1
|
Eibauer M, Weber MS, Kronenberg-Tenga R, Beales CT, Boujemaa-Paterski R, Turgay Y, Sivagurunathan S, Kraxner J, Köster S, Goldman RD, Medalia O. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol 2024; 31:939-949. [PMID: 38632361 PMCID: PMC11189308 DOI: 10.1038/s41594-024-01261-2] [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] [Received: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
Collapse
Affiliation(s)
- Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Charlie T Beales
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Yagmur Turgay
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- MDC Berlin-Buch, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
2
|
Cruz-León S, Majtner T, Hoffmann PC, Kreysing JP, Kehl S, Tuijtel MW, Schaefer SL, Geißler K, Beck M, Turoňová B, Hummer G. High-confidence 3D template matching for cryo-electron tomography. Nat Commun 2024; 15:3992. [PMID: 38734767 PMCID: PMC11088655 DOI: 10.1038/s41467-024-47839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.
Collapse
Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Tomáš Majtner
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Sebastian Kehl
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Katharina Geißler
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| |
Collapse
|
3
|
Liu HF, Zhou Y, Huang Q, Piland J, Jin W, Mandel J, Du X, Martin J, Bartesaghi A. nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography. Nat Methods 2023; 20:1909-1919. [PMID: 37884796 PMCID: PMC10703682 DOI: 10.1038/s41592-023-02045-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP ( http://nextpyp.app ).
Collapse
Affiliation(s)
- Hsuan-Fu Liu
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Qinwen Huang
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Jonathan Piland
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA
| | - Weisheng Jin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Justin Mandel
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Xiaochen Du
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey Martin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
| |
Collapse
|
4
|
Zhao C, Lu D, Zhao Q, Ren C, Zhang H, Zhai J, Gou J, Zhu S, Zhang Y, Gong X. Computational methods for in situ structural studies with cryogenic electron tomography. Front Cell Infect Microbiol 2023; 13:1135013. [PMID: 37868346 PMCID: PMC10586593 DOI: 10.3389/fcimb.2023.1135013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/29/2023] [Indexed: 10/24/2023] Open
Abstract
Cryo-electron tomography (cryo-ET) plays a critical role in imaging microorganisms in situ in terms of further analyzing the working mechanisms of viruses and drug exploitation, among others. A data processing workflow for cryo-ET has been developed to reconstruct three-dimensional density maps and further build atomic models from a tilt series of two-dimensional projections. Low signal-to-noise ratio (SNR) and missing wedge are two major factors that make the reconstruction procedure challenging. Because only few near-atomic resolution structures have been reconstructed in cryo-ET, there is still much room to design new approaches to improve universal reconstruction resolutions. This review summarizes classical mathematical models and deep learning methods among general reconstruction steps. Moreover, we also discuss current limitations and prospects. This review can provide software and methods for each step of the entire procedure from tilt series by cryo-ET to 3D atomic structures. In addition, it can also help more experts in various fields comprehend a recent research trend in cryo-ET. Furthermore, we hope that more researchers can collaborate in developing computational methods and mathematical models for high-resolution three-dimensional structures from cryo-ET datasets.
Collapse
Affiliation(s)
- Cuicui Zhao
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Da Lu
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Qian Zhao
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Chongjiao Ren
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Huangtao Zhang
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Jiaqi Zhai
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Jiaxin Gou
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Shilin Zhu
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Yaqi Zhang
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Xinqi Gong
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
- Beijing Academy of Intelligence, Beijing, China
| |
Collapse
|
5
|
Vuillemot R, Rouiller I, Jonić S. MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations. Sci Rep 2023; 13:10596. [PMID: 37391578 PMCID: PMC10313669 DOI: 10.1038/s41598-023-37037-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023] Open
Abstract
Cryo electron tomography (cryo-ET) allows observing macromolecular complexes in their native environment. The common routine of subtomogram averaging (STA) allows obtaining the three-dimensional (3D) structure of abundant macromolecular complexes, and can be coupled with discrete classification to reveal conformational heterogeneity of the sample. However, the number of complexes extracted from cryo-ET data is usually small, which restricts the discrete-classification results to a small number of enough populated states and, thus, results in a largely incomplete conformational landscape. Alternative approaches are currently being investigated to explore the continuity of the conformational landscapes that in situ cryo-ET studies could provide. In this article, we present MDTOMO, a method for analyzing continuous conformational variability in cryo-ET subtomograms based on Molecular Dynamics (MD) simulations. MDTOMO allows obtaining an atomic-scale model of conformational variability and the corresponding free-energy landscape, from a given set of cryo-ET subtomograms. The article presents the performance of MDTOMO on a synthetic ABC exporter dataset and an in situ SARS-CoV-2 spike dataset. MDTOMO allows analyzing dynamic properties of molecular complexes to understand their biological functions, which could also be useful for structure-based drug discovery.
Collapse
Affiliation(s)
- Rémi Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, CC 115, 4 Place Jussieu, 75005, Paris, France
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Isabelle Rouiller
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC, 3052, Australia
| | - Slavica Jonić
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, CC 115, 4 Place Jussieu, 75005, Paris, France.
| |
Collapse
|
6
|
Kim HHS, Uddin MR, Xu M, Chang YW. Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data. J Mol Biol 2023; 435:168068. [PMID: 37003470 PMCID: PMC10164694 DOI: 10.1016/j.jmb.2023.168068] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/19/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Cryo-electron tomography can uniquely probe the native cellular environment for macromolecular structures. Tomograms feature complex data with densities of diverse, densely crowded macromolecular complexes, low signal-to-noise, and artifacts such as the missing wedge effect. Post-processing of this data generally involves isolating regions or particles of interest from tomograms, organizing them into related groups, and rendering final structures through subtomogram averaging. Template-matching and reference-based structure determination are popular analysis methods but are vulnerable to biases and can often require significant user input. Most importantly, these approaches cannot identify novel complexes that reside within the imaged cellular environment. To reliably extract and resolve structures of interest, efficient and unbiased approaches are therefore of great value. This review highlights notable computational software and discusses how they contribute to making automated structural pattern discovery a possibility. Perspectives emphasizing the importance of features for user-friendliness and accessibility are also presented.
Collapse
Affiliation(s)
- Hannah Hyun-Sook Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. https://twitter.com/hannahinthelab
| | - Mostofa Rafid Uddin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. https://twitter.com/duran_rafid
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
7
|
Zabeo D, Davies KM. Studying membrane modulation mechanisms by electron cryo-tomography. Curr Opin Struct Biol 2022; 77:102464. [PMID: 36174286 DOI: 10.1016/j.sbi.2022.102464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022]
Abstract
Membrane modulation is a key part of cellular life. Critical to processes like energy production, cell division, trafficking, migration and even pathogen entry, defects in membrane modulation are often associated with diseases. Studying the molecular mechanisms of membrane modulation is challenging due to the highly dynamic nature of the oligomeric assemblies involved, which adopt multiple conformations depending on the precise event they are participating in. With the development of electron cryo-tomography and subtomogram averaging, many of these challenges are being resolved as it is now possible to observe complex macromolecular assemblies inside a cell at nanometre to sub-nanometre resolutions. Here, we review the different ways electron cryo-tomography is being used to help uncover the molecular mechanisms used by cells to shape their membranes.
