1
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Ilett M, Afzali M, Abdulkarim B, Aslam Z, Foster S, Burgos-Ruiz M, Kim YY, Meldrum FC, Drummond-Brydson RM. Studying crystallisation processes using electron microscopy: The importance of sample preparation. J Microsc 2024; 295:243-256. [PMID: 38594963 DOI: 10.1111/jmi.13300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/12/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
We present a comparison of common electron microscopy sample preparation methods for studying crystallisation processes from solution using both scanning and transmission electron microscopy (SEM and TEM). We focus on two widely studied inorganic systems: calcium sulphate, gypsum (CaSO4·2H2O) and calcium carbonate (CaCO3). We find significant differences in crystallisation kinetics and polymorph selection between the different sample preparation methods, which indicate that drying and chemical quenching can induce severe artefacts that are capable of masking the true native state of the crystallising solution. Overall, these results highlight the importance of cryogenic (cryo)-quenching crystallising solutions and the use of full cryo-TEM as the most reliable method for studying the early stages of crystallisation.
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Affiliation(s)
- Martha Ilett
- School of Chemical and Process Engineering, University of Leeds, Leeds, UK
| | - Maryam Afzali
- School of Chemical and Process Engineering, University of Leeds, Leeds, UK
| | - Bilal Abdulkarim
- School of Chemical and Process Engineering, University of Leeds, Leeds, UK
| | - Zabeada Aslam
- School of Chemical and Process Engineering, University of Leeds, Leeds, UK
| | - Stephanie Foster
- School of Chemical and Process Engineering, University of Leeds, Leeds, UK
| | - Miguel Burgos-Ruiz
- Department of Mineralogy and Petrology, University of Granada, Granada, UK
| | - Yi-Yeoun Kim
- School of Chemistry, University of Leeds, Leeds, UK
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2
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Falk M, Tobiasson V, Bock A, Hansen C, Ynnerman A. A Visual Environment for Data Driven Protein Modeling and Validation. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2024; 30:5063-5073. [PMID: 37327104 PMCID: PMC11273209 DOI: 10.1109/tvcg.2023.3286582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In structural biology, validation and verification of new atomic models are crucial and necessary steps which limit the production of reliable molecular models for publications and databases. An atomic model is the result of meticulous modeling and matching and is evaluated using a variety of metrics that provide clues to improve and refine the model so it fits our understanding of molecules and physical constraints. In cryo electron microscopy (cryo-EM) the validation is also part of an iterative modeling process in which there is a need to judge the quality of the model during the creation phase. A shortcoming is that the process and results of the validation are rarely communicated using visual metaphors. This work presents a visual framework for molecular validation. The framework was developed in close collaboration with domain experts in a participatory design process. Its core is a novel visual representation based on 2D heatmaps that shows all available validation metrics in a linear fashion, presenting a global overview of the atomic model and provide domain experts with interactive analysis tools. Additional information stemming from the underlying data, such as a variety of local quality measures, is used to guide the user's attention toward regions of higher relevance. Linked with the heatmap is a three-dimensional molecular visualization providing the spatial context of the structures and chosen metrics. Additional views of statistical properties of the structure are included in the visual framework. We demonstrate the utility of the framework and its visual guidance with examples from cryo-EM.
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3
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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4
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Hu L, Rossetti M, Bergua JF, Parolo C, Álvarez-Diduk R, Rivas L, Idili A, Merkoçi A. Harnessing Bioluminescent Bacteria to Develop an Enzymatic-free Enzyme-linked immunosorbent assay for the Detection of Clinically Relevant Biomarkers. ACS APPLIED MATERIALS & INTERFACES 2024; 16:30636-30647. [PMID: 38651970 PMCID: PMC11194763 DOI: 10.1021/acsami.4c01744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Enzyme-linked immunosorbent assay (ELISA) is the gold standard technique for measuring protein biomarkers due to its high sensitivity, specificity, and throughput. Despite its success, continuous advancements in ELISA and immunoassay formats are crucial to meet evolving global challenges and to address new analytical needs in diverse applications. To expand the capabilities and applications of immunoassays, we introduce a novel ELISA-like assay that we call Bioluminescent-bacteria-linked immunosorbent assay (BBLISA). BBLISA is an enzyme-free assay that utilizes the inner filter effect between the bioluminescent bacteriaAllivibrio fischeriand metallic nanoparticles (gold nanoparticles and gold iridium oxide nanoflowers) as molecular absorbers. Functionalizing these nanoparticles with antibodies induces their accumulation in wells upon binding to molecular targets, forming the classical immune-sandwich complex. Thanks to their ability to adsorb the light emitted by the bacteria, the nanoparticles can suppress the bioluminescence signal, allowing the rapid quantification of the target. To demonstrate the bioanalytical properties of the novel immunoassay platform, as a proof of principle, we detected two clinically relevant biomarkers (human immunoglobulin G and SARS-CoV-2 nucleoprotein) in human serum, achieving the same sensitivity and precision as the classic ELISA. We believe that BBLISA can be a promising alternative to the standard ELISA techniques, offering potential advancements in biomarker detection and analysis by combining nanomaterials with a low-cost, portable bioluminescent platform.
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Affiliation(s)
- Liming Hu
- Nanobioelectronics
& Biosensors Group, Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra 08193, Barcelona, Spain
| | - Marianna Rossetti
- Nanobioelectronics
& Biosensors Group, Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra 08193, Barcelona, Spain
| | - José Francisco Bergua
- Nanobioelectronics
& Biosensors Group, Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra 08193, Barcelona, Spain
| | - Claudio Parolo
- Barcelona
Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona 08036, Spain
| | - Ruslan Álvarez-Diduk
- Nanobioelectronics
& Biosensors Group, Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra 08193, Barcelona, Spain
| | - Lourdes Rivas
- Nanobioelectronics
& Biosensors Group, Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra 08193, Barcelona, Spain
| | - Andrea Idili
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Arben Merkoçi
- Nanobioelectronics
& Biosensors Group, Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra 08193, Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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5
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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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6
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589090. [PMID: 38712113 PMCID: PMC11071277 DOI: 10.1101/2024.04.12.589090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
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
- Dept. of Electrical Engineering, Stanford University
| | | | - Liyue Shen
- Dept. of Electrical and Computer Engineering, University of Michigan
| | - Philip Baldwin
- Dept. of Biochemistry and Molecular Pharmacology, Baylor College of Medicine
- Dept. of Genetics, The Salk Institute for Biological Sciences
| | | | - Dmitry Lyumkis
- Dept. of Genetics, The Salk Institute for Biological Sciences
- Graduate School of Biological Sciences, University of California San Diego
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
| | - Wah Chiu
- Dept. of Bioengineering, Stanford University
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
- Dept. of Microbiology and Immunology, Stanford University
| | - John Pauly
- Dept. of Electrical Engineering, Stanford University
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7
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Parkhurst JM, Cavalleri A, Dumoux M, Basham M, Clare D, Siebert CA, Evans G, Naismith JH, Kirkland A, Essex JW. Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. Ultramicroscopy 2024; 256:113882. [PMID: 37979542 PMCID: PMC10730944 DOI: 10.1016/j.ultramic.2023.113882] [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: 04/28/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations. Although practical for small sample volumes; for simulation of cryo-EM data from large sample volumes, this can be too computationally expensive. We have evaluated a Gaussian Random Field (GRF) ice model which is shown to be more computationally efficient for large sample volumes. The simulated EM images are compared with the gold standard atom-based ice model approach and shown to be directly comparable. Comparison with experimentally acquired data shows the Gaussian random field ice model produces realistic simulations. The software required has been implemented in the Parakeet software package and the underlying atomic models are available online for use by the wider community.
