X-ray Absorption Spectroscopy of Dilute Metalloenzymes at X-ray Free-Electron Lasers in a Shot-by-Shot Mode

Bogacz, Isabel; Szilagyi, Erzsi; Makita, Hiroki; Simon, Philipp S.; Zhang, Miao; Doyle, Margaret D.; Chatterjee, Kuntal; Kretzschmar, Moritz; Chernev, Petko; Croy, Nicholas; Cheah, Mun-Hon; Dasgupta, Medhanjali; Nangca, Isabela; Fransson, Thomas; Bhowmick, Asmit; Brewster, Aaron S.; Sauter, Nicholas K.; Owada, Shigeki; Tono, Kensuke; Zerdane, Serhane; Oggenfuss, Alexander; Babich, Danylo; Sander, Mathias; Mankowsky, Roman; Lemke, Henrik T.; Gee, Leland B.; Sato, Takahiro; Kroll, Thomas; Messinger, Johannes; Alonso-Mori, Roberto; Bergmann, Uwe; Sokaras, Dimosthenis; Yachandra, Vittal K.; Kern, Jan; Yano, Junko

doi:10.1021/acs.jpclett.5c00399

X-ray Absorption Spectroscopy of Dilute Metalloenzymes at X-ray Free-Electron Lasers in a Shot-by-Shot Mode

Journal Article · Mon Apr 07 00:00:00 EDT 2025 · Journal of Physical Chemistry Letters

DOI:https://doi.org/10.1021/acs.jpclett.5c00399· OSTI ID:2565631

^[1]; ^[2]; Makita, Hiroki ^[1]; ^[1]; Zhang, Miao ^[1]; ^[1]; Chatterjee, Kuntal ^[1]; Kretzschmar, Moritz ^[3]; Chernev, Petko ^[4]; Croy, Nicholas ^[4]; ^[4]; Dasgupta, Medhanjali ^[1]; ^[1]; ^[5]; ^[1]; ^[1]; ^[1]; Owada, Shigeki ^[6]; Tono, Kensuke ^[6]; Zerdane, Serhane ^[7] more »

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Wisconsin, Madison, WI (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Humboldt Univ. of Berlin (Germany)
Uppsala Univ. (Sweden)
KTH Royal Inst. of Technology, Stockholm (Sweden)
Japan Synchrotron Radiation Research Institute, Sayo, Hyogo (Japan); RIKEN SPring-8 Center, Sayo (Japan)
Paul Scherrer Inst. (PSI), Villigen (Switzerland). SwissFEL
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Uppsala Univ. (Sweden); Umea Univ. (Sweden)
Univ. of Wisconsin, Madison, WI (United States)

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515

OSTI ID:: 2565631

Journal Information:: Journal of Physical Chemistry Letters, Journal Name: Journal of Physical Chemistry Letters Journal Issue: 15 Vol. 16; ISSN 1948-7185

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (54)

