1
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Cuadrado AF, Van Damme D. Unlocking protein-protein interactions in plants: a comprehensive review of established and emerging techniques. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5220-5236. [PMID: 38437582 DOI: 10.1093/jxb/erae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions orchestrate plant development and serve as crucial elements for cellular and environmental communication. Understanding these interactions offers a gateway to unravel complex protein networks that will allow a better understanding of nature. Methods for the characterization of protein-protein interactions have been around over 30 years, yet the complexity of some of these interactions has fueled the development of new techniques that provide a better understanding of the underlying dynamics. In many cases, the application of these techniques is limited by the nature of the available sample. While some methods require an in vivo set-up, others solely depend on protein sequences to study protein-protein interactions via an in silico set-up. The vast number of techniques available to date calls for a way to select the appropriate tools for the study of specific interactions. Here, we classify widely spread tools and new emerging techniques for the characterization of protein-protein interactions based on sample requirements while providing insights into the information that they can potentially deliver. We provide a comprehensive overview of commonly used techniques and elaborate on the most recent developments, showcasing their implementation in plant research.
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Affiliation(s)
- Alvaro Furones Cuadrado
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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2
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Van Blerkom P, Bezault A, Sauvanet C, Hanein D, Volkmann N. The GoldX Fiducial Eraser. Int J Mol Sci 2024; 25:7442. [PMID: 39000548 PMCID: PMC11242485 DOI: 10.3390/ijms25137442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Gold nanoparticles with sizes in the range of 5-15 nm are a standard method of providing fiducial markers to assist with alignment during reconstruction in cryogenic electron tomography. However, due to their high electron density and resulting contrast when compared to standard cellular or biological samples, they introduce artifacts such as streaking in the reconstructed tomograms. Here, we demonstrate a tool that automatically detects these nanoparticles and suppresses them by replacing them with a local background as a post-processing step, providing a cleaner tomogram without removing any sample relevant information or introducing new artifacts or edge effects from uniform density replacements.
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Affiliation(s)
- Peter Van Blerkom
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Armel Bezault
- Structural Image Analysis Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, 75724 Paris, France
| | - Cécile Sauvanet
- Institut de Biologie Intégrative de la Cellule, CNRS CEA, Université Paris Saclay, 91190 Gif-sur-Yvette, France
| | - Dorit Hanein
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Biological Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Niels Volkmann
- Department of Biological Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Electrical and Computer Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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3
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. Int J Mol Sci 2024; 25:5473. [PMID: 38791508 PMCID: PMC11121946 DOI: 10.3390/ijms25105473] [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: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Jesús G. Galaz-Montoya
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
| | - Liyue Shen
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Philip Baldwin
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
| | | | - Dmitry Lyumkis
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
- Graduate School of Biological Sciences, University of California San Diego, La Jolla, CA 92037, USA
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Pauly
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
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4
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Yeganeh FA, Summerill C, Hu Z, Rahmani H, Taylor DW, Taylor KA. The cryo-EM 3D image reconstruction of isolated Lethocerus indicus Z-discs. J Muscle Res Cell Motil 2023; 44:271-286. [PMID: 37661214 PMCID: PMC10843718 DOI: 10.1007/s10974-023-09657-1] [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: 02/14/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023]
Abstract
The Z-disk of striated muscle defines the ends of the sarcomere, which repeats many times within the muscle fiber. Here we report application of cryoelectron tomography and subtomogram averaging to Z-disks isolated from the flight muscles of the large waterbug Lethocerus indicus. We use high salt solutions to remove the myosin containing filaments and use gelsolin to remove the actin filaments of the A- and I-bands leaving only the thin filaments within the Z-disk which were then frozen for cryoelectron microscopy. The Lethocerus Z-disk structure is similar in many ways to the previously studied Z-disk of the honeybee Apis mellifera. At the corners of the unit cell are positioned trimers of paired antiparallel F-actins defining a large solvent channel, whereas at the trigonal positions are positioned F-actin trimers converging slowly towards their (+) ends defining a small solvent channel through the Z-disk. These near parallel F-actins terminate at different Z-heights within the Z-disk. The two types of solvent channel in Lethocerus are similar in size compared to those of Apis which are very different in size. Two types of α-actinin crosslinks were observed between oppositely oriented actin filaments. In one of these, the α-actinin long axis is almost parallel to the F-actins it crosslinks. In the other, the α-actinins are at a small but distinctive angle with respect to the crosslinked actin filaments. The utility of isolated Z-disks for structure determination is discussed.