Collapse
Affiliation(s)
- Davide Zabeo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karen M Davies
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
| |
Collapse
|
8
|
Harastani M, Vuillemot R, Hamitouche I, Moghadam NB, Jonic S. ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data. J Struct Biol 2022; 214:107906. [PMID: 36244611 DOI: 10.1016/j.jsb.2022.107906] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
ContinuousFlex is a user-friendly open-source software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy (cryo-EM) and cryo electron tomography (cryo-ET) data. In 2019, ContinuousFlex became available as a plugin for Scipion, an image processing software package extensively used in the cryo-EM field. Currently, ContinuousFlex contains software for running (1) recently published methods HEMNMA-3D, TomoFlow, and NMMD; (2) earlier published methods HEMNMA and StructMap; and (3) methods for simulating cryo-EM and cryo-ET data with conformational variability and methods for data preprocessing. It also includes external software for molecular dynamics simulation (GENESIS) and normal mode analysis (ElNemo), used in some of the mentioned methods. The HEMNMA software has been presented in the past, but not the software of other methods. Besides, ContinuousFlex currently also offers a deep learning extension of HEMNMA, named DeepHEMNMA. In this article, we review these methods in the context of the ContinuousFlex package, developed to facilitate their use by the community.
Collapse
Affiliation(s)
- Mohamad Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Rémi Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Ilyes Hamitouche
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Nima Barati Moghadam
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Slavica Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
| |
Collapse
|
9
|
Rodríguez de Francisco B, Bezault A, Xu XP, Hanein D, Volkmann N. MEPSi: A tool for simulating tomograms of membrane-embedded proteins. J Struct Biol 2022; 214:107921. [PMID: 36372192 DOI: 10.1016/j.jsb.2022.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.
Collapse
Affiliation(s)
- Borja Rodríguez de Francisco
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | - Armel Bezault
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | | | - Dorit Hanein
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Scintillon Institute, San Diego, CA 92121, USA
| | - Niels Volkmann
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France.
| |
Collapse
|
10
|
Pyle E, Hutchings J, Zanetti G. Strategies for picking membrane-associated particles within subtomogram averaging workflows. Faraday Discuss 2022; 240:101-113. [PMID: 35924570 PMCID: PMC9642003 DOI: 10.1039/d2fd00022a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryo-electron tomography (cryo-ET) with subtomogram averaging (STA) has emerged as a key tool for determining macromolecular structure(s) in vitro and in situ. However, processing cryo-ET data with STA currently requires significant user expertise. Recent efforts have streamlined several steps in STA workflows; however, particle picking remains a time-consuming bottleneck for many projects and requires considerable user input. Here, we present several strategies for the time-efficient and accurate picking of membrane-associated particles using the COPII inner coat as a case study. We also discuss a range of particle cleaning solutions to remove both poor quality and false-positive particles from STA datasets. We provide a step-by-step guide and the necessary scripts for users to independently carry out the particle picking and cleaning strategies discussed.
Collapse
Affiliation(s)
- Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck CollegeMalet St.LondonWC1E 7HXUK
| | - Joshua Hutchings
- Division of Biological Sciences, University of California San DiegoLa JollaCAUSA
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck CollegeMalet St.LondonWC1E 7HXUK
| |
Collapse
|
11
|
Förster F. Subtomogram analysis: The sum of a tomogram's particles reveals molecular structure in situ. J Struct Biol X 2022; 6:100063. [PMID: 36684812 PMCID: PMC9846452 DOI: 10.1016/j.yjsbx.2022.100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/25/2023] Open
Abstract
Cryo-electron tomography is uniquely suited to provide insights into the molecular architecture of cells and tissue in the native state. While frozen hydrated specimens tolerate sufficient electron doses to distinguish different types of particles in a tomogram, the accumulating beam damage does not allow resolving their detailed molecular structure individually. Statistical methods for subtomogram averaging and classification that coherently enhance the signal of particles corresponding to copies of the same type of macromolecular allow obtaining much higher resolution insights into macromolecules. Here, I review the developments in subtomogram analysis at Wolfgang Baumeister's laboratory that make the dream of structural biology in the native cell become reality.
Collapse
Affiliation(s)
- Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Uni-versiteitsweg 99, 3584 CG Utrecht, the Netherlands
| |
Collapse
|
12
|
Wu JG, Yan Y, Zhang DX, Liu BW, Zheng QB, Xie XL, Liu SQ, Ge SX, Hou ZG, Xia NS. Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022; 33:452-472. [PMID: 34932487 DOI: 10.1109/tnnls.2021.3131325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recently, single-particle cryo-electron microscopy (cryo-EM) has become an indispensable method for determining macromolecular structures at high resolution to deeply explore the relevant molecular mechanism. Its recent breakthrough is mainly because of the rapid advances in hardware and image processing algorithms, especially machine learning. As an essential support of single-particle cryo-EM, machine learning has powered many aspects of structure determination and greatly promoted its development. In this article, we provide a systematic review of the applications of machine learning in this field. Our review begins with a brief introduction of single-particle cryo-EM, followed by the specific tasks and challenges of its image processing. Then, focusing on the workflow of structure determination, we describe relevant machine learning algorithms and applications at different steps, including particle picking, 2-D clustering, 3-D reconstruction, and other steps. As different tasks exhibit distinct characteristics, we introduce the evaluation metrics for each task and summarize their dynamics of technology development. Finally, we discuss the open issues and potential trends in this promising field.
Collapse
|
13
|
Ni T, Frosio T, Mendonça L, Sheng Y, Clare D, Himes BA, Zhang P. High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity. Nat Protoc 2022; 17:421-444. [PMID: 35022621 PMCID: PMC9251519 DOI: 10.1038/s41596-021-00648-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022]
Abstract
Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA.
