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Mäeots ME, Enchev RI. Structural dynamics: review of time-resolved cryo-EM. Acta Crystallogr D Struct Biol 2022; 78:927-935. [PMID: 35916218 PMCID: PMC9344476 DOI: 10.1107/s2059798322006155] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022] Open
Abstract
Time-resolved cryo-EM is an emerging technique in structural biology that allows the user to capture structural states which would otherwise be too transient for standard methods. There has been a resurgence in technical advancements in this field in the last five years and this review provides a summary of the technical highlights. The structural determination of biological macromolecules has been transformative for understanding biochemical mechanisms and developing therapeutics. However, the ultimate goal of characterizing how structural dynamics underpin biochemical processes has been difficult. This is largely due to significant technical challenges that hinder data collection and analysis on the native timescales of macromolecular dynamics. Single-particle cryo-EM provides a powerful platform to approach this challenge, since samples can be frozen faster than the single-turnover timescales of most biochemical reactions. In order to enable time-resolved analysis, significant innovations in the handling and preparation of cryo-EM samples have been implemented, bringing us closer to the goal of the direct observation of protein dynamics in the milliseconds to seconds range. Here, the current state of time-resolved cryo-EM is reviewed and the most promising future research directions are discussed.
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Castells-Graells R, Ribeiro JRS, Domitrovic T, Hesketh EL, Scarff CA, Johnson JE, Ranson NA, Lawson DM, Lomonossoff GP. Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus. Commun Biol 2021; 4:619. [PMID: 34031522 PMCID: PMC8144610 DOI: 10.1038/s42003-021-02134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus maturation, we transiently expressed the capsid protein of the insect virus Nudaurelia capensis omega virus (NωV) in Nicotiana benthamiana and were able to purify both immature procapsids and mature capsids from infiltrated leaves by varying the expression time. Cryo-EM analysis of the plant-produced procapsids and mature capsids to 6.6 Å and 2.7 Å resolution, respectively, reveals that in addition to large scale rigid body motions, internal regions of the subunits are extensively remodelled during maturation, creating the active site required for autocatalytic cleavage and infectivity. The mature particles are biologically active in terms of their ability to lyse membranes and have a structure that is essentially identical to authentic virus. The ability to faithfully recapitulate and visualize a complex maturation process in plants, including the autocatalytic cleavage of the capsid protein, has revealed a ~30 Å translation-rotation of the subunits during maturation as well as conformational rearrangements in the N and C-terminal helical regions of each subunit.
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Affiliation(s)
- Roger Castells-Graells
- Department of Biological Chemistry, John Innes Centre, Colney, UK
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Jonas R S Ribeiro
- Virology Department, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana Domitrovic
- Virology Department, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emma L Hesketh
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Charlotte A Scarff
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Colney, UK
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Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G. Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis. Sci Rep 2020; 10:16301. [PMID: 33004869 PMCID: PMC7530986 DOI: 10.1038/s41598-020-73199-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/11/2020] [Indexed: 01/21/2023] Open
Abstract
Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.
