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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Holstad TS, Dresselhaus-Marais LE, Ræder TM, Kozioziemski B, van Driel T, Seaberg M, Folsom E, Eggert JH, Knudsen EB, Nielsen MM, Simons H, Haldrup K, Poulsen HF. Real-time imaging of acoustic waves in bulk materials with X-ray microscopy. Proc Natl Acad Sci U S A 2023; 120:e2307049120. [PMID: 37725646 PMCID: PMC10523471 DOI: 10.1073/pnas.2307049120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
The dynamics of lattice vibrations govern many material processes, such as acoustic wave propagation, displacive phase transitions, and ballistic thermal transport. The maximum velocity of these processes and their effects is determined by the speed of sound, which therefore defines the temporal resolution (picoseconds) needed to resolve these phenomena on their characteristic length scales (nanometers). Here, we present an X-ray microscope capable of imaging acoustic waves with subpicosecond resolution within mm-sized crystals. We directly visualize the generation, propagation, branching, and energy dissipation of longitudinal and transverse acoustic waves in diamond, demonstrating how mechanical energy thermalizes from picosecond to microsecond timescales. Bulk characterization techniques capable of resolving this level of structural detail have previously been available on millisecond time scales-orders of magnitude too slow to capture these fundamental phenomena in solid-state physics and geoscience. As such, the reported results provide broad insights into the interaction of acoustic waves with the structure of materials, and the availability of ultrafast time-resolved dark-field X-ray microscopy opens a vista of new opportunities for 3D imaging of materials dynamics on their intrinsic submicrosecond time scales.
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Affiliation(s)
- Theodor S. Holstad
- Department of Physics, Technical University of Denmark, Kongens Lyngby2800, Denmark
| | - Leora E. Dresselhaus-Marais
- Department of Materials Science & Engineering, Stanford University, Stanford, CA94305
- SLAC National Accelerator Laboratory, Menlo Park, CA94025-7015
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA94550-9234
| | - Trygve Magnus Ræder
- Department of Physics, Technical University of Denmark, Kongens Lyngby2800, Denmark
| | - Bernard Kozioziemski
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA94550-9234
| | - Tim van Driel
- SLAC National Accelerator Laboratory, Menlo Park, CA94025-7015
| | - Matthew Seaberg
- SLAC National Accelerator Laboratory, Menlo Park, CA94025-7015
| | - Eric Folsom
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA94550-9234
| | - Jon H. Eggert
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA94550-9234
| | | | | | - Hugh Simons
- Department of Physics, Technical University of Denmark, Kongens Lyngby2800, Denmark
| | - Kristoffer Haldrup
- Department of Physics, Technical University of Denmark, Kongens Lyngby2800, Denmark
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3
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Støckler LJ, Christensen RS, Kløve M, Bertelsen AD, Borup AB, Krause L, Takahashi S, Fujita T, Kasai H, Inoue I, Nishibori E, Iversen BB. Pair Distribution Function from Liquid Jet Nanoparticle Suspension using Femtosecond X-ray Pulses. Chemphyschem 2023:e202300407. [PMID: 37705300 DOI: 10.1002/cphc.202300407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023]
Abstract
X-ray scattering data measured on femtosecond timescales at the SACLA X-ray Free Electron Laser (XFEL) facility on a suspension of HfO2 nanoparticles in a liquid jet were used for pair distribution function (PDF) analysis. Despite a non-optimal experimental setup resulting in a modest Qmax of ~8 Å-1 , a promising PDF was obtained. The main features were reproduced when comparing the XFEL PDF to a PDF obtained from data measured at the PETRA III synchrotron light source. Refining structural parameters such as unit cell dimension and particle size from the XFEL PDF provided reliable values. Although the reachable Qmax limited the obtainable information, the present results indicate that good quality PDFs can be obtained on femtosecond timescales if the experimental conditions are further optimized. The study therefore encourages a new direction in ultrafast structural science where structural features of amorphous and disordered systems can be studied.