Collapse
Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas Frosio
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Luiza Mendonça
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Benjamin A Himes
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
| |
Collapse
|
14
|
Zivanov J, Otón J, Ke Z, von Kügelgen A, Pyle E, Qu K, Morado D, Castaño-Díez D, Zanetti G, Bharat TAM, Briggs JAG, Scheres SHW. A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. eLife 2022; 11:83724. [PMID: 36468689 PMCID: PMC9815803 DOI: 10.7554/elife.83724] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
Collapse
Affiliation(s)
- Jasenko Zivanov
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Laboratory of Biomedical Imaging (LIB)LausanneSwitzerland,BioEM lab, Biozentrum, University of BaselBaselSwitzerland
| | - Joaquín Otón
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,ALBA SynchrotronBarcelonaSpain
| | - Zunlong Ke
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Max Planck Institute of BiochemistryMartinsriedGermany
| | - Andriko von Kügelgen
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Kun Qu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Dustin Morado
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Max Planck Institute of BiochemistryMartinsriedGermany
| | - Daniel Castaño-Díez
- BioEM lab, Biozentrum, University of BaselBaselSwitzerland,Instituto BiofisikaLeioaSpain
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Tanmay AM Bharat
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Sir William Dunn School of Pathology, University of OxfordOxfordUnited Kingdom
| | - John AG Briggs
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom,Max Planck Institute of BiochemistryMartinsriedGermany
| | | |
Collapse
|
15
|
Harastani M, Eltsov M, Leforestier A, Jonic S. TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow. J Mol Biol 2021; 434:167381. [PMID: 34848215 DOI: 10.1016/j.jmb.2021.167381] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 01/14/2023]
Abstract
Cryogenic Electron Tomography (cryo-ET) allows structural and dynamics studies of macromolecules in situ. Averaging different copies of imaged macromolecules is commonly used to obtain their structure at higher resolution and discrete classification to analyze their dynamics. Instrumental and data processing developments are progressively equipping cryo-ET studies with the ability to escape the trap of classification into a complete continuous conformational variability analysis. In this work, we propose TomoFlow, a method for analyzing macromolecular continuous conformational variability in cryo-ET subtomograms based on a three-dimensional dense optical flow (OF) approach. The resultant lower-dimensional conformational space allows generating movies of macromolecular motion and obtaining subtomogram averages by grouping conformationally similar subtomograms. The animations and the subtomogram group averages reveal accurate trajectories of macromolecular motion based on a novel mathematical model that makes use of OF properties. This paper describes TomoFlow with tests on simulated datasets generated using different techniques, namely Normal Mode Analysis and Molecular Dynamics Simulation. It also shows an application of TomoFlow on a dataset of nucleosomes in situ, which provided promising results coherent with previous findings using the same dataset but without imposing any prior knowledge on the analysis of the conformational variability. The method is discussed with its potential uses and limitations.
Collapse
Affiliation(s)
- Mohamad Harastani
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France; Laboratoire de Physique des Solides (LPS), UMR 8502 CNRS, Université Paris-Saclay, Orsay, France. https://twitter.com/moh_harastani
| | - Mikhail Eltsov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France. https://twitter.com/EltsovMikhail
| | - Amélie Leforestier
- Laboratoire de Physique des Solides (LPS), UMR 8502 CNRS, Université Paris-Saclay, Orsay, France
| | - Slavica Jonic
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
| |
Collapse
|
16
|
Moebel E, Martinez-Sanchez A, Lamm L, Righetto RD, Wietrzynski W, Albert S, Larivière D, Fourmentin E, Pfeffer S, Ortiz J, Baumeister W, Peng T, Engel BD, Kervrann C. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nat Methods 2021; 18:1386-1394. [PMID: 34675434 DOI: 10.1038/s41592-021-01275-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/18/2021] [Indexed: 11/10/2022]
Abstract
Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules. Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (roughly 3.2 MDa), ribulose 1,5-bisphosphate carboxylase-oxygenase (roughly 560 kDa soluble complex) and photosystem II (roughly 550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semiautomated analysis of a wide range of molecular targets in cellular tomograms.
Collapse
Affiliation(s)
- Emmanuel Moebel
- Serpico Project-Team, Centre Inria Rennes-Bretagne Atlantique and CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, Campus Universitaire de Beaulieu, Rennes Cedex, France
| | - Antonio Martinez-Sanchez
- Department of Computer Science, Faculty of Sciences, University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, Oviedo, Spain.,Institute of Neuropathology, Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells', University of Göttingen, Göttingen, Germany
| | - Lorenz Lamm
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.,Helmholtz AI, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ricardo D Righetto
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Damien Larivière
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Eric Fourmentin
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Stefan Pfeffer
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Julio Ortiz
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Ernst Ruska-Centre, Wilhelm-Johnen-Straße, Jülich, Germany
| | | | - Tingying Peng
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, Germany
| | - Benjamin D Engel
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany. .,Department of Chemistry, Technical University of Munich, Garching, Germany.
| | - Charles Kervrann
- Serpico Project-Team, Centre Inria Rennes-Bretagne Atlantique and CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, Campus Universitaire de Beaulieu, Rennes Cedex, France.
| |
Collapse
|
17
|
Lucas BA, Himes BA, Xue L, Grant T, Mahamid J, Grigorieff N. Locating macromolecular assemblies in cells by 2D template matching with cisTEM. eLife 2021; 10:e68946. [PMID: 34114559 PMCID: PMC8219381 DOI: 10.7554/elife.68946] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells with high precision and sensitivity, demonstrating that this is a versatile tool for in situ visual proteomics and in situ structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.
Collapse
Affiliation(s)
- Bronwyn A Lucas
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Benjamin A Himes
- Howard Hughes Medical Institute, RNA Therapeutics Institute, The University of Massachusetts Medical SchoolWorcesterUnited States
| | - Liang Xue
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Timothy Grant
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Nikolaus Grigorieff
- Howard Hughes Medical Institute, RNA Therapeutics Institute, The University of Massachusetts Medical SchoolWorcesterUnited States
| |
Collapse
|
18
|
Wang Z, Zhang Q, Mim C. Coming of Age: Cryo-Electron Tomography as a Versatile Tool to Generate High-Resolution Structures at Cellular/Biological Interfaces. Int J Mol Sci 2021; 22:6177. [PMID: 34201105 PMCID: PMC8228724 DOI: 10.3390/ijms22126177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last few years, cryo electron microscopy has become the most important method in structural biology. While 80% of deposited maps are from single particle analysis, electron tomography has grown to become the second most important method. In particular sub-tomogram averaging has matured as a method, delivering structures between 2 and 5 Å from complexes in cells as well as in vitro complexes. While this resolution range is not standard, novel developments point toward a promising future. Here, we provide a guide for the workflow from sample to structure to gain insight into this emerging field.
Collapse
Affiliation(s)
| | | | - Carsten Mim
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute (KTH), Hälsovägen 11C, 141 27 Huddinge, Sweden; (Z.W.); (Q.Z.)
| |
Collapse
|
19
|
Pyle E, Zanetti G. Current data processing strategies for cryo-electron tomography and subtomogram averaging. Biochem J 2021; 478:1827-1845. [PMID: 34003255 PMCID: PMC8133831 DOI: 10.1042/bcj20200715] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 12/25/2022]
Abstract
Cryo-electron tomography (cryo-ET) can be used to reconstruct three-dimensional (3D) volumes, or tomograms, from a series of tilted two-dimensional images of biological objects in their near-native states in situ or in vitro. 3D subvolumes, or subtomograms, containing particles of interest can be extracted from tomograms, aligned, and averaged in a process called subtomogram averaging (STA). STA overcomes the low signal to noise ratio within the individual subtomograms to generate structures of the particle(s) of interest. In recent years, cryo-ET with STA has increasingly been capable of reaching subnanometer resolution due to improvements in microscope hardware and data processing strategies. There has also been an increase in the number and quality of software packages available to process cryo-ET data with STA. In this review, we describe and assess the data processing strategies available for cryo-ET data and highlight the recent software developments which have enabled the extraction of high-resolution information from cryo-ET datasets.
