1
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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2
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Makita H, Simon PS, Kern J, Yano J, Yachandra VK. Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography. Curr Opin Struct Biol 2023; 80:102604. [PMID: 37148654 PMCID: PMC10793627 DOI: 10.1016/j.sbi.2023.102604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023]
Abstract
With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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3
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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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4
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Patra KK, Eliah Dawod I, Martin AV, Greaves TL, Persson D, Caleman C, Timneanu N. Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1296-1308. [PMID: 34475279 PMCID: PMC8415341 DOI: 10.1107/s1600577521007657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/26/2021] [Indexed: 05/30/2023]
Abstract
X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.
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Affiliation(s)
- Kajwal Kumar Patra
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ibrahim Eliah Dawod
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany
| | - Andrew V. Martin
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L. Greaves
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Daniel Persson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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5
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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6
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Nass K. Pixel modelling - a new age in SFX data analysis. IUCRJ 2020; 7:949-950. [PMID: 33209307 PMCID: PMC7642796 DOI: 10.1107/s2052252520014281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A new program, diffBragg, employs per-pixel maximum likelihood optimization of X-ray pulse and crystal parameters to improve the accuracy of structure factor amplitudes attainable in SFX experiments.
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Affiliation(s)
- Karol Nass
- SwissFEL, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
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7
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A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography. CRYSTALS 2020. [DOI: 10.3390/cryst10070585] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.
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8
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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9
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Hybrid Plasma/Molecular-Dynamics Approach for Efficient XFEL Radiation Damage Simulations. CRYSTALS 2020. [DOI: 10.3390/cryst10060478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb forces. The accurate simulation of these dynamical effects is critical in designing feasible XFEL experiments and interpreting the results. Current molecular dynamics simulations are, however, computationally intensive, particularly when they treat unbound electrons as classical point particles. On the other hand, plasma simulations are computationally efficient but do not model atomic motion. Here we present a hybrid approach to XFEL damage simulation that combines molecular dynamics for the nuclear motion and plasma models to describe the evolution of the low-energy electron continuum. The plasma properties of the unbound electron gas are used to define modified inter-ionic potentials for the molecular dynamics, including Debye screening and drag forces. The hybrid approach is significantly faster than damage simulations that treat unbound electrons as classical particles, enabling simulations to be performed on large sample volumes.
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10
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Miller KR, Paretsky JD, Follmer AH, Heinisch T, Mittra K, Gul S, Kim IS, Fuller FD, Batyuk A, Sutherlin KD, Brewster AS, Bhowmick A, Sauter NK, Kern J, Yano J, Green MT, Ward TR, Borovik AS. Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases. Inorg Chem 2020; 59:6000-6009. [PMID: 32309932 PMCID: PMC7219546 DOI: 10.1021/acs.inorgchem.9b03791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.
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Affiliation(s)
- Kelsey R. Miller
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Jonathan D. Paretsky
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Alec H. Follmer
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Kaustuv Mittra
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Michael T. Green
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - A. S. Borovik
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
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11
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Martiel I, Mozzanica A, Opara NL, Panepucci E, Leonarski F, Redford S, Mohacsi I, Guzenko V, Ozerov D, Padeste C, Schmitt B, Pedrini B, Wang M. X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:329-339. [PMID: 32153271 PMCID: PMC7064105 DOI: 10.1107/s1600577519016758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/14/2019] [Indexed: 05/06/2023]
Abstract
Detection of heavy elements, such as metals, in macromolecular crystallography (MX) samples by X-ray fluorescence is a function traditionally covered at synchrotron MX beamlines by silicon drift detectors, which cannot be used at X-ray free-electron lasers because of the very short duration of the X-ray pulses. Here it is shown that the hybrid pixel charge-integrating detector JUNGFRAU can fulfill this function when operating in a low-flux regime. The feasibility of precise position determination of micrometre-sized metal marks is also demonstrated, to be used as fiducials for offline prelocation in serial crystallography experiments, based on the specific fluorescence signal measured with JUNGFRAU, both at the synchrotron and at SwissFEL. Finally, the measurement of elemental absorption edges at a synchrotron beamline using JUNGFRAU is also demonstrated.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Aldo Mozzanica
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Nadia L. Opara
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel 4058, Switzerland
- SwissNanoscience Institute, University of Basel, Basel 4056, Switzerland
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Filip Leonarski
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Sophie Redford
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Istvan Mohacsi
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Vitaliy Guzenko
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Bernd Schmitt
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Bill Pedrini
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
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12
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Sauter NK, Kern J, Yano J, Holton JM. Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction. Acta Crystallogr D Struct Biol 2020; 76:176-192. [PMID: 32038048 PMCID: PMC7008510 DOI: 10.1107/s2059798320000418] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/14/2020] [Indexed: 12/25/2022] Open
Abstract
Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 × 10-4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10-3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.
