A., Inhester L., Hanasaki K., Li X., Robatjazi S.J., Erk B., Boll R., Toyota K., Hao Y., Vendrell O. et al. Femtosecond response of polyatomic molecules to ultra-intense hard X-rays. Nature. 2017;546:129–132. doi: 10.1038/nature22373
  66. Takanashi T., Nakamura K., Kukk E., Motomura K., Fukuzawa H., Nagaya K., Wada S.-I., Kumagai Y., Iablonskyi D., Ito Y. et al. Ultrafast Coulomb explosion of a diiodomethane molecule induced by an X-ray free-electron laser pulse. Phys. Chem. Chem. Phys. 2017;19:19707–19721. doi: 10.1039/C7CP01669G
  67. Motomura K., Fukuzawa H., Son S.-K., Mondal S., Tachibana T., Ito Y., Kimura M., Nagaya K., Sakai T., Matsunami K. Sequential multiphoton multiple ionization of atomic argon and xenon irradiated by x-ray free-electron laser pulses from SACLA. J. Phys. B. 2013;46:164024. doi: 10.1088/0953-4075/46/16/164024
  68. Fukuzawa H., Takanashi T., Kukk E., Motomura K., Wada S.I., Nagaya K., Ito Y., Nishiyama T., Nicolas C., Kumagai Y. et al. Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2. Nat. Commun. 2019;10:2186. doi: 10.1038/s41467-019-10060-z
  69. Wallner M., Eland J.H.D., Squibb R.J., Andersson J., Roos A.H., Singh R., Talaee O., Koulentianos D., Piancastelli M.N., Simon M. et al. Coulomb explosion of CD3I induced by single photon deep inner-shell ionization. Sci. Rep. 2020;1:1246.
  70. Murphy B.F., Osipov T., Jurek Z., Fang L., Son S.K., Mucke M., Eland J.H., Zhaunerchyk V., Feifel R., Avaldi L. et al. Femtosecond X-ray-induced explosion of C60 at extreme intensity. Nat. Commun. 2014;5:4281. doi: 10.1038/ncomms5281
  71. Berrah N., Sanchez-Gonzalez A., Jurek Z., Obaid R. , Xiong H., Squibb R.J., Osipov T., Lutman A., Fang L., Barillot T. et al. Author Correction: Femtosecond-resolved observation of the fragmentation of buckminsterfullerene following X-ray multiphoton ionization. Nat. Phys. 2019;15:1301. doi: 10.1038/s41567-019-0706-2
  72. Nass K., Foucar L., Barends T.R.M., Hartmann E., Botha S., Shoeman R.L., Doak R.B., Alonso-Mori R., Aquila A., Bajt, S. et al. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. J. Synchrotron Rad. 2015;22:225–238. doi: 10.1107/S1600577515002349
  73. Wang J. Destruction-and-diffraction by X-ray free-electron laser. Protein Sci. 2016;25:1585–1592. doi: 10.1002/pro.2959
  74. Inoue I., Inubushi Y., Sato T., Tono K., Katayama T., Kameshima T., Ogawa K., Togashi T., Owada S., Amemiya Y. et al. Observation of femtosecond X-ray interactions with matter using an X-ray-X-ray pump-probe scheme. Proc. Natl. Acad. Sci. USA. 2016;113:1492–1497. doi: 10.1073/pnas
  75. Nass K., Gorel A., Abdullah M.M., Martin A.V., Kloos M., Marinelli A., Aquila A., Barends T.R.M., Decker F.J., Doak B. et al. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat. Commun. 2020;11:1814. doi: 10.1038/s41467-020-15610-4
  76. Opara N.L., Mohacsi I., Makita M., Castano-Diez D., Diaz A., Juranić P., Marsh M., Meents A., Milne C.J., Mozzanica A. et al. Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals. Struct. Dyn. 2018;5:054303. doi: 10.1063/1.5050618
  77. Munke A., Andreasson J., Aquila A., Awel S., Ayyer K., Barty A., Bean R.J., Berntsen P., Bielecki J., Boutet S. et al. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Sci. Data. 2016;3:160064. doi: 10.1038/sdata.2016.64
  78. Kurta R.P., Donatelli J.J., Yoon C.H., Berntsen P., Bielecki J., Daurer B.J., DeMirci H., Fromme P., Hantke M.F., Maia F.R.N.C. et al. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses. Phys. Rev. Lett. 2017;119:158102. doi: 10.1103/PhysRevLett.119.158102
  79. Östlin C., Tîmneanu N., Jönsson H.O., Ekeberg T., Martin A.V., Caleman C. Reproducibility of single protein explosions induced by X-ray lasers. Phys. Chem. Chem. Phys. 2018;20:12381–12389. doi: 10.1039/C7CP07267H
  80. Östlin C., Timneanu N., Caleman C., Martin A.V. Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers? Struct. Dyn. 2019;6:044103. 