Transient X‐Ray Absorption Near Edge Structure Spectroscopy Using Broadband Free‐Electron Laser Pulses Juranić, Pavle; Cirelli, Claudio; Mamyrbayev, Talgat Small Methods, Vol. 8, Issue 8 https://doi.org/10.1002/smtd.202301328	journal	March 2024
Photosystem I Golbeck, John H. Advances in Photosynthesis and Respiration https://doi.org/10.1007/978-1-4020-4256-0	book	January 2006
X-Ray Absorption Spectroscopy of Metalloproteins Ward, Jesse; Ollmann, Emily; Maxey, Evan Methods in Molecular Biology https://doi.org/10.1007/978-1-62703-794-5_12	book	January 2014
Metal ions in biological catalysis: from enzyme databases to general principles Andreini, Claudia; Bertini, Ivano; Cavallaro, Gabriele JBIC Journal of Biological Inorganic Chemistry, Vol. 13, Issue 8 https://doi.org/10.1007/s00775-008-0404-5	journal	July 2008
Solar energy conversion by photosystem II: principles and structures Shevela, Dmitry; Kern, Jan F.; Govindjee, Govindjee Photosynthesis Research, Vol. 156, Issue 3 https://doi.org/10.1007/s11120-022-00991-y	journal	February 2023
Improved isolation and crystallization of photosystem I for structural analysis Fromme, Petra; Witt, Horst Tobias Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1365, Issue 1-2 https://doi.org/10.1016/S0005-2728(98)00059-0	journal	June 1998
Room temperature crystallography and X-ray spectroscopy of metalloenzymes Makita, Hiroki; Zhang, Miao; Yano, Junko Methods in Enzymology https://doi.org/10.1016/bs.mie.2023.07.009	book	January 2023
Purification, characterisation and crystallisation of photosystem II from Thermosynechococcus elongatus cultivated in a new type of photobioreactor Kern, J.; Loll, B.; Lüneberg, C. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1706, Issue 1-2 https://doi.org/10.1016/j.bbabio.2004.10.007	journal	January 2005
High resolution 1s core hole X-ray spectroscopy in 3d transition metal complexes—electronic and structural information Glatzel, Pieter; Bergmann, Uwe Coordination Chemistry Reviews, Vol. 249, Issue 1-2 https://doi.org/10.1016/j.ccr.2004.04.011	journal	January 2005
Ultrafast photophysics and photochemistry of iron hexacyanides in solution: Infrared to X-ray spectroscopic studies Chergui, M. Coordination Chemistry Reviews, Vol. 372 https://doi.org/10.1016/j.ccr.2018.05.021	journal	October 2018
Pixel array detector for X-ray free electron laser experiments Philipp, Hugh T.; Hromalik, Marianne; Tate, Mark Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 649, Issue 1 https://doi.org/10.1016/j.nima.2010.11.189	journal	September 2011
Targeting Metalloenzymes for Therapeutic Intervention Chen, Allie Y.; Adamek, Rebecca N.; Dick, Benjamin L. Chemical Reviews, Vol. 119, Issue 2 https://doi.org/10.1021/acs.chemrev.8b00201	journal	September 2018
Antivitamins B ₁₂ in a Microdrop: The Excited-State Structure of a Precious Sample Using Transient Polarized X-ray Absorption Near-Edge Structure Miller, Nicholas A.; Michocki, Lindsay B.; Alonso-Mori, Roberto The Journal of Physical Chemistry Letters, Vol. 10, Issue 18 https://doi.org/10.1021/acs.jpclett.9b02202	journal	August 2019
Mn ₄ Ca Cluster in Photosynthesis: Where and How Water is Oxidized to Dioxygen Yano, Junko; Yachandra, Vittal Chemical Reviews, Vol. 114, Issue 8 https://doi.org/10.1021/cr4004874	journal	March 2014
Introduction: Bioinorganic Enzymology II Holm, Richard H.; Solomon, Edward I. Chemical Reviews, Vol. 114, Issue 7 https://doi.org/10.1021/cr500118g	journal	January 2014
High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States Srinivas, Vivek; Banerjee, Rahul; Lebrette, Hugo Journal of the American Chemical Society, Vol. 142, Issue 33 https://doi.org/10.1021/jacs.0c05613	journal	July 2020
Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography Ishigami, Izumi; Carbajo, Sergio; Zatsepin, Nadia Journal of the American Chemical Society, Vol. 145, Issue 41 https://doi.org/10.1021/jacs.3c07803	journal	September 2023
Ultrafast Excited State Relaxation of a Metalloporphyrin Revealed by Femtosecond X-ray Absorption Spectroscopy Shelby, Megan L.; Lestrange, Patrick J.; Jackson, Nicholas E. Journal of the American Chemical Society, Vol. 138, Issue 28 https://doi.org/10.1021/jacs.6b02176	journal	July 2016
