1
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Stransky M, E J, Jurek Z, Santra R, Bean R, Ziaja B, Mancuso AP. Computational study of diffraction image formation from XFEL irradiated single ribosome molecule. Sci Rep 2024; 14:10617. [PMID: 38720133 PMCID: PMC11078940 DOI: 10.1038/s41598-024-61314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX, available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation.
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Affiliation(s)
- Michal Stransky
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Krakow, Poland.
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21, Prague 8, Czech Republic.
| | - Juncheng E
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Krakow, Poland
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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2
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Round A, Jungcheng E, Fortmann-Grote C, Giewekemeyer K, Graceffa R, Kim C, Kirkwood H, Mills G, Round E, Sato T, Pascarelli S, Mancuso A. Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:141-162. [PMID: 38507205 DOI: 10.1007/978-3-031-52193-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.
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Affiliation(s)
| | | | | | | | | | - Chan Kim
- European XFEL, Schenefeld, Germany
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3
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Xu H, Wu L, Xue Y, Yang T, Xiong T, Wang C, He S, Sun H, Cao Z, Liu J, Wang S, Li Z, Naeem A, Yin X, Zhang J. Advances in Structure Pharmaceutics from Discovery to Evaluation and Design. Mol Pharm 2023; 20:4404-4429. [PMID: 37552597 DOI: 10.1021/acs.molpharmaceut.3c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Drug delivery systems (DDSs) play an important role in delivering active pharmaceutical ingredients (APIs) to targeted sites with a predesigned release pattern. The chemical and biological properties of APIs and excipients have been extensively studied for their contribution to DDS quality and effectiveness; however, the structural characteristics of DDSs have not been adequately explored. Structure pharmaceutics involves the study of the structure of DDSs, especially the three-dimensional (3D) structures, and its interaction with the physiological and pathological structure of organisms, possibly influencing their release kinetics and targeting abilities. A systematic overview of the structures of a variety of dosage forms, such as tablets, granules, pellets, microspheres, powders, and nanoparticles, is presented. Moreover, the influence of structures on the release and targeting capability of DDSs has also been discussed, especially the in vitro and in vivo release correlation and the structure-based organ- and tumor-targeting capabilities of particles with different structures. Additionally, an in-depth discussion is provided regarding the application of structural strategies in the DDSs design and evaluation. Furthermore, some of the most frequently used characterization techniques in structure pharmaceutics are briefly described along with their potential future applications.
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Affiliation(s)
- Huipeng Xu
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wu
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, School of Pharmacy, Ministry of Education, Yantai University, Yantai 264005, China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Yanling Xue
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Ting Yang
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ting Xiong
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Caifen Wang
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Siyu He
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyu Sun
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zeying Cao
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Liu
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Siwen Wang
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Li
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Abid Naeem
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
| | - Xianzhen Yin
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Lingang Laboratory, Shanghai 201602, China
| | - Jiwen Zhang
- Center for Drug Delivery Systems, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang 330004, China
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, National Institutes for Food and Drug Control, No.2 Tiantan Xili, Beijing 100050, China
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4
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Nakano M, Miyashita O, Tama F. Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:024101. [PMID: 36942031 PMCID: PMC10024609 DOI: 10.1063/4.0000175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 05/03/2023]
Abstract
Single-particle analysis using x-ray free-electron lasers (XFELs) is a novel method for obtaining structural information of samples in a state close to nature. In particular, it is suitable for observing the inner structure of large biomolecules by taking advantage of the high transmittance of x-rays. However, systematic studies on the resolution achievable for large molecules are lacking. In this study, the molecular size dependence of the resolution of a three-dimensional (3D) structure resulting from XFEL single-particle reconstruction is evaluated using synthetic data. Evidently, 3D structures of larger molecules can be restored with higher detail (defined relative to the molecular sizes) than smaller ones; however, reconstruction with high absolute resolution (defined in nm-1) is challenging. Our results provide useful information for the experimental design of 3D structure reconstruction using coherent x-ray diffraction patterns of single-particles.
