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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. SCIENCE ADVANCES 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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2
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Dhakal A, Gyawali R, Wang L, Cheng J. A large expert-curated cryo-EM image dataset for machine learning protein particle picking. Sci Data 2023; 10:392. [PMID: 37349345 PMCID: PMC10287764 DOI: 10.1038/s41597-023-02280-2] [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: 03/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA.
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3
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Dhakal A, Gyawali R, Wang L, Cheng J. CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529443. [PMID: 36865277 PMCID: PMC9980126 DOI: 10.1101/2023.02.21.529443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is currently the most powerful technique for determining the structures of large protein complexes and assemblies. Picking single-protein particles from cryo-EM micrographs (images) is a key step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though the emerging machine learning-based particle picking can potentially automate the process, its development is severely hindered by lack of large, high-quality, manually labelled training data. Here, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for single protein particle picking and analysis to address this bottleneck. It consists of manually labelled cryo-EM micrographs of 32 non-redundant, representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). It includes 9,089 diverse, high-resolution micrographs (∼300 cryo-EM images per EMPIAR dataset) in which the coordinates of protein particles were labelled by human experts. The protein particle labelling process was rigorously validated by both 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of machine learning and artificial intelligence methods for automated cryo-EM protein particle picking. The dataset and data processing scripts are available at https://github.com/BioinfoMachineLearning/cryoppp.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
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4
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Assalauova D, Vartanyants IA. The structure of tick-borne encephalitis virus determined at X-ray free-electron lasers. Simulations. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:24-34. [PMID: 36601923 PMCID: PMC9814066 DOI: 10.1107/s1600577522011341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
The study of virus structures by X-ray free-electron lasers (XFELs) has attracted increased attention in recent decades. Such experiments are based on the collection of 2D diffraction patterns measured at the detector following the application of femtosecond X-ray pulses to biological samples. To prepare an experiment at the European XFEL, the diffraction data for the tick-borne encephalitis virus (TBEV) was simulated with different parameters and the optimal values were identified. Following the necessary steps of a well established data-processing pipeline, the structure of TBEV was obtained. In the structure determination presented, a priori knowledge of the simulated virus orientations was used. The efficiency of the proposed pipeline was demonstrated.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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5
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Fremdling P, Esser TK, Saha B, Makarov AA, Fort KL, Reinhardt-Szyba M, Gault J, Rauschenbach S. A Preparative Mass Spectrometer to Deposit Intact Large Native Protein Complexes. ACS NANO 2022; 16:14443-14455. [PMID: 36037396 PMCID: PMC9527803 DOI: 10.1021/acsnano.2c04831] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study the structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase, where they can be accurately manipulated and purified, followed by controlled deposition onto various substrates. In combination with imaging techniques, direct structural information on well-defined molecules can be obtained, which is essential to test and interpret results from indirect mass spectrometry techniques. To date, ion-beam deposition experiments are limited to a small number of custom instruments worldwide, and there are no commercial alternatives. Here we present a module that adds ion-beam deposition capabilities to a popular commercial MS platform (Thermo Scientific Q Exactive UHMR mass spectrometer). This combination significantly reduces the overhead associated with custom instruments, while benefiting from established high performance and reliability. We present current performance characteristics including beam intensity, landing-energy control, and deposition spot size for a broad range of molecules. In combination with atomic force microscopy (AFM) and transmission electron microscopy (TEM), we distinguish near-native from unfolded proteins and show retention of the native shape of protein assemblies after dehydration and deposition. Further, we use an enzymatic assay to quantify the activity of a noncovalent protein complex after deposition on a dry surface. Together, these results not only indicate a great potential of ES-IBD for applications in structural biology, but also outline the challenges that need to be solved for it to reach its full potential.