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Affiliation(s)
- Eileen L. Murphy
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
| | - Kavindra V. Singh
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Bryant Avila
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Torsten Kleffmann
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Steven T. Gregory
- grid.20431.340000 0004 0416 2242Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881 USA
| | - Barbara E. Murray
- grid.267308.80000 0000 9206 2401Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030 USA
| | - Kurt L. Krause
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, 9054 New Zealand
| | - Reza Khayat
- grid.254250.40000 0001 2264 7145Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031 USA
| | - Gerwald Jogl
- grid.40263.330000 0004 1936 9094Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912 USA
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Shi J, Zeng X, Jiang R, Jiang T, Xu M. A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection. QUANTITATIVE BIOLOGY 2020; 8:51-63. [PMID: 32477613 PMCID: PMC7259590 DOI: 10.1007/s40484-019-0191-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/10/2019] [Accepted: 11/08/2019] [Indexed: 10/24/2022]
Abstract
BACKGROUND Cryo-electron microscopy (Cryo-EM) and tomography (Cryo-ET) have emerged as important imaging techniques for studying structures of macromolecular complexes. In 3D reconstruction of large macromolecular complexes, many 2D projection images of macromolecular complex particles are usually acquired with low signal-to-noise ratio. Therefore, it is meaningful to select multiple images containing the same structure with identical orientation. The selected images are averaged to produce a higher-quality representation of the underlying structure with improved resolution. Existing approaches of selecting such images have limited accuracy and speed. METHODS We propose a simulated annealing-based algorithm (SA) to pick the homogeneous image set with best average. Its performance is compared with two baseline methods based on both 2D and 3D datasets. When tested on simulated and experimental 3D Cryo-ET images of Ribosome complex, SA sometimes stopped at a local optimal solution. Restarting is applied to settle this difficulty and significantly improved the performance of SA on 3D datasets. RESULTS Experimented on simulated and experimental 2D Cryo-EM images of Ribosome complex datasets respectively with SNR = 10 and SNR = 0.5, our method achieved better accuracy in terms of F-measure, resolution score, and time cost than two baseline methods. Additionally, SA shows its superiority when the proportion of homogeneous images decreases. CONCLUSIONS SA is introduced for homogeneous image selection to realize higher accuracy with faster processing speed. Experiments on both simulated and real 2D Cryo-EM and 3D Cryo-ET images demonstrated that SA achieved expressively better performance. This approach serves as an important step for improving the resolution of structural recovery of macromolecular complexes captured by Cryo-EM and Cryo-ET.
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Affiliation(s)
- Jie Shi
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Rui Jiang
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California-Riverside, Riverside, CA 92521, USA
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Nakane T, Kimanius D, Lindahl E, Scheres SH. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. eLife 2018; 7:36861. [PMID: 29856314 PMCID: PMC6005684 DOI: 10.7554/elife.36861] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022] Open
Abstract
Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.
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Affiliation(s)
- Takanori Nakane
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Dari Kimanius
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
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Heymann JB. Guidelines for using Bsoft for high resolution reconstruction and validation of biomolecular structures from electron micrographs. Protein Sci 2017; 27:159-171. [PMID: 28891250 DOI: 10.1002/pro.3293] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/12/2022]
Abstract
Cryo-electron microscopy (cryoEM) is becoming popular as a tool to solve biomolecular structures with the recent availability of direct electron detectors allowing automated acquisition of high resolution data. The Bsoft software package, developed over 20 years for analyzing electron micrographs, offers a full workflow for validated single particle analysis with extensive functionality, enabling customization for specific cases. With the increasing use of cryoEM and its automation, proper validation of the results is a bigger concern. The three major validation approaches, independent data sets, resolution-limited processing, and coherence testing, can be incorporated into any Bsoft workflow. Here, the main workflow is divided into four phases: (i) micrograph preprocessing, (ii) particle picking, (iii) particle alignment and reconstruction, and (iv) interpretation. Each of these phases represents a conceptual unit that can be automated, followed by a check point to assess the results. The aim in the first three phases is to reconstruct one or more validated maps at the best resolution possible. Map interpretation then involves identification of components, segmentation, quantification, and modeling. The algorithms in Bsoft are well established, with future plans focused on ease of use, automation and institutionalizing validation.
