journal article·2025-09-01Open access

Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide

Peter Smyth, Sofia Jaho, Lewis J. Williams, Gabriel Karras, Ann Fitzpatrick, Amy J. Thompson, Sinan Battah, Danny Axford, Sam Horrell, Marina Lučić, Kotone Ishihara, Machika Kataoka, Hiroaki Matsuura, Kanji Shimba, Kensuke Tono, Takehiko Tosha, Hiroshi Sugimoto, Shigeki Owada, Michael A. Hough, Jonathan A.R. Worrall, Robin L. Owen

IUCrJ· Volume 12· Issue 5

Abstract

Time-resolved X-ray crystallography is undergoing a renaissance due to the development of serial crystallography at synchrotron and XFEL beamlines. Crucial to such experiments are efficient and effective methods for uniformly initiating time-dependent processes within microcrystals, such as ligand binding, enzymatic reactions or signalling. A widely applicable approach is the use of photocaged substrates, where the photocage is soaked into the crystal in advance and then activated using a laser pulse to provide uniform initiation of the reaction throughout the crystal. This work characterizes photocage release of nitric oxide and binding of this ligand to two heme protein systems, cytochrome c ′-β and dye-decolourizing peroxidase B using a fixed target sample delivery system. Laser parameters for photoactivation are systematically explored, and time-resolved structures over timescales ranging from 100 µs to 1.4 s using synchrotron and XFEL beamlines are described. The effective use of this photocage for time-resolved crystallography is demonstrated and appropriate illumination conditions for such experiments are determined.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Hemoglobin structure and function · Porphyrin and Phthalocyanine Chemistry · Heme Oxygenase-1 and Carbon Monoxide

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (53)