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Affiliation(s)
- James M Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom.
| | - Anna Cavalleri
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - James H Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom; Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
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8
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Agostini M, Traldi P, Hamdan M. Mass Spectrometry Investigation of Some ATP-Binding Cassette (ABC) Proteins. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:200. [PMID: 38399488 PMCID: PMC10890348 DOI: 10.3390/medicina60020200] [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: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024]
Abstract
Drug resistance remains one of the main causes of poor outcome in cancer therapy. It is also becoming evident that drug resistance to both chemotherapy and to antibiotics is driven by more than one mechanism. So far, there are at least eight recognized mechanisms behind such resistance. In this review, we choose to discuss one of these mechanisms, which is known to be partially driven by a class of transmembrane proteins known as ATP-binding cassette (ABC) transporters. In normal tissues, ABC transporters protect the cells from the toxic effects of xenobiotics, whereas in tumor cells, they reduce the intracellular concentrations of anticancer drugs, which ultimately leads to the emergence of multidrug resistance (MDR). A deeper understanding of the structures and the biology of these proteins is central to current efforts to circumvent resistance to both chemotherapy, targeted therapy, and antibiotics. Understanding the biology and the function of these proteins requires detailed structural and conformational information for this class of membrane proteins. For many years, such structural information has been mainly provided by X-ray crystallography and cryo-electron microscopy. More recently, mass spectrometry-based methods assumed an important role in the area of structural and conformational characterization of this class of proteins. The contribution of this technique to structural biology has been enhanced by its combination with liquid chromatography and ion mobility, as well as more refined labelling protocols and the use of more efficient fragmentation methods, which allow the detection and localization of labile post-translational modifications. In this review, we discuss the contribution of mass spectrometry to efforts to characterize some members of the ATP-binding cassette (ABC) proteins and why such a contribution is relevant to efforts to clarify the link between the overexpression of these proteins and the most widespread mechanism of chemoresistance.
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Affiliation(s)
| | - Pietro Traldi
- Corso Stati Uniti 4, Istituto di Ricerca Pediatrica Città della Speranza, 35100 Padova, Italy; (M.A.)
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9
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Deniaud A, Kabasakal BV, Bufton JC, Schaffitzel C. Sample Preparation for Electron Cryo-Microscopy of Macromolecular Machines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:173-190. [PMID: 38507207 DOI: 10.1007/978-3-031-52193-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
High-resolution structure determination by electron cryo-microscopy underwent a step change in recent years. This now allows study of challenging samples which previously were inaccessible for structure determination, including membrane proteins. These developments shift the focus in the field to the next bottlenecks which are high-quality sample preparations. While the amounts of sample required for cryo-EM are relatively small, sample quality is the key challenge. Sample quality is influenced by the stability of complexes which depends on buffer composition, inherent flexibility of the sample, and the method of solubilization from the membrane for membrane proteins. It further depends on the choice of sample support, grid pre-treatment and cryo-grid freezing protocol. Here, we discuss various widely applicable approaches to improve sample quality for structural analysis by cryo-EM.
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Affiliation(s)
- Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG - Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Burak V Kabasakal
- School of Biochemistry, University of Bristol, Bristol, UK
- Turkish Accelerator and Radiation Laboratory, Gölbaşı, Ankara, Türkiye
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10
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Roberge H, Moreau P, Couallier E, Abellan P. Lipids and Proteins Differentiation in Membrane Fouling Using Heavy Metal Staining and Electron Microscopy at Cryogenic Temperatures. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2090-2098. [PMID: 37966971 DOI: 10.1093/micmic/ozad114] [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: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/24/2023] [Indexed: 11/17/2023]
Abstract
The detailed characterization of fouling in membranes is essential to understand any observed improvement or reduction on filtration performance. Electron microscopy allows detailed structural characterization, and its combination with labeling techniques, using electron-dense probes, typically allows for the differentiation of biomolecules. Developing specific protocols that allow for differentiation of biomolecules in membrane fouling by electron microscopy is a major challenge due to both as follows: the necessity to preserve the native state of fouled membranes upon real filtration conditions as well as the inability of the electron-dense probes to penetrate the membranes once they have been fouled. In this study, we present the development of a heavy metal staining technique for identification and differentiation of biomolecules in membrane fouling, which is compatible with cryofixation methods. A general contrast enhancement of biomolecules and fouling is achieved. Our observations indicate a strong interaction between biomolecules: A tendency of proteins, both in solution as well as in the fouling, to surround the lipids is observed. Using transmission electron microscopy and scanning electron microscopy at cryogenic conditions, cryo-SEM, in combination with energy-dispersive X-ray spectroscopy, the spatial distribution of proteins and lipids within fouling is shown and the role of proteins in fouling discussed.
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Affiliation(s)
- Hélène Roberge
- Nantes Université, CNRS, Institut des Matériaux de Nantes Jean Rouxel, IMN, 2 rue de la Houssinère, 44000 Nantes, France
- Laboratoire de Génie des Procédés, Nantes Université, CNRS, ONIRIS, Environnement et Agroalimentaire, 37 boulevard de l'université, GEPEA, 44600 Saint-Nazaire, France
| | - Philippe Moreau
- Nantes Université, CNRS, Institut des Matériaux de Nantes Jean Rouxel, IMN, 2 rue de la Houssinère, 44000 Nantes, France
| | - Estelle Couallier
- Laboratoire de Génie des Procédés, Nantes Université, CNRS, ONIRIS, Environnement et Agroalimentaire, 37 boulevard de l'université, GEPEA, 44600 Saint-Nazaire, France
| | - Patricia Abellan
- Nantes Université, CNRS, Institut des Matériaux de Nantes Jean Rouxel, IMN, 2 rue de la Houssinère, 44000 Nantes, France
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11
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Sheikh A, Zechmann B, Sayes CM, Taube JH, Greathouse KL. A preparation of bacterial outer membrane with osmium tetroxide and uranyl acetate co-stain enables improved structural determination by transmission electron microscopy. Microscopy (Oxf) 2023; 72:515-519. [PMID: 37148329 PMCID: PMC10673695 DOI: 10.1093/jmicro/dfad027] [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: 01/20/2023] [Revised: 04/10/2023] [Accepted: 05/04/2023] [Indexed: 05/08/2023] Open
Abstract
Biological nanoparticles, such as bacterial outer membrane vesicles (OMVs), are routinely characterized through transmission electron microscopy (TEM). In this study, we report a novel method to prepare OMVs for TEM imaging. To preserve vesicular shape and structure, we developed a dual fixation protocol involving osmium tetroxide incubation prior to negative staining with uranyl acetate. Combining osmium tetroxide with uranyl acetate resulted in preservation of sub-50 nm vesicles and improved morphological stability, enhancing characterization of lipid-based nanoparticles by TEM.
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Affiliation(s)
- Aadil Sheikh
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Bernd Zechmann
- Center for Microscopy and Imaging, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Christie M Sayes
- Department of Environmental Science, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - Joseph H Taube
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
| | - K Leigh Greathouse
- Department of Biology, Baylor University, One Bear Place #97046, Waco, TX 76798, USA
- Nutrition Sciences, Baylor University, One Bear Place #97311, Waco, TX 76798, USA
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12
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Ramlaul K, Feng Z, Canavan C, de Martín Garrido N, Carreño D, Crone M, Jensen KE, Li B, Barnett H, Riglar DT, Freemont PS, Miller D, Aylett CHS. A 3D-printed flow-cell for on-grid purification of electron microscopy samples directly from lysate. J Struct Biol 2023; 215:107999. [PMID: 37451560 DOI: 10.1016/j.jsb.2023.107999] [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: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
While recent advances in cryo-EM, coupled with single particle analysis, have the potential to allow structure determination in a near-native state from vanishingly few individual particles, this vision has yet to be realised in practise. Requirements for particle numbers that currently far exceed the theoretical lower limits, challenges with the practicalities of achieving high concentrations for difficult-to-produce samples, and inadequate sample-dependent imaging conditions, all result in significant bottlenecks preventing routine structure determination using cryo-EM. Therefore, considerable efforts are being made to circumvent these bottlenecks by developing affinity purification of samples on-grid; at once obviating the need to produce large amounts of protein, as well as more directly controlling the variable, and sample-dependent, process of grid preparation. In this proof-of-concept study, we demonstrate a further practical step towards this paradigm, developing a 3D-printable flow-cell device to allow on-grid affinity purification from raw inputs such as whole cell lysates, using graphene oxide-based affinity grids. Our flow-cell device can be interfaced directly with routinely-used laboratory equipment such as liquid chromatographs, or peristaltic pumps, fitted with standard chromatographic (1/16") connectors, and can be used to allow binding of samples to affinity grids in a controlled environment prior to the extensive washing required to remove impurities. Furthermore, by designing a device which can be 3D printed and coupled to routinely used laboratory equipment, we hope to increase the accessibility of the techniques presented herein to researchers working towards single-particle macromolecular structures.