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Affiliation(s)
- Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James M. Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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13
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Galler A, Gawelda W, Biednov M, Bomer C, Britz A, Brockhauser S, Choi TK, Diez M, Frankenberger P, French M, Görries D, Hart M, Hauf S, Khakhulin D, Knoll M, Korsch T, Kubicek K, Kuster M, Lang P, Alves Lima F, Otte F, Schulz S, Zalden P, Bressler C. Scientific instrument Femtosecond X-ray Experiments (FXE): instrumentation and baseline experimental capabilities. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1432-1447. [PMID: 31490131 PMCID: PMC6730617 DOI: 10.1107/s1600577519006647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/08/2019] [Indexed: 05/15/2023]
Abstract
The European X-ray Free-Electron Laser (EuXFEL) delivers extremely intense (>1012 photons pulse-1 and up to 27000 pulses s-1), ultrashort (<100 fs) and transversely coherent X-ray radiation, at a repetition rate of up to 4.5 MHz. Its unique X-ray beam parameters enable novel and groundbreaking experiments in ultrafast photochemistry and material sciences at the Femtosecond X-ray Experiments (FXE) scientific instrument. This paper provides an overview of the currently implemented experimental baseline instrumentation and its performance during the commissioning phase, and a preview of planned improvements. FXE's versatile instrumentation combines the simultaneous application of forward X-ray scattering and X-ray spectroscopy techniques with femtosecond time resolution. These methods will eventually permit exploitation of wide-angle X-ray scattering studies and X-ray emission spectroscopy, along with X-ray absorption spectroscopy, including resonant inelastic X-ray scattering and X-ray Raman scattering. A suite of ultrafast optical lasers throughout the UV-visible and near-IR ranges (extending up to mid-IR in the near future) with pulse length down to 15 fs, synchronized to the X-ray source, serve to initiate dynamic changes in the sample. Time-delayed hard X-ray pulses in the 5-20 keV range are used to probe the ensuing dynamic processes using the suite of X-ray probe tools. FXE is equipped with a primary monochromator, a primary and secondary single-shot spectrometer, and a timing tool to correct the residual timing jitter between laser and X-ray pulses.
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Affiliation(s)
- Andreas Galler
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Wojciech Gawelda
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Mykola Biednov
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Christina Bomer
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
| | - Alexander Britz
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Sandor Brockhauser
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt 62, H-6726 Szeged, Hungary
| | - Tae-Kyu Choi
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Diez
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
| | - Paul Frankenberger
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marcus French
- STFC Technology, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, UK
| | - Dennis Görries
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthiew Hart
- STFC Technology, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, UK
| | - Steffen Hauf
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Dmitry Khakhulin
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Martin Knoll
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Timo Korsch
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Katharina Kubicek
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Markus Kuster
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Philipp Lang
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Frederico Alves Lima
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Florian Otte
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
- Fakultät Physik, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Sebastian Schulz
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Peter Zalden
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Christian Bressler
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22607 Hamburg, Germany
- Correspondence e-mail:
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14
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Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
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Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
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15
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Nass K. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr D Struct Biol 2019; 75:211-218. [PMID: 30821709 PMCID: PMC6400258 DOI: 10.1107/s2059798319000317] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/07/2019] [Indexed: 01/17/2023] Open
Abstract
Radiation damage is still the most limiting factor in obtaining high-resolution structures of macromolecules in crystallographic experiments at synchrotrons. With the advent of X-ray free-electron lasers (XFELs) that produce ultrashort and highly intense X-ray pulses, it became possible to outrun most of the radiation-damage processes occurring in the sample during exposure to XFEL radiation. Although this is generally the case, several experimental and theoretical studies have indicated that structures from XFELs may not always be radiation-damage free. This is especially true when higher intensity pulses are used and protein molecules that contain heavy elements in their structures are studied. Here, the radiation-damage mechanisms that occur in samples exposed to XFEL pulses are summarized, results that show indications of radiation damage are reviewed and methods that can partially overcome it are discussed.
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Affiliation(s)
- Karol Nass
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
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16
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Martiel I, Müller-Werkmeister HM, Cohen AE. Strategies for sample delivery for femtosecond crystallography. Acta Crystallogr D Struct Biol 2019; 75:160-177. [PMID: 30821705 PMCID: PMC6400256 DOI: 10.1107/s2059798318017953] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 11/11/2022] Open
Abstract
Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.