Collapse
Affiliation(s)
- Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck College, Malet St., London WC1E 7HX, U.K
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College, Malet St., London WC1E 7HX, U.K
| |
Collapse
|
20
|
Harastani M, Eltsov M, Leforestier A, Jonic S. HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes. Front Mol Biosci 2021; 8:663121. [PMID: 34095222 PMCID: PMC8170028 DOI: 10.3389/fmolb.2021.663121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022] Open
Abstract
Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (in situ). Its potential of providing information on the dynamics of macromolecular complexes in cells is still largely unexploited, due to the challenges of the data analysis. The crowded cell environment and continuous conformational changes of complexes make difficult disentangling the data heterogeneity. We present HEMNMA-3D, which is, to the best of our knowledge, the first method for analyzing cryo electron subtomograms in terms of continuous conformational changes of complexes. HEMNMA-3D uses a combination of elastic and rigid-body 3D-to-3D iterative alignments of a flexible 3D reference (atomic structure or electron microscopy density map) to match the conformation, orientation, and position of the complex in each subtomogram. The elastic matching combines molecular mechanics simulation (Normal Mode Analysis of the 3D reference) and experimental, subtomogram data analysis. The rigid-body alignment includes compensation for the missing wedge, due to the limited tilt angle of cryo-ET. The conformational parameters (amplitudes of normal modes) of the complexes in subtomograms obtained through the alignment are processed to visualize the distribution of conformations in a space of lower dimension (typically, 2D or 3D) referred to as space of conformations. This allows a visually interpretable insight into the dynamics of the complexes, by calculating 3D averages of subtomograms with similar conformations from selected (densest) regions and by recording movies of the 3D reference's displacement along selected trajectories through the densest regions. We describe HEMNMA-3D and show its validation using synthetic datasets. We apply HEMNMA-3D to an experimental dataset describing in situ nucleosome conformational variability. HEMNMA-3D software is available freely (open-source) as part of ContinuousFlex plugin of Scipion V3.0 (http://scipion.i2pc.es).
Collapse
Affiliation(s)
- Mohamad Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Mikhail Eltsov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Saclay, Paris, France
| | - Slavica Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| |
Collapse
|
21
|
Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation. Proc Natl Acad Sci U S A 2021; 118:2020054118. [PMID: 33397805 PMCID: PMC7826355 DOI: 10.1073/pnas.2020054118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 particle assembly is driven by the viral Gag protein, which oligomerizes into a hexameric array on the inner surface of the viral envelope, forming a truncated spherical lattice containing large and small gaps. Gag is then cut by the viral protease, disassembles, and rearranges to form the mature, infectious virus. Here, we present structures and molecular dynamics simulations of the edges of the immature Gag lattice. Our analysis shows that Gag dimers are the basic assembly unit of the HIV-1 particle, lattice edges are partial hexamers, and partial hexamers are prone to structural changes allowing protease to cut Gag. These findings provide insights into assembly of the immature virus, its structure, and how it disassembles during maturation. The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.
Collapse
|
22
|
Bouvette J, Liu HF, Du X, Zhou Y, Sikkema AP, da Fonseca Rezende E Mello J, Klemm BP, Huang R, Schaaper RM, Borgnia MJ, Bartesaghi A. Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography. Nat Commun 2021; 12:1957. [PMID: 33785757 PMCID: PMC8009872 DOI: 10.1038/s41467-021-22251-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/08/2021] [Indexed: 11/19/2022] Open
Abstract
Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by up to an order of magnitude and improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300 kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved. Tomographic reconstructions of cryopreserved specimens enable in-situ structural studies. Here, the authors present the beam image-shift electron cryo-tomography (BISECT) approach that accelerates data collection speed and improves the map resolution compared to earlier approaches and present the in vitro structure of a 300 kDa protein complex that was solved at 3.6 Å resolution as a test case.
Collapse
Affiliation(s)
- Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Xiaochen Du
- Department of Computer Science, Duke University, Durham, NC, USA.,Department of Chemistry, Duke University, Durham, NC, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Andrew P Sikkema
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Juliana da Fonseca Rezende E Mello
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Bradley P Klemm
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA.
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA. .,Department of Computer Science, Duke University, Durham, NC, USA. .,Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
| |
Collapse
|
23
|
Singla J, White KL, Stevens RC, Alber F. Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography. J Struct Biol 2021; 213:107727. [PMID: 33753204 DOI: 10.1016/j.jsb.2021.107727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022]
Abstract
Cryo-electron tomography provides the opportunity for unsupervised discovery of endogenous complexes in situ. This process usually requires particle picking, clustering and alignment of subtomograms to produce an average structure of the complex. When applied to heterogeneous samples, template-free clustering and alignment of subtomograms can potentially lead to the discovery of structures for unknown endogenous complexes. However, such methods require scoring functions to measure and accurately rank the quality of aligned subtomogram clusters, which can be compromised by contaminations from misclassified complexes and alignment errors. Here, we provide the first study to assess the effectiveness of more than 15 scoring functions for evaluating the quality of subtomogram clusters, which differ in the amount of structural misalignments and contaminations due to misclassified complexes. We assessed both experimental and simulated subtomograms as ground truth data sets. Our analysis showed that the robustness of scoring functions varies largely. Most scores were sensitive to the signal-to-noise ratio of subtomograms and often required Gaussian filtering as preprocessing for improved performance. Two scoring functions, Spectral SNR-based Fourier Shell Correlation and Pearson Correlation in the Fourier domain with missing wedge correction, showed a robust ranking of subtomogram clusters without any preprocessing and irrespective of SNR levels of subtomograms. Of these two scoring functions, Spectral SNR-based Fourier Shell Correlation was fastest to compute and is a better choice for handling large numbers of subtomograms. Our results provide a guidance for choosing an accurate scoring function for template-free approaches to detect complexes from heterogeneous samples.
Collapse
Affiliation(s)
- Jitin Singla
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA; Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Kate L White
- Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Raymond C Stevens
- Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA.
| |
Collapse
|
24
|
Leneva N, Kovtun O, Morado DR, Briggs JAG, Owen DJ. Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. SCIENCE ADVANCES 2021; 7:7/13/eabf8598. [PMID: 33762348 PMCID: PMC7990337 DOI: 10.1126/sciadv.abf8598] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/05/2021] [Indexed: 05/12/2023]
Abstract
Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes.