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Affiliation(s)
- Fatemeh Abbasi Yeganeh
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Corinne Summerill
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
- Department of Life and Earth Sciences, Perimeter College, Georgia State University, 33 Gilmer Street SE, Atlanta, GA, 30303, USA
| | - Zhongjun Hu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
- Facebook, Inc, 1 Hacker Way, Menlo Park, CA, 94025, USA
| | - Hamidreza Rahmani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dianne W Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA.
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5
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Liang J, Koo B, Wu Y, Manna S, Noble JM, Patel M, Park JH, Kozak D, Wang Y, Zheng J. Characterization of Complex Drug Formulations Using Cryogenic Scanning Electron Microscopy (Cryo-SEM). Curr Protoc 2022; 2:e406. [PMID: 35384403 DOI: 10.1002/cpz1.406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The physicochemical properties of complex drug formulations, including liposomes, suspensions, and emulsions, are important for understanding drug release mechanisms, quality control, and regulatory assessment. It is ideal to characterize these complex drug formulations in their native hydrated state. This article describes the characterization of complex drug formulations in a frozen-hydrated state using cryogenic scanning electron microscopy (cryo-SEM). In comparison to other techniques, such as optical microscopy or room-temperature scanning electron microscopy, cryo-SEM combines the advantage of studying hydrated samples with high-resolution imaging capability. Detailed information regarding cryo-fixation, cryo-fracture, freeze-etching, sputter-coating, and cryo-SEM imaging is included in this article. A multivesicular liposomal complex drug formulation is used to illustrate the impact of different cryogenic sample preparation conditions. In addition to drug formulations, this approach can also be applied to biological samples (e.g., cells, bacteria) and soft-matter samples (e.g., hydrogels). © Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: Cryo-fixation to preserve the native structure of samples using planchettes Alternate Protocol: Cryo-fixation to preserve the native structure of biological samples on sapphire disks Basic Protocol 2: Sample preparation for cross-sectional cryo-SEM imaging Basic Protocol 3: Cryo-SEM imaging and microanalysis.
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Affiliation(s)
- Jing Liang
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Bonhye Koo
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Yong Wu
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Soumyarwit Manna
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Jade M Noble
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Mehulkumar Patel
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Jin H Park
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Darby Kozak
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Yan Wang
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Jiwen Zheng
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
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6
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Yang JE, Rossignol ED, Chang D, Zaia J, Forrester I, Raja K, Winbigler H, Nicastro D, Jackson WT, Bullitt E. Complexity and ultrastructure of infectious extracellular vesicles from cells infected by non-enveloped virus. Sci Rep 2020; 10:7939. [PMID: 32409751 PMCID: PMC7224179 DOI: 10.1038/s41598-020-64531-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses support cell-to-cell viral transmission prior to their canonical lytic spread of virus. Poliovirus (PV), a prototype for human pathogenic positive-sense RNA enteroviruses, and picornaviruses in general, transport multiple virions en bloc via infectious extracellular vesicles, 100~1000 nm in diameter, secreted from host cells. Using biochemical and biophysical methods we identify multiple components in secreted microvesicles, including mature PV virions; positive-sense genomic and negative-sense replicative, template viral RNA; essential viral replication proteins; and cellular proteins. Using cryo-electron tomography, we visualize the near-native three-dimensional architecture of secreted infectious microvesicles containing both virions and a unique morphological component that we describe as a mat-like structure. While the composition of these mat-like structures is not yet known, based on our biochemical data they are expected to be comprised of unencapsidated RNA and proteins. In addition to infectious microvesicles, CD9-positive exosomes released from PV-infected cells are also infectious and transport virions. Thus, our data show that, prior to cell lysis, non-enveloped viruses are secreted within infectious vesicles that also transport viral unencapsidated RNAs, viral and host proteins. Understanding the structure and function of these infectious particles helps elucidate the mechanism by which extracellular vesicles contribute to the spread of non-enveloped virus infection.
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Affiliation(s)
- Jie E Yang
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, United States.,Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, United States
| | - Evan D Rossignol
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, United States
| | - Deborah Chang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, United States
| | - Joseph Zaia
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, United States
| | - Isaac Forrester
- Department of Biochemistry, Baylor College of Medicine, Houston, United States
| | - Kiran Raja
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Holly Winbigler
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 20201, United States
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75235, United States
| | - William T Jackson
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 20201, United States
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, United States.
