1
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Wollter A, De Santis E, Ekeberg T, Marklund EG, Caleman C. Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging. J Chem Phys 2024; 160:114108. [PMID: 38506290 DOI: 10.1063/5.0188772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins' orientation as each protein is randomly oriented when exposed to x-rays. Algorithms such as the expand, maximize, and compress (EMC) exist that can solve the orientation problem and reconstruct the three-dimensional diffraction intensity space, given sufficient measurements. If information about orientation were known, for example, by using an electric field to orient the particles, the reconstruction would benefit and potentially reach better results. We used simulated diffraction experiments to test how the reconstructions from EMC improve with particles' orientation to a preferred axis. Our reconstructions converged to correct maps of the three-dimensional diffraction space with fewer measurements if biased orientation information was considered. Even for a moderate bias, there was still significant improvement. Biased orientations also substantially improved the results in the case of missing central information, in particular in the case of small datasets. The effects were even more significant when adding a background with 50% the strength of the averaged diffraction signal photons to the diffraction patterns, sometimes reducing the data requirement for convergence by a factor of 10. This demonstrates the usefulness of having biased orientation information in single particle imaging experiments, even for a weaker bias than what was previously known. This could be a key component in overcoming the problems with background noise that currently plague these experiments.
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Affiliation(s)
- August Wollter
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Husargatan 3, 75124 Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Husargatan 3, 75124 Uppsala, Sweden
| | - Erik G Marklund
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, DE-22607 Hamburg, Germany
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2
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Ota F, Abe S, Hatada K, Ueda K, Díaz-Tendero S, Martín F. Imaging intramolecular hydrogen migration with time- and momentum-resolved photoelectron diffraction. Phys Chem Chem Phys 2021; 23:20174-20182. [PMID: 34473148 DOI: 10.1039/d1cp02055b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imaging ultrafast hydrogen migration with few- or sub-femtosecond time resolution is a challenge for ultrafast spectroscopy due to the lightness and small scattering cross-section of the moving hydrogen atom. Here we propose time- and momentum-resolved photoelectron diffraction (TMR-PED) as a way to overcome limitations of existing methodologies and illustrate its performance in the ethanol molecule. By combining different theoretical methods, namely molecular dynamics and electron scattering methods, we show that TMR-PED, along with a judicious choice of the reference frame for multi-coincidence detection, allows for direct imaging of single and double hydrogen migration in doubly-charged ethanol with both few-fs and Å resolutions, all the way from its birth to the very end. It also provides hints of proton extraction following H2 roaming. The signature of hydrogen dynamics shows up in polarization-averaged molecular-frame photoelectron angular distributions (PA-MFPADs) as moving features that allow for a straightforward visualization in space.
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Affiliation(s)
- Fukiko Ota
- Department of Physics, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
| | - Shigeru Abe
- Department of Physics, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
| | - Keisuke Hatada
- Department of Physics, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
| | - Kiyoshi Ueda
- Department of Chemistry, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan.