Collapse
Affiliation(s)
- Natalya Leneva
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Oleksiy Kovtun
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - John A G Briggs
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - David J Owen
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| |
Collapse
|
25
|
Martins B, Sorrentino S, Chung WL, Tatli M, Medalia O, Eibauer M. Unveiling the polarity of actin filaments by cryo-electron tomography. Structure 2021; 29:488-498.e4. [PMID: 33476550 PMCID: PMC8111420 DOI: 10.1016/j.str.2020.12.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 01/01/2023]
Abstract
The actin cytoskeleton plays a fundamental role in numerous cellular processes, such as cell motility, cytokinesis, and adhesion to the extracellular matrix. Revealing the polarity of individual actin filaments in intact cells would foster an unprecedented understanding of cytoskeletal processes and their associated mechanical forces. Cryo-electron tomography provides the means for high-resolution structural imaging of cells. However, the low signal-to-noise ratio of cryo-tomograms obscures the high frequencies, and therefore the polarity of actin filaments cannot be directly measured. Here, we developed a method that enables us to determine the polarity of actin filaments in cellular cryo-tomograms. We applied it to reveal the actin polarity distribution in focal adhesions, and show a linear relation between actin polarity and distance from the apical boundary of the adhesion site. Determining the polarity of individual actin filaments inside cells Reconstruction of actin networks from cryo-tomograms The polarity of actin changes from mixed to uniform along focal adhesions
Collapse
Affiliation(s)
- Bruno Martins
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Simona Sorrentino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wen-Lu Chung
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Meltem Tatli
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| |
Collapse
|
26
|
Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
Collapse
Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
27
|
Zeng X, Xu M. Gum-Net: Unsupervised Geometric Matching for Fast and Accurate 3D Subtomogram Image Alignment and Averaging. PROCEEDINGS. IEEE COMPUTER SOCIETY CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION 2020; 2020:4072-4082. [PMID: 33716478 PMCID: PMC7955792 DOI: 10.1109/cvpr42600.2020.00413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We propose a Geometric unsupervised matching Network (Gum-Net) for finding the geometric correspondence between two images with application to 3D subtomogram alignment and averaging. Subtomogram alignment is the most important task in cryo-electron tomography (cryo-ET), a revolutionary 3D imaging technique for visualizing the molecular organization of unperturbed cellular landscapes in single cells. However, subtomogram alignment and averaging are very challenging due to severe imaging limits such as noise and missing wedge effects. We introduce an end-to-end trainable architecture with three novel modules specifically designed for preserving feature spatial information and propagating feature matching information. The training is performed in a fully unsupervised fashion to optimize a matching metric. No ground truth transformation information nor category-level or instance-level matching supervision information is needed. After systematic assessments on six real and nine simulated datasets, we demonstrate that Gum-Net reduced the alignment error by 40 to 50% and improved the averaging resolution by 10%. Gum-Net also achieved 70 to 110 times speedup in practice with GPU acceleration compared to state-of-the-art subtomogram alignment methods. Our work is the first 3D unsupervised geometric matching method for images of strong transformation variation and high noise level. The training code, trained model, and datasets are available in our open-source software AITom.
Collapse
Affiliation(s)
- Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213
| |
Collapse
|
28
|
Abstract
The endoplasmic reticulum (ER) translocon complex is the main gate into the secretory pathway, facilitating the translocation of nascent peptides into the ER lumen or their integration into the lipid membrane. Protein biogenesis in the ER involves additional processes, many of them occurring co-translationally while the nascent protein resides at the translocon complex, including recruitment of ER-targeted ribosome-nascent-chain complexes, glycosylation, signal peptide cleavage, membrane protein topogenesis and folding. To perform such varied functions on a broad range of substrates, the ER translocon complex has different accessory components that associate with it either stably or transiently. Here, we review recent structural and functional insights into this dynamically constituted central hub in the ER and its components. Recent cryo-electron microscopy (EM) studies have dissected the molecular organization of the co-translational ER translocon complex, comprising the Sec61 protein-conducting channel, the translocon-associated protein complex and the oligosaccharyl transferase complex. Complemented by structural characterization of the post-translational import machinery, key molecular principles emerge that distinguish co- and post-translational protein import and biogenesis. Further cryo-EM structures promise to expand our mechanistic understanding of the various biochemical functions involving protein biogenesis and quality control in the ER.
Collapse
Affiliation(s)
- Max Gemmer
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
29
|
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is an essential process that removes misfolded proteins from the ER, preventing cellular dysfunction and disease. While most of the key components of ERAD are known, their specific localization remains a mystery. This study uses in situ cryo-electron tomography to directly visualize the ERAD machinery within the native cellular environment. Proteasomes and Cdc48, the complexes that extract and degrade ER proteins, cluster together in non–membrane-bound cytosolic microcompartments that contact ribosome-free patches on the ER membrane. This discrete molecular organization may facilitate efficient ERAD. Structural analysis reveals that proteasomes directly engage ER-localized substrates, providing evidence for a noncanonical “direct ERAD” pathway. In addition, live-cell fluorescence microscopy suggests that these ER-associated proteasome clusters form by liquid–liquid phase separation. To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non–membrane-bound regions. It is unknown whether this strategy is used to facilitate protein degradation at specific locations within the cell. Leveraging in situ cryo-electron tomography to image the native molecular landscape of the unicellular alga Chlamydomonas reinhardtii, we discovered that the cytosolic protein degradation machinery is concentrated within ∼200-nm foci that contact specialized patches of endoplasmic reticulum (ER) membrane away from the ER–Golgi interface. These non–membrane-bound microcompartments exclude ribosomes and consist of a core of densely clustered 26S proteasomes surrounded by a loose cloud of Cdc48. Active proteasomes in the microcompartments directly engage with putative substrate at the ER membrane, a function canonically assigned to Cdc48. Live-cell fluorescence microscopy revealed that the proteasome clusters are dynamic, with frequent assembly and fusion events. We propose that the microcompartments perform ER-associated degradation, colocalizing the degradation machinery at specific ER hot spots to enable efficient protein quality control.
Collapse
|
30
|
Zhang P. Advances in cryo-electron tomography and subtomogram averaging and classification. Curr Opin Struct Biol 2019; 58:249-258. [PMID: 31280905 PMCID: PMC6863431 DOI: 10.1016/j.sbi.2019.05.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022]
Abstract
Cryo-electron tomography (cryoET) can provide 3D reconstructions, or tomograms, of pleomorphic objects such as organelles or cells in their close-to-native states. Subtomograms that contain repetitive structures can be further extracted and subjected to averaging and classification to improve resolution, and this process has become an emerging structural biology method referred to as cryoET subtomogram averaging and classification (cryoSTAC). Recent technical advances in cryoSTAC have had a profound impact on many fields in biology. Here, I review recent exciting work on several macromolecular assemblies demonstrating the power of cryoSTAC for in situ structure analysis and discuss challenges and future directions.