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Affiliation(s)
- Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ziyi Feng
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Caoimhe Canavan
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Natàlia de Martín Garrido
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - David Carreño
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Michael Crone
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Kirsten E Jensen
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Bing Li
- Hamlyn Centre, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Harry Barnett
- Imperial College Advanced Hackspace, Imperial College London, London, United Kingdom
| | - David T Riglar
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Paul S Freemont
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - David Miller
- Imperial College Advanced Hackspace, Imperial College London, London, United Kingdom.
| | - Christopher H S Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom.
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13
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Wójcik-Mieszawska S, Lewtak K, Skwarek E, Dębowski D, Gitlin-Domagalska A, Nowak J, Wydrych J, Pawelec J, Fiołka MJ. Autophagy of Candida albicans cells after the action of earthworm Venetin-1 nanoparticle with protease inhibitor activity. Sci Rep 2023; 13:14228. [PMID: 37648723 PMCID: PMC10468520 DOI: 10.1038/s41598-023-41281-4] [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: 03/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
The present studies show the effect of the Venetin-1 protein-polysaccharide complex obtained from the coelomic fluid of the earthworm Dendrobaena veneta on Candida albicans cells. They are a continuation of research on the mechanisms of action, cellular targets, and modes of cell death. After the action of Venetin-1, a reduced survival rate of the yeast cells was noted. The cells were observed to be enlarged compared to the controls and deformed. In addition, an increase in the number of cells with clearly enlarged vacuoles was noted. The detected autophagy process was confirmed using differential interference contrast, fluorescence microscopy, and transmission electron microscopy. Autophagic vesicles were best visible after incubation of fungus cells with the Venetin-1 complex at a concentration of 50 and 100 µg mL-1. The changes in the vacuoles were accompanied by changes in the size of mitochondria, which is probably related to the previously documented oxidative stress. The aggregation properties of Venetin-1 were characterized. Based on the results of the zeta potential at the Venetin-1/KCl interface, the pHiep = 4 point was determined, i.e. the zeta potential becomes positive above pH = 4 and is negative below this value, which may affect the electrostatic interactions with other particles surrounding Venetin-1.
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Affiliation(s)
- Sylwia Wójcik-Mieszawska
- Department of Immunobiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kinga Lewtak
- Department of Cell Biology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Ewa Skwarek
- Department of Radiochemistry and Environmental Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Dębowski
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Agata Gitlin-Domagalska
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Jakub Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Jerzy Wydrych
- Department of Functional Anatomy and Cytobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jarosław Pawelec
- Department of Functional Anatomy and Cytobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marta J Fiołka
- Department of Immunobiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland.
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14
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Fineberg A, Takagi Y, Thirumurugan K, Andrecka J, Billington N, Young G, Cole D, Burgess SA, Curd AP, Hammer JA, Sellers JR, Kukura P, Knight PJ. Myosin-5 varies its steps along the irregular F-actin track. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.16.549178. [PMID: 37503193 PMCID: PMC10370000 DOI: 10.1101/2023.07.16.549178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Molecular motors employ chemical energy to generate unidirectional mechanical output against a track. By contrast to the majority of macroscopic machines, they need to navigate a chaotic cellular environment, potential disorder in the track and Brownian motion. Nevertheless, decades of nanometer-precise optical studies suggest that myosin-5a, one of the prototypical molecular motors, takes uniform steps spanning 13 subunits (36 nm) along its F-actin track. Here, we use high-resolution interferometric scattering (iSCAT) microscopy to reveal that myosin takes strides spanning 22 to 34 actin subunits, despite walking straight along the helical actin filament. We show that cumulative angular disorder in F-actin accounts for the observed proportion of each stride length, akin to crossing a river on variably-spaced stepping stones. Electron microscopy revealed the structure of the stepping molecule. Our results indicate that both motor and track are soft materials that can adapt to function in complex cellular conditions.
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Affiliation(s)
- Adam Fineberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Yasuharu Takagi
- Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Kavitha Thirumurugan
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
- Present address: Structural Biology Lab, Pearl Research Park, SBST, Vellore Institute of Technology, Vellore-632 014, India
| | - Joanna Andrecka
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Present address: Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Neil Billington
- Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
- Present address: Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, U.S.A
| | - Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Present address: Refeyn Ltd., Unit 9, Trade City, Sandy Ln W, Littlemore, Oxford OX4 6FF, U.K
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Present address: Refeyn Ltd., Unit 9, Trade City, Sandy Ln W, Littlemore, Oxford OX4 6FF, U.K
| | - Stan A. Burgess
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Alistair P. Curd
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - John A. Hammer
- Cell and Developmental Biology Center, NHLBI, National Institutes of Health, Bethesda, MD 20892, U.S.A
| | - James R. Sellers
- Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, U.K
| | - Peter J. Knight
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
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15
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Beraza-Millor M, Rodríguez-Castejón J, Miranda J, Del Pozo-Rodríguez A, Rodríguez-Gascón A, Solinís MÁ. Novel Golden Lipid Nanoparticles with Small Interference Ribonucleic Acid for Substrate Reduction Therapy in Fabry Disease. Pharmaceutics 2023; 15:1936. [PMID: 37514122 PMCID: PMC10385692 DOI: 10.3390/pharmaceutics15071936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Substrate reduction therapy (SRT) has been proposed as a new gene therapy for Fabry disease (FD) to prevent the formation of globotriaosylceramide (Gb3). Nanomedicines containing different siRNA targeted to Gb3 synthase (Gb3S) were designed. Formulation factors, such as the composition, solid lipid nanoparticles (SLNs) preparation method and the incorporation of different ligands, such as gold nanoparticles (GNs), protamine (P) and polysaccharides, were evaluated. The new siRNA-golden LNPs were efficiently internalized in an FD cell model (IMFE-1), with GNs detected in the cytoplasm and in the nucleus. Silencing efficacy (measured by RT-qPCR) depended on the final composition and method of preparation, with silencing rates up to 90% (expressed as the reduction in Gb3S-mRNA). GNs conferred a higher system efficacy and stability without compromising cell viability and hemocompatibility. Immunocytochemistry assays confirmed Gb3S silencing for at least 15 days with the most effective formulations. Overall, these results highlight the potential of the new siRNA-golden LNP system as a promising nanomedicine to address FD by specific SRT.
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Affiliation(s)
- Marina Beraza-Millor
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (Pharma Nano Gene), Faculty of Pharmacy, Centro de Investigación Lascaray Ikergunea, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - Julen Rodríguez-Castejón
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (Pharma Nano Gene), Faculty of Pharmacy, Centro de Investigación Lascaray Ikergunea, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - Jonatan Miranda
- GLUTEN3S Research Group, Faculty of Pharmacy, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Nutrition and Food Safety, 01006 Vitoria-Gasteiz, Spain
| | - Ana Del Pozo-Rodríguez
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (Pharma Nano Gene), Faculty of Pharmacy, Centro de Investigación Lascaray Ikergunea, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - Alicia Rodríguez-Gascón
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (Pharma Nano Gene), Faculty of Pharmacy, Centro de Investigación Lascaray Ikergunea, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
| | - María Ángeles Solinís
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (Pharma Nano Gene), Faculty of Pharmacy, Centro de Investigación Lascaray Ikergunea, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents and Gene Therapy, 01006 Vitoria-Gasteiz, Spain
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16
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Perdigão LMA, Ho EML, Cheng ZC, Yee NBY, Glen T, Wu L, Grange M, Dumoux M, Basham M, Darrow MC. Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images. BIOLOGICAL IMAGING 2023; 3:e9. [PMID: 38487692 PMCID: PMC10936406 DOI: 10.1017/s2633903x23000119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2024]
Abstract
An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming.
