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Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [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: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
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Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
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2
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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3
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DeRonja J, Nowell M, Wright S, Kacher J. Generational assessment of EBSD detectors for cross-correlation-based analysis: From scintillators to direct detection. Ultramicroscopy 2024; 257:113913. [PMID: 38141535 DOI: 10.1016/j.ultramic.2023.113913] [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: 06/20/2023] [Revised: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Introduced over ten years ago, cross-correlation-based electron backscatter diffraction has enabled high precision measurements of crystallographic rotations and elastic strain gradients at high spatial resolution. Since that time, there have been remarkable improvements in electron detector technology, including the advent of ultra-high speed detectors and the commercialization of direct detectors. In this study, we assess the efficacy of multiple generations of electron detectors for cross-correlation-based analysis using a single crystal Si sample as a reference. We show that, while improvements in precision are modest, there have been significant gains in the rate at which high-quality diffraction patterns can be collected. This has important implications in the size of datasets that can be collected and reduces the impact of drift and sample contamination.
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Affiliation(s)
| | | | | | - Josh Kacher
- Georgia Institute of Technology, Atlanta, GA 30332, United States.
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4
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Ding Y, Xue X. Medicinal Chemistry Strategies for the Modification of Bioactive Natural Products. Molecules 2024; 29:689. [PMID: 38338433 PMCID: PMC10856770 DOI: 10.3390/molecules29030689] [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: 12/14/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Natural bioactive compounds are valuable resources for drug discovery due to their diverse and unique structures. However, these compounds often lack optimal drug-like properties. Therefore, structural optimization is a crucial step in the drug development process. By employing medicinal chemistry principles, targeted molecular operations can be applied to natural products while considering their size and complexity. Various strategies, including structural fragmentation, elimination of redundant atoms or groups, and exploration of structure-activity relationships, are utilized. Furthermore, improvements in physicochemical properties, chemical and metabolic stability, biophysical properties, and pharmacokinetic properties are sought after. This article provides a concise analysis of the process of modifying a few marketed drugs as illustrative examples.
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Affiliation(s)
- Yuyang Ding
- Shenzhen Borui Pharmaceutical Technology Co., Ltd., Shenzhen 518055, China;
| | - Xiaoqian Xue
- Medi-X Pingshan, Southern University of Science and Technology, Shenzhen 518055, China
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5
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Ignatiou A, Macé K, Redzej A, Costa TRD, Waksman G, Orlova EV. Structural Analysis of Protein Complexes by Cryo-Electron Microscopy. Methods Mol Biol 2024; 2715:431-470. [PMID: 37930544 DOI: 10.1007/978-1-0716-3445-5_27] [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] [Indexed: 11/07/2023]
Abstract
Structural studies of bio-complexes using single particle cryo-Electron Microscopy (cryo-EM) is nowadays a well-established technique in structural biology and has become competitive with X-ray crystallography. Development of digital registration systems for electron microscopy images and algorithms for the fast and efficient processing of the recorded images and their following analysis has facilitated the determination of structures at near-atomic resolution. The latest advances in EM have enabled the determination of protein complex structures at 1.4-3 Å resolution for an extremely broad range of sizes (from ~100 kDa up to hundreds of MDa (Bartesaghi et al., Science 348(6239):1147-1151, 2015; Herzik et al., Nat Commun 10:1032, 2019; Wu et al., J Struct Biol X 4:100020, 2020; Zhang et al., Nat Commun 10:5511, 2019; Zhang et al., Cell Res 30(12):1136-1139, 2020; Yip et al., Nature 587(7832):157-161, 2020; https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_year )). In 2022, nearly 1200 structures deposited to the EMDB database were at a resolution of better than 3 Å ( https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_year ).To date, the highest resolutions have been achieved for apoferritin, which comprises a homo-oligomer of high point group symmetry (O432) and has rigid organization together with high stability (Zhang et al., Cell Res 30(12):1136-1139, 2020; Yip et al., Nature 587(7832):157-161, 2020). It has been used as a test object for the assessments of modern cryo-microscopes and processing methods during the last 5 years. In contrast to apoferritin bacterial secretion systems are typical examples of multi protein complexes exhibiting high flexibility owing to their functions relating to the transportation of small molecules, proteins, and DNA into the extracellular space or target cells. This makes their structural characterization extremely challenging (Barlow, Methods Mol Biol 532:397-411, 2009; Costa et al., Nat Rev Microbiol 13:343-359, 2015). The most feasible approach to reveal their spatial organization and functional modification is cryo-electron microscopy (EM). During the last decade, structural cryo-EM has become broadly used for the analysis of the bio-complexes that comprise multiple components and are not amenable to crystallization (Lyumkis, J Biol Chem 294:5181-5197, 2019; Orlova and Saibil, Methods Enzymol 482:321-341, 2010; Orlova and Saibil, Chem Rev 111(12):7710-7748, 2011).In this review, we will describe the basics of sample preparation for cryo-EM, the principles of digital data collection, and the logistics of image analysis focusing on the common steps required for reconstructions of both small and large biological complexes together with refinement of their structures to nearly atomic resolution. The workflow of processing will be illustrated by examples of EM analysis of Type IV Secretion System.
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Affiliation(s)
- Athanasios Ignatiou
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Kévin Macé
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Adam Redzej
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK
| | - Gabriel Waksman
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK
| | - Elena V Orlova
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London, UK.
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6
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Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
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Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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7
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Dwyer C. Quantum Limits of Transmission Electron Microscopy. PHYSICAL REVIEW LETTERS 2023; 130:056101. [PMID: 36800479 DOI: 10.1103/physrevlett.130.056101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
New-generation transmission electron microscopes (TEMs) are equipped with detectors that approach the shot-noise limit. Hence it is pertinent to ask: What are the quantum limits of electron scattering experiments in the TEM? For example, for a given electron dose, what is the ultimate accuracy allowed by quantum mechanics for the atomic structure of a material? We provide quantitative answers based on quantum estimation theory. We also show that, for an arbitrary set of sample parameters, the quantum limit is achievable under conditions of weak scattering, but not strong multiple scattering (this conclusion extends to scattering of other types of radiation). Implications for structure determination of radiation-sensitive materials are discussed.