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Affiliation(s)
- J Bernard Heymann
- Laboratory for Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, 20892
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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8
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Abstract
The herpes simplex virus 1 (HSV-1) capsid is a massive particle (~200 MDa; 1,250-Å diameter) with T=16 icosahedral symmetry. It initially assembles as a procapsid with ~4,000 protein subunits of 11 different kinds. The procapsid undergoes major changes in structure and composition as it matures, a process driven by proteolysis and expulsion of the internal scaffolding protein. Assembly also relies on an external scaffolding protein, the triplex, an α2β heterotrimer that coordinates neighboring capsomers in the procapsid and becomes a stabilizing clamp in the mature capsid. To investigate the mechanisms that regulate its assembly, we developed a novel isolation procedure for the metastable procapsid and collected a large set of cryo-electron microscopy data. In addition to procapsids, these preparations contain maturation intermediates, which were distinguished by classifying the images and calculating a three-dimensional reconstruction for each class. Appraisal of the procapsid structure led to a new model for assembly; in it, the protomer (assembly unit) consists of one triplex, surrounded by three major capsid protein (MCP) subunits. The model exploits the triplexes’ departure from 3-fold symmetry to explain the highly skewed MCP hexamers, the triplex orientations at each 3-fold site, and the T=16 architecture. These observations also yielded new insights into maturation. This paper addresses the molecular mechanisms that govern the self-assembly of large, structurally complex, macromolecular particles, such as the capsids of double-stranded DNA viruses. Although they may consist of thousands of protein subunits of many different kinds, their assembly is precise, ranking them among the largest entities in the biosphere whose structures are uniquely defined to the atomic level. Assembly proceeds in two stages: formation of a precursor particle (procapsid) and maturation, during which major changes in structure and composition take place. Our analysis of the HSV procapsid by cryo-electron microscopy suggests a hierarchical pathway in which multisubunit “protomers” are the building blocks of the procapsid but their subunits are redistributed into different subcomplexes upon being incorporated into a nascent procapsid and are redistributed again in maturation. Assembly is a highly virus-specific process, making it a potential target for antiviral intervention.
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9
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Zhang J, Reza Malmirchegini G, Clubb RTCT, Loo JA. Native top-down mass spectrometry for the structural characterization of human hemoglobin. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:221-31. [PMID: 26307702 PMCID: PMC4731028 DOI: 10.1255/ejms.1340] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and noncovalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down MS using electrospray ionization and a 15-Tesla Fourier transform ion cyclotron resonance mass spectrometer. Native MS preserves the noncovalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of the Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore a low fragmentation efficiency. Precursor ion activation allows a steady increase in N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and four z ions on the α chain; 36 c ions and two z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer shows similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. It may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.
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Affiliation(s)
| | | | - Robert T Clubb T Clubb
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, 90095, United States.
| | - Joseph A Loo
- De partment of Chemistry and Biochemistry, Department of Biological Chemistry, David Geffen School of Medicine, UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, California, 90095, United States.
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Cohen MR, Moiseenkova-Bell VY. Structure of thermally activated TRP channels. CURRENT TOPICS IN MEMBRANES 2014; 74:181-211. [PMID: 25366237 DOI: 10.1016/b978-0-12-800181-3.00007-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Temperature sensation is important for adaptation and survival of organisms. While temperature has the potential to affect all biological macromolecules, organisms have evolved specific thermosensitive molecular detectors that are able to transduce temperature changes into physiologically relevant signals. Among these thermosensors are ion channels from the transient receptor potential (TRP) family. Prime candidates include TRPV1-4, TRPA1, and TRPM8 (the so-called "thermoTRP" channels), which are expressed in sensory neurons and gated at specific temperatures. Electrophysiological and thermodynamic approaches have been employed to determine the nature by which thermoTRPs detect temperature and couple temperature changes to channel gating. To further understand how thermoTRPs sense temperature, high-resolution structures of full-length thermoTRPs channels will be required. Here, we will discuss current progress in unraveling the structures of thermoTRP channels.
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Affiliation(s)
- Matthew R Cohen
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vera Y Moiseenkova-Bell
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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11
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Cossio P, Hummer G. Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. J Struct Biol 2013; 184:427-37. [PMID: 24161733 DOI: 10.1016/j.jsb.2013.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 10/05/2013] [Accepted: 10/09/2013] [Indexed: 10/26/2022]
Abstract
We develop a method to extract structural information from electron microscopy (EM) images of dynamic and heterogeneous molecular assemblies. To overcome the challenge of disorder in the imaged structures, we analyze each image individually, avoiding information loss through clustering or averaging. The Bayesian inference of EM (BioEM) method uses a likelihood-based probabilistic measure to quantify the consistency between each EM image and given structural models. The likelihood function accounts for uncertainties in the molecular position and orientation, variations in the relative intensities and noise in the experimental images. The BioEM formalism is physically intuitive and mathematically simple. We show that for experimental GroEL images, BioEM correctly identifies structures according to the functional state. The top-ranked structure is the corresponding X-ray crystal structure, followed by an EM structure generated previously from a superset of the EM images used here. To analyze EM images of highly flexible molecules, we propose an ensemble refinement procedure, and validate it with synthetic EM maps of the ESCRT-I-II supercomplex. Both the size of the ensemble and its structural members are identified correctly. BioEM offers an alternative to 3D-reconstruction methods, extracting accurate population distributions for highly flexible structures and their assemblies. We discuss limitations of the method, and possible applications beyond ensemble refinement, including the cross-validation and unbiased post-assessment of model structures, and the structural characterization of systems where traditional approaches fail. Overall, our results suggest that the BioEM framework can be used to analyze EM images of both ordered and disordered molecular systems.