  81. Nass K. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr. D. Struct. Biol. 2019;75:211–218. doi: 10.1107/S2059798319000317
  82. Campbell J.L., Papp T. Widths of the atomic K-N7 levels. At. Data Nucl. Data Tables. 2001;77:1–56. doi: 10.1006/adnd.2000.0848
  83. Son S.-K., Young L., Santra R. Impact of hollow-atom formation on coherent x-ray scattering at high intensity. Phys. Rev. A. 2011;83:033402. doi: 10.1103/PhysRevA.83.033402
  84. Lunin V.Y., Grum-Grzhimailo A.N., Gryzlova E.V., Sinitsyn D.O., Petrova T.E., Lunina N.L., Balabaev N.K., Tereshkina K.B., Stepanov A.S., Krupyanskii Y.F. Efficient calculation of diffracted intensities in the case of non-stationary scattering by biological macromolecules under XFEL pulse. Acta Crystallographica D. 2015;71:293–303. doi: 10.1107/S1399004714025450
  85. Chapman H.N., Barty A., Bogan M., Boutet S., Frank M., Hau-Riege S.P., Marchesini S. et al. Femtosecond diffractive imaging with a soft-X-ray free-electron laser. Nat. Phys. 2006;2:839–843. doi: 10.1038/nphys461
  86. Seibert M.M., Ekeberg T., Maia F.R., Svenda M., Andreasson J., Jönsson O., Odić D., Iwan B., Rocker A., Westphal D. et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature. 2011;470:78–81. doi: 10.1038/nature09748
  87. Hantke M.F., Hasse D., Maia F.R.N.C., Ekeberg T., John K., Svenda M., Loh N.D., Martin A.V., Timneanu N., Larsson D.S.D. et al. High-throughput imaging of heterogeneous cell organelles with an x-ray laser. Nat. Photonics. 2014;8:943–949. doi: 10.1038/nphoton.2014.27
  88. van der Schot G., Svenda M., Maia F.R.N.C., Hantke M., DePonte D.P., Seibert M.M., Aquila A., Schulz J., Kirian R., Liang M., Stellato F. et al. Imaging single cells in a beam of live cyanobacteria with an x-ray laser. Nat. Commun. 2015;6:5704. doi: 10.1038/ncomms6704
  89. Ekeberg T., Svenda M., Abergel C., Maia F.R.N.C., Seltzer V., Claverie J.M., Hantke M., Jönsson O., Nettelblad C., van der Schot G. et al. Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser. Phys. Rev. Lett. 2015;114:098102. doi: 10.1103/PhysRevLett.114.098102
  90. Reddy H.K.N., Yoon C.H., Aquila A., Awel S., Ayyer K., Barty A., Berntsen P., Bielecki J., Bobkov S., Bucher M. Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source. Sci. Data. 2017;4:170079. doi: 10.1038/sdata.2017.79
  91. Daurer B.J., Okamoto K., Bielecki J., Maia F.R.N.C., Muhlig K., Seibert M.M., Hantke M.F., Nettelblad C., Benner W.H., Svenda M. et al. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ. 2017;4:251–262. doi: 10.1107/S2052252517003591
  92. Lundholm I.V., Sellberg J.A., Ekeberg T., Hantke M.F., Okamoto K., van der Schot G., Andreasson J., Barty A., Bielecki J., Bruza P. et al. Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. IUCrJ. 2018;5:531–541. doi: 10.1107/S2052252518010047
  93. DePonte D.P., Weierstall U., Schmidt K., Warner J., Starodub D., Spence J.C.H., Doak R.B. Gas dynamic virtual nozzle for generation of microscopic droplet streams. J. Phys. D Appl. Phys. 2008;41:195505. doi: 10.1088/0022-3727/41/19/195505