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Affiliation(s)
- Christian Dwyer
- Electron Imaging and Spectroscopy Tools, PO Box 506, Sans Souci, NSW 2219, Australia and Physics, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
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8
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [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] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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9
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Shi D, Huang R. Analysis and comparison of electron radiation damage assessments in Cryo-EM by single particle analysis and micro-crystal electron diffraction. Front Mol Biosci 2022; 9:988928. [PMID: 36275612 PMCID: PMC9585622 DOI: 10.3389/fmolb.2022.988928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Electron radiation damage to macromolecules is an inevitable resolution limit factor in all major structural determination applications using cryo-electron microscopy (cryo-EM). Single particle analysis (SPA) and micro-crystal electron diffraction (MicroED) have been employed to assess radiation damage with a variety of protein complexes. Although radiation induced sidechain density loss and resolution decay were observed by both methods, the minimum dose of electron irradiation reducing high-resolution limit reported by SPA is more than ten folds higher than measured by MicroED using the conventional dose concept, and there is a gap between the attained resolutions assessed by these two methods. We compared and analyzed these two approaches side-by-side in detail from several aspects to identify some crucial determinants and to explain this discrepancy. Probability of a high energy electron being inelastically scattered by a macromolecule is proportional to number of layers of the molecules in its transmission path. As a result, the same electron dose could induce much more site-specific damage to macromolecules in 3D protein crystal than single particle samples. Major differences in data collection and processing scheme are the key factors to different levels of sensitivity to radiation damage at high resolution between the two methods. High resolution electron diffraction in MicroED dataset is very sensitive to global damage to 3D protein crystals with low dose accumulation, and its intensity attenuation rates at atomic resolution shell could be applied for estimating ratio of damaged and total selected single particles for SPA. More in-depth systematically radiation damage assessments using SPA and MicroED will benefit all applications of cryo-EM, especially cellular structure analysis by tomography.
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Affiliation(s)
- Dan Shi
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
- *Correspondence: Dan Shi,
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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10
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Kelly DF, DiCecco LA, Jonaid GM, Dearnaley WJ, Spilman MS, Gray JL, Dressel-Dukes MJ. Liquid-EM goes viral - visualizing structure and dynamics. Curr Opin Struct Biol 2022; 75:102426. [PMID: 35868163 DOI: 10.1016/j.sbi.2022.102426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
Liquid-electron microscopy (EM), the room temperature correlate to cryo-EM, is an exciting new technique delivering real-time data of dynamic reactions in solution. Here, we explain how liquid-EM gained popularity in recent years by examining key experiments conducted on viral assemblies and host-pathogen interactions. We describe developing workflows for specimen preparation, data collection, and computing processes that led to the first high-resolution virus structures in a liquid environment. Equally important, we review why liquid-electron tomography may become the next big thing in biomedical research due to its ability to monitor live viruses entering cells within seconds. Taken together, we pose the idea that liquid-EM can serve as a dynamic complement to current cryo-EM methods, inspiring the "real-time revolution" in nanoscale imaging.
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Affiliation(s)
- Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA; Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA.
| | - Liza-Anastasia DiCecco
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Department of Materials Science and Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada. https://twitter.com/LizaDiCecco
| | - G M Jonaid
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA; Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA. https://twitter.com/PennStateMRI
| | - Michael S Spilman
- Direct Electron, LP, San Diego, CA 92128, USA. https://twitter.com/DirectElectron
| | - Jennifer L Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
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11
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J Piper
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M Johnson
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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12
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Peck A, Carter SD, Mai H, Chen S, Burt A, Jensen GJ. Montage electron tomography of vitrified specimens. J Struct Biol 2022; 214:107860. [PMID: 35487464 PMCID: PMC10081539 DOI: 10.1016/j.jsb.2022.107860] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023]
Abstract
Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view to provide more cellular context requires reducing magnification during data collection, which in turn restricts the resolution. To circumvent this trade-off between field of view and resolution, we have developed a montage data collection scheme that uniformly distributes the dose throughout the specimen. In this approach, sets of slightly overlapping circular tiles are collected at high magnification and stitched to form a composite projection image at each tilt angle. These montage tilt-series are then reconstructed into massive tomograms with a small pixel size but a large field of view. For proof-of-principle, we applied this method to the thin edge of HeLa cells. Thon rings to better than 10 Å were detected in the montaged tilt-series, and diverse cellular features were observed in the resulting tomograms. These results indicate that the additional dose required by this technique is not prohibitive to performing structural analysis to intermediate resolution across a large field of view. We anticipate that montage tomography will prove particularly useful for lamellae, increase the likelihood of imaging rare cellular events, and facilitate visual proteomics.
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Affiliation(s)
- Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen D Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Huanghao Mai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Songye Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alister Burt
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA.
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13
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Peters JJ, Leitz J, Guo Q, Beck F, Baumeister W, Brunger AT. A feature-guided, focused 3D signal permutation method for subtomogram averaging. J Struct Biol 2022; 214:107851. [PMID: 35346811 PMCID: PMC9149098 DOI: 10.1016/j.jsb.2022.107851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023]
Abstract
Advances in electron microscope instrumentation, cryo-electron tomography data collection, and subtomogram averaging have allowed for the in-situ visualization of molecules and their complexes in their native environment. Current data processing pipelines commonly extract subtomograms as a cubic subvolume with the key assumption that the selected object of interest is discrete from its surroundings. However, in instances when the object is in its native environment, surrounding densities may negatively affect the subsequent alignment and refinement processes, leading to loss of information due to misalignment. For example, the strong densities from surrounding membranes may dominate the alignment process for membrane proteins. Here, we developed methods for feature-guided subtomogram alignment and 3D signal permutation for subtomogram averaging. Our 3D signal permutation method randomizes and filters voxels outside a mask of any shape and blurs the boundary of the mask that encapsulates the object of interest. The randomization preserves global statistical properties such as mean density and standard deviation of voxel density values, effectively producing a featureless background surrounding the object of interest. This signal permutation process can be repeatedly applied with intervening alignments of the 3D signal-permuted subvolumes, recentering of the mask, and optional adjustments of the shape of the mask. We have implemented these methods in a new processing pipeline which starts from tomograms, contains feature-guided subtomogram extraction and alignment, 3D signal-permutation, and subtomogram visualization tools. As an example, feature-guided alignment and 3D signal permutation leads to improved subtomogram average maps for a dataset of synaptic protein complexes in their native environment.