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Affiliation(s)
- Lise Joost Støckler
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Rasmus Stubkjaer Christensen
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Magnus Kløve
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Andreas Dueholm Bertelsen
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Anders Baek Borup
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Lennard Krause
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Seiya Takahashi
- Department of Physics, Faculty of Pure and Applied Sciences and TREMS, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Tomoki Fujita
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
- Department of Physics, Faculty of Pure and Applied Sciences and TREMS, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Hidetaka Kasai
- Department of Physics, Faculty of Pure and Applied Sciences and TREMS, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Ichiro Inoue
- RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Eiji Nishibori
- Department of Physics, Faculty of Pure and Applied Sciences and TREMS, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Bo Brummerstedt Iversen
- Center for Integrated Materials Research, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
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Jang H, Ueda H, Kim HD, Kim M, Shin KW, Kim KH, Park SY, Shin HJ, Borisov P, Rosseinsky MJ, Jang D, Choi H, Eom I, Staub U, Chun SH. 4D Visualization of a Nonthermal Coherent Magnon in a Laser Heated Lattice by an X-ray Free Electron Laser. Adv Mater 2023; 35:e2303032. [PMID: 37391904 DOI: 10.1002/adma.202303032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/02/2023]
Abstract
Ultrafast optical manipulation of magnetic phenomena is an exciting achievement of mankind, expanding one's horizon of knowledge toward the functional nonequilibrium states. The dynamics acting on an extremely short timescale push the detection limits that reveal fascinating light-matter interactions for nonthermal creation of effective magnetic fields. While some cases are benchmarked by emergent transient behaviors, otherwise identifying the nonthermal effects remains challenging. Here, a femtosecond time-resolved resonant magnetic X-ray diffraction experiment is introduced, which uses an X-ray free-electron laser (XFEL) to distinguish between the effective field and the photoinduced thermal effect. It is observed that a multiferroic Y-type hexaferrite exhibits magnetic Bragg peak intensity oscillations manifesting entangled antiferromagnetic (AFM) and ferromagnetic (FM) Fourier components of a coherent AFM magnon. The magnon trajectory constructed in 3D space and time domains is decisive to evince ultrafast field formation preceding the lattice thermalization. A remarkable impact of photoexcitation across the electronic bandgap is directly unraveled, amplifying the photomagnetic coupling that is one of the highest among AFM dielectrics. Leveraging the above-bandgap photoexcitation, this energy-efficient optical process further suggests a novel photomagnetic control of ferroelectricity in multiferroics.
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Affiliation(s)
- Hoyoung Jang
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hiroki Ueda
- Swiss Light Source, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
- SwissFEL, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
| | - Hyeong-Do Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Kwang Woo Shin
- Center for Novel States of Complex Materials Research, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kee Hoon Kim
- Center for Novel States of Complex Materials Research, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Youn Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hee Jun Shin
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Pavel Borisov
- Department of Physics, Loughborough University, Loughborough, LE11 3TU, UK
- Department of Chemistry, University of Liverpool, Liverpool, L7 3NY, UK
| | | | - Dogeun Jang
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyeongi Choi
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Urs Staub
- Swiss Light Source, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
| | - Sae Hwan Chun
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea
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5
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Makita H, Zhang M, Yano J, Kern J. Room temperature crystallography and X-ray spectroscopy of metalloenzymes. Methods Enzymol 2023; 688:307-348. [PMID: 37748830 PMCID: PMC10799221 DOI: 10.1016/bs.mie.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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6
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Nango E, Iwata S. Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins. Curr Opin Struct Biol 2023; 81:102629. [PMID: 37354789 DOI: 10.1016/j.sbi.2023.102629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/26/2023]
Abstract
Microbial rhodopsin is a membrane protein with a domain of seven-transmembrane helices and a retinal chromophore. The main function of this protein is to perform light-induced ion transport, either actively or passively, by acting as pumps, channels, and light sensors. It is widely used for optogenetic application to control the activity of specific cells in living tissues by light. Time-resolved serial femtosecond crystallography (TR-SFX) with the use of X-ray free electron lasers is an effective technique for capturing dynamic ion transport and efflux structures across membranes with high spatial and temporal resolutions. Here, we outline recent TR-SFX studies of microbial rhodopsins, including a pump and a channel. We also discuss differences and similarities observed in the structural dynamics derived from the TR-SFX structures.
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Affiliation(s)
- Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. https://twitter.com/@enango_5
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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7
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Shin J, Jung C, Ihm Y, Heo SP, Nam D, Kim S, Kim M, Eom I, Shim JH, Noh DY, Song C. Ultrafast Energy Transfer Process in Confined Gold Nanospheres Revealed by Femtosecond X-ray Imaging and Diffraction. Nano Lett 2023; 23:1481-1488. [PMID: 36723175 DOI: 10.1021/acs.nanolett.2c04920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Femtosecond laser pulses drive nonequilibrium phase transitions via reaction paths hidden in thermal equilibrium. This stimulates interest to understand photoinduced ultrafast melting processes, which remains incomplete due to challenges in resolving accompanied kinetics at the relevant space-time resolution. Here, by newly establishing a multiplexing femtosecond X-ray probe, we have successfully revealed ultrafast energy transfer processes in confined Au nanospheres. Real-time images of electron density distributions with the corresponding lattice structures elucidate that the energy transfer begins with subpicosecond melting at the specimen boundary earlier than the lattice thermalization, and proceeds by forming voids. Two temperature molecular dynamics simulations uncovered the presence of both heterogeneous melting with the melting front propagation from surface and grain boundaries and homogeneous melting with random melting seeds and nanoscale voids. Supported by experimental and theoretical results, we provide a comprehensive atomic-scale picture that accounts for the ultrafast laser-induced melting and evaporation kinetics.
