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Tegze M, Bortel G. Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments. IUCRJ 2021; 8:980-991. [PMID: 34804550 PMCID: PMC8562656 DOI: 10.1107/s205225252100868x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
In single-particle imaging (SPI) experiments, diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. The crucial step of the data processing of SPI is finding the orientations of the recorded diffraction patterns in reciprocal space and reconstructing the 3D intensity distribution. Here, two orientation methods are compared: the expansion maximization compression (EMC) algorithm and the correlation maximization (CM) algorithm. To investigate the efficiency, reliability and accuracy of the methods at various XFEL pulse fluences, simulated diffraction patterns of biological molecules are used.
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Affiliation(s)
- Miklós Tegze
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Konkoly Thege Miklós út 29-33, Budapest, H-1121, Hungary
| | - Gábor Bortel
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Konkoly Thege Miklós út 29-33, Budapest, H-1121, Hungary
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Shen Z, Teo CZW, Ayyer K, Loh ND. An encryption-decryption framework to validating single-particle imaging. Sci Rep 2021; 11:971. [PMID: 33441629 PMCID: PMC7806625 DOI: 10.1038/s41598-020-79589-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/17/2020] [Indexed: 11/11/2022] Open
Abstract
We propose an encryption-decryption framework for validating diffraction intensity volumes reconstructed using single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) when the ground truth volume is absent. This conceptual framework exploits each reconstructed volumes' ability to decipher latent variables (e.g. orientations) of unseen sentinel diffraction patterns. Using this framework, we quantify novel measures of orientation disconcurrence, inconsistency, and disagreement between the decryptions by two independently reconstructed volumes. We also study how these measures can be used to define data sufficiency and its relation to spatial resolution, and the practical consequences of focusing XFEL pulses to smaller foci. This conceptual framework overcomes critical ambiguities in using Fourier Shell Correlation (FSC) as a validation measure for SPI. Finally, we show how this encryption-decryption framework naturally leads to an information-theoretic reformulation of the resolving power of XFEL-SPI, which we hope will lead to principled frameworks for experiment and instrument design.
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Affiliation(s)
- Zhou Shen
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557, Singapore, Singapore
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117551, Singapore, Singapore
| | - Colin Zhi Wei Teo
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557, Singapore, Singapore
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117551, Singapore, Singapore
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - N Duane Loh
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557, Singapore, Singapore.
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117551, Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117557, Singapore, Singapore.
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Bielecki J, Maia FRNC, Mancuso AP. Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:040901. [PMID: 32818147 PMCID: PMC7413746 DOI: 10.1063/4.0000024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/21/2020] [Indexed: 05/20/2023]
Abstract
X-ray free electron lasers (XFELs) now routinely produce millijoule level pulses of x-ray photons with tens of femtoseconds duration. Such x-ray intensities gave rise to the idea that weakly scattering particles-perhaps single biomolecules or viruses-could be investigated free of radiation damage. Here, we examine elements from the past decade of so-called single particle imaging with hard XFELs. We look at the progress made to date and identify some future possible directions for the field. In particular, we summarize the presently achieved resolutions as well as identifying the bottlenecks and enabling technologies to future resolution improvement, which in turn enables application to samples of scientific interest.
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Affiliation(s)
- Johan Bielecki
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Author to whom correspondence should be addressed:
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
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Nakano M, Miyashita O, Tama F. Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching. Biophys Physicobiol 2020; 16:367-376. [PMID: 31984191 PMCID: PMC6975998 DOI: 10.2142/biophysico.16.0_367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/09/2019] [Indexed: 12/01/2022] Open
Abstract
Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL.
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Affiliation(s)
- Miki Nakano
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aich 464-8602, Japan
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Tegze M, Bortel G. Incorporating particle symmetry into orientation determination in single-particle imaging. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2018; 74:512-517. [PMID: 30182937 DOI: 10.1107/s2053273318008999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/20/2018] [Indexed: 11/10/2022]
Abstract
In coherent-diffraction-imaging experiments X-ray diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. If the particle has symmetry, finding the orientation of a pattern can be ambiguous. With some modifications, the correlation-maximization method can find the relative orientations of the diffraction patterns for the case of symmetric particles as well. After convergence, the correlation maps show the symmetry of the particle and can be used to determine the symmetry elements and their orientations. The C factor, slightly modified for the symmetric case, can indicate the consistency of the assembled three-dimensional intensity distribution.
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Affiliation(s)
- Miklós Tegze
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49, Hungary
| | - Gábor Bortel
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49, Hungary
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Nakano M, Miyashita O, Jonic S, Tokuhisa A, Tama F. Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1010-1021. [PMID: 29979162 DOI: 10.1107/s1600577518005568] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Three-dimensional (3D) structures of biomolecules provide insight into their functions. Using X-ray free-electron laser (XFEL) scattering experiments, it was possible to observe biomolecules that are difficult to crystallize, under conditions that are similar to their natural environment. However, resolving 3D structure from XFEL data is not without its challenges. For example, strong beam intensity is required to obtain sufficient diffraction signal and the beam incidence angles to the molecule need to be estimated for diffraction patterns with significant noise. Therefore, it is important to quantitatively assess how the experimental conditions such as the amount of data and their quality affect the expected resolution of the resulting 3D models. In this study, as an example, the restoration of 3D structure of ribosome from two-dimensional diffraction patterns created by simulation is shown. Tests are performed using the diffraction patterns simulated for different beam intensities and using different numbers of these patterns. Guidelines for selecting parameters for slice-matching 3D reconstruction procedures are established. Also, the minimum requirements for XFEL experimental conditions to obtain diffraction patterns for reconstructing molecular structures to a high-resolution of a few nanometers are discussed.
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Affiliation(s)
- Miki Nakano
- Advanced Institute of Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Osamu Miyashita
- Advanced Institute of Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Slavica Jonic
- IMPMC, Sorbonne Universités - CNRS UMR 7590, UPMC Université Paris 6, MNHN, IRD UMR 206, Paris 75005, France
| | - Atsushi Tokuhisa
- Advanced Institute of Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- Advanced Institute of Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Tegze M, Bortel G. Coherent diffraction imaging: consistency of the assembled three-dimensional distribution. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2016; 72:459-64. [PMID: 27357847 DOI: 10.1107/s2053273316008366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/23/2016] [Indexed: 11/10/2022]
Abstract
The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.
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Affiliation(s)
- Miklós Tegze
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, PO Box 49, Budapest, H-1525, Hungary
| | - Gábor Bortel
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, PO Box 49, Budapest, H-1525, Hungary
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Tokuhisa A, Jonic S, Tama F, Miyashita O. Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns. J Struct Biol 2016; 194:325-36. [DOI: 10.1016/j.jsb.2016.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
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Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser. PHOTONICS 2015. [DOI: 10.3390/photonics2010256] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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