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Affiliation(s)
- John Jacob Peters
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Beck
- CryoEM Technology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States.
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14
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Jannis D, Hofer C, Gao C, Xie X, Béché A, Pennycook TJ, Verbeeck J. Event driven 4D STEM acquisition with a Timepix3 detector: Microsecond dwell time and faster scans for high precision and low dose applications. Ultramicroscopy 2022; 233:113423. [PMID: 34837737 DOI: 10.1016/j.ultramic.2021.113423] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/11/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022]
Abstract
Four dimensional scanning transmission electron microscopy (4D STEM) records the scattering of electrons in a material in great detail. The benefits offered by 4D STEM are substantial, with the wealth of data it provides facilitating for instance high precision, high electron dose efficiency phase imaging via centre of mass or ptychography based analysis. However the requirement for a 2D image of the scattering to be recorded at each probe position has long placed a severe bottleneck on the speed at which 4D STEM can be performed. Recent advances in camera technology have greatly reduced this bottleneck, with the detection efficiency of direct electron detectors being especially well suited to the technique. However even the fastest frame driven pixelated detectors still significantly limit the scan speed which can be used in 4D STEM, making the resulting data susceptible to drift and hampering its use for low dose beam sensitive applications. Here we report the development of the use of an event driven Timepix3 direct electron camera that allows us to overcome this bottleneck and achieve 4D STEM dwell times down to 100 ns; orders of magnitude faster than what has been possible with frame based readout. We characterize the detector for different acceleration voltages and show that the method is especially well suited for low dose imaging and promises rich datasets without compromising dwell time when compared to conventional STEM imaging.
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Affiliation(s)
- D Jannis
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - C Hofer
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - C Gao
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - X Xie
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - A Béché
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - T J Pennycook
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - J Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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15
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Vankadari N, Shepherd DC, Carter SD, Ghosal D. Three-dimensional insights into human enveloped viruses in vitro and in situ. Biochem Soc Trans 2022; 50:95-105. [PMID: 35076655 PMCID: PMC9022983 DOI: 10.1042/bst20210433] [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: 09/14/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022]
Abstract
Viruses can be enveloped or non-enveloped, and require a host cell to replicate and package their genomes into new virions to infect new cells. To accomplish this task, viruses hijack the host-cell machinery to facilitate their replication by subverting and manipulating normal host cell function. Enveloped viruses can have severe consequences for human health, causing various diseases such as acquired immunodeficiency syndrome (AIDS), seasonal influenza, COVID-19, and Ebola virus disease. The complex arrangement and pleomorphic architecture of many enveloped viruses pose a challenge for the more widely used structural biology techniques, such as X-ray crystallography. Cryo-electron tomography (cryo-ET), however, is a particularly well-suited tool for overcoming the limitations associated with visualizing the irregular shapes and morphology enveloped viruses possess at macromolecular resolution. The purpose of this review is to explore the latest structural insights that cryo-ET has revealed about enveloped viruses, with particular attention given to their architectures, mechanisms of entry, replication, assembly, maturation and egress during infection. Cryo-ET is unique in its ability to visualize cellular landscapes at 3-5 nanometer resolution. Therefore, it is the most suited technique to study asymmetric elements and structural rearrangements of enveloped viruses during infection in their native cellular context.
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Affiliation(s)
- Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Doulin C. Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen D. Carter
- Centre for Virus Research, Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, U.K
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
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16
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Jonaid GM, Casasanta MA, Dearnaley WJ, Berry S, Kaylor L, Dressel-Dukes MJ, Spilman MS, Gray JL, Kelly DF. Automated Tools to Advance High-Resolution Imaging in Liquid. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 35048845 DOI: 10.1017/s1431927621013921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Liquid-electron microscopy (EM), the room-temperature correlate to cryo-EM, is a rapidly growing field providing high-resolution insights of macromolecules in solution. Here, we describe how liquid-EM experiments can incorporate automated tools to propel the field to new heights. We demonstrate fresh workflows for specimen preparation, data collection, and computing processes to assess biological structures in liquid. Adeno-associated virus (AAV) and the SARS-CoV-2 nucleocapsid (N) were used as model systems to highlight the technical advances. These complexes were selected based on their major differences in size and natural symmetry. AAV is a highly symmetric, icosahedral assembly with a particle diameter of ~25 nm. At the other end of the spectrum, N protein is an asymmetric monomer or dimer with dimensions of approximately 5–7 nm, depending upon its oligomerization state. Equally important, both AAV and N protein are popular subjects in biomedical research due to their high value in vaccine development and therapeutic efforts against COVID-19. Overall, we demonstrate how automated practices in liquid-EM can be used to decode molecules of interest for human health and disease.
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Affiliation(s)
- G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
| | | | | | - Jennifer L Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
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17
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Khan YA, White KI, Brunger AT. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol 2021; 57:156-187. [PMID: 34632886 DOI: 10.1080/10409238.2021.1979460] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
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Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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18
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Jonaid GM, Dearnaley WJ, Casasanta MA, Kaylor L, Berry S, Dukes MJ, Spilman MS, Gray JL, Kelly DF. High-Resolution Imaging of Human Viruses in Liquid Droplets. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103221. [PMID: 34302401 PMCID: PMC8440499 DOI: 10.1002/adma.202103221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/28/2021] [Indexed: 05/29/2023]
Abstract
Liquid-phase electron microscopy (LP-EM) is an exciting new area in the materials imaging field, providing unprecedented views of molecular processes. Time-resolved insights from LP-EM studies are a strong complement to the remarkable results achievable with other high-resolution techniques. Here, the opportunities to expand LP-EM technology beyond 2D temporal assessments and into the 3D regime are described. The results show new structures and dynamic insights of human viruses contained in minute volumes of liquid while acquired in a rapid timeframe. To develop this strategy, adeno-associated virus (AAV) is used as a model system. AAV is a well-known gene therapy vehicle with current applications involving drug delivery and vaccine development for COVID-19. Improving the understanding of the physical properties of biological entities in a liquid state, as maintained in the human body, has broad societal implications for human health and disease.