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Affiliation(s)
- Jaeyong Shin
- Department of Physics, POSTECH; Pohang37673, Korea
- Korea Research Initiative, Center for Ultrafast Science on Quantum Matter, Max Planck POSTECH; Pohang37673, Korea
- Photon Science Center, POSTECH, Pohang37673, Korea
| | - Chulho Jung
- Department of Physics, POSTECH; Pohang37673, Korea
- Korea Research Initiative, Center for Ultrafast Science on Quantum Matter, Max Planck POSTECH; Pohang37673, Korea
- Photon Science Center, POSTECH, Pohang37673, Korea
| | - Yungok Ihm
- Photon Science Center, POSTECH, Pohang37673, Korea
- Department of Chemistry, POSTECH, Pohang37673, Korea
| | - Seung-Phil Heo
- Department of Physics, POSTECH; Pohang37673, Korea
- Korea Research Initiative, Center for Ultrafast Science on Quantum Matter, Max Planck POSTECH; Pohang37673, Korea
- Photon Science Center, POSTECH, Pohang37673, Korea
| | - Daewoong Nam
- Photon Science Center, POSTECH, Pohang37673, Korea
- Pohang Accelerator Laboratory, Pohang37673, Korea
| | - Sangsoo Kim
- Pohang Accelerator Laboratory, Pohang37673, Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, Pohang37673, Korea
| | - Intae Eom
- Photon Science Center, POSTECH, Pohang37673, Korea
- Pohang Accelerator Laboratory, Pohang37673, Korea
| | - Ji Hoon Shim
- Photon Science Center, POSTECH, Pohang37673, Korea
- Department of Chemistry, POSTECH, Pohang37673, Korea
| | - Do Young Noh
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology; Gwangju61005, Korea
- Institute for Basic Science, Daejeon34126, Korea
| | - Changyong Song
- Department of Physics, POSTECH; Pohang37673, Korea
- Korea Research Initiative, Center for Ultrafast Science on Quantum Matter, Max Planck POSTECH; Pohang37673, Korea
- Photon Science Center, POSTECH, Pohang37673, Korea
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8
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Stagno JR. Preparation of RNA Microcrystals for Serial Femtosecond Crystallography Experiments. Methods Mol Biol 2023; 2568:233-242. [PMID: 36227572 DOI: 10.1007/978-1-0716-2687-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Serial femtosecond crystallography (SFX) experiments using an X-ray free electron laser (XFEL) is a burgeoning method for time-resolved structural studies of biomacromolecules. As with any crystallography experiment, the most important component is quality sample preparation. Whereas dozens of SFX experiments, including batch crystallization methods, have been reported for proteins, very few have been reported for RNA. This chapter outlines standard procedures for preparing RNA microcrystalline samples suitable for SFX studies.
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Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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Stagno JR, Knoska J, Chapman HN, Wang YX. Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates. Methods Mol Biol 2023; 2568:243-249. [PMID: 36227573 DOI: 10.1007/978-1-0716-2687-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers (XFEL), a new frontier has emerged in time-resolved crystallography whereby crystals can be mixed with ligand and then probed with X-rays (mix-and-inject) in real time and at room temperature. This chapter outlines the basic setup and procedures for mix-and-inject experiments for recording time-resolved crystallographic data of riboswitch RNA reaction states using serial femtosecond crystallography (SFX) and an XFEL.
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Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
- Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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Abstract
Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, nonvisual light effects, to bacterial light sensing and harvesting. Light-driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here, I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps, hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond together with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
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11
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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12
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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13
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Cho DH, Shen Z, Ihm Y, Wi DH, Jung C, Nam D, Kim S, Park SY, Kim KS, Sung D, Lee H, Shin JY, Hwang J, Lee SY, Lee SY, Han SW, Noh DY, Loh ND, Song C. High-Throughput 3D Ensemble Characterization of Individual Core-Shell Nanoparticles with X-ray Free Electron Laser Single-Particle Imaging. ACS Nano 2021; 15:4066-4076. [PMID: 33506675 DOI: 10.1021/acsnano.0c07961] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The structures as building blocks for designing functional nanomaterials have fueled the development of versatile nanoprobes to understand local structures of noncrystalline specimens. Progress in analyzing structures of individual specimens with atomic scale accuracy has been notable recently. In most cases, however, only a limited number of specimens are inspected lacking statistics to represent the systems with structural inhomogeneity. Here, by employing single-particle imaging with X-ray free electron lasers and algorithms for multiple-model 3D imaging, we succeeded in investigating several thousand specimens in a couple of hours and identified intrinsic heterogeneities with 3D structures. Quantitative analysis has unveiled 3D morphology, facet indices, and elastic strain. The 3D elastic energy distribution is further corroborated by molecular dynamics simulations to gain mechanical insight at the atomic level. This work establishes a route to high-throughput characterization of individual specimens in large ensembles, hence overcoming statistical deficiency while providing quantitative information at the nanoscale.