  94. Yamashita M., Fenn J.B. Electrospray ion source. Another variation on the free-jet theme. J. Phys. Chem. 1984;88:4451–4459. doi: 10.1021/j150664a002
  95. Gañán-Calvo A.M., Montanero J.M. Revision of capillary cone-jet physics: Electrospray and flow focusing. Phys. Rev. E. 2009;79:066305. doi: 10.1103/PhysRevE.79.066305
  96. Hantke M.F., Bielecki J., Kulyk O., Westphal D., Larsson D.S.D., Svenda M., Reddy H.K.N., Kirian R.A., Andreasson J., Hajdu J. et al. Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams. IUCrJ. 2018;5:673–680. doi: 10.1107/S2052252518010837
  97. Bielecki J., Hantke M.F., Daurer B.J., Reddy H.K.N., Hasse D., Larsson D.S.D., Gunn L.H., Svenda M., Munke A., Sellberg J.A. et al. Electrospray sample injection for single-particle imaging with x-ray lasers. Sci. Adv. 2019;5:eaav8801. doi: 10.1126/sciadv.aav8801
  98. Miao J., Hodgson K.O., Ishikawa T., Larabell C.A., LeGros M.A., Nishino Y. Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction. Proc. Natl. Acad. Sci. USA. 2003;100:110–112. doi: 10.1073/pnas.232691299
  99. Shapiro D., Thibault P., Beetz T., Elser V., Howells M., Jacobsen C., Kirz J., Lima E., Miao H., Neiman A.M. et al. Biological imaging by soft x-ray diffraction microscopy. Proc. Natl. Acad. Sci. USA. 2005;102:15343–15346. doi: 10.1073/pnas.0503305102
  100. Song C., Tono K., Park J., Ebisu T., Kim S., Shimada H., Kim S., Gallagher-Jones M., Nam D., Sato T. et al. Multiple application X-ray imaging chamber for single-shot diffraction experiments with femtosecond X-ray laser pulses. J. Appl. Cryst. 2014;47:188–197. doi: 10.1107/S1600576713029944
  101. Robinson I., Schwenke J., Yusuf M., Estandarte A., Zhang F., Chen B., Clark J., Song Ch., Nam D., Joti Y. et al. Towards single particle imaging of human chromosomes at SACLA. J. Phys. B: At. Mol. Opt. Phys. 2015;48:244007. doi: 10.1088/0953-4075/48/24/244007
  102. Seuring C., Ayyer K., Filippaki E., Barthelmess M., Longchamp J.N., Ringler P., Pardini T., Wojtas D.H., Coleman M.A., Dörner K. et al. Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene. Nat. Commun. 2018;9:1836. doi: 10.1038/s41467-018-04116-9
  103. Takayama Y., Yonekura K. Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy. Acta Crystallogr. A. 2016;72:179–189. doi: 10.1107/S2053273315023980
  104. Altarelli M. The European X-ray free-electron laser facility in Hamburg. Nucl. Instrum. Methods. Phys. Res. B. 2011;269:2845–2849. doi: 10.1016/j.nimb.2011.04.034
  105. von Ardenne B., Mechelke M., Grubmüller H. Structure determination from single molecule X-ray scattering with three photons per image. Nat. Commun. 2018;9:2375. doi: 10.1038/s41467-018-04830-4
  106. Allahgholi A., Becker J., Bianco L., Bradford R., Delfs A., Dinapoli R., Goettlicher P., Gronewald M., Graafsma H., Greiffenberg D. et al. The adaptive gain integrating pixel detector. J. Instrum. 2016;11:C02066. doi: 10.1088/1748-0221/11/02/C02066