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Affiliation(s)
- Miki Nakano
- RIKEN Center for Computational Science, 6-7-1, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, 6-7-1, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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5
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E J, Kim Y, Bielecki J, Sikorski M, de Wijn R, Fortmann-Grote C, Sztuk-Dambietz J, Koliyadu JCP, Letrun R, Kirkwood HJ, Sato T, Bean R, Mancuso AP, Kim C. Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:064101. [PMID: 36411869 PMCID: PMC9675053 DOI: 10.1063/4.0000169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 05/15/2023]
Abstract
The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.
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Affiliation(s)
- Juncheng E
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Bielecki
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Sikorski
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R. de Wijn
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - R. Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - T. Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R. Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - C. Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Author to whom correspondence should be addressed:
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6
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Yumoto H, Koyama T, Suzuki A, Joti Y, Niida Y, Tono K, Bessho Y, Yabashi M, Nishino Y, Ohashi H. High-fluence and high-gain multilayer focusing optics to enhance spatial resolution in femtosecond X-ray laser imaging. Nat Commun 2022; 13:5300. [PMID: 36100607 PMCID: PMC9470745 DOI: 10.1038/s41467-022-33014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
With the emergence of X-ray free-electron lasers (XFELs), coherent diffractive imaging (CDI) has acquired a capability for single-particle imaging (SPI) of non-crystalline objects under non-cryogenic conditions. However, the single-shot spatial resolution is limited to ~5 nanometres primarily because of insufficient fluence. Here, we present a CDI technique whereby high resolution is achieved with very-high-fluence X-ray focusing using multilayer mirrors with nanometre precision. The optics can focus 4-keV XFEL down to 60 nm × 110 nm and realize a fluence of >3 × 105 J cm−2 pulse−1 or >4 × 1012 photons μm−2 pulse−1 with a tenfold increase in the total gain compared to conventional optics due to the high demagnification. Further, the imaging of fixed-target metallic nanoparticles in solution attained an unprecedented 2-nm resolution in single-XFEL-pulse exposure. These findings can further expand the capabilities of SPI to explore the relationships between dynamic structures and functions of native biomolecular complexes. Here, the authors realize an ultra-high fluence X-ray laser by high-gain multilayer focusing optics. This enables in-solution imaging with 2-nm resolution in a single-pulse exposure, making strides toward biomolecular imaging under physiological conditions.
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Affiliation(s)
- Hirokatsu Yumoto
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan. .,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
| | - Takahisa Koyama
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Akihiro Suzuki
- Research Institute for Electronic Science, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yoshiya Niida
- Research Institute for Electronic Science, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.,Institute of Biological Chemistry, Academia Sinica, 128, Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yoshinori Nishino
- Research Institute for Electronic Science, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Japan.
| | - Haruhiko Ohashi
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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7
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Tokuhisa A, Akinaga Y, Terayama K, Okamoto Y, Okuno Y. Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network. J Chem Inf Model 2022; 62:3352-3364. [PMID: 35820663 PMCID: PMC9326892 DOI: 10.1021/acs.jcim.2c00660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Femtosecond X-ray pulse lasers are promising probes for
the elucidation
of the multiconformational states of biomolecules because they enable
snapshots of single biomolecules to be observed as coherent diffraction
images. Multi-image processing using an X-ray free-electron laser
has proven to be a successful structural analysis method for viruses.
However, the performance of single-particle analysis (SPA) for flexible
biomolecules with sizes ≤100 nm remains difficult. Owing to
the multiconformational states of biomolecules and noisy character
of diffraction images, diffraction image improvement by multi-image
processing is often ineffective for such molecules. Herein, a single-image
super-resolution (SR) model was constructed using an SR convolutional
neural network (SRCNN). Data preparation was performed in silico to
consider the actual observation situation with unknown molecular orientations
and the fluctuation of molecular structure and incident X-ray intensity.
It was demonstrated that the trained SRCNN model improved the single-particle
diffraction image quality, corresponding to an observed image with
an incident X-ray intensity (approximately three to seven times higher
than the original X-ray intensity), while retaining the individuality
of the diffraction images. The feasibility of SPA for flexible biomolecules
with sizes ≤100 nm was dramatically increased by introducing
the SRCNN improvement at the beginning of the various structural analysis
schemes.