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Affiliation(s)
- GM Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael A. Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | | | | | - Jennifer L. Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
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19
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Liang S, Chaplin AK, Stavridi AK, Appleby R, Hnizda A, Blundell TL. Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:60-73. [PMID: 33285184 PMCID: PMC8224183 DOI: 10.1016/j.pbiomolbio.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/26/2020] [Indexed: 01/10/2023]
Abstract
Non-homologous end joining (NHEJ) is the preferred pathway for the repair of DNA double-strand breaks in humans. Here we describe three structural aspects of the repair pathway: stages, scaffolds and strings. We discuss the orchestration of DNA repair to guarantee robust and efficient NHEJ. We focus on structural studies over the past two decades, not only using X-ray diffraction, but also increasingly exploiting cryo-EM to investigate the macromolecular assemblies.
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Affiliation(s)
- Shikang Liang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Antonia Kefala Stavridi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Robert Appleby
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Ales Hnizda
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, Cambridgeshire, UK.
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20
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An overview of the recent advances in cryo-electron microscopy for life sciences. Emerg Top Life Sci 2021; 5:151-168. [PMID: 33760078 DOI: 10.1042/etls20200295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.
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21
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Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder. Sci Rep 2021; 11:8395. [PMID: 33863933 PMCID: PMC8052451 DOI: 10.1038/s41598-021-87183-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/22/2021] [Indexed: 12/22/2022] Open
Abstract
Recently, the structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method. Many results of cryo-EM SPA are based on data acquired on state-of-the-art cryo-electron microscopes customized for SPA. These are currently only available in limited locations around the world, where securing machine time is highly competitive. One potential solution for this time-competitive situation is to reuse existing multi-purpose equipment, although this comes with performance limitations. Here, a multi-purpose TEM with a side entry cryo-holder was used to evaluate the potential of high-resolution SPA, resulting in a 3 Å resolution map of apoferritin with local resolution extending to 2.6 Å. This map clearly showed two positions of an aromatic side chain. Further, examination of optimal imaging conditions depending on two different multi-purpose electron microscope and camera combinations was carried out, demonstrating that higher magnifications are not always necessary or desirable. Since automation is effectively a requirement for large-scale data collection, and augmenting the multi-purpose equipment is possible, we expanded testing by acquiring data with SerialEM using a β-galactosidase test sample. This study demonstrates the possibilities of more widely available and established electron microscopes, and their applications for cryo-EM SPA.
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22
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Feathers JR, Spoth KA, Fromme JC. Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM. J Struct Biol X 2021; 5:100047. [PMID: 33817625 PMCID: PMC8008246 DOI: 10.1016/j.yjsbx.2021.100047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/19/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In principle, super-resolution imaging should enable reconstructions to surpass the physical Nyquist limit by increasing sampling frequency, yet there are few reports of reconstructions that do so. Here we directly examine the contribution of super-resolution information, obtained with the K3 direct electron detector using a 2-condenser microscope, to single-particle cryo-EM reconstructions surpassing the physical Nyquist limit. We also present a comparative analysis of a sample imaged at four different magnifications. This analysis demonstrates that lower magnifications can be beneficial, despite the loss of higher resolution signal, due to the increased number of particle images obtained. To highlight the potential utility of lower magnification data collection, we produced a 3.5 Å reconstruction of jack bean urease with particles from a single micrograph.
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Affiliation(s)
- J. Ryan Feathers
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853 USA
| | - Katherine A. Spoth
- Cornell Center for Materials Research, Cornell University, Ithaca, NY 14853 USA
| | - J. Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853 USA
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23
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Zhong ED, Bepler T, Berger B, Davis JH. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat Methods 2021; 18:176-185. [PMID: 33542510 PMCID: PMC8183613 DOI: 10.1038/s41592-020-01049-4] [Citation(s) in RCA: 223] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022]
Abstract
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many imaged protein complexes exhibit conformational and compositional heterogeneity that poses a major challenge to existing three-dimensional reconstruction methods. Here, we present cryoDRGN, an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. Using cryoDRGN, we uncovered residual heterogeneity in high-resolution datasets of the 80S ribosome and the RAG complex, revealed a new structural state of the assembling 50S ribosome, and visualized large-scale continuous motions of a spliceosome complex. CryoDRGN contains interactive tools to visualize a dataset's distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions. CryoDRGN is open-source software freely available at http://cryodrgn.csail.mit.edu .
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Affiliation(s)
- Ellen D Zhong
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan Bepler
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph H Davis
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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24
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Nuclear Import of Adeno-Associated Viruses Imaged by High-Speed Single-Molecule Microscopy. Viruses 2021; 13:v13020167. [PMID: 33499411 PMCID: PMC7911914 DOI: 10.3390/v13020167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding the detailed nuclear import kinetics of adeno-associated virus (AAV) through the nuclear pore complex (NPC) is essential for the application of AAV capsids as a nuclear delivery instrument as well as a target for drug development. However, a comprehensive understanding of AAV transport through the sub-micrometer NPCs in live cells calls for new techniques that can conquer the limitations of conventional fluorescence microscopy and electron microscopy. With recent technical advances in single-molecule fluorescence microscopy, we are now able to image the entire nuclear import process of AAV particles and also quantify the transport dynamics of viral particles through the NPCs in live human cells. In this review, we initially evaluate the necessity of single-molecule live-cell microscopy in the study of nuclear import for AAV particles. Then, we detail the application of high-speed single-point edge-excitation sub-diffraction (SPEED) microscopy in tracking the entire process of nuclear import for AAV particles. Finally, we summarize the major findings for AAV nuclear import by using SPEED microscopy.