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Affiliation(s)
- Isabelle Martiel
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Henrike M. Müller-Werkmeister
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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17
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Porcaro F, Roudeau S, Carmona A, Ortega R. Advances in element speciation analysis of biomedical samples using synchrotron-based techniques. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.09.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Wherland S, Pecht I. Radiation chemists look at damage in redox proteins induced by X-rays. Proteins 2018; 86:817-826. [DOI: 10.1002/prot.25521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Scot Wherland
- Department of Chemistry; Washington State University; Pullman Washington
| | - Israel Pecht
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
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19
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Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Short-wavelength free-electron laser sources and science: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:115901. [PMID: 29059048 DOI: 10.1088/1361-6633/aa7cca] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.
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Affiliation(s)
- E A Seddon
- ASTeC, STFC Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom. The School of Physics and Astronomy and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The Cockcroft Institute, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom
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20
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Chergui M, Collet E. Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods. Chem Rev 2017; 117:11025-11065. [DOI: 10.1021/acs.chemrev.6b00831] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU), ISIC, and Lausanne Centre for
Ultrafast Science (LACUS), Faculté des Sciences de Base, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Eric Collet
- Univ Rennes 1, CNRS, Institut de Physique de Rennes, UMR 6251, UBL, Rennes F-35042, France
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21
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Spence JCH. XFELs for structure and dynamics in biology. IUCRJ 2017; 4:322-339. [PMID: 28875020 PMCID: PMC5571796 DOI: 10.1107/s2052252517005760] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/17/2017] [Indexed: 05/20/2023]
Abstract
The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
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Affiliation(s)
- J. C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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22
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Altissimo M, Kiskinova M, Mincigrucci R, Vaccari L, Guarnaccia C, Masciovecchio C. Perspective: A toolbox for protein structure determination in physiological environment through oriented, 2D ordered, site specific immobilization. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044017. [PMID: 28428974 PMCID: PMC5392127 DOI: 10.1063/1.4981224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/05/2017] [Indexed: 05/19/2023]
Abstract
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment. Today, the ultra-short and ultra-bright pulses of X-ray free-electron lasers have made attainable the dream to determine protein structures before radiation damage starts to destroy the samples. However, the signal-to-noise ratio remains a great challenge to obtain usable diffraction patterns from a single protein molecule. With the perspective to overcome these challenges, we describe here a new methodology that has the potential to overcome the signal-to-noise-ratio and protein crystallization limits. Using a multidisciplinary approach, we propose to create ordered, two dimensional protein arrays with defined orientation attached on a self-assembled-monolayer. We develop a literature-based flexible toolbox capable of assembling different kinds of proteins on a functionalized surface and consider using a graphene cover layer that will allow performing experiments with proteins in physiological conditions.
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Affiliation(s)
- M Altissimo
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - M Kiskinova
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - R Mincigrucci
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - L Vaccari
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - C Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - C Masciovecchio
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
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23
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24
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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25
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A Practical Guide to High-resolution X-ray Spectroscopic Measurements and their Applications in Bioinorganic Chemistry. Isr J Chem 2016. [DOI: 10.1002/ijch.201600037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Hirata K, Foadi J, Evans G, Hasegawa K, Zeldin OB. Structural Biology with Microfocus Beamlines. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-4-431-56030-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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27
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Kimberg V, Rohringer N. Stochastic stimulated electronic x-ray Raman spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:034101. [PMID: 26958585 PMCID: PMC4752554 DOI: 10.1063/1.4940916] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/15/2016] [Indexed: 05/09/2023]
Abstract
Resonant inelastic x-ray scattering (RIXS) is a well-established tool for studying electronic, nuclear, and collective dynamics of excited atoms, molecules, and solids. An extension of this powerful method to a time-resolved probe technique at x-ray free electron lasers (XFELs) to ultimately unravel ultrafast chemical and structural changes on a femtosecond time scale is often challenging, due to the small signal rate in conventional implementations at XFELs that rely on the usage of a monochromator setup to select a small frequency band of the broadband, spectrally incoherent XFEL radiation. Here, we suggest an alternative approach, based on stochastic spectroscopy, which uses the full bandwidth of the incoming XFEL pulses. Our proposed method is relying on stimulated resonant inelastic x-ray scattering, where in addition to a pump pulse that resonantly excites the system a probe pulse on a specific electronic inelastic transition is provided, which serves as a seed in the stimulated scattering process. The limited spectral coherence of the XFEL radiation defines the energy resolution in this process and stimulated RIXS spectra of high resolution can be obtained by covariance analysis of the transmitted spectra. We present a detailed feasibility study and predict signal strengths for realistic XFEL parameters for the CO molecule resonantly pumped at the [Formula: see text] transition. Our theoretical model describes the evolution of the spectral and temporal characteristics of the transmitted x-ray radiation, by solving the equation of motion for the electronic and vibrational degrees of freedom of the system self consistently with the propagation by Maxwell equations.
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