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Affiliation(s)
- Atsushi Tokuhisa
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshinobu Akinaga
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,VINAS Co., Ltd., Keihan Dojima Bldg., Dojima 2 1 31, Kita-ku, Osaka 530-0003, Japan
| | - Kei Terayama
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Yuji Okamoto
- Graduate School of Medicine, Kyoto University, Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Center for Cluster Development and Coordination, Foundation for Biomedical Research and Innovation at Kobe, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Graduate School of Medicine, Kyoto University, Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
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8
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Tiwari SP, Tama F, Miyashita O. Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns. J Chem Inf Model 2021; 61:4108-4119. [PMID: 34357759 DOI: 10.1021/acs.jcim.1c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
X-ray free-electron laser (XFEL) scattering promises to probe single biomolecular complexes without crystallization, enabling the study of biomolecular structures under near-physiological conditions at room temperature. However, such structural determination of biomolecules is extremely challenging thus far. In addition to the large numbers of diffraction patterns required, the orientation of each diffraction pattern needs to be accurately estimated and the missing phase information needs to be recovered for three-dimensional (3D) structure reconstruction. Given the current limitations to the amount and resolution of the data available from single-particle XFEL scattering experiments, we propose an alternative approach to find plausible 3D biological shapes from a limited number of diffraction patterns to serve as a starting point for further analyses. In our proposed strategy, small sets of input (e.g., five) XFEL diffraction patterns were matched against a library of diffraction patterns simulated from 1628 electron microscopy (EM) models to find potential matching 3D models that are consistent with the input diffraction patterns. This approach was tested for three example cases: EMD-3457 (Thermoplasma acidophilum 20S proteasome), EMD-5141 (Escherichia coli 70S ribosome complex), and EMD-5152 (budding yeast Nup84 complex). We observed that choosing the best strategy to define matching regions on the diffraction patterns is critical for identifying correctly matching diffraction patterns. While increasing the number of input diffraction patterns improved the matches in some cases, we found that the resulting matches are more dependent on the uniqueness or complexity of the shape as captured in the individual input diffraction patterns and the availability of a similar 3D biological shape in the search library. The protocol could be useful for finding candidate models for a limited amount of low-resolution data, even when insufficient for reconstruction, performing a quick exploration of new data upon collection, and the analysis of the conformational heterogeneity of the particle of interest as captured within the diffraction patterns.
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Affiliation(s)
- Sandhya P Tiwari
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan.,Graduate School of Science, Department of Physics, Nagoya University, Nagoya, Aichi 464-8601, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
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9
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Marcus G, Halavanau A, Huang Z, Krzywinski J, MacArthur J, Margraf R, Raubenheimer T, Zhu D. Refractive Guide Switching a Regenerative Amplifier Free-Electron Laser for High Peak and Average Power Hard X Rays. PHYSICAL REVIEW LETTERS 2020; 125:254801. [PMID: 33416365 DOI: 10.1103/physrevlett.125.254801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
We present an x-ray regenerative amplifier free-electron laser design capable of producing fully coherent hard x-ray pulses across a broad tuning range at a high steady state repetition rate. The scheme leverages a strong undulator taper and an apertured diamond output-coupling cavity crystal to produce both high peak and average spectral brightness radiation that is 2 to 3 orders of magnitude greater than conventional single-pass self-amplified spontaneous emission free-electron laser amplifiers. Refractive guiding in the postsaturation regime is found to play a key role in passively controlling the stored cavity power. The scheme is explored both analytically and numerically in the context of the Linac Coherent Light Source II High Energy upgrade.