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25
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Haberfehlner G, Hoefler SF, Rath T, Trimmel G, Kothleitner G, Hofer F. Benefits of direct electron detection and PCA for EELS investigation of organic photovoltaics materials. Micron 2020; 140:102981. [PMID: 33202362 DOI: 10.1016/j.micron.2020.102981] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
Electron energy-loss spectroscopy (EELS) is a powerful tool for imaging chemical variations at the nanoscale. Here, we investigate a polymer/organic small molecule-blend used as absorber layer in an organic solar cell and employ EELS for distinguishing polymer donor and small molecule acceptor domains in the nanostructured blend based on elemental maps of light elements, such as nitrogen, sulfur or fluorine. Especially for beam sensitive samples, the electron dose needs to be limited, therefore optimized acquisition and data processing strategies are required. We compare data acquired on a post-column energy filter with a direct electron detection camera to data from a conventional CCD camera on the same filter and we investigate the impact of statistical data processing methods (principal components analysis, PCA) on acquired spectra and elemental maps extracted from spectrum images. Our work shows, that the quality of spectra on a direct electron detection camera is far superior to conventional CCD imaging, and thereby allows clear identification of ionization edges and the fine structure of these edges. For the quality of the elemental maps, the application of PCA is essential to allow a clear separation between the donor and acceptor phase in the bulk heterojunction absorber layer of a non-fullerene organic solar cell.
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Affiliation(s)
- Georg Haberfehlner
- Institute of Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010, Graz, Austria.
| | - Sebastian F Hoefler
- Institute for Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Thomas Rath
- Institute for Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Gregor Trimmel
- Institute for Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Gerald Kothleitner
- Institute of Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010, Graz, Austria; Graz Centre for Electron Microscopy, Steyrergasse 17, Graz, 8010, Austria
| | - Ferdinand Hofer
- Institute of Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010, Graz, Austria; Graz Centre for Electron Microscopy, Steyrergasse 17, Graz, 8010, Austria
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26
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Wang F, Echlin MP, Taylor AA, Shin J, Bammes B, Levin BDA, De Graef M, Pollock TM, Gianola DS. Electron backscattered diffraction using a new monolithic direct detector: High resolution and fast acquisition. Ultramicroscopy 2020; 220:113160. [PMID: 33197699 DOI: 10.1016/j.ultramic.2020.113160] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/19/2020] [Accepted: 11/01/2020] [Indexed: 11/19/2022]
Abstract
A monolithic active pixel sensor based direct detector that is optimized for the primary beam energies in scanning electron microscopes is implemented for electron back-scattered diffraction (EBSD) applications. The high detection efficiency of the detector and its large array of pixels allow sensitive and accurate detection of Kikuchi bands arising from primary electron beam excitation energies of 4 keV to 28 keV, with the optimal contrast occurring in the range of 8-16 keV. The diffraction pattern acquisition speed is substantially improved via a sparse sampling mode, resulting from the acquisition of a reduced number of pixels on the detector. Standard inpainting algorithms are implemented to effectively estimate the information in the skipped regions in the acquired diffraction pattern. For EBSD mapping, an acquisition speed as high as 5988 scan points per second is demonstrated, with a tolerable fraction of indexed points and accuracy. The collective capabilities spanning from high angular resolution EBSD patterns to high speed pattern acquisition are achieved on the same detector, facilitating simultaneous detection modalities that enable a multitude of advanced EBSD applications, including lattice strain mapping, structural refinement, low-dose characterization, 3D-EBSD and dynamic in situ EBSD.
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Affiliation(s)
- Fulin Wang
- Materials Department, University of California Santa Barbara, Santa Barbara, CA 93117, USA
| | - McLean P Echlin
- Materials Department, University of California Santa Barbara, Santa Barbara, CA 93117, USA
| | - Aidan A Taylor
- Materials Department, University of California Santa Barbara, Santa Barbara, CA 93117, USA
| | - Jungho Shin
- Materials Department, University of California Santa Barbara, Santa Barbara, CA 93117, USA
| | | | | | - Marc De Graef
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tresa M Pollock
- Materials Department, University of California Santa Barbara, Santa Barbara, CA 93117, USA
| | - Daniel S Gianola
- Materials Department, University of California Santa Barbara, Santa Barbara, CA 93117, USA.
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27
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Chen X, Hauwiller MR, Kumar A, Penn AN, LeBeau JM. Expanding the Dimensions of a Small, Two-Dimensional Diffraction Detector. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:938-943. [PMID: 32778194 DOI: 10.1017/s1431927620024277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report an approach to expand the effective number of pixels available to small, two-dimensional electron detectors. To do so, we acquire subsections of a diffraction pattern that are then accurately stitched together in post-processing. Using an electron microscopy pixel array detector (EMPAD) that has only 128 × 128 pixels, we show that the field of view can be expanded while achieving high reciprocal-space sampling. Further, we highlight the need to properly account for the detector position (rotation) and the non-orthonormal diffraction shift axes to achieve an accurate reconstruction. Applying the method, we provide examples of spot and convergent beam diffraction patterns acquired with a pixelated detector.
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Affiliation(s)
- Xi Chen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139, USA
| | - Matthew R Hauwiller
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139, USA
| | - Abinash Kumar
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139, USA
| | - Aubrey N Penn
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC27606, USA
| | - James M LeBeau
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA02139, USA
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28
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Investigating the Structure of Neurotoxic Protein Aggregates Inside Cells. Trends Cell Biol 2020; 30:951-966. [PMID: 32981805 DOI: 10.1016/j.tcb.2020.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022]
Abstract
Neurodegenerative diseases affect the lives of millions of people across the world, being particularly prevalent in the aging population. Despite huge research efforts, conclusive insights into the disease mechanisms are still lacking. Therefore, therapeutic strategies are limited to symptomatic treatments. A common histopathological hallmark of many neurodegenerative diseases is the presence of large pathognomonic protein aggregates, but their role in the disease pathology is unclear and subject to controversy. Here, we discuss imaging methods allowing investigation of these structures within their cellular environment: conventional electron microscopy (EM), super-resolution light microscopy (SR-LM), and cryo-electron tomography (cryo-ET). Multidisciplinary approaches are key for understanding neurodegenerative diseases and may contribute to the development of effective treatments. For simplicity, we focus on huntingtin aggregates, characteristic of Huntington's disease.