Polarized XANES Monitors Femtosecond Structural Evolution of Photoexcited Vitamin B ₁₂ Miller, Nicholas A.; Deb, Aniruddha; Alonso-Mori, Roberto Journal of the American Chemical Society, Vol. 139, Issue 5 https://doi.org/10.1021/jacs.6b11295	journal	January 2017
Potential for biomolecular imaging with femtosecond X-ray pulses Neutze, Richard; Wouts, Remco; van der Spoel, David Nature, Vol. 406, Issue 6797 https://doi.org/10.1038/35021099	journal	August 2000
Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution Jordan, Patrick; Fromme, Petra; Witt, Horst Tobias Nature, Vol. 411, Issue 6840 https://doi.org/10.1038/35082000	journal	June 2001
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4195	journal	February 2017
Structural evidence for intermediates during O2 formation in photosystem II Bhowmick, Asmit; Hussein, Rana; Bogacz, Isabel Nature, Vol. 617, Issue 7961 https://doi.org/10.1038/s41586-023-06038-z	journal	May 2023
Single-shot X-ray absorption spectroscopy at X-ray free electron lasers Harmand, Marion; Cammarata, Marco; Chollet, Matthieu Scientific Reports, Vol. 13, Issue 1 https://doi.org/10.1038/s41598-023-44196-2	journal	October 2023
Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes Bergmann, Uwe; Kern, Jan; Schoenlein, Robert W. Nature Reviews Physics, Vol. 3, Issue 4 https://doi.org/10.1038/s42254-021-00289-3	journal	March 2021
Serial femtosecond crystallography Barends, Thomas R. M.; Stauch, Benjamin; Cherezov, Vadim Nature Reviews Methods Primers, Vol. 2, Issue 1 https://doi.org/10.1038/s43586-022-00141-7	journal	August 2022
CHAPTER 7. Damage-free Electronic and Geometric Structure Determination of Metalloproteins Alonso-Mori, Roberto; Kern, Jan Energy and Environment Series https://doi.org/10.1039/9781782624097-00141	book	January 2017
Recent advances on ultrafast X-ray spectroscopy in the chemical sciences Chen, L. X.; Zhang, X.; Shelby, M. L. Chem. Sci., Vol. 5, Issue 11 https://doi.org/10.1039/C4SC01333F	journal	January 2014
Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments Kameshima, Takashi; Ono, Shun; Kudo, Togo Review of Scientific Instruments, Vol. 85, Issue 3 https://doi.org/10.1063/1.4867668	journal	March 2014
ePix100 camera: Use and applications at LCLS Carini, G. A.; Alonso-Mori, R.; Blaj, G. PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION – SRI2015, AIP Conference Proceedings https://doi.org/10.1063/1.4952880	conference	January 2016
Time-resolved X-ray spectroscopies of chemical systems: New perspectives Chergui, Majed Structural Dynamics, Vol. 3, Issue 3 https://doi.org/10.1063/1.4953104	journal	May 2016
Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode Alonso-Mori, R.; Kern, J.; Gildea, R. J. Proceedings of the National Academy of Sciences, Vol. 109, Issue 47, p. 19103-19107 https://doi.org/10.1073/pnas.1211384109	journal	November 2012
Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies Bacellar, Camila; Kinschel, Dominik; Mancini, Giulia F. Proceedings of the National Academy of Sciences, Vol. 117, Issue 36 https://doi.org/10.1073/pnas.2009490117	journal	August 2020
Structural Changes of the Oxygen-evolving Complex in Photosystem II during the Catalytic Cycle Glöckner, Carina; Kern, Jan; Broser, Matthias Journal of Biological Chemistry, Vol. 288, Issue 31 https://doi.org/10.1074/jbc.M113.476622	journal	June 2013
The JUNGFRAU Detector for Applications at Synchrotron Light Sources and XFELs Mozzanica, A.; Andrä, M.; Barten, R. Synchrotron Radiation News, Vol. 31, Issue 6 https://doi.org/10.1080/08940886.2018.1528429	journal	November 2018
Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers Neutze, Richard Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647 https://doi.org/10.1098/rstb.2013.0318	journal	July 2014
Range-extended EXAFS at the L edge of rare earths using high-energy-resolution fluorescence detection: A study of La in LaOCl Glatzel, P.; de Groot, F. M. F.; Manoilova, O. Physical Review B, Vol. 72, Issue 1 https://doi.org/10.1103/PhysRevB.72.014117	journal	July 2005
The X-ray Pump–Probe instrument at the Linac Coherent Light Source Chollet, Matthieu; Alonso-Mori, Roberto; Cammarata, Marco Journal of Synchrotron Radiation, Vol. 22, Issue 3 https://doi.org/10.1107/S1600577515005135	journal	April 2015