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Affiliation(s)
- Gabriel Marcus
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alex Halavanau
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Zhirong Huang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jacek Krzywinski
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - James MacArthur
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Rachel Margraf
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Tor Raubenheimer
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Diling Zhu
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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10
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Shelby M, Gilbile D, Grant T, Bauer W, Segelke B, He W, Evans A, Crespo N, Fischer P, Pakendorf T, Hennicke V, Hunter M, Batyuk A, Barthelmess M, Meents A, Kuhl T, Frank M, Coleman M. Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies. CRYSTALS 2020; 10. [PMID: 35686136 PMCID: PMC9175823 DOI: 10.3390/cryst10100886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
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Affiliation(s)
- M.L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - D. Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - T.D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - W.J. Bauer
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - B. Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - W. He
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - A.C. Evans
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - N. Crespo
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - P. Fischer
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - V. Hennicke
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - M.S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T.L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - M. Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
| | - M.A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
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11
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Tokuhisa A, Kanada R, Chiba S, Terayama K, Isaka Y, Ma B, Kamiya N, Okuno Y. Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. J Chem Inf Model 2020; 60:2803-2818. [PMID: 32469517 DOI: 10.1021/acs.jcim.0c00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biomolecular imaging using X-ray free-electron lasers (XFELs) has been successfully applied to serial femtosecond crystallography. However, the application of single-particle analysis for structure determination using XFELs with 100 nm or smaller biomolecules has two practical problems: the incomplete diffraction data sets for reconstructing 3D assembled structures and the heterogeneous conformational states of samples. A new diffraction template matching method is thus presented here to retrieve a plausible 3D structural model based on single noisy target diffraction patterns, assuming candidate structures. Two concepts are introduced here: prompt candidate diffraction, generated by enhanced sampled coarse-grain (CG) candidate structures, and efficient molecular orientation searching for matching based on Bayesian optimization. A CG model-based diffraction-matching protocol is proposed that achieves a 100-fold speed increase compared to exhaustive diffraction matching using an all-atom model. The conditions that enable multiconformational analysis were also investigated by simulated diffraction data for various conformational states of chromatin and ribosomes. The proposed method can enable multiconformational analysis, with a structural resolution of at least 20 Å for 270-800 Å flexible biomolecules, in experimental single-particle structure analyses that employ XFELs.
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Affiliation(s)
- Atsushi Tokuhisa
- RIKEN Cluster for Science and Technology Hub, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Center for Computational Science, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Ryo Kanada
- RIKEN Cluster for Science and Technology Hub, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Chiba
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kei Terayama
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan.,Graduate School of Medicine, Kyoto University, Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuta Isaka
- RIKEN Cluster for Science and Technology Hub, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Center for Cluster Development and Coordination, Foundation for Biomedical Research and Innovation at Kobe, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Biao Ma
- RIKEN Cluster for Science and Technology Hub, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Center for Cluster Development and Coordination, Foundation for Biomedical Research and Innovation at Kobe, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasushi Okuno
- RIKEN Cluster for Science and Technology Hub, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Medicine, Kyoto University, Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan.,Center for Cluster Development and Coordination, Foundation for Biomedical Research and Innovation at Kobe, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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12
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Shelby ML, Gilbile D, Grant TD, Seuring C, Segelke BW, He W, Evans AC, Pakendorf T, Fischer P, Hunter MS, Batyuk A, Barthelmess M, Meents A, Coleman MA, Kuhl TL, Frank M. A fixed-target platform for serial femtosecond crystallography in a hydrated environment. IUCRJ 2020; 7:30-41. [PMID: 31949902 PMCID: PMC6949605 DOI: 10.1107/s2052252519014003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/15/2019] [Indexed: 05/19/2023]
Abstract
For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.
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Affiliation(s)
- M. L. Shelby
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - D. Gilbile
- University of California at Davis, California, USA
| | - T. D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, Hauptman-Woodward Institute, SUNY University at Buffalo, Buffalo, New York, USA
| | - C. Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - B. W. Segelke
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - W. He
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - A. C. Evans
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - P. Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. A. Coleman
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. L. Kuhl
- University of California at Davis, California, USA
| | - M. Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
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13
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Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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14
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Halavanau A, Decker FJ, Emma C, Sheppard J, Pellegrini C. Very high brightness and power LCLS-II hard X-ray pulses. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:635-646. [PMID: 31074426 DOI: 10.1107/s1600577519002492] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/18/2019] [Indexed: 05/22/2023]
Abstract
The feasibility of generating X-ray pulses in the 4-8 keV fundamental photon energy range with 0.65 TW peak power, 15 fs pulse duration and 9 × 10-5 bandwidth using the LCLS-II copper linac and hard X-ray (HXR) undulator is shown. In addition, third-harmonic pulses with 8-12 GW peak power and narrow bandwidth are also generated. High-power and small-bandwidth X-rays are obtained using two electron bunches separated by about 1 ns, one to generate a high-power seed signal, the other to amplify it through the process of the HXR undulator tapering. The bunch delay is compensated by delaying the seed pulse with a four-crystal monochromator. The high-power seed leads to higher output power and better spectral properties, with more than 94% of the X-ray power within the near-transform-limited bandwidth. Some of the experiments made possible by X-ray pulses with these characteristics are discussed, such as single-particle imaging and high-field physics.