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Ahmed I, Akram Z, Sahar MSU, Iqbal HMN, Landsberg MJ, Munn AL. WITHDRAWN: Structural studies of vitrified biological proteins and macromolecules - A review on the microimaging aspects of cryo-electron microscopy. Int J Biol Macromol 2020:S0141-8130(20)33915-5. [PMID: 32710963 DOI: 10.1016/j.ijbiomac.2020.07.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/03/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Ishtiaq Ahmed
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia.
| | - Zain Akram
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia
| | - M Sana Ullah Sahar
- School of Engineering, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alan L Munn
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia
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30
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The performance evaluation of direct detection electron energy-loss spectroscopy at 200 kV and 80 kV accelerating voltages. Ultramicroscopy 2020; 212:112942. [DOI: 10.1016/j.ultramic.2020.112942] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/10/2020] [Accepted: 01/19/2020] [Indexed: 11/20/2022]
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31
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Franken LE, Grünewald K, Boekema EJ, Stuart MCA. A Technical Introduction to Transmission Electron Microscopy for Soft-Matter: Imaging, Possibilities, Choices, and Technical Developments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906198. [PMID: 32130784 DOI: 10.1002/smll.201906198] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/30/2019] [Indexed: 05/24/2023]
Abstract
With a significant role in material sciences, physics, (soft matter) chemistry, and biology, the transmission electron microscope is one of the most widely applied structural analysis tool to date. It has the power to visualize almost everything from the micrometer to the angstrom scale. Technical developments keep opening doors to new fields of research by improving aspects such as sample preservation, detector performance, computational power, and workflow automation. For more than half a century, and continuing into the future, electron microscopy has been, and is, a cornerstone methodology in science. Herein, the technical considerations of imaging with electrons in terms of optics, technology, samples and processing, and targeted soft materials are summarized. Furthermore, recent advances and their potential for application to soft matter chemistry are highlighted.
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Affiliation(s)
- Linda E Franken
- Department of Structural Cell Biology of Viruses, Heinrich-Pette Institute-Leibniz-Institute of Experimental Virology University of Hamburg, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany
| | - Kay Grünewald
- Department of Structural Cell Biology of Viruses, Heinrich-Pette Institute-Leibniz-Institute of Experimental Virology University of Hamburg, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany
| | - Egbert J Boekema
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Marc C A Stuart
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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32
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Chen Q, Dwyer C, Sheng G, Zhu C, Li X, Zheng C, Zhu Y. Imaging Beam-Sensitive Materials by Electron Microscopy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1907619. [PMID: 32108394 DOI: 10.1002/adma.201907619] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/20/2019] [Indexed: 05/15/2023]
Abstract
Electron microscopy allows the extraction of multidimensional spatiotemporally correlated structural information of diverse materials down to atomic resolution, which is essential for figuring out their structure-property relationships. Unfortunately, the high-energy electrons that carry this important information can cause damage by modulating the structures of the materials. This has become a significant problem concerning the recent boost in materials science applications of a wide range of beam-sensitive materials, including metal-organic frameworks, covalent-organic frameworks, organic-inorganic hybrid materials, 2D materials, and zeolites. To this end, developing electron microscopy techniques that minimize the electron beam damage for the extraction of intrinsic structural information turns out to be a compelling but challenging need. This article provides a comprehensive review on the revolutionary strategies toward the electron microscopic imaging of beam-sensitive materials and associated materials science discoveries, based on the principles of electron-matter interaction and mechanisms of electron beam damage. Finally, perspectives and future trends in this field are put forward.
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Affiliation(s)
- Qiaoli Chen
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Christian Dwyer
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Guan Sheng
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongzhi Zhu
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaonian Li
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Changlin Zheng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, 200438, China
| | - Yihan Zhu
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
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Abstract
Cryo electron microscopy (cryo-EM) is a powerful technique that can be used to elucidate the structural architecture of a protein molecule in a physiologically relevant environment. In this method, purified protein is frozen in its aqueous buffer in a thin layer of vitreous ice in which the biological macromolecules are embedded in various orientations. Images of this frozen sample are collected with an electron microscope, and the data is processed using different software algorithms resulting in high-resolution structures of the protein. Proteins in the presence of various ligands or other macromolecular complexes can also be studied by this method. Here, we present a protocol for the purification and vitrification of TRP channels for single particle cryo-EM.
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Affiliation(s)
- Amrita Samanta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor E T Hughes
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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34
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McBride JR, Rosenthal SJ. Real colloidal quantum dot structures revealed by high resolution analytical electron microscopy. J Chem Phys 2019; 151:160903. [DOI: 10.1063/1.5128366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- James R. McBride
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Nanoscale Science and Engineering, Nashville, Tennessee 37235, USA
| | - Sandra J. Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Nanoscale Science and Engineering, Nashville, Tennessee 37235, USA
- Department of Interdisciplinary Materials Science, Department of Chemical and Biomolecular Engineering, Department of Physics and Astronomy, Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, USA
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35
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Li Y, Junod SL, Ruba A, Kelich JM, Yang W. Nuclear export of mRNA molecules studied by SPEED microscopy. Methods 2019; 153:46-62. [PMID: 30125665 PMCID: PMC7138453 DOI: 10.1016/j.ymeth.2018.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
The nuclear exit of messenger RNA (mRNA) molecules through the nuclear pore complex (NPC) is an essential step in the translation process of all proteins. The current limitations of conventional fluorescence and electron microscopy have prevented elucidation of how mRNA exports through the NPCs of live cells. In the recent years, various single-molecule fluorescence (SMF) microscopy techniques have been developed to improve the temporal and spatial resolutions of live-cell imaging allowing a more comprehensive understanding of the dynamics of mRNA export through native NPCs. In this review, we firstly evaluate the necessity of single-molecule live-cell microscopy in the study of mRNA nuclear export. Then, we highlight the application of single-point edge-excitation sub-diffraction (SPEED) microscopy that combines high-speed SMF microscopy and a 2D-to-3D transformation algorithm in the studies of nuclear transport kinetics and route for mRNAs. Finally, we summarize the new features of mRNA nuclear export found with SPEED microscopy as well as the reliability and accuracy of SPEED microscopy in mapping the 3D spatial locations of transport routes adopted by proteins and mRNAs through the NPCs.
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Affiliation(s)
- Yichen Li
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Samuel L Junod
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Joseph M Kelich
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA.