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7
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Gibson KH, Trajtenberg F, Wunder EA, Brady MR, San Martin F, Mechaly A, Shang Z, Liu J, Picardeau M, Ko A, Buschiazzo A, Sindelar CV. An asymmetric sheath controls flagellar supercoiling and motility in the leptospira spirochete. eLife 2020; 9:e53672. [PMID: 32157997 PMCID: PMC7065911 DOI: 10.7554/elife.53672] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/27/2020] [Indexed: 12/25/2022] Open
Abstract
Spirochete bacteria, including important pathogens, exhibit a distinctive means of swimming via undulations of the entire cell. Motility is powered by the rotation of supercoiled 'endoflagella' that wrap around the cell body, confined within the periplasmic space. To investigate the structural basis of flagellar supercoiling, which is critical for motility, we determined the structure of native flagellar filaments from the spirochete Leptospira by integrating high-resolution cryo-electron tomography and X-ray crystallography. We show that these filaments are coated by a highly asymmetric, multi-component sheath layer, contrasting with flagellin-only homopolymers previously observed in exoflagellated bacteria. Distinct sheath proteins localize to the filament inner and outer curvatures to define the supercoiling geometry, explaining a key functional attribute of this spirochete flagellum.
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Affiliation(s)
- Kimberley H Gibson
- Department of Molecular Biophysics and Biochemistry, Yale School of MedicineNew HavenUnited States
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de MontevideoMontevideoUruguay
| | - Elsio A Wunder
- Departament of Epidemiology of Microbial Diseases, Yale School of Public HealthNew HavenUnited States
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of HealthSalvadorBrazil
| | - Megan R Brady
- Department of Molecular Biophysics and Biochemistry, Yale School of MedicineNew HavenUnited States
| | - Fabiana San Martin
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de MontevideoMontevideoUruguay
| | - Ariel Mechaly
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de MontevideoMontevideoUruguay
| | - Zhiguo Shang
- Department of Molecular Biophysics and Biochemistry, Yale School of MedicineNew HavenUnited States
| | - Jun Liu
- Department of Microbial Pathogenesis, School of Medicine, Yale UniversityNew HavenUnited States
| | - Mathieu Picardeau
- Biology of Spirochetes Unit, Institut PasteurParisFrance
- Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut PasteurParisFrance
| | - Albert Ko
- Departament of Epidemiology of Microbial Diseases, Yale School of Public HealthNew HavenUnited States
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Brazilian Ministry of HealthSalvadorBrazil
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de MontevideoMontevideoUruguay
- Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut PasteurParisFrance
| | - Charles Vaughn Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale School of MedicineNew HavenUnited States
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8
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Bollschweiler D, Radu L, Pellegrini L. Cryo-electron tomography of SYCP3 fibers under native conditions. Methods Cell Biol 2018; 145:347-371. [PMID: 29957214 DOI: 10.1016/bs.mcb.2018.03.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The synaptonemal complex (SC) forms during the early stages of meiotic prophase I, when it mediates the pairing of homologous chromosomes. Despite the crucial role of the SC in chromosome synapsis and genetic recombination, the molecular details of its function are still unclear. High-resolution information on the structure of SC proteins would be very valuable to elucidate the molecular basis of their function in meiosis. Here we show how cryo-electron tomography and subtomographic averaging can be usefully applied to provide insights into the structure of the helical SYCP3 protein in its filamentous state. The establishment of such method should prove of use for structural studies of other SC proteins, such as SYCP1 and the TEX12-SYCE2 complex, which can form physiologically relevant filamentous assemblies, and ultimately for the structural analysis of the SC.
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Affiliation(s)
| | - Laura Radu
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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9
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Morphew MK, Giddings TH, McIntosh JR. Cryoelectron Microscopy of Fission Yeast. Cold Spring Harb Protoc 2017; 2017:2017/1/pdb.prot091330. [PMID: 28049779 DOI: 10.1101/pdb.prot091330] [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] [Indexed: 06/06/2023]
Abstract
Fission yeast cells can be prepared for electron microscopy (EM) in the frozen-hydrated state. This eliminates the requirement for dehydration and heavy metal staining when preparing samples for EM. As with room temperature imaging, however, the yeast must be sectioned to make them thin enough for transmission of the electron beam. Cutting sections of vitreous ice with a microtome is challenging. An alternative method that uses a focused ion beam to make a thin sample by milling away much of the sample at liquid nitrogen temperatures is under development but is not yet available for routine use. Imaging frozen-hydrated samples by EM is also a challenge. The technique involves battling low image contrast, high sensitivity to the electron beam, and mechanical distortions produced during the sectioning process. When used successfully, however, the method holds promise of providing excellent molecular detail without the disruption characteristic of dehydration or isolating a structure from its cellular environment. Cryo-EM of tilted views can be used to examine small structures and macromolecular complexes in their native cellular environment. If a structure exists in multiple copies, or has a repeating unit, it can be investigated at higher resolution using subvolume averaging. This protocol focuses on the preparation of cells for cryo-EM.