X-ray optics for advanced ultrafast pump–probe X-ray experiments at SACLA Katayama, Tetsuo; Hirano, Takashi; Morioka, Yuki Journal of Synchrotron Radiation, Vol. 26, Issue 2 https://doi.org/10.1107/S1600577518018362	journal	February 2019
Experimental station Bernina at SwissFEL: condensed matter physics on femtosecond time scales investigated by X-ray diffraction and spectroscopic methods Ingold, Gerhard; Abela, Rafael; Arrell, Christopher Journal of Synchrotron Radiation, Vol. 26, Issue 3 https://doi.org/10.1107/S160057751900331X	journal	April 2019
XANES and EXAFS of dilute solutions of transition metals at XFELs Chatterjee, Ruchira; Weninger, Clemens; Loukianov, Anton Journal of Synchrotron Radiation, Vol. 26, Issue 5 https://doi.org/10.1107/S1600577519007550	journal	August 2019
X-ray lasers for structure and dynamics in biology Spence, John C. H. IUCrJ, Vol. 5, Issue 3 https://doi.org/10.1107/S2052252518005365	journal	April 2018
Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography Pandey, Suraj; Calvey, George; Katz, Andrea M. IUCrJ, Vol. 8, Issue 6 https://doi.org/10.1107/S2052252521008125	journal	September 2021
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned Hadjidemetriou, Kyprianos; Coquelle, Nicolas; Barends, Thomas R. M. Acta Crystallographica Section D Structural Biology, Vol. 78, Issue 9 https://doi.org/10.1107/S2059798322007525	journal	August 2022
High-resolution large-acceptance analyzer for x-ray fluorescence and Raman spectroscopy Bergmann, Uwe; Cramer, Stephen P. SPIE's International Symposium on Optical Science, Engineering, and Instrumentation, SPIE Proceedings https://doi.org/10.1117/12.332507	conference	December 1998
X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis Rabe, Patrick; Kamps, Jos J. A. G.; Sutherlin, Kyle D. Science Advances, Vol. 7, Issue 34 https://doi.org/10.1126/sciadv.abh0250	journal	August 2021
Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography Smith, Nathan; Dasgupta, Medhanjali; Wych, David C. Science Advances, Vol. 10, Issue 13 https://doi.org/10.1126/sciadv.adk7201	journal	March 2024
Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy Mara, Michael W.; Hadt, Ryan G.; Reinhard, Marco Eli Science, Vol. 356, Issue 6344 https://doi.org/10.1126/science.aam6203	journal	June 2017
Advances and challenges in time-resolved macromolecular crystallography Brändén, Gisela; Neutze, Richard Science, Vol. 373, Issue 6558 https://doi.org/10.1126/science.aba0954	journal	August 2021
Structure and Energy Transfer in Photosystems of Oxygenic Photosynthesis Nelson, Nathan; Junge, Wolfgang Annual Review of Biochemistry, Vol. 84, Issue 1 https://doi.org/10.1146/annurev-biochem-092914-041942	journal	June 2015
Structure Function Studies of Photosystem II Using X-Ray Free Electron Lasers Yano, Junko; Kern, Jan; Yachandra, Vittal K. Annual Review of Biophysics, Vol. 53, Issue 1 https://doi.org/10.1146/annurev-biophys-071723-102519	journal	July 2024
Structure and Function of Photosystems i and ii Nelson, Nathan; Yocum, Charles F. Annual Review of Plant Biology, Vol. 57, Issue 1 https://doi.org/10.1146/annurev.arplant.57.032905.105350	journal	June 2006
X-ray Absorption Spectroscopy George, Graham N.; Pickering, Ingrid J. https://doi.org/10.1515/9783110570441	book	January 2025
Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs Bogacz, Isabel; Makita, Hiroki; Simon, Philipp S. Pure and Applied Chemistry, Vol. 95, Issue 8 https://doi.org/10.1515/pac-2023-0213	journal	April 2023

Similar Records

Single-shot X-ray absorption spectroscopy at X-ray free electron lasers

Journal Article · Mon Oct 23 20:00:00 EDT 2023 · Scientific Reports · OSTI ID:2280900

Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes

Journal Article · Thu Mar 18 20:00:00 EDT 2021 · Nature Reviews Physics · OSTI ID:1775134

X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser

Journal Article · Wed Apr 04 20:00:00 EDT 2018 · Biochemistry · OSTI ID:1465465

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
crystals
fluorescence
fluorescence detection
scattering
transition metals

X-ray Absorption Spectroscopy of Dilute Metalloenzymes at X-ray Free-Electron Lasers in a Shot-by-Shot Mode

Citation Formats

References (54)

Similar Records

Related Subjects