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Affiliation(s)
- Do Hyung Cho
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Zhou Shen
- Department of Physics, National University of Singapore, Singapore 117551
| | - Yungok Ihm
- Department of Chemistry, POSTECH, Pohang 37673, Korea
| | - Dae Han Wi
- Center for Nanotectonics, Department of Chemistry and KI for the NanoCentury, KAIST, Daejeon 34141, Korea
| | - Chulho Jung
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Daewoong Nam
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Korea
| | - Sangsoo Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Korea
| | - Sang-Youn Park
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Korea
| | - Kyung Sook Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Korea
| | - Daeho Sung
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Heemin Lee
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Jae-Yong Shin
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Junha Hwang
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Sung Yun Lee
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
| | - Su Yong Lee
- Pohang Accelerator Laboratory, POSTECH, Pohang 37673, Korea
| | - Sang Woo Han
- Center for Nanotectonics, Department of Chemistry and KI for the NanoCentury, KAIST, Daejeon 34141, Korea
| | - Do Young Noh
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Institute for Basic Science (IBS), Daejeon 34126, Korea
| | - N Duane Loh
- Department of Physics, National University of Singapore, Singapore 117551
- Department of Biological Sciences, National University of Singapore, Singapore 117557
| | - Changyong Song
- Department of Physics and Photon Science Center, POSTECH, Pohang 37673, Korea
- Asia Pacific Center for Theoretical Physics (APCTP), POSTECH, Pohang 37673, Korea
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14
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Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A 2020; 117:12624-12635. [PMID: 32434915 PMCID: PMC7293653 DOI: 10.1073/pnas.2000529117] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
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Affiliation(s)
- Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Casper de Lichtenberg
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Petko Chernev
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, OX11 0FA Didcot, United Kingdom
| | - Nicholas Saichek
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Trent Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
| | - Shigeki Owada
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bolotovsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany;
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden;
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
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15
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Nakasako M, Kobayashi A, Takayama Y, Asakura K, Oide M, Okajima K, Oroguchi T, Yamamoto M. Methods and application of coherent X-ray diffraction imaging of noncrystalline particles. Biophys Rev 2020; 12:541-567. [PMID: 32180121 DOI: 10.1007/s12551-020-00690-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/05/2020] [Indexed: 11/26/2022] Open
Abstract
Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. The structure of the particle projected along the direction of the beam is, in principle, retrieved from a finely recorded diffraction pattern alone by using iterative phase-retrieval algorithms. Here, we describe fundamental theory and experimental methods of coherent X-ray diffraction imaging and the recent application in structural studies of noncrystalline specimens by using X-rays available at Super Photon Ring of 8-Gev and SPring-8 Angstrom Compact Free Electron Laser in Japan.
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Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan.
| | - Amane Kobayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Kenta Asakura
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan
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16
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Ishikawa T. Accelerator-based X-ray sources: synchrotron radiation, X-ray free electron lasers and beyond. Philos Trans A Math Phys Eng Sci 2019; 377:20180231. [PMID: 31030654 DOI: 10.1098/rsta.2018.0231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
The evolution of synchrotron radiation (SR) sources and related sciences is discussed to explain the 'generation' of the SR sources. Most of the contemporary SR sources belong to the third generation, where the storage rings are optimized for the use of undulator radiation. The undulator development allowed to reduction of the electron energy of the storage ring necessary for delivering 10 keV X-rays from the initial 6-8 GeV to the current 3 Gev. Now is the transitional period from the double-bend-achromat lattice-based storage ring to the multi-bend-achromat lattice to achieve much smaller electron beam emittance. Free electron lasers are the other important accelerator-based light sources which recently reached hard X-ray regime by using self-amplified spontaneous emission scheme. Future accelerator-based X-ray sources should be continuous wave X-ray free electron lasers and pulsed X-ray free electron lasers. Some pathways to reach the future case are discussed. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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Affiliation(s)
- Tetsuya Ishikawa
- RIKEN SPring-8 Center, RIKEN , Kouto 1-1-1, Sayo-cho, Hyogo 679-5148 , Japan
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17
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Hutchison CDM, van Thor JJ. Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography. Philos Trans A Math Phys Eng Sci 2019; 377:20170474. [PMID: 30929625 PMCID: PMC6452057 DOI: 10.1098/rsta.2017.0474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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18
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Coffee RN, Cryan JP, Duris J, Helml W, Li S, Marinelli A. Development of ultrafast capabilities for X-ray free-electron lasers at the linac coherent light source. Philos Trans A Math Phys Eng Sci 2019; 377:20180386. [PMID: 30929632 PMCID: PMC6452055 DOI: 10.1098/rsta.2018.0386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/18/2019] [Indexed: 05/07/2023]
Abstract