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Affiliation(s)
- Pilar Cossio
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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12
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Abstract
At 37°C, the structure of poliovirus is dynamic, and internal polypeptides VP4 and N terminus of VP1 (residues 1 to 53) externalize reversibly. An Fab fragment of a monospecific antibody, which binds to residues 39 to 55 of VP1, was utilized to locate the N termini of VP1 in native (160S) particles in this "breathing" state. Fab and virus were mixed and imaged via cryogenic electron microscopy. The resulting reconstruction showed the capsid expands similarly to the irreversibly altered cell entry intermediate (135S) particle, but the N terminus of VP1 is located near the 2-fold axes, instead of the "propeller tip" as in 135S particles.
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13
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Nemecek D, Cheng N, Qiao J, Mindich L, Steven AC, Heymann JB. Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates. J Mol Biol 2011; 414:260-71. [PMID: 22019738 DOI: 10.1016/j.jmb.2011.10.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/30/2011] [Accepted: 10/05/2011] [Indexed: 12/31/2022]
Abstract
The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state.
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Affiliation(s)
- Daniel Nemecek
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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14
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An externalized polypeptide partitions between two distinct sites on genome-released poliovirus particles. J Virol 2011; 85:9974-83. [PMID: 21775460 DOI: 10.1128/jvi.05013-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to 53). Externalization of these entities is followed by release of the RNA genome (uncoating), leaving an empty (80S) particle. The antigen-binding fragment (Fab) of a monospecific peptide 1 (P1) antibody, which was raised against a peptide corresponding to amino-terminal residues 24 to 40 of VP1, was utilized to track the location of the amino terminus of VP1 in the 135S and 80S states of poliovirus particles via cryogenic electron microscopy (cryo-EM) and three-dimensional image reconstruction. On 135S, P1 Fabs bind to a prominent feature on the external surface known as the "propeller tip." In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, at least 50 Å distant, at the icosahedral 2-fold axes. Further analysis showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips, P1 Fabs bound only at the 2-fold axes, or P1 Fabs simultaneously bound at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Hence, this portion of VP1 does not change conformation synchronously when switching from the 135S state. These conclusions are compatible with previous observations of multiple conformations of the 80S state and suggest that movement of the amino terminus of VP1 has a role in uncoating. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions.
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15
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Benesch JLP, Ruotolo BT, Simmons DA, Barrera NP, Morgner N, Wang L, Saibil HR, Robinson CV. Separating and visualising protein assemblies by means of preparative mass spectrometry and microscopy. J Struct Biol 2010; 172:161-8. [PMID: 20227505 DOI: 10.1016/j.jsb.2010.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 10/19/2022]
Abstract
Many multi-protein assemblies exhibit characteristics which hamper their structural and dynamical characterization. These impediments include low copy number, heterogeneity, polydispersity, hydrophobicity, and intrinsic disorder. It is becoming increasingly apparent that both novel and hybrid structural biology approaches need to be developed to tackle the most challenging targets. Nanoelectrospray mass spectrometry has matured over the last decade to enable the elucidation of connectivity and composition of large protein assemblies. Moreover, comparing mass spectrometry data with transmission electron microscopy images has enabled the mapping of subunits within topological models. Here we describe a preparative form of mass spectrometry designed to isolate specific protein complexes from within a heterogeneous ensemble, and to 'soft-land' these target complexes for ex situ imaging. By building a retractable probe incorporating a versatile target holder, and modifying the ion optics of a commercial mass spectrometer, we show that we can steer the macromolecular ion beam onto a target for imaging by means of transmission electron microscopy and atomic force microscopy. Our data for the tetradecameric chaperonin GroEL show that not only are the molecular volumes of the landed particles consistent with the overall dimensions of the complex, but also that their gross topological features can be maintained.