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Affiliation(s)
- Luís M. A. Perdigão
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
| | - Elaine M. L. Ho
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
| | - Zhiyuan C. Cheng
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
- School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Neville B.-Y. Yee
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
| | - Thomas Glen
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Liang Wu
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michael Grange
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Mark Basham
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
- Diamond Light Source, Didcot, UK
| | - Michele C. Darrow
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Didcot, UK
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17
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Kumar R. Cryo-EM technique and its application: Structure of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:385-397. [PMID: 37717991 DOI: 10.1016/bs.vh.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become one of the most powerful tools to solve the 3-D structure of macromolecules. Unlike X-ray crystallography, the cryo-EM method has advantage of providing an in-depth insight into the dynamic behavior of macromolecules, which is particularly useful to determine 3-D structural analyses of large protein complexes. Due to recent technical advancements, cryo-EM has become the method of choice for the determination of protein structures. Among other proteins, solving 3-D structure of steroid hormone receptors (SHRs) complexed with DNA and coactivators has been a challenge for decades. The limitations with X-ray crystallography and NMR to solve SHR protein structures prompted investigators to move towards cryo-EM technique. The cryo-EM structural analyses have been successful in revealing structural dynamics of several SHRs in recent years. Though, limited by low-resolution, the structural analyses of these SHRs may be useful in understanding many receptor functions as well as provide a platform to refine high-resolution structural analyses in future. This review article discusses the cryo-EM technique in general as well as structural information gained for SHRs using cryo-EM.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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18
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Malawska KJ, Takano S, Oisaki K, Yanagisawa H, Kikkawa M, Tsukuda T, Kanai M. Bioconjugation of Au 25 Nanocluster to Monoclonal Antibody at Tryptophan. Bioconjug Chem 2023. [PMID: 36893358 DOI: 10.1021/acs.bioconjchem.3c00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
We report the first bioconjugation of Au25 nanocluster to a monoclonal antibody at scarcely exposed tryptophan (Trp) residues toward the development of high-resolution probes for cryogenic electron microscopy (cryo-EM) and tomography (cryo-ET). To achieve this, we improved the Trp-selective bioconjugation using hydroxylamine (ABNOH) reagents instead of previously developed N-oxyl radicals (ABNO). This new protocol allowed for the application of Trp-selective bioconjugation to acid-sensitive proteins such as antibodies. We found that a two-step procedure utilizing first Trp-selective bioconjugation for the introduction of azide groups to the protein and then strain-promoted azide-alkyne cycloaddition (SPAAC) to attach a bicyclononyne (BCN)-presenting redox-sensitive Au25 nanocluster was essential for a scalable procedure. Covalent labeling of the antibody with gold nanoclusters was confirmed by various analytical methods, including cryo-EM analysis of the Au25 nanocluster conjugates.
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Affiliation(s)
- Katarzyna Joanna Malawska
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinjiro Takano
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kounosuke Oisaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsuya Tsukuda
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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19
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Harrison PJ, Vecerkova T, Clare DK, Quigley A. A review of the approaches used to solve sub-100 kDa membrane proteins by cryo-electron microscopy. J Struct Biol 2023; 215:107959. [PMID: 37004781 DOI: 10.1016/j.jsb.2023.107959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/07/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Membrane proteins (MPs) are essential components of all biological membranes, contributing to key cellular functions that include signalling, molecular transport and energy metabolism. Consequently, MPs are important biomedical targets for therapeutics discovery. Despite hardware and software developments in cryo-electron microscopy, as well as MP sample preparation, MPs smaller than 100 kDa remain difficult to study structurally. Significant investment is required to overcome low levels of naturally abundant protein, MP hydrophobicity as well as conformational and compositional instability. Here we have reviewed the sample preparation approaches that have been taken to successfully express, purify and prepare small MPs for analysis by cryo-EM (those with a total solved molecular weight of under 100 kDa), as well as examining the differing approaches towards data processing and ultimately obtaining a structural solution. We highlight common challenges at each stage in the process as well as strategies that have been developed to overcome these issues. Finally, we discuss future directions and opportunities for the study of sub-100 kDa membrane proteins by cryo-EM.
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20
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Dumoux M, Glen T, Smith JLR, Ho EML, Perdigão LMA, Pennington A, Klumpe S, Yee NBY, Farmer DA, Lai PYA, Bowles W, Kelley R, Plitzko JM, Wu L, Basham M, Clare DK, Siebert CA, Darrow MC, Naismith JH, Grange M. Cryo-plasma FIB/SEM volume imaging of biological specimens. eLife 2023; 12:83623. [PMID: 36805107 PMCID: PMC9995114 DOI: 10.7554/elife.83623] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/20/2023] [Indexed: 02/23/2023] Open
Abstract
Serial focussed ion beam scanning electron microscopy (FIB/SEM) enables imaging and assessment of subcellular structures on the mesoscale (10 nm to 10 µm). When applied to vitrified samples, serial FIB/SEM is also a means to target specific structures in cells and tissues while maintaining constituents' hydration shells for in situ structural biology downstream. However, the application of serial FIB/SEM imaging of non-stained cryogenic biological samples is limited due to low contrast, curtaining, and charging artefacts. We address these challenges using a cryogenic plasma FIB/SEM. We evaluated the choice of plasma ion source and imaging regimes to produce high-quality SEM images of a range of different biological samples. Using an automated workflow we produced three-dimensional volumes of bacteria, human cells, and tissue, and calculated estimates for their resolution, typically achieving 20-50 nm. Additionally, a tag-free localisation tool for regions of interest is needed to drive the application of in situ structural biology towards tissue. The combination of serial FIB/SEM with plasma-based ion sources promises a framework for targeting specific features in bulk-frozen samples (>100 µm) to produce lamellae for cryogenic electron tomography.
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Affiliation(s)
- Maud Dumoux
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Thomas Glen
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Jake LR Smith
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Elaine ML Ho
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Luis MA Perdigão
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - Avery Pennington
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Sven Klumpe
- Research Group Cryo-EM Technology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Neville BY Yee
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - David Andrew Farmer
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Pui YA Lai
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - William Bowles
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Ron Kelley
- Materials and Structural Analysis Division, Thermo Fisher ScientificEindhovenNetherlands
| | - Jürgen M Plitzko
- Research Group Cryo-EM Technology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Liang Wu
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Mark Basham
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Daniel K Clare
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science & Innovation CampusDidcotUnited Kingdom
| | - Michele C Darrow
- Artificial Intelligence and Informatics, Rosalind Franklin InstituteDidcotUnited Kingdom
| | - James H Naismith
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Michael Grange
- Structural Biology, Rosalind Franklin InstituteDidcotUnited Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
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21
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Three-Dimensional Reconstruction of the Hepatitis C Virus Envelope Glycoprotein E1E2 Heterodimer by Electron Microscopic Analysis. J Virol 2023; 97:e0178822. [PMID: 36519897 PMCID: PMC9888182 DOI: 10.1128/jvi.01788-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Despite the development of highly effective hepatitis C virus (HCV) treatments, an effective prophylactic vaccine is still lacking. HCV infection is mediated by its envelope glycoproteins, E1 and E2, during the entry process, with E2 binding to cell receptors and E1 mediating endosomal fusion. The structure of E1E2 has only been partially resolved by X-ray crystallography of the core domain of E2 protein (E2c) and its complex with various neutralizing antibodies. Structural understanding of the E1E2 heterodimer in its native form can advance the design of candidates for HCV vaccine development. Here, we analyze the structure of the recombinant HCV E1E2 heterodimer with the aid of well-defined monoclonal anti-E1 and E2 antibodies, as well as a small-molecule chlorcyclizine-diazirine-biotin that can target and cross-link the putative E1 fusion domain. Three-dimensional (3D) models were generated after extensive 2D classification analysis with negative-stain single-particle data sets. We modeled the available crystal structures of the E2c and Fabs into 3D volumes of E1E2-Fab complexes based on the shape and dimension of the domain density. The E1E2 heterodimer exists in monomeric form and consists of a main globular body, presumably depicting the E1 and E2 stem/transmembrane domain, and a protruding structure representing the E2c region, based on anti-E2 Fab binding. At low resolution, a model generated from negative-stain analysis revealed the unique binding and orientation of individual or double Fabs onto the E1 and E2 components of the complex. Cryo-electron microscopy (cryo-EM) of the double Fab complexes resulted in a refined structural model of the E1E2 heterodimer, presented here. IMPORTANCE Recombinant HCV E1E2 heterodimer is being developed as a vaccine candidate. Using electron microscopy, we demonstrated unique features of E1E2 in complex with various neutralizing antibodies and small molecule inhibitors that are important to understanding its antigenicity and induction of immune response.