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36
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Sgro GG, Costa TRD. Cryo-EM Grid Preparation of Membrane Protein Samples for Single Particle Analysis. Front Mol Biosci 2018; 5:74. [PMID: 30131964 PMCID: PMC6090150 DOI: 10.3389/fmolb.2018.00074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/10/2018] [Indexed: 11/26/2022] Open
Abstract
Recent advances in cryo-electron microscopy (cryo-EM) have made it possible to solve structures of biological macromolecules at near atomic resolution. Development of more stable microscopes, improved direct electron detectors and faster software for image processing has enabled structural solution of not only large macromolecular (megadalton range) complexes but also small (~60 kDa) proteins. As a result of the widespread use of the technique, we have also witnessed new developments of techniques for cryo-EM grid preparation of membrane protein samples. This includes new types of solubilization strategies that better stabilize these protein complexes and the development of new grid supports with proven efficacy in reducing the motion of the molecules during electron beam exposure. Here, we discuss the practicalities and recent challenges of membrane protein sample preparation and vitrification, as well as grid support and foil treatment in the context of the structure determination of protein complexes by single particle cryo-EM.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago R. D. Costa
- Department of Life Sciences, Imperial College London, MRC Centre for Molecular Microbiology and Infection, London, United Kingdom
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37
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Hujsak KA, Roth EW, Kellogg W, Li Y, Dravid VP. High speed/low dose analytical electron microscopy with dynamic sampling. Micron 2018; 108:31-40. [DOI: 10.1016/j.micron.2018.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 10/17/2022]
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38
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Biyani N, Scherer S, Righetto RD, Kowal J, Chami M, Stahlberg H. Image processing techniques for high-resolution structure determination from badly ordered 2D crystals. J Struct Biol 2018; 203:120-134. [PMID: 29689299 DOI: 10.1016/j.jsb.2018.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 11/19/2022]
Abstract
2D electron crystallography can be used to study small membrane proteins in their native environment. Obtaining highly ordered 2D crystals is difficult and time-consuming. However, 2D crystals diffracting to only 10-12 Å can be prepared relatively conveniently in most cases. We have developed image-processing algorithms allowing to generate a high resolution 3D structure from cryo-electron crystallography images of badly ordered crystals. These include movie-mode unbending, refinement over sub-tiles of the images in order to locally refine the sample tilt geometry, implementation of different CTF correction schemes, and an iterative method to apply known constraints in the real and reciprocal space to approximate amplitudes and phases in the so-called missing cone regions. These algorithms applied to a dataset of the potassium channel MloK1 show significant resolution improvements to better than 5 Å.
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Affiliation(s)
- Nikhil Biyani
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Sebastian Scherer
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland; BioEM Lab, C-CINA, Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel, Switzerland.
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39
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Workflw of Cryo-Electron Microscopy and Status of Domestic Infrastructure. Appl Microsc 2018. [DOI: 10.9729/am.2018.48.1.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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40
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Abstract
Structural studies of biocomplexes using single-particle cryo-electron microscopy (cryo-EM) is now a well-established technique in structural biology and has become competitive with X-ray crystallography. The latest advances in EM enable us to determine structures of protein complexes at 3-5 Å resolution for an extremely broad range of sizes from ~200 kDa up to hundreds of megadaltons (Bartesaghi et al., Science 348(6239):1147-1151, 2051; Bai et al., Nature 525(7568):212-217, 2015; Vinothkumar et al., Nature 515(7525):80-84, 2014; Grigorieff and Harrison, Curr Opin Struct Biol 21(2):265-273, 2011). The majority of biocomplexes comprise a number of different components and are not amenable to crystallisation. Secretion systems are typical examples of such multi-protein complexes, and structural studies of them are extremely challenging. The only feasible approach to revealing their spatial organisation and functional modification is cryo-EM. The development of systems for digital registration of images and algorithms for the fast and efficient processing of recorded images and subsequent analysis facilitated the determination of structures at near-atomic resolution. In this review we will describe sample preparation for cryo-EM, how data are collected by new detectors, and the logistics of image analysis through the basic steps required for reconstructions of both small and large biological complexes and their refinement to nearly atomic resolution. The processing workflow is illustrated using examples of EM analysis of a Type IV Secretion System.
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41
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Mak J, de Marco A. Recent advances in retroviruses via cryo-electron microscopy. Retrovirology 2018; 15:23. [PMID: 29471854 PMCID: PMC5824478 DOI: 10.1186/s12977-018-0405-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy.
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Affiliation(s)
- Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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42
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Reagan BC, Kim PJY, Perry PD, Dunlap JR, Burch-Smith TM. Spatial distribution of organelles in leaf cells and soybean root nodules revealed by focused ion beam-scanning electron microscopy. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:180-191. [PMID: 32291032 DOI: 10.1071/fp16347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/23/2016] [Indexed: 06/11/2023]
Abstract
Analysis of cellular ultrastructure has been dominated by transmission electron microscopy (TEM), so images collected by this technique have shaped our current understanding of cellular structure. More recently, three-dimensional (3D) analysis of organelle structures has typically been conducted using TEM tomography. However, TEM tomography application is limited by sample thickness. Focused ion beam-scanning electron microscopy (FIB-SEM) uses a dual beam system to perform serial sectioning and imaging of a sample. Thus FIB-SEM is an excellent alternative to TEM tomography and serial section TEM tomography. Animal tissue samples have been more intensively investigated by this technique than plant tissues. Here, we show that FIB-SEM can be used to study the 3D ultrastructure of plant tissues in samples previously prepared for TEM via commonly used fixation and embedding protocols. Reconstruction of FIB-SEM sections revealed ultra-structural details of the plant tissues examined. We observed that organelles packed tightly together in Nicotiana benthamiana Domin leaf cells may form membrane contacts. 3D models of soybean nodule cells suggest that the bacteroids in infected cells are contained within one large membrane-bound structure and not the many individual symbiosomes that TEM thin-sections suggest. We consider the implications of these organelle arrangements for intercellular signalling.