The ability to produce ultrashort, high-brightness X-ray pulses is revolutionizing the field of ultrafast X-ray spectroscopy. Free-electron laser (FEL) facilities are driving this revolution, but unique aspects of the FEL process make the required characterization and use of the pulses challenging. In this paper, we describe a number of developments in the generation of ultrashort X-ray FEL pulses, and the concomitant progress in the experimental capabilities necessary for their characterization and use at the Linac Coherent Light Source. This includes the development of sub-femtosecond hard and soft X-ray pulses, along with ultrafast characterization techniques for these pulses. We also describe improved techniques for optical cross-correlation as needed to address the persistent challenge of external optical laser synchronization with these ultrashort X-ray pulses. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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Affiliation(s)
- Ryan N. Coffee
- SLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA 94025, USA
- SLAC National Accelerator Laboratory, Stanford Pulse Institute, Menlo Park, CA 94025, USA
| | - James P. Cryan
- SLAC National Accelerator Laboratory, Linac Coherent Light Source, Menlo Park, CA 94025, USA
- SLAC National Accelerator Laboratory, Stanford Pulse Institute, Menlo Park, CA 94025, USA
| | - Joseph Duris
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Wolfram Helml
- Zentrum für Synchrotronstrahlung, Technische Universität Dortmund, Maria-Goeppert-Mayer-Straße 2, 44227 Dortmund, Germany
- Physik-Department E11, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Siqi Li
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Physics, Stanford University, Stanford, CA 94305, USA
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19
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Cao Y, Mazzone DG, Meyers D, Hill JP, Liu X, Wall S, Dean MPM. Ultrafast dynamics of spin and orbital correlations in quantum materials: an energy- and momentum-resolved perspective. Philos Trans A Math Phys Eng Sci 2019; 377:20170480. [PMID: 30929631 PMCID: PMC6452052 DOI: 10.1098/rsta.2017.0480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 05/07/2023]
Abstract
Many remarkable properties of quantum materials emerge from states with intricate coupling between the charge, spin and orbital degrees of freedom. Ultrafast photo-excitation of these materials holds great promise for understanding and controlling the properties of these states. Here, we introduce time-resolved resonant inelastic X-ray scattering (tr-RIXS) as a means of measuring the charge, spin and orbital excitations out of equilibrium. These excitations encode the correlations and interactions that determine the detailed properties of the states generated. After outlining the basic principles and instrumentations of tr-RIXS, we review our first observations of transient antiferromagnetic correlations in quasi two dimensions in a photo-excited Mott insulator and present possible future routes of this fast-developing technique. The increasing number of X-ray free electron laser facilities not only enables tackling long-standing fundamental scientific problems, but also promises to unleash novel inelastic X-ray scattering spectroscopies. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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Affiliation(s)
- Y. Cao
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - D. G. Mazzone
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - D. Meyers
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - J. P. Hill
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - X. Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - S. Wall
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - M. P. M. Dean
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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20
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Buzzi M, Först M, Cavalleri A. Measuring non-equilibrium dynamics in complex solids with ultrashort X-ray pulses. Philos Trans A Math Phys Eng Sci 2019; 377:20170478. [PMID: 30929635 PMCID: PMC6452049 DOI: 10.1098/rsta.2017.0478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Strong interactions between electrons give rise to the complexity of quantum materials, which exhibit exotic functional properties and extreme susceptibility to external perturbations. A growing research trend involves the study of these materials away from equilibrium, especially in cases in which the stimulation with optical pulses can coherently enhance cooperative orders. Time-resolved X-ray probes are integral to this type of research, as they can be used to track atomic and electronic structures as they evolve on ultrafast timescales. Here, we review a series of recent experiments where femtosecond X-ray diffraction was used to measure dynamics of complex solids. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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Affiliation(s)
- Michele Buzzi
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Michael Först
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Andrea Cavalleri
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
- Department of Physics, Oxford University, Clarendon Laboratory, Oxford, UK
- e-mail:
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21
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Katayama T, Hirano T, Morioka Y, Sano Y, Osaka T, Owada S, Togashi T, Yabashi M. X-ray optics for advanced ultrafast pump-probe X-ray experiments at SACLA. J Synchrotron Radiat 2019; 26:333-338. [PMID: 30855240 PMCID: PMC6412179 DOI: 10.1107/s1600577518018362] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/27/2018] [Indexed: 05/17/2023]
Abstract
X-ray optics were implemented for advanced ultrafast X-ray experiments with different techniques at the hard X-ray beamline BL3 of SPring-8 Ångstrom Compact free-electron LAser. A double channel-cut crystal monochromator (DCCM) and compound refractive lenses (CRLs) were installed to tailor the beam conditions. These X-ray optics can work simultaneously with an arrival-timing monitor that compensates for timing jitter and drift. Inner-walls of channel-cut crystals (CCs) in the DCCM were processed by plasma chemical vaporization machining to remove crystallographic damage. Four-bounced reflection profiles of the CCs were investigated and excellent diffraction qualities were achieved. The use of CRLs enabled two-dimensional X-ray focusing with a spot size of ∼1.5 µm × 1.5 µm full width at half-maximum, while keeping reasonable throughputs for a wide photon energy range of 5-15 keV.