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22
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Baymukhametov TN, Lyabin DN, Chesnokov YM, Sorokin II, Pechnikova E, Vasiliev A, Afonina Z. Polyribosomes of circular topology are prevalent in mammalian cells. Nucleic Acids Res 2022; 51:908-918. [PMID: 36583341 PMCID: PMC9881139 DOI: 10.1093/nar/gkac1208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been shown to possess various spatial conformations, including a ring-shaped configuration which was considered to be functionally important. However, a recent in situ cryo-ET analysis of predominant regular inter-ribosome contacts did not confirm the abundance of ring-shaped polyribosomes in a cell cytoplasm. To address this discrepancy, here we analyzed the cryo-ET structure of polyribosomes in diluted lysates of HeLa cells. It was shown that the vast majority of the ribosomes were combined into polysomes and were proven to be translationally active. Tomogram analysis revealed that circular polyribosomes are indeed very common in the cytoplasm, but they mostly possess pseudo-regular structures without specific inter-ribosomal contacts. Although the size of polyribosomes varied widely, most circular polysomes were relatively small in size (4-8 ribosomes). Our results confirm the recent data that it is cellular mRNAs with short ORF that most commonly form circular structures providing an enhancement of translation.
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Affiliation(s)
- Timur N Baymukhametov
- Structural biology department, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia
| | - Dmitry N Lyabin
- Institute of Protein Research RAS, Pushchino, Moscow Region 142290, Russia
| | - Yury M Chesnokov
- Probe and Electron Microscopy Resource Center, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia
| | - Ivan I Sorokin
- Institute of Protein Research RAS, Pushchino, Moscow Region 142290, Russia
| | - Evgeniya V Pechnikova
- Probe and Electron Microscopy Resource Center, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia,Electron Microscopy Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ RAS, Moscow 119333, Russia
| | - Alexander L Vasiliev
- Probe and Electron Microscopy Resource Center, National Research Center ‘Kurchatov Institute’, Moscow 123182, Russia,Electron Microscopy Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ RAS, Moscow 119333, Russia
| | - Zhanna A Afonina
- To whom correspondence should be addressed. Tel: +7 985 7232812; Fax: +7 4967 318435;
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23
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ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation. Mol Cell 2022; 82:4324-4339.e8. [PMID: 36347259 DOI: 10.1016/j.molcel.2022.10.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
ATG9A and ATG2A are essential core members of the autophagy machinery. ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer, whereas ATG2A facilitates lipid flow between tethered membranes. Although both have been functionally linked during the formation of autophagosomes, the molecular details and consequences of their interaction remain unclear. By combining data from peptide arrays, crosslinking, and hydrogen-deuterium exchange mass spectrometry together with cryoelectron microscopy, we propose a molecular model of the ATG9A-2A complex. Using this integrative structure modeling approach, we identify several interfaces mediating ATG9A-2A interaction that would allow a direct transfer of lipids from ATG2A into the lipid-binding perpendicular branch of ATG9A. Mutational analyses combined with functional activity assays demonstrate their importance for autophagy, thereby shedding light on this protein complex at the heart of autophagy.
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24
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Yang H, Talledge N, Arndt WG, Zhang W, Mansky LM. Human Immunodeficiency Virus Type 2 Capsid Protein Mutagenesis Reveals Amino Acid Residues Important for Virus Particle Assembly. J Mol Biol 2022; 434:167753. [PMID: 35868362 PMCID: PMC11057910 DOI: 10.1016/j.jmb.2022.167753] [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: 05/11/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Human immunodeficiency virus (HIV) Gag drives virus particle assembly. The capsid (CA) domain is critical for Gag multimerization mediated by protein-protein interactions. The Gag protein interaction network defines critical aspects of the retroviral lifecycle at steps such as particle assembly and maturation. Previous studies have demonstrated that the immature particle morphology of HIV-2 is intriguingly distinct relative to that of HIV-1. Based upon this observation, we sought to determine the amino acid residues important for virus assembly that might help explain the differences between HIV-1 and HIV-2. To do this, we conducted site-directed mutagenesis of targeted locations in the HIV-2 CA domain of Gag and analyzed various aspects of virus particle assembly. A panel of 31 site-directed mutants of residues that reside at the HIV-2 CA inter-hexamer interface, intra-hexamer interface and CA inter-domain linker were created and analyzed for their effects on the efficiency of particle production, particle morphology, particle infectivity, Gag subcellular distribution and in vitro protein assembly. Seven conserved residues between HIV-1 and HIV-2 (L19, A41, I152, K153, K157, N194, D196) and two non-conserved residues (G38, N127) were found to significantly impact Gag multimerization and particle assembly. Taken together, these observations complement structural analyses of immature HIV-2 particle morphology and Gag lattice organization as well as provide important comparative insights into the key amino acid residues that can help explain the observed differences between HIV immature particle morphology and its association with virus replication and particle infectivity.
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Affiliation(s)
- Huixin Yang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA
| | - Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - William G Arndt
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology & Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA; Biochemistry, Molecular Biology & Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
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25
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Mazumder A, Mozammal M, Talukder MA. Three-dimensional imaging of biological cells using surface plasmon coupled emission. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:106002. [PMID: 36203237 PMCID: PMC9535299 DOI: 10.1117/1.jbo.27.10.106002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
SIGNIFICANCE Biological cell imaging has become one of the most crucial research interests because of its applications in biomedical and microbiology studies. However, three-dimensional (3D) imaging of biological cells is critically challenging and often involves prohibitively expensive and complex equipment. Therefore, a low-cost imaging technique with a simpler optical arrangement is immensely needed. AIM The proposed approach will provide an accurate cell image at a low cost without needing any microscope or extensive processing of the collected data, often used in conventional imaging techniques. APPROACH We propose that patterns of surface plasmon coupled emission (SPCE) features from a fluorescently labeled biological cell can be used to image the cell. An imaging methodology has been developed and theoretically demonstrated to create 3D images of cells from the detected SPCE patterns. The 3D images created from the different SPCE properties at the far-field closely match the actual cell structures. RESULTS The developed technique has been applied to different regular and irregular cell shapes. In each case, the calculated root-mean-square error (RMSE) of the created images from the cell structures remains within a few percentages. Our work recreates the base of a circular-shaped cell with an RMSE of ≲1.4 % . In addition, the images of irregular-shaped cell bases have an RMSE of ≲2.8 % . Finally, we obtained a 3D image with an RMSE of ≲6.5 % for a random cellular structure. CONCLUSIONS Despite being in its initial stage of development, the proposed technique shows promising results considering its simplicity and the nominal cost it would require.
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Affiliation(s)
- Anik Mazumder
- Bangladesh University of Engineering and Technology, Department of Electrical and Electronic Engineering, Dhaka, Bangladesh
- United International University, Department of Computer Science and Engineering, Dhaka, Bangladesh
| | - Mohammad Mozammal
- Bangladesh University of Engineering and Technology, Department of Electrical and Electronic Engineering, Dhaka, Bangladesh
| | - Muhammad Anisuzzaman Talukder
- Bangladesh University of Engineering and Technology, Department of Electrical and Electronic Engineering, Dhaka, Bangladesh
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26
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Ranno N, Si D. Neural representations of cryo-EM maps and a graph-based interpretation. BMC Bioinformatics 2022; 23:397. [PMID: 36171544 PMCID: PMC9517980 DOI: 10.1186/s12859-022-04942-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Producing a protein structure from the discrete voxel grid data of cryo-EM maps involves interpolation into the continuous spatial domain. We present a novel data format called the neural cryo-EM map, which is formed from a set of neural networks that accurately parameterize cryo-EM maps and provide native, spatially continuous data for density and gradient. As a case study of this data format, we create graph-based interpretations of high resolution experimental cryo-EM maps. Results Normalized cryo-EM map values interpolated using the non-linear neural cryo-EM format are more accurate, consistently scoring less than 0.01 mean absolute error, than a conventional tri-linear interpolation, which scores up to 0.12 mean absolute error. Our graph-based interpretations of 115 experimental cryo-EM maps from 1.15 to 4.0 Å resolution provide high coverage of the underlying amino acid residue locations, while accuracy of nodes is correlated with resolution. The nodes of graphs created from atomic resolution maps (higher than 1.6 Å) provide greater than 99% residue coverage as well as 85% full atomic coverage with a mean of 0.19 Å root mean squared deviation. Other graphs have a mean 84% residue coverage with less specificity of the nodes due to experimental noise and differences of density context at lower resolutions. Conclusions The fully continuous and differentiable nature of the neural cryo-EM map enables the adaptation of the voxel data to alternative data formats, such as a graph that characterizes the atomic locations of the underlying protein or macromolecular structure. Graphs created from atomic resolution maps are superior in finding atom locations and may serve as input to predictive residue classification and structure segmentation methods. This work may be generalized to transform any 3D grid-based data format into non-linear, continuous, and differentiable format for downstream geometric deep learning applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04942-1.