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Affiliation(s)
- Brandon C Reagan
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
| | - Paul J-Y Kim
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
| | - Preston D Perry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
| | - John R Dunlap
- Advanced Microscopy and Imaging Center, University of Tennessee, Knoxville, 1499 Circle Dr Knoxville, TN 37996, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
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43
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Chen Z, Wang B. How priors of initial hyperparameters affect Gaussian process regression models. Neurocomputing 2018. [DOI: 10.1016/j.neucom.2017.10.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Razi A, Britton RA, Ortega J. The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly. Nucleic Acids Res 2017; 45:1027-1040. [PMID: 28180306 PMCID: PMC5388408 DOI: 10.1093/nar/gkw1231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/20/2016] [Accepted: 11/25/2016] [Indexed: 01/14/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process.
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Affiliation(s)
- Aida Razi
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology and Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
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45
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Direct Detection Electron Energy-Loss Spectroscopy: A Method to Push the Limits of Resolution and Sensitivity. Sci Rep 2017; 7:8243. [PMID: 28811485 PMCID: PMC5557959 DOI: 10.1038/s41598-017-07709-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/03/2017] [Indexed: 12/17/2022] Open
Abstract
In many cases, electron counting with direct detection sensors offers improved resolution, lower noise, and higher pixel density compared to conventional, indirect detection sensors for electron microscopy applications. Direct detection technology has previously been utilized, with great success, for imaging and diffraction, but potential advantages for spectroscopy remain unexplored. Here we compare the performance of a direct detection sensor operated in counting mode and an indirect detection sensor (scintillator/fiber-optic/CCD) for electron energy-loss spectroscopy. Clear improvements in measured detective quantum efficiency and combined energy resolution/energy field-of-view are offered by counting mode direct detection, showing promise for efficient spectrum imaging, low-dose mapping of beam-sensitive specimens, trace element analysis, and time-resolved spectroscopy. Despite the limited counting rate imposed by the readout electronics, we show that both core-loss and low-loss spectral acquisition are practical. These developments will benefit biologists, chemists, physicists, and materials scientists alike.
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46
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Chiu W, Downing KH. Editorial overview: Cryo Electron Microscopy: Exciting advances in CryoEM Herald a new era in structural biology. Curr Opin Struct Biol 2017; 46:iv-viii. [PMID: 28801059 DOI: 10.1016/j.sbi.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wah Chiu
- Departments of Bioengineering and Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
| | - Kenneth H Downing
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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47
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Roh SH, Hryc CF, Jeong HH, Fei X, Jakana J, Lorimer GH, Chiu W. Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. Proc Natl Acad Sci U S A 2017; 114:8259-8264. [PMID: 28710336 PMCID: PMC5547627 DOI: 10.1073/pnas.1704725114] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10-12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer.
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Affiliation(s)
- Soung-Hun Roh
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
| | - Hyun-Hwan Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Xue Fei
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030;
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
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48
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Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit. Structure 2017; 25:1436-1441.e2. [PMID: 28757144 DOI: 10.1016/j.str.2017.06.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/16/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022]
Abstract
The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A single-particle reconstruction of the T4 baseplate was able to generate a 4.1 Å resolution map for the first two rings of the tube using the overall baseplate for alignment. We have now reconstructed the T4 tail tube at a resolution of 3.4 Å, more than a 1,000-fold increase in information content for the tube from 1968. We have used legacy software (Spider) to show that we can do better than the typical 2/3 Nyquist frequency. A reasonable map can be generated with only 1.5 electrons/Å2 using the higher dose images for alignment, but increasing the dose results in a better map, consistent with other reports that electron dose does not represent the main limitation on resolution in cryo-electron microscopy.
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49
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Abstract
Recently, dozens of virus structures have been solved to resolutions between 2.5 and 5.0 Å by means of electron cryomicroscopy. With these structures we are now firmly within the "atomic age" of electron cryomicroscopy, as these studies can reveal atomic details of protein and nucleic acid topology and interactions between specific residues. This improvement in resolution has been the result of direct electron detectors and image processing advances. Although enforcing symmetry facilitates reaching near-atomic resolution with fewer particle images, it unfortunately obscures some biologically interesting components of a virus. New approaches on relaxing symmetry and exploring structure dynamics and heterogeneity of viral assemblies have revealed important insights into genome packaging, virion assembly, cell entry, and other stages of the viral life cycle. In the future, novel methods will be required to reveal yet-unknown structural conformations of viruses, relevant to their biological activities. Ultimately, these results hold the promise of answering many unresolved questions linking structural diversity of viruses to their biological functions.
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Affiliation(s)
- Jason T Kaelber
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030;
| | - Wah Chiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030;
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50
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Li S, Rissanen I, Zeltina A, Hepojoki J, Raghwani J, Harlos K, Pybus OG, Huiskonen JT, Bowden TA. A Molecular-Level Account of the Antigenic Hantaviral Surface. Cell Rep 2016; 15:959-967. [PMID: 27117403 PMCID: PMC4858563 DOI: 10.1016/j.celrep.2016.03.082] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/29/2016] [Accepted: 03/22/2016] [Indexed: 11/26/2022] Open
Abstract
Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high-resolution crystal structure of the antigenic ectodomain of Gn from Puumala hantavirus (PUUV), a causative agent of hemorrhagic fever with renal syndrome. Fitting of PUUV Gn into an electron cryomicroscopy reconstruction of intact Gn-Gc spike complexes from the closely related but non-pathogenic Tula hantavirus localized Gn tetramers to the membrane-distal surface of the virion. The accuracy of the fitting was corroborated by epitope mapping and genetic analysis of available PUUV sequences. Interestingly, Gn exhibits greater non-synonymous sequence diversity than the less accessible Gc, supporting a role of the host humoral immune response in exerting selective pressure on the virus surface. The fold of PUUV Gn is likely to be widely conserved across hantaviruses. We describe the high-resolution crystal structure of a hantaviral Gn ectodomain Electron cryotomography analysis reveals the ultrastructure of Gn-Gc assembly X-ray fitting and mapping analysis reveals the antigenic hantavirus surface The Gn fold is likely to be widely conserved across this group of viruses
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Affiliation(s)
- Sai Li
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ilona Rissanen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jussi Hepojoki
- Department of Virology, Haartman Institute, University of Helsinki, 00014 Helsinki, Finland
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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