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Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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16
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Lu Z, Shaikh TR, Barnard D, Meng X, Mohamed H, Yassin A, Mannella CA, Agrawal RK, Lu TM, Wagenknecht T. Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy. J Struct Biol 2009; 168:388-95. [PMID: 19683579 DOI: 10.1016/j.jsb.2009.08.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 07/14/2009] [Accepted: 08/10/2009] [Indexed: 11/19/2022]
Abstract
The goal of time-resolved cryo-electron microscopy is to determine structural models for transient functional states of large macromolecular complexes such as ribosomes and viruses. The challenge of time-resolved cryo-electron microscopy is to rapidly mix reactants, and then, following a defined time interval, to rapidly deposit them as a thin film and freeze the sample to the vitreous state. Here we describe a methodology in which reaction components are mixed and allowed to react, and are then sprayed onto an EM grid as it is being plunged into cryogen. All steps are accomplished by a monolithic, microfabricated silicon device that incorporates a mixer, reaction channel, and pneumatic sprayer in a single chip. We have found that microdroplets produced by air atomization spread to sufficiently thin films on a millisecond time scale provided that the carbon supporting film is made suitably hydrophilic. The device incorporates two T-mixers flowing into a single channel of four butterfly-shaped mixing elements that ensure effective mixing, followed by a microfluidic reaction channel whose length can be varied to achieve the desired reaction time. The reaction channel is flanked by two ports connected to compressed humidified nitrogen gas (at 50 psi) to generate the spray. The monolithic mixer-sprayer is incorporated into a computer-controlled plunging apparatus. To test the mixing performance and the suitability of the device for preparation of biological macromolecules for cryo-EM, ribosomes and ferritin were mixed in the device and sprayed onto grids. Three-dimensional reconstructions of the ribosomes demonstrated retention of native structure, and 30S and 50S subunits were shown to be capable of reassociation into ribosomes after passage through the device.
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Affiliation(s)
- Zonghuan Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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17
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JONIĆ S, SORZANO C, BOISSET N. Comparison of single-particle analysis and electron tomography approaches: an overview. J Microsc 2008; 232:562-79. [DOI: 10.1111/j.1365-2818.2008.02119.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Steven AC, Baumeister W. The future is hybrid. J Struct Biol 2008; 163:186-95. [DOI: 10.1016/j.jsb.2008.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 06/02/2008] [Indexed: 11/29/2022]
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19
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Chu JW, Voth GA. Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. Biophys J 2007; 93:3860-71. [PMID: 17704151 PMCID: PMC2084241 DOI: 10.1529/biophysj.107.112060] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle points, and is hence a "rough" free energy landscape. In this implementation of the DWNM, the free energy function is reduced to an elastic-network model representation near the two reference states. The effects of free energy function roughness on the reaction pathways of protein conformational change is demonstrated by applying the DWNM to the conformational changes of two protein systems: the coil-to-helix transition of the DB-loop in G-actin and the open-to-closed transition of adenylate kinase. In both systems, the rough free energy function of the DWNM leads to the identification of distinct minimum free energy paths connecting two conformational states. These results indicate that while the elastic-network model captures the low-frequency vibrational motions of a protein, the roughness in the free energy function introduced by the DWNM can be used to characterize the transition mechanism between protein conformations.
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Affiliation(s)
- Jhih-Wei Chu
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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20
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Scheres SHW, Gao H, Valle M, Herman GT, Eggermont PPB, Frank J, Carazo JM. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat Methods 2006; 4:27-9. [PMID: 17179934 DOI: 10.1038/nmeth992] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 11/06/2006] [Indexed: 11/08/2022]
Abstract
Although three-dimensional electron microscopy (3D-EM) permits structural characterization of macromolecular assemblies in distinct functional states, the inability to classify projections from structurally heterogeneous samples has severely limited its application. We present a maximum likelihood-based classification method that does not depend on prior knowledge about the structural variability, and demonstrate its effectiveness for two macromolecular assemblies with different types of conformational variability: the Escherichia coli ribosome and Simian virus 40 (SV40) large T-antigen.