  107. Mezza D., Allahgholi A., Arino-Estrada G., Bianco L., Delfs A., Dinapoli R., Goettlicher P., Graafsma H., Greiffenberg D., Hirsemann H. et al. Characterization of AGIPD1.0: the full scale chip. Nucl. Instrum. Methods Phys. Res. A. 2016;838:39–46. doi: 10.1016/j.nima.2016.09.007
  108. Allahgholi A., Becker J., Delfs A., Dinapoli R., Goettlicher P., Greiffenberg D., Henrich B., Hirsemann H., Kuhn M., Klanner R. et al. The Adaptive Gain Integrating Pixel Detector at the European XFEL. J. Synchrotron Radiat. 2019;26:74–82. doi: 10.1107/S1600577518016077
  109. Philipp H.T., Hromalik M., Tate M., Koerner L., Gruner S.M. Pixel array detector for X-ray free electron laser experiments. Nucl. Instrum. Methods Phys. Res. A. 2011;649:67–69. doi: 10.1016/j.nima.2010.11.189
  110. Blaj G., Caragiulo P., Carini G., Dragone A., Haller G., Hart P., Hasi J., Herbst R., Kenney C., Markovic B. et al. Future of ePix detectors for high repetition rate FELs. AIP Conference Proceedings. 2016;1741:040012. doi: 10.1063/1.495288.
  111. Leonarski F., Redford S., Mozzanica A., Lopez-Cuenca C., Panepucci E., Nass K., Ozerov D., Vera L., Olieric V., Buntschu D. et al. Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector. Nat. Methods. 2018;15:799–804. doi: 10.1038/s41592-018-0143-7
  112. Redford S., Bergamaschi A., Brückner M., Cartier S., Dinapoli R., Ekinci Y., Fröjdh E., Greiffenberg D., Mayilyan D., Mezza D. et al. Calibration status and plans for the charge integrating JUNGFRAU pixel detector for SwissFEL. J. Instrum. 2016;11:C11013. doi: 10.1088/1748-0221/11/11/C11013
  113. Goettlicher P., Allahgholi A., Becker J., Bianco L., Delfs A., Dinapoli R., Fretwurst E., Fretwurst E., Graafsma H., Greiffenberg D. et al. AGIPD, the electronics for a high speed X-ray imager at the Eu-XFEL. In: Proceedings of TIPP2014 – Technology and Instrumentation in Particle Physic. 2014. 253 p.
  114. Mancuso A.P., Aquila A., Batchelor L., Bean R.J., Bielecki J., Borchers G., Doerner K., Giewekemeyer K., Graceffa R., Kelsey O.D. et al. The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation. J. Synchrotron Radiat. 2019;26:660–676. doi: 10.1107/S1600577519003308
  115. Gasthuber M., Dietrich S., Malka J., Kuhn M., Ensslin U., Wrona K., Szuba J. Online & Offline data storage and data processing at the European XFEL facility. J. Phys.: Conf. Ser. 2017;898:062049. doi: 10.1088/1742-6596/898/6/062049
  116. Hauf S., Heisen B., Aplin S., Beg M., Bergemann M., Bondar V., Boukhelef D., Danilevsky C., Ehsan W., Essenov S. et al. The Karabo distributed control system. J. Synchrotron Radiat. 2019;26:1448–1461. doi: 10.1107/S1600577519006696
  117. Fangohr H., Beg M., Bondar V., Boukhelef D., Brockhauser S., Danilevski C., Ehsan W., Esenov S.G., Flucke G., Giovanetti G. et al. Data Analysis Support in Karabo at European XFEL. In: Proc. 16th Int. Conf. on Accelerator and Large Experimental Control Systems (ICALEPCS‘17) (Barcelona, Spain, Oct. 2017). 2018:245–252. doi: Cite to nonCR doi: 10.18429/JACoW-ICALEPCS2017-TUCPA01