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Affiliation(s)
- Paul Fremdling
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim K. Esser
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bodhisattwa Saha
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alexander A. Makarov
- Thermo
Fisher Scientific, Bremen 28199, Germany
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
| | | | | | - Joseph Gault
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Stephan Rauschenbach
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart 70569, Germany
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6
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Brillault L, Landsberg MJ. Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy. Methods Mol Biol 2020; 2073:221-246. [PMID: 31612445 DOI: 10.1007/978-1-4939-9869-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.
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Affiliation(s)
- Lou Brillault
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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7
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Downing KH, Glaeser RM. Estimating the effect of finite depth of field in single-particle cryo-EM. Ultramicroscopy 2017; 184:94-99. [PMID: 28869854 DOI: 10.1016/j.ultramic.2017.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/05/2017] [Accepted: 08/15/2017] [Indexed: 01/30/2023]
Abstract
The extent to which the resolution varies within a three-dimensional (3-D) reconstruction, when the diameter of an object is large, is investigated computationally. Numerical simulation is used to model ideal three-dimensional point-spread functions at different radial positions within an object. It is shown that reconstructed density maps are affected less than might have been expected when particles are larger than the depth of field. This favorable outcome is attributed mainly to the fact that a point which lies outside the depth of field relative to the center, for some orientations of the object, will also lie within the depth of field for other orientations. We find, as a result, that the diameter of a particle can be as much as four times the depth of field (as defined by a 90° phase-error criterion) before curvature of the Ewald sphere becomes a limiting factor in determining the resolution that can be achieved.
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Affiliation(s)
- Kenneth H Downing
- Lawrence Berkeley National Laboratory, University of California, Berkeley CA 94720, USA
| | - Robert M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley CA 94720, USA.
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8
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Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf) 2015; 65:43-56. [PMID: 26671944 DOI: 10.1093/jmicro/dfv369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/06/2015] [Indexed: 11/12/2022] Open
Abstract
Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.
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Affiliation(s)
- Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA 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
| | - Anchi Cheng
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA 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, New York Structural Biology Center, New York, NY 10027, USA 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
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9
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Wu S, Armache JP, Cheng Y. Single-particle cryo-EM data acquisition by using direct electron detection camera. Microscopy (Oxf) 2015; 65:35-41. [PMID: 26546989 DOI: 10.1093/jmicro/dfv355] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/08/2015] [Indexed: 11/14/2022] Open
Abstract
Recent advances in single-particle electron cryo-microscopy (cryo-EM) were largely facilitated by the application of direct electron detection cameras. These cameras feature not only a significant improvement in detective quantum efficiency but also a high frame rate that enables images to be acquired as 'movies' made of stacks of many frames. In this review, we discuss how the applications of direct electron detection cameras in cryo-EM have changed the way the data are acquired.
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Affiliation(s)
- Shenping Wu
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA Howard Hughes Medical Institute, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
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10
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Passos DO, Lyumkis D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. J Struct Biol 2015; 192:235-44. [PMID: 26470814 DOI: 10.1016/j.jsb.2015.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 11/17/2022]
Abstract
A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of ∼75,000 particles. The gold-standard and frequency-limited approaches to single-particle refinement were each independently used to determine orientation parameters for the final reconstruction. Both approaches showed similar resolution curves and nominal resolution values for the 60S dataset, estimated at 2.9 Å. The amount of over-fitting present during frequency-limited refinement was quantitatively analyzed using the high-resolution phase-randomization test, and the results showed no apparent over-fitting. The number of asymmetric subunits required to reach specific resolutions was subsequently analyzed by refining subsets of the data in an ab initio manner. With our data collection and processing strategies, sub-nanometer resolution was obtained with ∼200 asymmetric subunits (or, equivalently for the ribosomal subunit, particles). Resolutions of 5.6 Å, 4.5 Å, and 3.8 Å were reached with ∼1000, ∼1600, and ∼5000 asymmetric subunits, respectively. At these resolutions, one would expect to detect alpha-helical pitch, separation of beta-strands, and separation of Cα atoms, respectively. Using this map, together with strategies for ab initio model building and model refinement, we built a region of the ribosomal protein eL6, which was missing in previous models of the yeast ribosome. The relevance for more routine high-resolution structure determination is discussed.