Collapse
Affiliation(s)
- Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
| |
Collapse
|
31
|
Lü Y, Zeng X, Zhao X, Li S, Li H, Gao X, Xu M. Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization. BMC Bioinformatics 2019; 20:443. [PMID: 31455212 PMCID: PMC6712796 DOI: 10.1186/s12859-019-3003-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microscopy technology, the image quality of three-dimensional reconstruction of cryo-electron tomography has greatly improved. However, cryo-ET images are characterized by low resolution, partial data loss and low signal-to-noise ratio (SNR). In order to tackle these challenges and improve resolution, a large number of subtomograms containing the same structure needs to be aligned and averaged. Existing methods for refining and aligning subtomograms are still highly time-consuming, requiring many computationally intensive processing steps (i.e. the rotations and translations of subtomograms in three-dimensional space). RESULTS In this article, we propose a Stochastic Average Gradient (SAG) fine-grained alignment method for optimizing the sum of dissimilarity measure in real space. We introduce a Message Passing Interface (MPI) parallel programming model in order to explore further speedup. CONCLUSIONS We compare our stochastic average gradient fine-grained alignment algorithm with two baseline methods, high-precision alignment and fast alignment. Our SAG fine-grained alignment algorithm is much faster than the two baseline methods. Results on simulated data of GroEL from the Protein Data Bank (PDB ID:1KP8) showed that our parallel SAG-based fine-grained alignment method could achieve close-to-optimal rigid transformations with higher precision than both high-precision alignment and fast alignment at a low SNR (SNR=0.003) with tilt angle range ±60∘ or ±40∘. For the experimental subtomograms data structures of GroEL and GroEL/GroES complexes, our parallel SAG-based fine-grained alignment can achieve higher precision and fewer iterations to converge than the two baseline methods.
Collapse
Affiliation(s)
- Yongchun Lü
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Xiangrui Zeng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Xiaofang Zhao
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Shirui Li
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Hua Li
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| |
Collapse
|
32
|
Zhao Y, Zeng X, Guo Q, Xu M. An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification. Bioinformatics 2019; 34:i227-i236. [PMID: 29949977 PMCID: PMC6022576 DOI: 10.1093/bioinformatics/bty267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motivation Cellular Electron CryoTomography (CECT) is an emerging 3D imaging technique that visualizes subcellular organization of single cells at sub-molecular resolution and in near-native state. CECT captures large numbers of macromolecular complexes of highly diverse structures and abundances. However, the structural complexity and imaging limits complicate the systematic de novo structural recovery and recognition of these macromolecular complexes. Efficient and accurate reference-free subtomogram averaging and classification represent the most critical tasks for such analysis. Existing subtomogram alignment based methods are prone to the missing wedge effects and low signal-to-noise ratio (SNR). Moreover, existing maximum-likelihood based methods rely on integration operations, which are in principle computationally infeasible for accurate calculation. Results Built on existing works, we propose an integrated method, Fast Alignment Maximum Likelihood method (FAML), which uses fast subtomogram alignment to sample sub-optimal rigid transformations. The transformations are then used to approximate integrals for maximum-likelihood update of subtomogram averages through expectation–maximization algorithm. Our tests on simulated and experimental subtomograms showed that, compared to our previously developed fast alignment method (FA), FAML is significantly more robust to noise and missing wedge effects with moderate increases of computation cost. Besides, FAML performs well with significantly fewer input subtomograms when the FA method fails. Therefore, FAML can serve as a key component for improved construction of initial structural models from macromolecules captured by CECT. Availability and implementation http://www.cs.cmu.edu/mxu1
Collapse
Affiliation(s)
- Yixiu Zhao
- Computational Biology and Computer Science Departments, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiangrui Zeng
- Computational Biology and Computer Science Departments, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Qiang Guo
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Min Xu
- Computational Biology and Computer Science Departments, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| |
Collapse
|
33
|
Lin R, Zeng X, Kitani K, Xu M. Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms. Bioinformatics 2019; 35:i260-i268. [PMID: 31510673 PMCID: PMC6612867 DOI: 10.1093/bioinformatics/btz364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Since 2017, an increasing amount of attention has been paid to the supervised deep learning-based macromolecule in situ structural classification (i.e. subtomogram classification) in cellular electron cryo-tomography (CECT) due to the substantially higher scalability of deep learning. However, the success of such supervised approach relies heavily on the availability of large amounts of labeled training data. For CECT, creating valid training data from the same data source as prediction data is usually laborious and computationally intensive. It would be beneficial to have training data from a separate data source where the annotation is readily available or can be performed in a high-throughput fashion. However, the cross data source prediction is often biased due to the different image intensity distributions (a.k.a. domain shift). RESULTS We adapt a deep learning-based adversarial domain adaptation (3D-ADA) method to timely address the domain shift problem in CECT data analysis. 3D-ADA first uses a source domain feature extractor to extract discriminative features from the training data as the input to a classifier. Then it adversarially trains a target domain feature extractor to reduce the distribution differences of the extracted features between training and prediction data. As a result, the same classifier can be directly applied to the prediction data. We tested 3D-ADA on both experimental and realistically simulated subtomogram datasets under different imaging conditions. 3D-ADA stably improved the cross data source prediction, as well as outperformed two popular domain adaptation methods. Furthermore, we demonstrate that 3D-ADA can improve cross data source recovery of novel macromolecular structures. AVAILABILITY AND IMPLEMENTATION https://github.com/xulabs/projects. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Ruogu Lin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kris Kitani
- Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| |
Collapse
|
34
|
Castaño-Díez D, Zanetti G. In situ structure determination by subtomogram averaging. Curr Opin Struct Biol 2019; 58:68-75. [PMID: 31233977 DOI: 10.1016/j.sbi.2019.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/06/2019] [Accepted: 05/12/2019] [Indexed: 02/02/2023]
Abstract
Cryo-tomography and subtomogram averaging are increasingly popular techniques for structural determination of macromolecular complexes in situ. They have the potential to achieve high-resolution views of native complexes, together with the details of their location relative to interacting molecules. The subtomogram averaging (StA) pipelines are well-established, with current developments aiming to optimise each step by reducing manual intervention and user decisions, following similar trends in single-particle approaches that have dramatically increased their popularity. Here, we review the main steps of typical StA workflows. We focus on considerations arising from the fact that the objects of study are embedded within unique crowded environments, and we emphasise those steps where careful decisions need to be made by the user.
Collapse
Affiliation(s)
- Daniel Castaño-Díez
- BioEM Lab, Center for Cellular Imaging and Nanoanalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College, Malet St., London, WC1E 7HX, UK.
| |
Collapse
|
35
|
Abstract
Cryo-electron tomography (cryo-ET) allows three-dimensional (3D) visualization of frozen-hydrated biological samples, such as protein complexes and cell organelles, in near-native environments at nanometer scale. Protein complexes that are present in multiple copies in a set of tomograms can be extracted, mutually aligned, and averaged to yield a signal-enhanced 3D structure up to sub-nanometer or even near-atomic resolution. This technique, called subtomogram averaging (StA), is powered by improvements in EM hardware and image processing software. Importantly, StA provides unique biological insights into the structure and function of cellular machinery in close-to-native contexts. In this chapter, we describe the principles and key steps of StA. We briefly cover sample preparation and data collection with an emphasis on image processing procedures related to tomographic reconstruction, subtomogram alignment, averaging, and classification. We conclude by summarizing current limitations and future directions of this technique with a focus on high-resolution StA.