  118. Rose M., Bobkov S., Ayyer K., Kurta R.P., Dzhigaev D., Kim Y.Y., Morgan A.J., Yoon C.H., Westphal D., Bielecki J. et al. Single-particle imaging without symmetry constraints at an X-ray free-electron laser. IUCrJ. 2018;5:727–736. doi: 10.1107/S205225251801120X
  119. Daurer B.J., Hantke M.F., Nettelblad C, Maia F.R.N.C. Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time. J. Appl. Cryst. 2016;49:1042–1047. doi: 10.1107/S1600576716005926
  120. Barty A., Kirian R.A., Maia F.R.N.C., Hantke M., Yoon C.H., White T.A., Chapman H. Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J. Appl. Cryst. 2014;47:1118–1131. doi: 10.1107/S1600576714007626
  121. Foucar L., Barty A., Coppola N., Hartmann R., Holl P., Hoppe U., Kassemeyer S., Kimmel N., Küpper J., Scholz et al. CASS–CFEL-ASG software suite. Comput. Phys. Commun. 2012;183:2207–2213. doi: 10.1016/j.cpc.2012.04.023
  122. Foucar L. CFEL-ASG Software Suite (CASS): usage for free-electron laser experiments with biological focus. J. Appl Crystallogr. 2016;49:1336–1346. doi: 10.1107/S1600576716009201
  123. Damiani D., Dubrovin M., Gaponenko I., Kroeger W., Lane T.J., Mitra A., O'Grady C.P., Salnikov A., Sanchez-Gonzalez A., Schneider D., Yoon C.H. Linac Coherent Light Source data analysis using psana. J. Appl. Cryst. 2016;49:672–679. doi: 10.1107/S1600576716004349
  124. Coifman R.R., Lafon S. Diffusion maps. Appl. Comput. Harmon. Anal. 2006;21:5–30. doi: 10.1016/j.acha.2006.04.006
  125. Giannakis D., Schwander P., Ourmazd A. The symmetries of image formation by scattering. I. Theoretical framework. Opt. Express. 2012;20:12799–12826. doi: 10.1364/OE.20.012799
  126. Yoon C.H., Schwander P., Abergel C., Andersson I., Andreasson J., Aquila A., Bajt S., Barthelmess M., Barty A., Bogan M.J., Bostedt C., Bozek J. et al. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. Opt. Express. 2011;19:16542–16549. doi: 10.1364/OE.19.016542
  127. Giewekemeyer K., Aquila A., Loh N.D., Chushkin Y., Shanks K.S., Weiss J.T., Tate M.W., Philipp H.T., Stern S., Vagovic P. et al. Experimental 3D coherent diffractive imaging from photon-sparse random projections. IUCrJ. 2019;20:357–365. doi: 10.1107/S2052252519002781
  128. Ayyer K., Morgan A.J., Aquila A., DeMirci H., Hogue B.G., Kirian R.A., Xavier P.L., Yoon C.H., Chapman H.N., Barty A. Low-signal limit of X-ray single particle diffractive imaging. Opt Express. 2019;27:37816–37833. doi: 10.1364/OE.27.037816
  129. Loh N.D., Elser V. Reconstruction algorithm for single-particle diffraction imaging experiments. Phys. Rev. E. 2009;80:026705. doi: 10.1103/PhysRevE.80.026705
  130. Ayyer K., Lan Ti-Yen, Elser V., Loh N.D. Dragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imaging. J. Appl. Crystallogr. 2016;49:1320–1335. doi: 10.1107/S1600576716008165
