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Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses.

<div class='caption-title'>Disulfide and thioether bonds.</div>
<div class='caption-title'>Changes in the protein backbone.</div>
<div class='caption-title'>Changes in aromatic side chains.</div>
Nass K, Gorel A, Abdullah MM, V Martin A, Kloos M, Marinelli A, Aquila A, Barends TRM, Decker FJ, Bruce Doak R, Foucar L, Hartmann E, Hilpert M, Hunter MS, Jurek Z, Koglin JE, Kozlov A, Lutman AA, Kovacs GN, Roome CM, Shoeman RL, Santra R, Quiney HM, Ziaja B, Boutet S, Schlichting I
OpenAccess logo Nat Commun 11 1814 (2020)
Related entries: 6sr0, 6sr1, 6sr2, 6sr3, 6sr4, 6sr5, 6srj, 6srk, 6srl, 6sro, 6srq

Cited: 27 times
EuropePMC logo PMID: 32286284

Abstract

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter's correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

Reviews citing this publication (4)

  1. Best practices for time-resolved serial synchrotron crystallography. Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Acta Crystallogr D Struct Biol 78 14-29 (2022)
  2. Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis. Hough MA, Owen RL. Curr Opin Struct Biol 71 232-238 (2021)
  3. Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Hekstra DR. Annu Rev Biophys 52 255-274 (2023)
  4. Growing and making nano- and microcrystals. Shoeman RL, Hartmann E, Schlichting I. Nat Protoc 18 854-882 (2023)

Articles citing this publication (23)

  1. Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering. Lee Y, Kim JG, Lee SJ, Muniyappan S, Kim TW, Ki H, Kim H, Jo J, Yun SR, Lee H, Lee KW, Kim SO, Cammarata M, Ihee H. Nat Commun 12 3677 (2021)
  2. Serial femtosecond crystallography. Barends TRM, Stauch B, Cherezov V, Schlichting I. Nat Rev Methods Primers 2 59 (2022)
  3. X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis. Rabe P, Kamps JJAG, Sutherlin KD, Linyard JDS, Aller P, Pham CC, Makita H, Clifton I, McDonough MA, Leissing TM, Shutin D, Lang PA, Butryn A, Brem J, Gul S, Fuller FD, Kim IS, Cheah MH, Fransson T, Bhowmick A, Young ID, O'Riordan L, Brewster AS, Pettinati I, Doyle M, Joti Y, Owada S, Tono K, Batyuk A, Hunter MS, Alonso-Mori R, Bergmann U, Owen RL, Sauter NK, Claridge TDW, Robinson CV, Yachandra VK, Yano J, Kern JF, Orville AM, Schofield CJ. Sci Adv 7 eabh0250 (2021)
  4. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. Vakili M, Bielecki J, Knoška J, Otte F, Han H, Kloos M, Schubert R, Delmas E, Mills G, de Wijn R, Letrun R, Dold S, Bean R, Round A, Kim Y, Lima FA, Dörner K, Valerio J, Heymann M, Mancuso AP, Schulz J. J Synchrotron Radiat 29 331-346 (2022)
  5. The XBI BioLab for life science experiments at the European XFEL. Han H, Round E, Schubert R, Gül Y, Makroczyová J, Meza D, Heuser P, Aepfelbacher M, Barák I, Betzel C, Fromme P, Kursula I, Nissen P, Tereschenko E, Schulz J, Uetrecht C, Ulicný J, Wilmanns M, Hajdu J, Lamzin VS, Lorenzen K. J Appl Crystallogr 54 7-21 (2021)
  6. Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Grünbein ML, Gorel A, Foucar L, Carbajo S, Colocho W, Gilevich S, Hartmann E, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Lewandowski J, Lutman A, Nass K, Nass Kovacs G, Roome CM, Sheppard J, Shoeman RL, Stricker M, van Driel T, Vetter S, Doak RB, Boutet S, Aquila A, Decker FJ, Barends TRM, Stan CA, Schlichting I. Nat Commun 12 1672 (2021)
  7. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Struct Dyn 8 064302 (2021)
  8. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser. E J, Stransky M, Jurek Z, Fortmann-Grote C, Juha L, Santra R, Ziaja B, Mancuso AP. Sci Rep 11 17976 (2021)
  9. editorial Radiation damage to biological samples: still a pertinent issue. Garman EF, Weik M. J Synchrotron Radiat 28 1278-1283 (2021)
  10. High-throughput in situ experimental phasing. Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J, Aller P. Acta Crystallogr D Struct Biol 76 790-801 (2020)
  11. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. Nass K, Bacellar C, Cirelli C, Dworkowski F, Gevorkov Y, James D, Johnson PJM, Kekilli D, Knopp G, Martiel I, Ozerov D, Tolstikova A, Vera L, Weinert T, Yefanov O, Standfuss J, Reiche S, Milne CJ. IUCrJ 8 905-920 (2021)
  12. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Šrajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA. IUCrJ 9 610-624 (2022)
  13. Density functional tight binding approach utilized to study X-ray-induced transitions in solid materials. Lipp V, Tkachenko V, Stransky M, Aradi B, Frauenheim T, Ziaja B. Sci Rep 12 1551 (2022)
  14. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers. Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthür D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barák I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dörner K, Gañán-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoška J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Münnich A, Peña Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C. Nat Commun 13 4708 (2022)
  15. Thioredoxin reductase from Bacillus cereus exhibits distinct reduction and NADPH-binding properties. Shoor M, Gudim I, Hersleth HP, Hammerstad M. FEBS Open Bio 11 3019-3031 (2021)
  16. Combination of an inject-and-transfer system for serial femtosecond crystallography. Lee K, Kim J, Baek S, Park J, Park S, Lee JL, Chung WK, Cho Y, Nam KH. J Appl Crystallogr 55 813-822 (2022)
  17. Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned. Hadjidemetriou K, Coquelle N, Barends TRM, De Zitter E, Schlichting I, Colletier JP, Weik M. Acta Crystallogr D Struct Biol 78 1131-1142 (2022)
  18. A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers. Wranik M, Kepa MW, Beale EV, James D, Bertrand Q, Weinert T, Furrer A, Glover H, Gashi D, Carrillo M, Kondo Y, Stipp RT, Khusainov G, Nass K, Ozerov D, Cirelli C, Johnson PJM, Dworkowski F, Beale JH, Stubbs S, Zamofing T, Schneider M, Krauskopf K, Gao L, Thorn-Seshold O, Bostedt C, Bacellar C, Steinmetz MO, Milne C, Standfuss J. Nat Commun 14 7956 (2023)
  19. DNA-Mediated Stack Formation of Nanodiscs. Subramanian M, Kielar C, Tsushima S, Fahmy K, Oertel J. Molecules 26 1647 (2021)
  20. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme. Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, Ros A. Lab Chip 23 3016-3033 (2023)
  21. Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging. Kozlov A, Gureyev TE, Paganin DM, Martin AV, Martin AV, Caleman C, Quiney HM. IUCrJ 7 1114-1123 (2020)
  22. The FUSION protein crystallization screen. Gorrec F, Bellini D. J Appl Crystallogr 55 310-319 (2022)
  23. Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses. Patra KK, Eliah Dawod I, Martin AV, Greaves TL, Persson D, Caleman C, Timneanu N. J Synchrotron Radiat 28 1296-1308 (2021)


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