Collapse
|
36
|
Danev R, Yanagisawa H, Kikkawa M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions. Trends Biochem Sci 2019; 44:837-848. [PMID: 31078399 DOI: 10.1016/j.tibs.2019.04.008] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/01/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of laboratories worldwide to determine high-resolution protein structures. Cryo-electron tomography (cryo-ET) is another powerful approach that enables visualization of protein complexes in their native cellular environment. Despite the wide-ranging success of cryo-EM, there are many methodological aspects that could be improved. Those include sample preparation, sample screening, data acquisition, image processing, and structure validation. Future developments will increase the reliability and throughput of the technique and reduce the cost and skill level barrier for its adoption.
Collapse
Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Haruaki Yanagisawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Kikkawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| |
Collapse
|
37
|
Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Curr Opin Struct Biol 2019; 58:1-9. [PMID: 31005754 DOI: 10.1016/j.sbi.2019.03.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023]
Abstract
Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein's location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA.
Collapse
Affiliation(s)
- Florian Km Schur
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria.
| |
Collapse
|
38
|
Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Structure 2019; 27:679-691.e14. [PMID: 30744995 DOI: 10.1016/j.str.2019.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022]
Abstract
Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called "Multi-Pattern Pursuit" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures. These initially detected structures can then serve as input for more targeted refinement efforts. Our tests on simulated and experimental tomograms show that our automated method is a promising tool for supporting large-scale template-free visual proteomics analysis.
Collapse
Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Jitin Singla
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond C Stevens
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
39
|
Che C, Lin R, Zeng X, Elmaaroufi K, Galeotti J, Xu M. Improved deep learning-based macromolecules structure classification from electron cryo-tomograms. MACHINE VISION AND APPLICATIONS 2018; 29:1227-1236. [PMID: 31511756 PMCID: PMC6738941 DOI: 10.1007/s00138-018-0949-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/16/2018] [Accepted: 05/18/2018] [Indexed: 05/30/2023]
Abstract
Cellular processes are governed by macromolecular complexes inside the cell. Study of the native structures of macromolecular complexes has been extremely difficult due to lack of data. With recent breakthroughs in Cellular Electron Cryo-Tomography (CECT) 3D imaging technology, it is now possible for researchers to gain accesses to fully study and understand the macro-molecular structures single cells. However, systematic recovery of macromolecular structures from CECT is very difficult due to high degree of structural complexity and practical imaging limitations. Specifically, we proposed a deep learning-based image classification approach for large-scale systematic macromolecular structure separation from CECT data. However, our previous work was only a very initial step toward exploration of the full potential of deep learning-based macromolecule separation. In this paper, we focus on improving classification performance by proposing three newly designed individual CNN models: an extended version of (Deep Small Receptive Field) DSRF3D, donated as DSRF3D-v2, a 3D residual block-based neural network, named as RB3D, and a convolutional 3D (C3D)-based model, CB3D. We compare them with our previously developed model (DSRF3D) on 12 datasets with different SNRs and tilt angle ranges. The experiments show that our new models achieved significantly higher classification accuracies. The accuracies are not only higher than 0.9 on normal datasets, but also demonstrate potentials to operate on datasets with high levels of noises and missing wedge effects presented.
Collapse
Affiliation(s)
- Chengqian Che
- The Robotics Institute, Carnegie Mellon University,Pittsburgh, USA
| | - Ruogu Lin
- Department of Automation, Tsinghua University, Beijing, China
| | - Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA
| | - Karim Elmaaroufi
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, USA
| | - John Galeotti
- The Robotics Institute, Carnegie Mellon University,Pittsburgh, USA
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA
| |
Collapse
|
40
|
Himes BA, Zhang P. emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. Nat Methods 2018; 15:955-961. [PMID: 30349041 PMCID: PMC6281437 DOI: 10.1038/s41592-018-0167-z] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 07/25/2018] [Indexed: 11/17/2022]
Abstract
Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single particle cryoEM. Such complexes may be studied using cryo-electron tomography combined with sub-tomogram alignment and classification, which in exceptional cases reaches sub-nanometer resolution, yielding insight into structure-function relationships. Extending this approach to specimens that exhibit conformational or compositional heterogeneity, and that may be present at low abundance, remains challenging. To address this challenge, we developed emClarity (https://github.com/bHimes/emClarity/wiki), a GPU-accelerated image processing package, which features an iterative tomographic tilt-series refinement algorithm using sub-tomograms as fiducial markers and a 3D-samping function compensated, multi-scale Principle Component Analysis classification method. We demonstrate substantial improvements in the resolution of maps and in the separation of different functional states of macromolecular complexes, compared to those generated using current state-of-the-art software.
Collapse
Affiliation(s)
- Benjamin A Himes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Electron Bio-Imaging Centre, Diamond Light Source, Didcot, UK.
| |
Collapse
|
41
|
Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
Collapse
Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| |
Collapse
|
42
|
Englmeier R, Förster F. Cryo-electron tomography for the structural study of mitochondrial translation. Tissue Cell 2018; 57:129-138. [PMID: 30197222 DOI: 10.1016/j.tice.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/29/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Cryo-electron tomography (cryo-ET) enables the three-dimensional (3D) structural characterization of macromolecular complexes in their physiological environment. Thus, cryo-ET is uniquely suited to study the structural basis of biomolecular processes that are extremely difficult or even impossible to reconstitute using purified components. Translation of mitochondrial genes, which occurs in the secluded interior of mitochondria, falls into this category. Here, we describe the principles of cryo-ET in the context of mitochondrial translation and outline recent developments and challenges of the method. The 3D image of a frozen-hydrated biological sample is computed from its 2D projections, which are acquired using a transmission electron microscope. In conjunction with automated detection of different copies of the molecule of interest and averaging of the corresponding subtomograms, cryo-ET enables macromolecular structure determination in the native environment (i.e. in situ) at sub-nanometer resolution. The preservation of the native environment furthermore allows the extraction of contextual information about the molecules, including the location of specific molecules with respect to membranes, their relative positioning and the spatial organization with respect to other types of macromolecules. Recent preparative developments extend the field of application of cryo-ET from isolated organelles to cultured eukaryotic cells and even tissue, making the traditional borders between molecular and cellular structural biology disappear.
Collapse
Affiliation(s)
- Robert Englmeier
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.
| |
Collapse
|
43
|
Xu M, Chai X, Muthakana H, Liang X, Yang G, Zeev-Ben-Mordehai T, Xing EP. Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. Bioinformatics 2018; 33:i13-i22. [PMID: 28881965 PMCID: PMC5946875 DOI: 10.1093/bioinformatics/btx230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Motivation Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. Results To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Availability and Implementation Source code freely available at http://www.cs.cmu.edu/∼mxu1/software. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaoqi Chai
- Biomedical Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hariank Muthakana
- Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaodan Liang
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ge Yang
- Biomedical Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tzviya Zeev-Ben-Mordehai
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Eric P Xing
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
| |
Collapse
|
44
|
Cyrklaff M, Frischknecht F, Kudryashev M. Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev 2018; 41:828-853. [PMID: 28962014 DOI: 10.1093/femsre/fux041] [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: 01/23/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
In recent years, novel imaging approaches revolutionised our understanding of the cellular and molecular biology of microorganisms. These include advances in fluorescent probes, dynamic live cell imaging, superresolution light and electron microscopy. Currently, a major transition in the experimental approach shifts electron microscopy studies from a complementary technique to a method of choice for structural and functional analysis. Here we review functional insights into the molecular architecture of viruses, bacteria and parasites as well as interactions with their respective host cells gained from studies using cryogenic electron tomography and related methodologies.