  131. Yoon C.H., Yurkov M.V., Schneidmiller E.A., Samoylova L., Buzmakov A., Jurek Z., Ziaja B., Santra R., Loh N.D., Tschentscher T. et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. Sci. Rep. 2016;6:24791. doi: 10.1038/srep24791
  132. Hantke M.F., Ekeberg T., Maia F.R.H.C. A simulation tool for flash X-ray imaging. J. Appl. Cryst. 2016;49:1356–1362. doi: 10.1107/S1600576716009213
  133. Lunin V.Y., Lunina N.L., Petrova T.E. Mask-Based Approach in Phasing and Restoring of Single-Particle Diffraction Data. Mathematical Biology and Bioinformatics. 2020;15(S):t1–t20. doi: 10.17537/2020.15.t1
  134. Bricogne G. Geometric sources of redundancy in intensity data and their use for phase determination. Acta Crystallographica A. 1974;30:395–405. doi: 10.1107/S0567739474010722
  135. Bricogne G. Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallographica A. 1976;32:832–847. doi: 10.1107/S0567739476001691
  136. Lunin V.Y. Use of the fast differentiation algorithm for phase refinement in protein crystallography. Acta Crystallographica. A. 1985;41:551–556. doi: 10.1107/S0108767385001209
  137. Podjarny A.D., Rees B., Urzhumtsev A.G. Density modification in X-ray crystallography. In: Methods in Molecular Biology, Crystallographic Methods and Protocols. Eds. Jones C., Milloy B, Sanderson M.R. Totowa, New Jersey: Humana Press, 1996. P. 205–226. (Methods in Molecular Biology, Vol. 56). doi: 10.1385/0-89603-259-0:205
  138. Zhang K.Y.J., Cowtan K.D., Main P. Phase improvement by iterative density modification. In: International Tables for Crystallography. Vol. F. Eds. Arnold E., Himmel D.M., Rossmann M.G. Chichester: John Wiley and Sons, 2012. P. 385–400. doi: 10.1107/97809553602060000847
  139. Fienup J.R. Reconstruction of an object from the modulus of its Fourier transform. Optics Letters. 1978;3(1):27–29. doi: 10.1364/OL.3.000027
  140. Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymology. 1985;115:90–111. doi: 10.1016/0076-6879(85)15009-3
  141. Abrahams J.P. Bias reduction in phase refinement by modified interference functions: introducing the g-correction. Acta Crystallographica D. 1997;53:371–376. doi: 10.1107/S0907444996015272
  142. Oslányi G., Sütő A. Ab initio structure solution by charge flipping. Acta Crystallographica A. 2004;60:134–141. doi: 10.1107/S0108767303027569
  143. Marchesini S. A unified evaluation of iterative projection algorithms for phase retrieval. Rev. Sci. Instrum. 2007;78:011301. doi: 10.1063/1.2403783
  144. Maia F.R.N.C., Ekeberg T., Spoel D., Hajdu J. Hawk: the image reconstruction package for coherent X-ray diffractive imaging. J. Applied Crystallography. 2010;43:1535–1539. doi: 10.1107/S0021889810036083
  145. Millane R., Lo V.L. Iterative projection algorithms in protein crystallography. I. Theory. Acta Crystallographica A. 2013;69:517–527. doi: 10.1107/S0108767313015249
  146. Urzhumtsev A.G. The use of local averaging in analysis of macromolecule images at electron density distribution maps: Preprint. Pushchino, 1985 (in Russ.).