| | - Sergio Díaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, EU, Spain. .,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, EU, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, EU, Spain
| | - Fernando Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, EU, Spain. .,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, EU, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nano), Campus de Cantoblanco, 28049 Madrid, EU, Spain
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3
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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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4
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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5
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Giewekemeyer K, Aquila A, Loh NTD, Chushkin Y, Shanks KS, Weiss J, Tate MW, Philipp HT, Stern S, Vagovic P, Mehrjoo M, Teo C, Barthelmess M, Zontone F, Chang C, Tiberio RC, Sakdinawat A, Williams GJ, Gruner SM, Mancuso AP. Experimental 3D coherent diffractive imaging from photon-sparse random projections. IUCRJ 2019; 6:357-365. [PMID: 31098017 PMCID: PMC6503918 DOI: 10.1107/s2052252519002781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/24/2019] [Indexed: 05/19/2023]
Abstract
The routine atomic resolution structure determination of single particles is expected to have profound implications for probing structure-function relationships in systems ranging from energy-storage materials to biological molecules. Extremely bright ultrashort-pulse X-ray sources - X-ray free-electron lasers (XFELs) - provide X-rays that can be used to probe ensembles of nearly identical nanoscale particles. When combined with coherent diffractive imaging, these objects can be imaged; however, as the resolution of the images approaches the atomic scale, the measured data are increasingly difficult to obtain and, during an X-ray pulse, the number of photons incident on the 2D detector is much smaller than the number of pixels. This latter concern, the signal 'sparsity', materially impedes the application of the method. An experimental analog using a conventional X-ray source is demonstrated and yields signal levels comparable with those expected from single biomolecules illuminated by focused XFEL pulses. The analog experiment provides an invaluable cross check on the fidelity of the reconstructed data that is not available during XFEL experiments. Using these experimental data, it is established that a sparsity of order 1.3 × 10-3 photons per pixel per frame can be overcome, lending vital insight to the solution of the atomic resolution XFEL single-particle imaging problem by experimentally demonstrating 3D coherent diffractive imaging from photon-sparse random projections.
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Affiliation(s)
| | - A. Aquila
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - N.-T. D. Loh
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117551 Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
| | - Y. Chushkin
- ESRF – The European Synchrotron, 71 avenue des Martyrs, 38000 Grenoble, France
| | - K. S. Shanks
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - J.T. Weiss
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - M. W. Tate
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - H. T. Philipp
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - S. Stern
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - P. Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - M. Mehrjoo
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Teo
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - F. Zontone
- ESRF – The European Synchrotron, 71 avenue des Martyrs, 38000 Grenoble, France
| | - C. Chang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - R. C. Tiberio
- Stanford Nano Shared Facilities, Stanford University, 348 Via Pueblo, Stanford, CA 94305, USA
| | - A. Sakdinawat
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - G. J. Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - S. M. Gruner
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - A. P. Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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6
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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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7
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Sun Z, Fan J, Li H, Liu H, Nam D, Kim C, Kim Y, Han Y, Zhang J, Yao S, Park J, Kim S, Tono K, Yabashi M, Ishikawa T, Song C, Fan C, Jiang H. Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers. ACS NANO 2018; 12:7509-7518. [PMID: 29986128 DOI: 10.1021/acsnano.8b01838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It has been proposed that the radiation damage to biological particles and soft condensed matter can be overcome by ultrafast and ultraintense X-ray free-electron lasers (FELs) with short pulse durations. The successful demonstration of the "diffraction-before-destruction" concept has made single-shot diffraction imaging a promising tool to achieve high resolutions under the native states of samples. However, the resolution is still limited because of the low signal-to-noise ratio, especially for biological specimens such as cells, viruses, and macromolecular particles. Here, we present a demonstration single-shot diffraction imaging experiment of DNA-based structures at SPring-8 Angstrom Compact Free Electron Laser (SACLA), Japan. Through quantitative analysis of the reconstructed images, the scattering abilities of gold and DNA were demonstrated. Suggestions for extracting valid DNA signals from noisy diffraction patterns were also explained and outlined. To sketch out the necessary experimental conditions for the 3D imaging of DNA origami or DNA macromolecular particles, we carried out numerical simulations with practical detector noise and experimental geometry using the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory, USA. The simulated results demonstrate that it is possible to capture images of DNA-based structures at high resolutions with the technique development of current and next-generation X-ray FEL facilities.