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Affiliation(s)
- Tetsuo Katayama
- XFEL Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Hirano
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuki Morioka
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yasuhisa Sano
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Taito Osaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- XFEL Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tadashi Togashi
- XFEL Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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22
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Abstract
Innovations are expanding the capabilities of experimental investigations of the structural properties of membrane proteins. Traditionally, three-dimensional structures have been determined by measuring x-ray diffraction using protein crystals with a size of least 100 μm. For membrane proteins, achieving crystals suitable for these measurements has been a significant challenge. The availabilities of micro-focus x-ray beams and the new instrumentation of x-ray free-electron lasers have opened up the possibility of using submicrometer-sized crystals. In addition, advances in cryo-electron microscopy have expanded the use of this technique for studies of protein crystals as well as studies of individual proteins as single particles. Together, these approaches provide unprecedented opportunities for the exploration of structural properties of membrane proteins, including dynamical changes during protein function.
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Affiliation(s)
- James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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23
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Ishigami I, Lewis-Ballester A, Echelmeier A, Brehm G, Zatsepin NA, Grant TD, Coe JD, Lisova S, Nelson G, Zhang S, Dobson ZF, Boutet S, Sierra RG, Batyuk A, Fromme P, Fromme R, Spence JCH, Ros A, Yeh SR, Rousseau DL. Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase. Proc Natl Acad Sci U S A 2019; 116:3572-7. [PMID: 30808749 DOI: 10.1073/pnas.1814526116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase (CcO) reduces dioxygen to water and harnesses the chemical energy to drive proton translocation across the inner mitochondrial membrane by an unresolved mechanism. By using time-resolved serial femtosecond crystallography, we identified a key oxygen intermediate of bovine CcO. It is assigned to the PR-intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a 3 iron atom is in a ferryl (Fe4+ = O2-) configuration, and heme a and CuB are oxidized while CuA is reduced. A Helix-X segment is poised in an open conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a distinct structure. These data offer insights into the mechanism by which the oxygen chemistry is coupled to unidirectional proton translocation.
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24
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Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. J Biol Chem 2018; 294:794-804. [PMID: 30455349 DOI: 10.1074/jbc.ra118.004038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.
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Affiliation(s)
- Ji-Hye Yun
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China
| | - Jae-Hyun Park
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Yang Wang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Mio Ohki
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Zeyu Jin
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Wonbin Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Hao Hu
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Chufeng Li
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Nadia Zatsepin
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Hyun-Soo Cho
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea
| | - Uwe Weierstall
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Leihan Tang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China,
| | - Weontae Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea,
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25
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Oroguchi T, Yoshidome T, Yamamoto T, Nakasako M. Growth of Cuprous Oxide Particles in Liquid-Phase Synthesis Investigated by X-ray Laser Diffraction. Nano Lett 2018; 18:5192-5197. [PMID: 29990436 DOI: 10.1021/acs.nanolett.8b02153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cuprous oxide (Cu2O) particles obtained by surfactant-assisted liquid-phase synthesis have cuboid shapes but the internal structures are difficult to be visualized by electron microscopy. Herein, we investigated the internal structures of numerous individual Cu2O particles with submicrometer dimensions by X-ray diffraction imaging (XDI) using X-ray free-electron laser (XFEL) pulses. The reconstructed two-dimensional electron density maps, which displayed inhomogeneous internal structures, were divided into five classes characterized by the positions and shapes of high and low electron density areas. Further analysis of the maps in each class by a manifold learning algorithm revealed that the internal structures of Cu2O particles varied in correlation with total electron density while retaining the characteristics within each class. On the basis of the analyses, we proposed a growth mechanism to yield the inhomogeneity in the internal structures of Cu2O particles in surfactant-mediated liquid-phase synthesis.