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Affiliation(s)
- Nathan Ranno
- Department of Computing and Software Systems, University of Washington, Bothell, WA, USA
| | - Dong Si
- Department of Computing and Software Systems, University of Washington, Bothell, WA, USA.
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27
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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 PMCID: PMC9480104 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [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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28
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Fan H, Sun F. Developing Graphene Grids for Cryoelectron Microscopy. Front Mol Biosci 2022; 9:937253. [PMID: 35911962 PMCID: PMC9326159 DOI: 10.3389/fmolb.2022.937253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cryogenic electron microscopy (cryo-EM) single particle analysis has become one of the major techniques used to study high-resolution 3D structures of biological macromolecules. Specimens are generally prepared in a thin layer of vitrified ice using a holey carbon grid. However, the sample quality using this type of grid is not always ideal for high-resolution imaging even when the specimens in the test tube behave ideally. Various problems occur during a vitrification procedure, including poor/nonuniform distribution of particles, preferred orientation of particles, specimen denaturation/degradation, high background from thick ice, and beam-induced motion, which have become important bottlenecks in high-resolution structural studies using cryo-EM in many projects. In recent years, grids with support films made of graphene and its derivatives have been developed to efficiently solve these problems. Here, the various advantages of graphene grids over conventional holey carbon film grids, functionalization of graphene support films, production methods of graphene grids, and origins of pristine graphene contamination are reviewed and discussed.
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Affiliation(s)
- Hongcheng Fan
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Bioland Laboratory, Guangzhou, China
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29
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Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 2022; 214:107880. [PMID: 35809758 DOI: 10.1016/j.jsb.2022.107880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022]
Abstract
Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.
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30
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Levitz TS, Weckener M, Fong I, Naismith JH, Drennan CL, Brignole EJ, Clare DK, Darrow MC. Approaches to Using the Chameleon: Robust, Automated, Fast-Plunge cryoEM Specimen Preparation. Front Mol Biosci 2022; 9:903148. [PMID: 35813832 PMCID: PMC9260054 DOI: 10.3389/fmolb.2022.903148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/31/2022] [Indexed: 01/21/2023] Open
Abstract
The specimen preparation process is a key determinant in the success of any cryo electron microscopy (cryoEM) structural study and until recently had remained largely unchanged from the initial designs of Jacques Dubochet and others in the 1980s. The process has transformed structural biology, but it is largely manual and can require extensive optimisation for each protein sample. The chameleon instrument with its self-wicking grids and fast-plunge freezing represents a shift towards a robust, automated, and highly controllable future for specimen preparation. However, these new technologies require new workflows and an understanding of their limitations and strengths. As early adopters of the chameleon technology, we report on our experiences and lessons learned through case studies. We use these to make recommendations for the benefit of future users of the chameleon system and the field of cryoEM specimen preparation generally.
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Affiliation(s)
- Talya S. Levitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, United Kingdom,Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ivan Fong
- SPT Labtech, Melbourn, United Kingdom
| | - James H. Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, United Kingdom,Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Edward J. Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States,MIT.nano, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Daniel K. Clare
- Diamond Light Source Ltd., Harwell Science Campus, Didcot, United Kingdom
| | - Michele C. Darrow
- SPT Labtech, Melbourn, United Kingdom,Artificial Intelligence and Informatics, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, United Kingdom,*Correspondence: Michele C. Darrow,
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31
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Okolo CA. A guide into the world of high-resolution 3D imaging: the case of soft X-ray tomography for the life sciences. Biochem Soc Trans 2022; 50:649-663. [PMID: 35257156 PMCID: PMC9162464 DOI: 10.1042/bst20210886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/27/2022]
Abstract
In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.
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Affiliation(s)
- Chidinma Adanna Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
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32
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Liedtke J, Depelteau JS, Briegel A. How advances in cryo-electron tomography have contributed to our current view of bacterial cell biology. J Struct Biol X 2022; 6:100065. [PMID: 35252838 PMCID: PMC8894267 DOI: 10.1016/j.yjsbx.2022.100065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Advancements in the field of cryo-electron tomography have greatly contributed to our current understanding of prokaryotic cell organization and revealed intracellular structures with remarkable architecture. In this review, we present some of the prominent advancements in cryo-electron tomography, illustrated by a subset of structural examples to demonstrate the power of the technique. More specifically, we focus on technical advances in automation of data collection and processing, sample thinning approaches, correlative cryo-light and electron microscopy, and sub-tomogram averaging methods. In turn, each of these advances enabled new insights into bacterial cell architecture, cell cycle progression, and the structure and function of molecular machines. Taken together, these significant advances within the cryo-electron tomography workflow have led to a greater understanding of prokaryotic biology. The advances made the technique available to a wider audience and more biological questions and provide the basis for continued advances in the near future.
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Affiliation(s)
- Janine Liedtke
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jamie S Depelteau
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ariane Briegel
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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33
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Ahn E, Tang T, Kim B, Lee HJ, Cho US. Development of an atmospheric plasma jet device for versatile treatment of electron microscope sample grids. J Biol Chem 2022; 298:101793. [PMID: 35248533 PMCID: PMC8980800 DOI: 10.1016/j.jbc.2022.101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/26/2022] Open
Abstract
Atmospheric-pressure plasmas have been widely applied for surface modification and biomedical treatment because of their ability to generate highly reactive radicals and charged particles. In negative-stain electron microscopy (Neg-EM) and cryogenic electron microscopy (cryo-EM), plasmas have been used to generate hydrophilic surfaces and eliminate surface contaminants to embed specimens onto grids. In addition, plasma treatment is a prerequisite for negative-stain and Quantifoil grids, whose surfaces are coated with hydrophobic amorphous carbon. Although the conventional glow discharge system has been used successfully in this purpose, there has been no further effort to take an advantage from the recent progress in the plasma field. Here, we developed a nonthermal atmospheric plasma jet system as an alternative tool for treatment of surfaces. The low-temperature plasma is a nonequilibrium system that has been widely used in biomedical area. Unlike conventional glow discharge systems, the plasma jet system successfully cleans and introduces hydrophilicity on the grid surface in the ambient environment without a vacuum. Therefore, we anticipate that the plasma jet system will have numerous benefits, such as convenience and versatility, as well as having potential applications in surface modification for both negative-stain and cryo-EM grid treatment.
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Affiliation(s)
- Eungjin Ahn
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Tianyu Tang
- Department of Electrical and Computer Engineering, Pusan National University, Busan 46241, South Korea
| | - Byungchul Kim
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hae June Lee
- Department of Electrical and Computer Engineering, Pusan National University, Busan 46241, South Korea
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
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34
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Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
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Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
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35
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Cho DH, Xie T, Mulcahey PJ, Kelleher NP, Hahm JI. Distinctive Adsorption Mechanism and Kinetics of Immunoglobulin G on a Nanoscale Polymer Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1458-1470. [PMID: 35037456 DOI: 10.1021/acs.langmuir.1c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Elucidation of protein adsorption beyond simple polymer surfaces to those presenting greater chemical complexity and nanoscopic features is critical to developing well-controlled nanobiomaterials and nanobiosensors. In this study, we repeatedly and faithfully track individual proteins on the same nanodomain areas of a block copolymer (BCP) surface and monitor the adsorption and assembly behavior of a model protein, immunoglobulin G (IgG), over time into a tight surface-packed structure. With discrete protein adsorption events unambiguously visualized at the biomolecular level, the detailed assembly and packing states of IgG on the BCP nanodomain surface are subsequently correlated to various regimes of IgG adsorption kinetic plots. Intriguing features, entirely different from those observed from macroscopic homopolymer templates, are identified from the IgG adsorption isotherms on the nanoscale, chemically varying BCP surface. They include the presence of two Langmuir-like adsorption segments and a nonmonotonic regime in the adsorption plot. Via correlation to time-corresponding topographic data, the unique isotherm features are explained with single biomolecule level details of the IgG adsorption pathway on the BCP. This work not only provides much needed, direct experimental evidence for time-resolved, single protein level, adsorption events on nanoscale polymer surfaces but also signifies mutual linking between specific topographic states of protein adsorption and assembly to particular segments of adsorption isotherms. From the fundamental research viewpoint, the correlative ability to examine the nanoscopic surface organizations of individual proteins and their local as well as global adsorption kinetic profiles will be highly valuable for accurately determining protein assembly mechanisms and interpreting protein adsorption kinetics on nanoscale surfaces. Application-wise, such knowledge will also be important for fundamentally guiding the design and development of biomaterials and biomedical devices that exploit nanoscale polymer architectures.