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Affiliation(s)
- Mary K Morphew
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347
| | - Thomas H Giddings
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - J Richard McIntosh
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
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10
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Fernandez JJ, Laugks U, Schaffer M, Bäuerlein FJB, Khoshouei M, Baumeister W, Lucic V. Removing Contamination-Induced Reconstruction Artifacts from Cryo-electron Tomograms. Biophys J 2015; 110:850-9. [PMID: 26743046 DOI: 10.1016/j.bpj.2015.10.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/06/2015] [Accepted: 10/26/2015] [Indexed: 01/03/2023] Open
Abstract
Imaging of fully hydrated, vitrified biological samples by electron tomography yields structural information about cellular protein complexes in situ. Here we present a computational procedure that removes artifacts of three-dimensional reconstruction caused by contamination present in samples during imaging by electron microscopy. Applying the procedure to phantom data and electron tomograms of cellular samples significantly improved the resolution and the interpretability of tomograms. Artifacts caused by surface contamination associated with thinning by focused ion beam, as well as those arising from gold fiducial markers and from common, lower contrast contamination, could be removed. Our procedure is widely applicable and is especially suited for applications that strive to reach a higher resolution and involve the use of recently developed, state-of-the-art instrumentation.
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Affiliation(s)
- Jose-Jesus Fernandez
- Centro Nacional de Biotecnologia (Consejo Superior de Investigaciones Científicas), Madrid, Spain.
| | - Ulrike Laugks
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | - Vladan Lucic
- Max-Planck-Institute of Biochemistry, Martinsried, Germany.
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11
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Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A. Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure 2015; 23:628-38. [PMID: 25728926 DOI: 10.1016/j.str.2015.01.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/16/2015] [Accepted: 01/22/2015] [Indexed: 12/23/2022]
Abstract
The visual pigment rhodopsin belongs to the family of G protein-coupled receptors that can form higher oligomers. It is controversial whether rhodopsin forms oligomers and whether oligomers are functionally relevant. Here, we study rhodopsin organization in cryosections of dark-adapted mouse rod photoreceptors by cryoelectron tomography. We identify four hierarchical levels of organization. Rhodopsin forms dimers; at least ten dimers form a row. Rows form pairs (tracks) that are aligned parallel to the disk incisures. Particle-based simulation shows that the combination of tracks with fast precomplex formation, i.e. rapid association and dissociation between inactive rhodopsin and the G protein transducin, leads to kinetic trapping: rhodopsin first activates transducin from its own track, whereas recruitment of transducin from other tracks proceeds more slowly. The trap mechanism could produce uniform single-photon responses independent of rhodopsin lifetime. In general, tracks might provide a platform that coordinates the spatiotemporal interaction of signaling molecules.
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Affiliation(s)
- Monika Gunkel
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Johannes Schöneberg
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Weaam Alkhaldi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Stephan Irsen
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Frank Noé
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
| | - Ashraf Al-Amoudi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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12
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Dent KC, Hagen C, Grünewald K. Critical step-by-step approaches toward correlative fluorescence/soft X-ray cryo-microscopy of adherent mammalian cells. Methods Cell Biol 2014; 124:179-216. [PMID: 25287842 DOI: 10.1016/b978-0-12-801075-4.00009-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Soft X-ray cryo-microscopy/tomography with its extraordinary capability to map vitreous cells with high absorption contrast in their full three-dimensional extent, and at a resolution exceeding super-resolution fluorescence microscopy, is a valuable tool for integrative structural cell biology. Focusing on cell biological applications, its ongoing methodological development gained momentum by combining it with fluorescence cryo-microscopy, thus correlating highly resolved structural and specific information in situ. In this chapter, we provide a basic description of the techniques, as well as an overview of equipment and methods available to carry out correlative soft X-ray cryo-tomography experiments on frozen-hydrated cells grown on a planar support. Our aim here is to suggest ways that biologically representative data can be recorded to the highest possible resolution, while also keeping in mind the limitations of the technique during data acquisition and analysis. We have written from our perspective as electron cryo-microscopists/structural cell biologists who have experience using correlative fluorescence/cryoXM/T at synchrotron beamlines presently available for external users in Europe (HZB TXM at U41-FSGM, BESSY II, Berlin/Germany; Carl Zeiss TXMs at MISTRAL, ALBA, Barcelona/Spain, and B24, DLS, Oxfordshire, UK).
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Affiliation(s)
- Kyle C Dent
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom; Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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