Show source-provided references
1. Adams · J. Biol. Inorg. Chem. · 2025 · 30 · 18110.1007/s00775-025-02102-3 ↗
2. Adams · Chem. Sci. · 2019 · 10 · 303110.1039/C8SC05210G ↗
3. Adams · J. Biol. Chem. · 2023 · 299 · 10474210.1016/j.jbc.2023.104742 ↗
4. Adams · Acta Cryst. D · 2010 · 66 · 21310.1107/S0907444909052925 ↗
5. Agirre · Acta Cryst. D · 2023 · 79 · 44910.1107/S2059798323003595 ↗
6. Aumonier · IUCrJ · 2022 · 9 · 75610.1107/S2052252522009150 ↗
7. Barends · Nature · 2024 · 626 · 90510.1038/s41586-024-07032-9 ↗
8. Beilsten-Edmands, J., Parkhurst, J. M., Winter, G. & Evans, G. (2024). Methods in Enzymology, Vol. 709, edited by P. Moody & H. Kwon, pp. 207-244. Academic Press.
9. Brändén · Science · 2021 · 373 · eaba095410.1126/science.aba0954 ↗
10. Cabail · J. Photochem. Photobiol. Chem. · 2002 · 152 · 10910.1016/S1010-6030(02)00231-9 ↗
11. Caramello · Acta Cryst. D · 2024 · 80 · 6010.1107/S2059798323011002 ↗
12. Chandra · FEMS Microbiol. Rev. · 2014 · 38 · 34510.1111/1574-6976.12047 ↗
13. Christou · Science · 2023 · 382 · 101510.1126/science.adj4270 ↗
14. Cooper · Biochim. Biophys. Acta · 1999 · 1411 · 29010.1016/S0005-2728(99)00021-3 ↗
15. De Zitter · Commun. Biol. · 2022 · 5 · 64010.1038/s42003-022-03575-7 ↗
16. Efremov · Biophys. J. · 2006 · 91 · 144110.1529/biophysj.106.083345 ↗
17. Elsliger · Acta Cryst. F · 2010 · 66 · 113710.1107/S1744309110038212 ↗
18. Emsley · Acta Cryst. D · 2010 · 66 · 48610.1107/S0907444910007493 ↗
19. Grünbein · Nat. Methods · 2020 · 17 · 68110.1038/s41592-020-0847-3 ↗
20. Horrell · JoVE · 2021 · 168 · e62200
21. Hough, M. A. & Andrew, C. R. (2015). Advances in Microbial Physiology, Vol. 67, edited by R. K. Poole, pp. 1-84. Academic Press.10.1016/bs.ampbs.2015.08.001 ↗
22. Hough · J. Mol. Biol. · 2011 · 405 · 39510.1016/j.jmb.2010.10.035 ↗
23. Keedy · Structure · 2014 · 22 · 89910.1016/j.str.2014.04.016 ↗
24. Kekilli · IUCrJ · 2017 · 4 · 26310.1107/S2052252517002159 ↗
25. Konold · Nat. Commun. · 2020 · 11 · 424810.1038/s41467-020-18065-9 ↗
26. Kupitz · Nature · 2014 · 513 · 26110.1038/nature13453 ↗
27. Lučić · Protein Sci. · 2024 · 33 · e507310.1002/pro.5073 ↗
28. Lučić · Angew. Chem. Int. Ed. · 2020 · 59 · 2165610.1002/anie.202008622 ↗
29. Lučić · ACS Catal. · 2022 · 12 · 1334910.1021/acscatal.2c03754 ↗
30. Mangubat-Medina · Chem. Soc. Rev. · 2021 · 50 · 1040310.1039/D0CS01434F ↗
31. Mehrabi · Science · 2019 · 365 · 116710.1126/science.aaw9904 ↗
32. Monteiro · Acta Cryst. D · 2021 · 77 · 121810.1107/S2059798321008809 ↗
33. Murshudov · Acta Cryst. D · 2011 · 67 · 35510.1107/S0907444911001314 ↗
34. Nakane · J. Appl. Cryst. · 2016 · 49 · 103510.1107/S1600576716005720 ↗
35. Namiki · J. Am. Chem. Soc. · 1997 · 119 · 384010.1021/ja962839d ↗
36. Nango · Science · 2016 · 354 · 155210.1126/science.aah3497 ↗
37. Orlans · Commun. Chem. · 2025 · 8 · 610.1038/s42004-024-01404-y ↗
38. Owen · Acta Cryst. D · 2017 · 73 · 37310.1107/S2059798317002996 ↗
39. Pandey · IUCrJ · 2021 · 8 · 87810.1107/S2052252521008125 ↗
40. Poddar · FEBS J. · 2022 · 289 · 57610.1111/febs.15880 ↗
41. Saavedra · J. Med. Chem. · 1996 · 39 · 436110.1021/jm960616s ↗
42. Schmidt · Crystals · 2020 · 10 · 11610.3390/cryst10020116 ↗
43. Schulz · Nat. Methods · 2018 · 15 · 90110.1038/s41592-018-0180-2 ↗
44. Sherrell · J. Synchrotron Rad. · 2015 · 22 · 137210.1107/S1600577515016938 ↗
45. Tono · J. Synchrotron Rad. · 2015 · 22 · 53210.1107/S1600577515004464 ↗
46. Tosha · Nat. Commun. · 2017 · 8 · 158510.1038/s41467-017-01702-1 ↗
47. Vagin · Acta Cryst. D · 2010 · 66 · 2210.1107/S0907444909042589 ↗
48. Werelusz · Biochim. Biophys. Acta · 2024 · 1871 · 11959810.1016/j.bbamcr.2023.119598 ↗
49. Wilamowski · Nat. Commun. · 2022 · 13 · 737910.1038/s41467-022-35029-3 ↗
50. Williams · Protein Sci. · 2018 · 27 · 29310.1002/pro.3330 ↗
51. Winter · J. Appl. Cryst. · 2010 · 43 · 18610.1107/S0021889809045701 ↗
52. Wolff · Nat. Chem. · 2023 · 15 · 154910.1038/s41557-023-01329-4 ↗
53. Yoshizumi, T., Shibui, Y., Kogo, M., Honma, S., Ito, S., Yajima, S. & Sasaki, Y. (2023). BMC Microbiol. 23, 285.10.1186/s12866-023-03036-z ↗