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Affiliation(s)
- David H Cho
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Tian Xie
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Patrick J Mulcahey
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Noah P Kelleher
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Jong-In Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
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36
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Pilsl M, Heiss FB, Pöll G, Höcherl M, Milkereit P, Engel C. Preparation of RNA Polymerase Complexes for Their Analysis by Single-Particle Cryo-Electron Microscopy. Methods Mol Biol 2022; 2533:81-96. [PMID: 35796984 PMCID: PMC9761500 DOI: 10.1007/978-1-0716-2501-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent technological progress revealed new prospects of high-resolution structure determination of macromolecular complexes using cryo-electron microscopy (cryo-EM) . In the field of RNA polymerase (Pol) I research, a number of cryo-EM studies contributed to understanding the highly specialized mechanisms underlying the transcription of ribosomal RNA genes . Despite a broad applicability of the cryo-EM method itself, preparation of samples for high-resolution data collection can be challenging. Here, we describe strategies for the purification and stabilization of Pol I complexes, exemplarily considering advantages and disadvantages of the methodology. We further provide an easy-to-implement protocol for the coating of EM-grids with self-made carbon support films. In sum, we present an efficient workflow for cryo-grid preparation and optimization, including early stage cryo-EM screening that can be adapted to a wide range of soluble samples for high-resolution structure determination .
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Affiliation(s)
- Michael Pilsl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Florian B Heiss
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Mona Höcherl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany.
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37
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Wood DM, Dobson RC, Horne CR. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Biochem Soc Trans 2021; 49:2711-2726. [PMID: 34854920 PMCID: PMC8786299 DOI: 10.1042/bst20210674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
Abstract
Transcription is the principal control point for bacterial gene expression, and it enables a global cellular response to an intracellular or environmental trigger. Transcriptional regulation is orchestrated by transcription factors, which activate or repress transcription of target genes by modulating the activity of RNA polymerase. Dissecting the nature and precise choreography of these interactions is essential for developing a molecular understanding of transcriptional regulation. While the contribution of X-ray crystallography has been invaluable, the 'resolution revolution' of cryo-electron microscopy has transformed our structural investigations, enabling large, dynamic and often transient transcription complexes to be resolved that in many cases had resisted crystallisation. In this review, we highlight the impact cryo-electron microscopy has had in gaining a deeper understanding of transcriptional regulation in bacteria. We also provide readers working within the field with an overview of the recent innovations available for cryo-electron microscopy sample preparation and image reconstruction of transcription complexes.
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Affiliation(s)
- David M. Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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38
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Lei C, Wang YH, Zhuang PX, Li YT, Wan QQ, Ma YX, Tay FR, Niu LN. Applications of Cryogenic Electron Microscopy in Biomineralization Research. J Dent Res 2021; 101:505-514. [PMID: 34918556 DOI: 10.1177/00220345211053814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biological mineralization is a natural process manifested by living organisms in which inorganic minerals crystallize under the scrupulous control of biomolecules, producing hierarchical organic-inorganic composite structures with physical properties and design that galvanize even the most ardent structural engineer and architect. Understanding the mechanisms that control the formation of biominerals is challenging in the biomimetic engineering of hard tissues. In this regard, the contribution of cryogenic electron microscopy (cryo-EM) has been nothing short of phenomenal. By preserving materials in their native hydrated status and reducing damage caused by ion beam radiation, cryo-EM outperforms conventional transmission electron microscopy in its ability to directly observe the morphologic evolution of mineral precursor phases at different stages of biomineralization with nanoscale spatial resolution and subsecond temporal resolution in 2 or 3 dimensions. In the present review, the development and applications of cryo-EM are discussed to support the use of this powerful technique in dental research. Because of the rapid development of cryogenic sample preparation techniques, direct electron detection, and image-processing algorithms, the last decade has witnessed an exponential increase in the use of cryo-EM in structural biology and materials research. By amalgamating with other analytic techniques, cryo-EM may be used for qualitative and quantitative analyses of the kinetics and thermodynamic mechanisms in which organic macromolecules participate in the transformation of mineral precursors from their original liquid state to amorphous and ultimately crystalline phases. The present review concentrates on the biomineralization of calcium phosphate mineral phases, while that of calcium carbonate, silica, and magnetite is only briefly mentioned. Bioinspired organic matrix-mediated inorganic crystallization strategies are discussed from the perspective of tissue regeneration engineering.
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Affiliation(s)
- C Lei
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - Y H Wang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - P X Zhuang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - Y T Li
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - Q Q Wan
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - Y X Ma
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - F R Tay
- The Graduate School, Augusta University, Augusta, GA, USA
| | - L N Niu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Key Laboratory of Stomatology, School of Stomatology, the Fourth Military Medical University, Xi'an, China
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39
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Grover A, Sinha R, Jyoti D, Faggio C. Imperative role of electron microscopy in toxicity assessment: A review. Microsc Res Tech 2021; 85:1976-1989. [PMID: 34904321 DOI: 10.1002/jemt.24029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
Electron microscope (EM) was developed in 1931 and since then microscopical examination of both the biological and non-biological samples has been revolutionized. Modifications in electron microscopy techniques, such as scanning EM and transmission EM, have widened their applicability in the various sectors such as understanding of drug toxicity, development of mechanism, criminal site investigation, and characterization of the nano-molecule. The present review summarizes its role in important aspects such as toxicity assessment and disease diagnosis in special reference to SARS-COV2. In the biological system, EM studies have elucidated the impact of toxicants at the ultra-structural level in various tissue in conformity to physiological alterations. Thus, EM can be concluded as an important tool in toxicity assessment and disease prognosis.
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Affiliation(s)
- Aseem Grover
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Reshma Sinha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Divya Jyoti
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
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40
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Pitz ME, Nukovic AM, Elpers MA, Alexander-Bryant AA. Factors Affecting Secondary and Supramolecular Structures of Self-Assembling Peptide Nanocarriers. Macromol Biosci 2021; 22:e2100347. [PMID: 34800001 DOI: 10.1002/mabi.202100347] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Indexed: 01/12/2023]
Abstract
Self-assembling peptides are a popular vector for therapeutic cargo delivery due to their versatility, tunability, and biocompatibility. Accurately predicting secondary and supramolecular structures of self-assembling peptides is essential for de novo peptide design. However, computational modeling of such assemblies is not yet able to accurately predict structure formation for many peptide sequences. This review identifies patterns in literature between secondary and supramolecular structures, primary sequences, and applications to provide a guide for informed peptide design. An overview of peptide structures, their applications as nanocarriers, and analytical methods for characterizing secondary and supramolecular structure is examined. A top-down approach is then used to identify trends between peptide sequence and assembly structure from the current literature, including an analysis of the drivers at work, such as local and nonlocal sequence effects and solution conditions.
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Affiliation(s)
- Megan E Pitz
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Alexandra M Nukovic
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Margaret A Elpers
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Angela A Alexander-Bryant
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
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41
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Parkhurst JM, Dumoux M, Basham M, Clare D, Siebert CA, Varslot T, Kirkland A, Naismith JH, Evans G. Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography. Open Biol 2021; 11:210160. [PMID: 34699732 PMCID: PMC8548082 DOI: 10.1098/rsob.210160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.
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Affiliation(s)
- James M. Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - C. Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Trond Varslot
- Thermo Fisher Scientific, Vlastimila Pecha, Brno, Czech Republic
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Electron Physical Science Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK,Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - James H. Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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42
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Tsegaye S, Dedefo G, Mehdi M. Biophysical applications in structural and molecular biology. Biol Chem 2021; 402:1155-1177. [PMID: 34218543 DOI: 10.1515/hsz-2021-0232] [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: 04/15/2021] [Accepted: 05/27/2021] [Indexed: 11/15/2022]
Abstract
The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn't be solved by X-ray crystallography or NMR. Now a day's low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.