  147. Urzhumtsev A.G., Lunin V.Y., Luzyanina T.B. Bounding a Molecule in a Noisy Synthesis. Acta Crystallographica A. 1989;45:34–39. doi: 10.1107/S0108767388008955
  148. Marchesini S., He H., Chapman H.N., Hau-Riege S.P., Noy A., Howells M.R., Weierstall U., Spence J.H.C. X-ray image reconstruction from a diffraction pattern alone. Phis. Rev. B. 2003;68:140101(R). doi: 10.1103/PhysRevB.68.140101
  149. Lunin V.Y., Lunina N.L., Petrova T.E. The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. Mathematical Biology and Bioinformatics. 2014;9:543–562. doi: 10.17537/2014.9.543
  150. Lunin V.Y., Lunina N.L., Petrova T.E., Baumstark M.W., Urzhumtsev A.G. Mask-based approach to phasing of single-particle diffraction data. Acta Crystallographica D. 2016;72:147–157. doi: 10.1107/S2059798315022652
  151. Lunin V.Y., Lunina N.L., Petrova T.E., Baumstark M.W., Urzhumtsev A.G. Mask-based approach to phasing of single-particle diffraction data. II. Likelihood-based selection criteria. Acta Crystallographica D. 2019;75:79–89. doi: 10.1107/S2059798318016959
  152. Lunina N.L., Petrova T.E., Urzhumtsev A.G., Lunin V.Y. The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. II. The Dependence of the Accuracy of the Solution on the Sampling Step of Experimental Data. Mathematical Biology and Bioinformatics. 2015;10:508–525. doi: 10.17537/2015.10.508
  153. Lunina N.L., Petrova T.E., Urzhumtsev A.G., Lunin V.Y. The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. III. Maximum-Likelihood Based Strategies to Select Solution of the Phase Problem. Mathematical Biology and Bioinformatics. 2017;12. С 521–535. doi: 10.17537/2017.12.521
  154. Mancuso A.P., Gorniak Th., Staier F., Yefanov O.M., Barth R., Christophis C., Reime B., Gulden J., Singer A., Pettit M.E. et al. Coherent imaging of biological samples with femtosecond pulses at the free electron laser FLASH. New J. Phys. 2010;12:035003. doi: 10.1088/1367-2630/12/3/035003
  155. Seibert M.M., Boutet S., Svenda M., Ekeberg T., Maia F.R.N.C., Bogan M.J., Nicusor Tîmneanu N., Anton Barty A., Stefan Hau-Riege S., Caleman C. Femtosecond diffractive imaging of biological cells. J. Phys. B: At. Mol. Opt. Phys. 2010;43:194015. doi: 10.1088/0953-4075/43/19/194015
  156. Gallagher-Jones M., Bessho Y., Kim S., Park J., Kim S., Nam D., Kim C., Kim Y., Noh do Y., Miyashita O. et al. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging. Nat. Commun. 2014;5:3798. doi: 10.1038/ncomms4798
  157. Xu R., Jiang H., Song C., Rodriguez J.A., Huang Z., Chen C.-C., Nam D., Park J., Gallagher-Jones M., Kim S. et al. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nat. Commun. 2014;5:4061. doi: 10.1038/ncomms5061
  158. Takayama Y., Inui Y., Sekiguchi Y., Kobayashi A., Oroguchi T., Yamamoto M., Matsunaga S., Nakasako M. Coherent X-Ray Diffraction Imaging of Chloroplasts from Cyanidioschyzon merolae by Using X-Ray Free Electron Laser. Plant Cell Physiol. 2015;56:1272–1286. doi: 10.1093/pcp/pcv032
  159. Nakano M., Osamu Miyashita O., Jonic S., Tokuhisa A., Tama F. Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution. J. Synchrotron Radiat. 2018;25:1010–1021. doi: 10.1107/S1600577518005568
  160. Maia F.R.N.C. The Coherent X-ray Imaging Data Bank. Nat. methods. 2012;9:854–855. doi: 10.1038/nmeth.2110
  161. Fan J., Sun Z., Wang Y., Park J., Kim S., Gallagher-Jones M., Kim Y., Song C., Yao S., Zhang J. et al. Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser. Sci. Rep. 2016;6:34008. doi: 10.1038/srep34008
  162. Hosseinizadeh A., Mashayekhi G., Copperman J., Schwander P., Dashti A., Sepehr R., Fung R., Schmidt M., Yoon C.H., Hogue B.G. et al. Conformational landscape of a virus by single-particle X-ray scattering. Nat. Methods. 2017;4:877–881. doi: 10.1038/nmeth.4395
  163. Aquila A., Barty A., Bostedt C., Boutet S., Carini G., dePonte D., Drell P., Doniach S., Downing K.H., Earnest T. The linac coherent light source single particle imaging road map. Structural Dynamics. 2015;2:041701. doi: 10.1063/1.4918726
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2020;15(2):195-234
doi: 10.17537/2020.15.195
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
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Перевод на англ. яз.
Мат. биол. и биоинф.
2020, 15(Suppl):t52-t87
doi: 10.17537/2020.15.t52

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