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Affiliation(s)
- Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama , 223-8522 Japan
- RIKEN SPring-8 Center , 1-1-1 Kohto, Sayo , Sayo-gun, Hyogo 679-5148 Japan
| | - Takashi Yoshidome
- Department of Applied Physics, Graduate School of Engineering , Tohoku University , 6-6-05, Aoba, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
| | - Takahiro Yamamoto
- Department of Physics, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama , 223-8522 Japan
- RIKEN SPring-8 Center , 1-1-1 Kohto, Sayo , Sayo-gun, Hyogo 679-5148 Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama , 223-8522 Japan
- RIKEN SPring-8 Center , 1-1-1 Kohto, Sayo , Sayo-gun, Hyogo 679-5148 Japan
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26
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Heimann P, Moeller S, Carbajo S, Song S, Dakovski G, Nordlund D, Fritz D. Laser power meters as an X-ray power diagnostic for LCLS-II. J Synchrotron Radiat 2018; 25:72-76. [PMID: 29271754 PMCID: PMC5741121 DOI: 10.1107/s1600577517014096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/29/2017] [Indexed: 05/23/2023]
Abstract
For the LCLS-II X-ray instruments, laser power meters are being developed as compact X-ray power diagnostics to operate at soft and tender X-ray photon energies. These diagnostics can be installed at various locations along an X-ray free-electron laser (FEL) beamline in order to monitor the transmission of X-ray optics along the beam path. In addition, the power meters will be used to determine the absolute X-ray power at the endstations. Here, thermopile power meters, which measure average power, and have been chosen primarily for their compatibility with the high repetition rates at LCLS-II, are evaluated. A number of characteristics in the soft X-ray range are presented including linearity, calibrations conducted with a photodiode and a gas monitor detector as well as ultra-high-vacuum compatibility tests using residual gas analysis. The application of these power meters for LCLS-II and other X-ray FEL sources is discussed.
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Affiliation(s)
- Philip Heimann
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Correspondence e-mail:
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Georgi Dakovski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dennis Nordlund
- Stanford Synchrotron Radiation Laboratory, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - David Fritz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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27
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Abstract
Membrane proteins, including G protein-coupled receptors (GPCRs), constitute the most important drug targets. The increasing number of targets requires new structural information, which has proven tremendously challenging due to the difficulties in growing diffraction-quality crystals. Recent developments of serial femtosecond crystallography at X-ray free electron lasers combined with the use of membrane-mimetic gel-like matrix of lipidic cubic phase (LCP-SFX) for crystal growth and delivery hold significant promise to accelerate structural studies of membrane proteins. This chapter describes the development and current status of the LCP-SFX technology and elaborates its future role in structural biology of membrane proteins.
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Affiliation(s)
- Lan Zhu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.,Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-1604, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Vadim Cherezov
- Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Wei Liu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287-1604, USA.
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28
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Johansson LC, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci 2017; 42:749-762. [PMID: 28733116 DOI: 10.1016/j.tibs.2017.06.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Benjamin Stauch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA.
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29
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Ishigami I, Zatsepin NA, Hikita M, Conrad CE, Nelson G, Coe JD, Basu S, Grant TD, Seaberg MH, Sierra RG, Hunter MS, Fromme P, Fromme R, Yeh SR, Rousseau DL. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Proc Natl Acad Sci U S A 2017; 114:8011-6. [PMID: 28698372 DOI: 10.1073/pnas.1705628114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe-C-O angle of ∼142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near CuB, which, in turn, moves closer to the heme a3 iron by ∼0.38 Å. Structural comparison reveals that ligand binding to the heme a3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.
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30
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André JM, Jonnard P. Ultra-short and ultra-intense X-ray free-electron laser single pulse in one-dimensional photonic crystals. J Synchrotron Radiat 2017; 24:376-385. [PMID: 28244430 DOI: 10.1107/s1600577517000820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 06/06/2023]
Abstract
The propagation within a one-dimensional photonic crystal of a single ultra-short and ultra-intense pulse delivered by an X-ray free-electron laser is analysed with the framework of the time-dependent coupled-wave theory in non-linear media. It is shown that the reflection and the transmission of an ultra-short pulse present a transient period conditioned by the extinction length and also the thickness of the structure for transmission. For ultra-intense pulses, non-linear effects are expected: they could give rise to numerous phenomena, bi-stability, self-induced transparency, gap solitons, switching, etc., which have been previously shown in the optical domain.