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Affiliation(s)
| | | | - Claudio Emma
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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15
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Beane G, Devkota T, Brown BS, Hartland GV. Ultrafast measurements of the dynamics of single nanostructures: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:016401. [PMID: 30485256 DOI: 10.1088/1361-6633/aaea4b] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ability to study single particles has revolutionized nanoscience. The advantage of single particle spectroscopy measurements compared to conventional ensemble studies is that they remove averaging effects from the different sizes and shapes that are present in the samples. In time-resolved experiments this is important for unraveling homogeneous and inhomogeneous broadening effects in lifetime measurements. In this report, recent progress in the development of ultrafast time-resolved spectroscopic techniques for interrogating single nanostructures will be discussed. The techniques include far-field experiments that utilize high numerical aperture (NA) microscope objectives, near-field scanning optical microscopy (NSOM) measurements, ultrafast electron microscopy (UEM), and time-resolved x-ray diffraction experiments. Examples will be given of the application of these techniques to studying energy relaxation processes in nanoparticles, and the motion of plasmons, excitons and/or charge carriers in different types of nanostructures.
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Affiliation(s)
- Gary Beane
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States of America
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16
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Imaging electron-density fluctuations by multidimensional X-ray photon-coincidence diffraction. Proc Natl Acad Sci U S A 2018; 116:395-400. [PMID: 30584098 DOI: 10.1073/pnas.1816730116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ultrafast spontaneous electron-density fluctuation dynamics in molecules is studied theoretically by off-resonant multiple X-ray diffraction events. The time- and wavevector-resolved photon-coincidence signals give an image of electron-density fluctuations expressed through the four-point correlation function of the charge density in momentum space. A Fourier transform of the signal provides a real-space image of the multipoint charge-density correlation functions, which reveal snapshots of the evolving electron density in between the diffraction events. The proposed technique is illustrated by ab initio simulations of the momentum- and real-space inelastic scattering signals from a linear cyanotetracetylene molecule.
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17
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Oberthür D. Biological single-particle imaging using XFELs - towards the next resolution revolution. IUCRJ 2018; 5:663-666. [PMID: 30443350 PMCID: PMC6211524 DOI: 10.1107/s2052252518015129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Better injectors resulting from careful iterative optimization used at high repetition XFELs in combination with better detectors and further developed algorithms might, in the not so distant future, result in a 'resolution revolution' in SPI, enabling the molecular and atomic imaging of the dynamics of biological macromolecules without the need to freeze or crystallize the sample.
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Affiliation(s)
- Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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18
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Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int J Mol Sci 2018; 19:E3401. [PMID: 30380757 PMCID: PMC6274748 DOI: 10.3390/ijms19113401] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
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Affiliation(s)
- Ashutosh Srivastava
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Arpita Srivastava
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Osamu Miyashita
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
| | - Florence Tama
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
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19
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Rouxel JR, Kowalewski M, Bennett K, Mukamel S. X-Ray Sum Frequency Diffraction for Direct Imaging of Ultrafast Electron Dynamics. PHYSICAL REVIEW LETTERS 2018; 120:243902. [PMID: 29956957 DOI: 10.1103/physrevlett.120.243902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Indexed: 05/23/2023]
Abstract
X-ray diffraction from molecules in the ground state produces an image of their charge density, and time-resolved x-ray diffraction can thus monitor the motion of the nuclei. However, the density change of excited valence electrons upon optical excitation can barely be monitored with regular diffraction techniques due to the overwhelming background contribution of the core electrons. We present a nonlinear x-ray technique made possible by novel free electron laser sources, which provides a spatial electron density image of valence electron excitations. The technique, sum frequency generation carried out with a visible pump and a broadband x-ray diffraction pulse, yields snapshots of the transition charge densities, which represent the electron density variations upon optical excitation. The technique is illustrated by ab initio simulations of transition charge density imaging for the optically induced electronic dynamics in a donor or acceptor substituted stilbene.
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Affiliation(s)
- Jérémy R Rouxel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - Markus Kowalewski
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - Kochise Bennett
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
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20
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