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Affiliation(s)
- Solomon Tsegaye
- Department of Biochemistry, College of Health Sciences, Arsi University, Oromia, Ethiopia
| | - Gobena Dedefo
- Department of Medical Laboratory Technology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mohammed Mehdi
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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43
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Harnden KA, Roy A, Hosseinzadeh P. Overview of Methods for Purification and Characterization of Metalloproteins. Curr Protoc 2021; 1:e234. [PMID: 34436821 DOI: 10.1002/cpz1.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metalloproteins make up one third of all proteins and perform some of the most essential reactions on earth. The unique properties of the metal ions within these proteins, and in particular of redox-active metal ions, enables the use of a number of characterization techniques. It also necessitates unique considerations in terms of purification and characterization. In this overview, we describe the considerations and methods used for metalloprotein purification and characterization. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
| | - Anindya Roy
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, Washington
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44
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SSA: Subset sum approach to protein β-sheet structure prediction. Comput Biol Chem 2021; 94:107552. [PMID: 34390958 DOI: 10.1016/j.compbiolchem.2021.107552] [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: 04/25/2020] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 11/22/2022]
Abstract
The three-dimensional structures of proteins provide their functions and incorrect folding of its β-strands can be the cause of many diseases. There are two major approaches for determining protein structures: computational prediction and experimental methods that employ technologies such as Cryo-electron microscopy. Due to experimental methods's high costs, extended wait times for its lengthy processes, and incompleteness of results, computational prediction is an attractive alternative. As the focus of the present paper, β-sheet structure prediction is a major portion of overall protein structure prediction. Prediction of other substructures, such as α-helices, is simpler with lower computational time complexities. Brute force methods are the most common approach and dynamic programming is also utilized to generate all possible conformations. The current study introduces the Subset Sum Approach (SSA) for the direct search space generation method, which is shown to outperform the dynamic programming approach in terms of both time and space. For the first time, the present work has calculated both the state space cardinality of the dynamic programming approach and the search space cardinality of the general brute force approaches. In regard to a set of pruning rules, SSA has demonstrated higher efficiency with respect to both time and accuracy in comparison to state-of-the-art methods.
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45
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Abstract
The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.
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Affiliation(s)
- Xuelang Mu
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA; .,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles, California 90095, USA
| | - Cody Gillman
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA; .,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles, California 90095, USA
| | - Chi Nguyen
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA;
| | - Tamir Gonen
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA; .,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles, California 90095, USA
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46
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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47
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Weng J, Xiang X, Ding L, Wong ALA, Zeng Q, Sethi G, Wang L, Lee SC, Goh BC. Extracellular vesicles, the cornerstone of next-generation cancer diagnosis? Semin Cancer Biol 2021; 74:105-120. [PMID: 33989735 DOI: 10.1016/j.semcancer.2021.05.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022]
Abstract
Cancer has risen up to be a major cause of mortality worldwide over the past decades. Despite advancements in cancer screening and diagnostics, a significant number of cancers are still diagnosed at a late stage with poor prognosis. Hence, the discovery of reliable and accurate methods to diagnose cancer early would be of great help in reducing cancer mortality. Extracellular vesicles (EVs) are phospholipid vesicles found in many biofluids and are released by almost all types of cells. In recent years, using EVs as cancer biomarkers has garnered attention as a novel technique of cancer diagnosis. Compared with traditional tissue biopsy, there are many advantages that this novel diagnostic tool presents - it is less invasive, detects early-stage asymptomatic cancers, and allows for monitoring of tumour progression. As such, EV biomarkers have great potential in improving the diagnostic accuracy of cancers and guiding subsequent therapeutic decisions. Efficient isolation and accurate characterization of EVs are essential for reliable outcomes of clinical application. However, these are complicated by the size and biomolecular diversity of EVs. In this review, we present an analysis and evaluation of the current techniques of EV isolation and characterization, as well as discuss the potential EV biomarkers for specific types of cancer. Taken together, EV biomarkers have a lot of potential as a novel method in cancer diagnostics and diagnosis. However, more work is still needed to streamline the purification, characterization and biomarker identification process to ensure optimal outcomes for patients.
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Affiliation(s)
- Jiayi Weng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Xiaoqiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai 20203, China
| | - Lingwen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andrea Li-Ann Wong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore 119228, Singapore
| | - Qi Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Soo Chin Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore 119228, Singapore.
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore 119228, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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48
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Weissenberger G, Henderikx RJM, Peters PJ. Understanding the invisible hands of sample preparation for cryo-EM. Nat Methods 2021; 18:463-471. [PMID: 33963356 DOI: 10.1038/s41592-021-01130-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is rapidly becoming an attractive method in the field of structural biology. With the exploding popularity of cryo-EM, sample preparation must evolve to prevent congestion in the workflow. The dire need for improved microscopy samples has led to a diversification of methods. This Review aims to categorize and explain the principles behind various techniques in the preparation of vitrified samples for the electron microscope. Various aspects and challenges in the workflow are discussed, from sample optimization and carriers to deposition and vitrification. Reliable and versatile specimen preparation remains a challenge, and we hope to give guidelines and posit future directions for improvement.
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Affiliation(s)
- Giulia Weissenberger
- CryoSol-World, Maastricht, the Netherlands.,Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Rene J M Henderikx
- CryoSol-World, Maastricht, the Netherlands.,Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands.
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49
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Casasanta MA, Jonaid GM, Kaylor L, Luqiu WY, Solares MJ, Schroen ML, Dearnaley WJ, Wilson J, Dukes MJ, Kelly DF. Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy. NANOSCALE 2021; 13:7285-7293. [PMID: 33889923 PMCID: PMC8135184 DOI: 10.1039/d1nr00388g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Interest in cryo-Electron Microscopy (EM) imaging has skyrocketed in recent years due to its pristine views of macromolecules and materials. As advances in instrumentation and computing algorithms spurred this progress, there is renewed focus to address specimen-related challenges. Here we contribute a microchip-based toolkit to perform complementary structural and biochemical analysis on low-molecular weight proteins. As a model system, we used the SARS-CoV-2 nucleocapsid (N) protein (48 kDa) due to its stability and important role in therapeutic development. Cryo-EM structures of the N protein monomer revealed a flexible N-terminal "top hat" motif and a helical-rich C-terminal domain. To complement our structural findings, we engineered microchip-based immunoprecipitation assays that led to the discovery of the first antibody binding site on the N protein. The data also facilitated molecular modeling of a variety of pandemic and common cold-related coronavirus proteins. Such insights may guide future pandemic-preparedness protocols through immuno-engineering strategies to mitigate viral outbreaks.
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Affiliation(s)
- Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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50
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Nguyen HT, O’Donovan LA, Venter H, Russell CC, McCluskey A, Page SW, Trott DJ, Ogunniyi AD. Comparison of Two Transmission Electron Microscopy Methods to Visualize Drug-Induced Alterations of Gram-Negative Bacterial Morphology. Antibiotics (Basel) 2021; 10:307. [PMID: 33802844 PMCID: PMC8002630 DOI: 10.3390/antibiotics10030307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/16/2023] Open
Abstract
In this study, we optimized and compared different transmission electron microscopy (TEM) methods to visualize changes to Gram-negative bacterial morphology induced by treatment with a robenidine analogue (NCL195) and colistin combination. Aldehyde-fixed bacterial cells (untreated, treated with colistin or NCL195 + colistin) were prepared using conventional TEM methods and compared with ultrathin Tokuyasu cryo-sections. The results of this study indicate superiority of ultrathin cryo-sections in visualizing the membrane ultrastructure of Escherichia coli and Pseudomonas aeruginosa, with a clear delineation of the outer and inner membrane as well as the peptidoglycan layer. We suggest that the use of ultrathin cryo-sectioning can be used to better visualize and understand drug interaction mechanisms on the bacterial cell membrane.
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Affiliation(s)
- Hang Thi Nguyen
- Australia Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, SA 5371, Australia;
- Department of Pharmacology, Toxicology, Internal Medicine and Diagnostics, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam
| | - Lisa A. O’Donovan
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture Food & Wine, Waite Campus, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia;
| | - Cecilia C. Russell
- Chemistry School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; (C.C.R.); (A.M.)
| | - Adam McCluskey
- Chemistry School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; (C.C.R.); (A.M.)
| | | | - Darren J. Trott
- Australia Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, SA 5371, Australia;
| | - Abiodun D. Ogunniyi
- Australia Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, SA 5371, Australia;
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