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Affiliation(s)
- Jean Michel André
- Laboratoire de Chimie Physique-Matière et Rayonnement, Sorbonne Universités, UPMC Université Paris 06, Boîte courrier 1140, 4 place Jussieu, F-75252 Paris Cedex 05, France
| | - Philippe Jonnard
- Laboratoire de Chimie Physique-Matière et Rayonnement, Sorbonne Universités, UPMC Université Paris 06, Boîte courrier 1140, 4 place Jussieu, F-75252 Paris Cedex 05, France
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31
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Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. eLife 2016; 5. [PMID: 27731796 PMCID: PMC5094853 DOI: 10.7554/elife.18740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/11/2016] [Indexed: 12/03/2022] Open
Abstract
X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models. DOI:http://dx.doi.org/10.7554/eLife.18740.001
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Affiliation(s)
- Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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32
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Barnes CO, Kovaleva EG, Fu X, Stevenson HP, Brewster AS, DePonte DP, Baxter EL, Cohen AE, Calero G. Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography. Arch Biochem Biophys 2016; 602:61-68. [PMID: 26944553 DOI: 10.1016/j.abb.2016.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Serial femtosecond crystallography (SFX) employing high-intensity X-ray free-electron laser (XFEL) sources has enabled structural studies on microcrystalline protein samples at non-cryogenic temperatures. However, the identification and optimization of conditions that produce well diffracting microcrystals remains an experimental challenge. Here, we report parallel SFX and transmission electron microscopy (TEM) experiments using fragmented microcrystals of wild type (WT) homoprotocatechuate 2,3-dioxygenase (HPCD) and an active site variant (H200Q). Despite identical crystallization conditions and morphology, as well as similar crystal size and density, the indexing efficiency of the diffraction data collected using the H200Q variant sample was over 7-fold higher compared to the diffraction results obtained using the WT sample. TEM analysis revealed an abundance of protein aggregates, crystal conglomerates and a smaller population of highly ordered lattices in the WT sample as compared to the H200Q variant sample. While not reported herein, the 1.75 Å resolution structure of the H200Q variant was determined from ∼16 min of beam time, demonstrating the utility of TEM analysis in evaluating sample monodispersity and lattice quality, parameters critical to the efficiency of SFX experiments.
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Affiliation(s)
- Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Aaron S Brewster
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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Siefermann KR, Pemmaraju CD, Neppl S, Shavorskiy A, Cordones AA, Vura-Weis J, Slaughter DS, Sturm FP, Weise F, Bluhm H, Strader ML, Cho H, Lin MF, Bacellar C, Khurmi C, Guo J, Coslovich G, Robinson JS, Kaindl RA, Schoenlein RW, Belkacem A, Neumark DM, Leone SR, Nordlund D, Ogasawara H, Krupin O, Turner JJ, Schlotter WF, Holmes MR, Messerschmidt M, Minitti MP, Gul S, Zhang JZ, Huse N, Prendergast D, Gessner O. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye-Semiconductor Interface. J Phys Chem Lett 2014; 5:2753-9. [PMID: 26277975 DOI: 10.1021/jz501264x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding interfacial charge-transfer processes on the atomic level is crucial to support the rational design of energy-challenge relevant systems such as solar cells, batteries, and photocatalysts. A femtosecond time-resolved core-level photoelectron spectroscopy study is performed that probes the electronic structure of the interface between ruthenium-based N3 dye molecules and ZnO nanocrystals within the first picosecond after photoexcitation and from the unique perspective of the Ru reporter atom at the center of the dye. A transient chemical shift of the Ru 3d inner-shell photolines by (2.3 ± 0.2) eV to higher binding energies is observed 500 fs after photoexcitation of the dye. The experimental results are interpreted with the aid of ab initio calculations using constrained density functional theory. Strong indications for the formation of an interfacial charge-transfer state are presented, providing direct insight into a transient electronic configuration that may limit the efficiency of photoinduced free charge-carrier generation.
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Affiliation(s)
- Katrin R Siefermann
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Chaitanya D Pemmaraju
- ‡The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stefan Neppl
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrey Shavorskiy
- §Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Amy A Cordones
- ∥Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Josh Vura-Weis
- ∥Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel S Slaughter
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Felix P Sturm
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Fabian Weise
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hendrik Bluhm
- §Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthew L Strader
- §Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hana Cho
- §Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ming-Fu Lin
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ∥Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Camila Bacellar
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ∥Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Champak Khurmi
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jinghua Guo
- #Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Giacomo Coslovich
- ⊥Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joseph S Robinson
- ⊥Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Robert A Kaindl
- ⊥Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert W Schoenlein
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ⊥Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ali Belkacem
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel M Neumark
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ∥Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Stephen R Leone
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ∥Department of Chemistry, University of California, Berkeley, California 94720, United States
- ○Department of Physics, University of California, Berkeley, California 94720, United States
| | - Dennis Nordlund
- ◆SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Hirohito Ogasawara
- ◆SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Oleg Krupin
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- ¶European XFEL GmbH, 22761 Hamburg, Germany
| | - Joshua J Turner
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - William F Schlotter
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael R Holmes
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Marc Messerschmidt
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Michael P Minitti
- ▽Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Sheraz Gul
- #Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- +Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Jin Z Zhang
- +Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Nils Huse
- ■Physics Department, University of Hamburg and Max-Planck Institute for Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - David Prendergast
- ‡The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oliver Gessner
- †Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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