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Affiliation(s)
- Dario Oliveira Passos
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Dmitry Lyumkis
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, United States.
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11
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Glaeser RM, Han BG, Csencsits R, Killilea A, Pulk A, Cate JHD. Factors that Influence the Formation and Stability of Thin, Cryo-EM Specimens. Biophys J 2015; 110:749-55. [PMID: 26386606 DOI: 10.1016/j.bpj.2015.07.050] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 11/27/2022] Open
Abstract
Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. Here we first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. We then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated. In fact, a surfactant layer (of uncontrolled composition and surface pressure) can hardly be avoided during standard cryo-EM specimen preparation. We thus suggest that better control over the composition and properties of the surfactant layer may result in more reliable production of cryo-EM specimens with the desired thickness.
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Affiliation(s)
- Robert M Glaeser
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California.
| | - Bong-Gyoon Han
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California
| | - Roseann Csencsits
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California
| | - Alison Killilea
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California
| | - Arto Pulk
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California; Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, California
| | - Jamie H D Cate
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, California; Department of Chemistry, University of California, Berkeley, Berkeley, California; Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California
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12
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Wu W, Yan C, Shi X, Li L, Liu W, Xu C. Lipid in T-cell receptor transmembrane signaling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:130-8. [DOI: 10.1016/j.pbiomolbio.2015.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
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13
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Affiliation(s)
- Christian Colliex
- Laboratoire de Physique des Solides (UMR CNRS8502), Université Paris Sud XI, 91405 Orsay, France
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14
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Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X, Milne JLS, Subramaniam S. 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor. Science 2015; 348:1147-51. [PMID: 25953817 DOI: 10.1126/science.aab1576] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/29/2015] [Indexed: 01/21/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM.
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Affiliation(s)
- Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Soojay Banerjee
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Doreen Matthies
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacqueline L S Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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15
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Abstract
Until only a few years ago, single-particle electron cryo-microscopy (cryo-EM) was usually not the first choice for many structural biologists due to its limited resolution in the range of nanometer to subnanometer. Now, this method rivals X-ray crystallography in terms of resolution and can be used to determine atomic structures of macromolecules that are either refractory to crystallization or difficult to crystallize in specific functional states. In this review, I discuss the recent breakthroughs in both hardware and software that transformed cryo-microscopy, enabling understanding of complex biomolecules and their functions at atomic level.
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Affiliation(s)
- Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
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Faruqi A, Henderson R, McMullan G. Progress and Development of Direct Detectors for Electron Cryomicroscopy. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2015. [DOI: 10.1016/bs.aiep.2015.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy. Proc Natl Acad Sci U S A 2014; 111:11709-14. [PMID: 25071206 DOI: 10.1073/pnas.1402809111] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the solution structure of Escherichia coli β-galactosidase (∼465 kDa), solved at ∼3.2-Å resolution by using single-particle cryo-electron microscopy (cryo-EM). Densities for most side chains, including those of residues in the active site, and a catalytic Mg(2+) ion can be discerned in the map obtained by cryo-EM. The atomic model derived from our cryo-EM analysis closely matches the 1.7-Å crystal structure with a global rmsd of ∼0.66 Å. There are significant local differences throughout the protein, with clear evidence for conformational changes resulting from contact zones in the crystal lattice. Inspection of the map reveals that although densities for residues with positively charged and neutral side chains are well resolved, systematically weaker densities are observed for residues with negatively charged side chains. We show that the weaker densities for negatively charged residues arise from their greater sensitivity to radiation damage from electron irradiation as determined by comparison of density maps obtained by using electron doses ranging from 10 to 30 e(-)/Å(2). In summary, we establish that it is feasible to use cryo-EM to determine near-atomic resolution structures of protein complexes (<500 kDa) with low symmetry, and that the residue-specific radiation damage that occurs with increasing electron dose can be monitored by using dose fractionation tools available with direct electron detector technology.
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