Collapse
Affiliation(s)
- Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Strasse 17, 60438 Frankfurt, Germany
| |
Collapse
|
45
|
Braunger K, Pfeffer S, Shrimal S, Gilmore R, Berninghausen O, Mandon EC, Becker T, Förster F, Beckmann R. Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. Science 2018. [PMID: 29519914 DOI: 10.1126/science.aar7899] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum.
Collapse
Affiliation(s)
- Katharina Braunger
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Otto Berninghausen
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany
| | - Elisabet C Mandon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, Netherlands.
| | - Roland Beckmann
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany.
| |
Collapse
|
46
|
Structural Biology in Situ Using Cryo-Electron Subtomogram Analysis. BIOLOGICAL AND MEDICAL PHYSICS, BIOMEDICAL ENGINEERING 2018. [DOI: 10.1007/978-3-319-68997-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
47
|
Baldwin PR, Tan YZ, Eng ET, Rice WJ, Noble AJ, Negro CJ, Cianfrocco MA, Potter CS, Carragher B. Big data in cryoEM: automated collection, processing and accessibility of EM data. Curr Opin Microbiol 2017; 43:1-8. [PMID: 29100109 DOI: 10.1016/j.mib.2017.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/27/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
Abstract
The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing.
Collapse
Affiliation(s)
- Philip R Baldwin
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - William J Rice
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Alex J Noble
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Carl J Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
48
|
Freeman Rosenzweig ES, Xu B, Kuhn Cuellar L, Martinez-Sanchez A, Schaffer M, Strauss M, Cartwright HN, Ronceray P, Plitzko JM, Förster F, Wingreen NS, Engel BD, Mackinder LCM, Jonikas MC. The Eukaryotic CO 2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization. Cell 2017; 171:148-162.e19. [PMID: 28938114 PMCID: PMC5671343 DOI: 10.1016/j.cell.2017.08.008] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/12/2017] [Accepted: 08/04/2017] [Indexed: 12/31/2022]
Abstract
Approximately 30%-40% of global CO2 fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is densely packed with the CO2-fixing enzyme Rubisco and is thought to be a crystalline or amorphous solid. Here, we show that the pyrenoid matrix of the unicellular alga Chlamydomonas reinhardtii is not crystalline but behaves as a liquid that dissolves and condenses during cell division. Furthermore, we show that new pyrenoids are formed both by fission and de novo assembly. Our modeling predicts the existence of a "magic number" effect associated with special, highly stable heterocomplexes that influences phase separation in liquid-like organelles. This view of the pyrenoid matrix as a phase-separated compartment provides a paradigm for understanding its structure, biogenesis, and regulation. More broadly, our findings expand our understanding of the principles that govern the architecture and inheritance of liquid-like organelles.
Collapse
Affiliation(s)
- Elizabeth S Freeman Rosenzweig
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Bin Xu
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Luis Kuhn Cuellar
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Antonio Martinez-Sanchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mike Strauss
- Cryo-EM Facility, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Heather N Cartwright
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Pierre Ronceray
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ 08544, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Luke C M Mackinder
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Martin C Jonikas
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
49
|
Englmeier R, Pfeffer S, Förster F. Structure of the Human Mitochondrial Ribosome Studied In Situ by Cryoelectron Tomography. Structure 2017; 25:1574-1581.e2. [PMID: 28867615 DOI: 10.1016/j.str.2017.07.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/12/2017] [Accepted: 07/26/2017] [Indexed: 01/26/2023]
Abstract
Mitochondria maintain their own genome and its corresponding protein synthesis machine, the mitochondrial ribosome (mitoribosome). Mitoribosomes primarily synthesize highly hydrophobic proteins of the inner mitochondrial membrane. Recent studies revealed the complete structure of the isolated mammalian mitoribosome, but its mode of membrane association remained hypothetical. In this study, we used cryoelectron tomography to visualize human mitoribosomes in isolated mitochondria. The subtomogram average of the membrane-associated human mitoribosome reveals a single major contact site with the inner membrane, mediated by the mitochondria-specific protein mL45. A second rRNA-mediated contact site that is present in yeast is absent in humans, resulting in a more variable association of the human mitoribosome with the inner membrane. Despite extensive structural differences of mammalian and fungal mitoribosomal structure, the principal organization of peptide exit tunnel and the mL45 homolog remains invariant, presumably to align the mitoribosome with the membrane-embedded insertion machinery.
Collapse
Affiliation(s)
- Robert Englmeier
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152 Martinsried, Germany
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152 Martinsried, Germany.
| |
Collapse
|
50
|
Scheffer MP, Gonzalez-Gonzalez L, Seybert A, Ratera M, Kunz M, Valpuesta JM, Fita I, Querol E, Piñol J, Martín-Benito J, Frangakis AS. Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium. Mol Microbiol 2017; 105:869-879. [PMID: 28671286 DOI: 10.1111/mmi.13743] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2017] [Indexed: 01/09/2023]
Abstract
Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its plasma membrane is the major surface adhesion complex, known as NAP that is essential for adhesion and gliding motility of the organism. Here, we have performed cryo-electron tomography of intact cells and detergent permeabilized M. genitalium cell aggregates, providing sub-tomogram averages of free and cell-attached NAPs respectively, revealing a tetrameric complex with two-fold rotational (C2) symmetry. Each NAP has two pairs of globular lobes (named α and β lobes), arranged as a dimer of heterodimers with each lobe connected by a stalk to the cell membrane. The β lobes are larger than the α lobes by 20%. Classification of NAPs showed that the complex can tilt with respect to the cell membrane. A protein complex containing exclusively the proteins P140 and P110, was purified from M. genitalium and was structurally characterized by negative-stain single particle EM reconstruction. The close structural similarity found between intact NAPs and the isolated P140/P110 complexes, shows that dimers of P140/P110 heterodimers are the only components of the extracellular region of intact NAPs in M. genitalium.
Collapse
Affiliation(s)
- Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - Luis Gonzalez-Gonzalez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - Mercè Ratera
- Parc Científic de Barcelona, Instituto de Biología Molecular de Barcelona del (IBMB-CSIC), Baldiri i Reixac 10, Barcelona 08028, Spain
| | - Michael Kunz
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - José M Valpuesta
- Department for Macromolecular Structures, Centro Nacional de Biotecnologıa (CNB-CSIC), Madrid 28049, Spain
| | - Ignacio Fita
- Parc Científic de Barcelona, Instituto de Biología Molecular de Barcelona del (IBMB-CSIC), Baldiri i Reixac 10, Barcelona 08028, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Jaime Martín-Benito
- Department for Macromolecular Structures, Centro Nacional de Biotecnologıa (CNB-CSIC), Madrid 28049, Spain
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| |
Collapse
|