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Affiliation(s)
- Zhibin Sun
- State Key Laboratory of Crystal Materials , Shandong University , Jinan 250100 , China
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Jiadong Fan
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Haoyuan Li
- Linac Coherent Light Source , SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
- Department of Physics , Stanford University , Stanford , California 94305 , United States
| | - Huajie Liu
- Laboratory of Physical Biology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Daewoong Nam
- Pohang Accelerator Laboratory , Pohang University of Science and Technology , Pohang 37673 , Korea
- Department of Physics , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Chan Kim
- European XFEL GmbH , Holzkoppel 4 , Schenefeld 22869 , Germany
- Department of Physics and Photon Science & School of Materials Science and Engineering , Gwangju Institute of Science and Technology , Gwangju 61005 , Korea
| | - Yoonhee Kim
- European XFEL GmbH , Holzkoppel 4 , Schenefeld 22869 , Germany
- Department of Physics and Photon Science & School of Materials Science and Engineering , Gwangju Institute of Science and Technology , Gwangju 61005 , Korea
| | - Yubo Han
- Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049 , China
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Jianhua Zhang
- State Key Laboratory of Crystal Materials , Shandong University , Jinan 250100 , China
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Shengkun Yao
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Jaehyun Park
- Pohang Accelerator Laboratory , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute , Kouto, Sayo-cho, Sayo-gun , Hyogo 679-5198 , Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center , Kouto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Tetsuya Ishikawa
- RIKEN SPring-8 Center , Kouto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Changyong Song
- Department of Physics , Pohang University of Science and Technology , Pohang 37673 , Korea
| | - Chunhai Fan
- Laboratory of Physical Biology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Huaidong Jiang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
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8
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Popp D, Koh F, Scipion CPM, Ghoshdastider U, Narita A, Holmes KC, Robinson RC. Advances in Structural Biology and the Application to Biological Filament Systems. Bioessays 2018; 40:e1700213. [PMID: 29484695 DOI: 10.1002/bies.201700213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Fujiet Koh
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Clement P M Scipion
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Akihiro Narita
- Nagoya University Graduate School of Science Structural Biology Research Center and Division of Biological Sciences, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kenneth C Holmes
- Max Planck Institute for Medical Research, D69120 Heidelberg, Germany
| | - Robert C Robinson
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore.,Research Institute for Interdisciplinary Science Okayama University, Okayama 700-8530, Japan
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9
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Miyashita O, Tama F. Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:199-217. [PMID: 30617831 DOI: 10.1007/978-981-13-2200-6_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hybrid approaches for the modeling of macromolecular complexes that combine computational molecular mechanics simulations with experimental data are discussed. Experimental data for biological molecular structures are often low-resolution, and thus, do not contain enough information to determine the atomic positions of molecules. This is especially true when the dynamics of large macromolecules are the focus of the study. However, computational modeling can complement missing information. Significant increase in computational power, as well as the development of new modeling algorithms allow us to model structures of biological macromolecules reliably, using experimental data as references. We review the basics of molecular mechanics approaches, such as atomic model force field, and coarse-grained models, molecular dynamics simulation and normal mode analysis and describe how they could be used for flexible fitting hybrid modeling with experimental data, especially from cryo-EM and SAXS.
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Affiliation(s)
| | - Florence Tama
- RIKEN R-CCS, Kobe, Hyōgo, Japan. .,Department of Physics and ITbM, Nagoya University, Nagoya, Japan.
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10
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Fortmann-Grote C, Buzmakov A, Jurek Z, Loh NTD, Samoylova L, Santra R, Schneidmiller EA, Tschentscher T, Yakubov S, Yoon CH, Yurkov MV, Ziaja-Motyka B, Mancuso AP. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser. IUCRJ 2017; 4:560-568. [PMID: 28989713 PMCID: PMC5619849 DOI: 10.1107/s2052252517009496] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/26/2017] [Indexed: 05/23/2023]
Abstract
Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.
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Affiliation(s)
| | - Alexey Buzmakov
- FSRC ‘Crystallography and Photonics’, Russian Academy of Sciences, Moscow, Russian Federation
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ne-Te Duane Loh
- Centre for Bio-Imaging Sciences, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Physics, National University of Singapore, Singapore
| | | | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | | | | | | | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park CA 94025, USA
| | | | - Beata Ziaja-Motyka
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
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11
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X-ray free electron laser single-particle analysis for biological systems. Curr Opin Struct Biol 2017; 43:163-169. [DOI: 10.1016/j.sbi.2017.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/24/2017] [Accepted: 03/30/2017] [Indexed: 02/01/2023]
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