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Affiliation(s)
- Sjors H W Scheres
- Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049, Madrid, Spain
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21
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Grob P, Cruse MJ, Inouye C, Peris M, Penczek PA, Tjian R, Nogales E. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 2006; 14:511-20. [PMID: 16531235 DOI: 10.1016/j.str.2005.11.020] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 11/11/2005] [Accepted: 11/16/2005] [Indexed: 11/20/2022]
Abstract
The multisubunit transcription factor TFIID is essential for directing eukaryotic promoter recognition and mediating interactions with activators/cofactors during assembly of the preinitiation complex. Despite its central role in transcription initiation and regulation, structural knowledge of the TFIID complex has so far been largely limited to electron microscopy studies of negatively stained samples. Here, we present a cryo-electron microscopy 3D reconstruction of the large endogenous human TFIID complex. The improved cryopreservation has allowed for a more detailed definition of the structural elements in the complex and for the detection, by an extensive statistical analysis of the data, of a conformational opening and closing of the cavity central to the TFIID architecture. We propose that these density rearrangements in the structure are a likely reflection of the plasticity of the interactions between TFIID and its many partner proteins.
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Affiliation(s)
- Patricia Grob
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, California 94720, USA
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22
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Fu J, Gao H, Frank J. Unsupervised classification of single particles by cluster tracking in multi-dimensional space. J Struct Biol 2006; 157:226-39. [PMID: 16931050 DOI: 10.1016/j.jsb.2006.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 06/07/2006] [Accepted: 06/11/2006] [Indexed: 11/17/2022]
Abstract
In cryo-electron microscopy (cryo-EM) single-particle reconstruction, the heterogeneity of two-dimensional projection image data resulting from the co-existence of different conformational or ligand binding states of a macromolecular complex remains a major obstacle as it impairs the validity of reconstructed density maps and limits the progress toward higher resolution. Classification of cryo-EM data according to the different conformations is difficult because of the coexistence of multiple orientations in a single dataset. Here, we present an unsupervised classification method, termed cluster tracking, which utilizes the continuity in multi-dimensional space induced by angular adjacency of projections in large datasets. In a proof of concept, the testing of cluster tracking on simulated projection data, which were generated from multiple conformations and orientations of an existing volume, produced clusters that are consistent with the conformational identity of the data. The application of the method to experimental cryo-EM projection data is found to result in a partition similar to the one generated by supervised classification.
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Affiliation(s)
- Jie Fu
- Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA
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23
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Heymann JB, Belnap DM. Bsoft: image processing and molecular modeling for electron microscopy. J Struct Biol 2006; 157:3-18. [PMID: 17011211 DOI: 10.1016/j.jsb.2006.06.006] [Citation(s) in RCA: 412] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Revised: 06/07/2006] [Accepted: 06/11/2006] [Indexed: 11/17/2022]
Abstract
Bsoft is a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing. The code is modularized to allow for rapid testing and deployment of new processing algorithms, while also providing sufficient infrastructure to deal with many file formats and parametric data. The design is deliberately open to allow interchange of information with other image and molecular processing software through a standard parameter file (currently a text-based encoding of parameters in the STAR format) and its support of multiple image and molecular formats. It also allows shell scripting of processes and allows subtasks to be distributed across multiple computers for concurrent processing. Bsoft has undergone many modifications and advancements since its initial release [Heymann, J.B., 2001. Bsoft: image and molecular processing in electron microscopy. J. Struct. Biol. 133, 156-169]. Much of the emphasis is on single particle analysis and tomography, and sufficient functionality is available in the package to support most needed operations for these techniques. The key graphical user interface is the program bshow, which displays an image and is used for many interactive purposes such as fitting the contrast transfer function or picking particles. Bsoft also offers various tools to manipulate atomic structures and to refine the fit of a known molecular structure to a density in a reconstruction.
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Affiliation(s)
- J Bernard Heymann
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Penczek PA, Frank J, Spahn CMT. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J Struct Biol 2006; 154:184-94. [PMID: 16520062 DOI: 10.1016/j.jsb.2005.12.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Accepted: 12/07/2005] [Indexed: 10/25/2022]
Abstract
The bootstrap-based method for calculation of the 3D variance in cryo-EM maps reconstructed from sets of their projections was applied to a dataset of functional ribosomal complexes containing the Escherichia coli 70S ribosome, tRNAs, and elongation factor G (EF-G). The variance map revealed regions of high variability in the intersubunit space of the ribosome: in the locations of tRNAs, in the putative location of EF-G, and in the vicinity of the L1 protein. This result indicated heterogeneity of the dataset. A method of focused classification was put forward in order to sort out the projection data into approximately homogenous subsets. The method is based on the identification and localization of a region of high variance that a subsequent classification step can be focused on by the use of a 3D spherical mask. After initial classification, template volumes are created and are subsequently refined using a multireference 3D projection alignment procedure. In the application to the ribosome dataset, the two resulting structures were interpreted as resulting from ribosomal complexes with bound EF-G and an empty A site, or, alternatively, from complexes that had no EF-G bound but had both A and P sites occupied by tRNA. The proposed method of focused classification proved to be a successful tool in the analysis of the heterogeneous cryo-EM dataset. The associated calculation of the correlations within the density map confirmed the conformational variability of the complex, which could be interpreted in terms of the ribosomal elongation cycle.
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Affiliation(s)
- Pawel A Penczek
- Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, 6431 Fannin, MSB 6.218, Houston, TX 77030, USA.
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25
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Scheres SHW, Valle M, Nuñez R, Sorzano COS, Marabini R, Herman GT, Carazo JM. Maximum-likelihood multi-reference refinement for electron microscopy images. J Mol Biol 2005; 348:139-49. [PMID: 15808859 DOI: 10.1016/j.jmb.2005.02.031] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 02/07/2005] [Accepted: 02/14/2005] [Indexed: 10/25/2022]
Abstract
A maximum-likelihood approach to multi-reference image refinement is presented. In contrast to conventional cross-correlation refinement, the new approach includes a formal description of the noise, implying that it is especially suited to cases with low signal-to-noise ratios. Application of this approach to a cryo-electron microscopy dataset revealed two major classes for projections of simian virus 40 large T-antigen in complex with an asymmetric DNA-probe, containing the origin of simian virus 40 replication. Strongly bent projections of dodecamers showed density that may be attributed to the complexed double-stranded DNA, while almost straight projections revealed a twist in the relative orientation of the hexameric subunits. This new level of detail for large T-antigen projections was not detected using conventional techniques. For a negative stain dataset, maximum-likelihood refinement yielded results that were practically identical to those obtained using conventional multi-reference refinement. Results obtained using simulated data suggest that the efficiency of the maximum-likelihood approach may be further enhanced by explicitly incorporating the microscope contrast transfer function in the image formation model.
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Affiliation(s)
- Sjors H W Scheres
- Biocomputing Unit, Centro Nacional de Biotecnología, Campus Universidad Autónoma, Cantoblanco, 28049, Madrid, Spain
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Abstract
Electron microscopy is arguably the most powerful tool for spatial imaging of structures. As such, 2D and 3D microscopies provide static structures with subnanometer and increasingly with angstrom-scale spatial resolution. Here we report the development of 4D ultrafast electron microscopy, whose capability imparts another dimension to imaging in general and to dynamics in particular. We demonstrate its versatility by recording images and diffraction patterns of crystalline and amorphous materials and images of biological cells. The electron packets, which were generated with femtosecond laser pulses, have a de Broglie wavelength of 0.0335 angstroms at 120 keV and have as low as one electron per pulse. With such few particles, doses of few electrons per square ångstrom, and ultrafast temporal duration, the long sought after but hitherto unrealized quest for ultrafast electron microscopy has been realized. Ultrafast electron microscopy should have an impact on all areas of microscopy, including biological imaging.
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Affiliation(s)
- Vladimir A Lobastov
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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