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Kapoor KS, Kong S, Sugimoto H, Guo W, Boominathan V, Chen YL, Biswal SL, Terlier T, McAndrews KM, Kalluri R. Single Extracellular Vesicle Imaging and Computational Analysis Identifies Inherent Architectural Heterogeneity. ACS NANO 2024; 18:11717-11731. [PMID: 38651873 DOI: 10.1021/acsnano.3c12556] [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: 04/25/2024]
Abstract
Evaluating the heterogeneity of extracellular vesicles (EVs) is crucial for unraveling their complex actions and biodistribution. Here, we identify consistent architectural heterogeneity of EVs using cryogenic transmission electron microscopy (cryo-TEM), which has an inherent ability to image biological samples without harsh labeling methods while preserving their native conformation. Imaging EVs isolated using different methodologies from distinct sources, such as cancer cells, normal cells, immortalized cells, and body fluids, we identify a structural atlas of their dominantly consistent shapes. We identify EV architectural attributes by utilizing a segmentation neural network model. In total, 7,576 individual EVs were imaged and quantified by our computational pipeline. Across all 7,576 independent EVs, the average eccentricity was 0.5366 ± 0.2, and the average equivalent diameter was 132.43 ± 67 nm. The architectural heterogeneity was consistent across all sources of EVs, independent of purification techniques, and compromised of single spherical, rod-like or tubular, and double shapes. This study will serve as a reference foundation for high-resolution images of EVs and offer insights into their potential biological impact.
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Affiliation(s)
- Kshipra S Kapoor
- Department of Cancer Biology and Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Seoyun Kong
- Department of Cancer Biology and Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Hikaru Sugimoto
- Department of Cancer Biology and Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Wenhua Guo
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Vivek Boominathan
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Yi-Lin Chen
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Sibani Lisa Biswal
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Tanguy Terlier
- SIMS Laboratory, Shared Equipment Authority, Rice University, Houston, Texas 77005, United States
| | - Kathleen M McAndrews
- Department of Cancer Biology and Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Raghu Kalluri
- Department of Cancer Biology and Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
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2
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Kapoor KS, Kong S, Sugimoto H, Guo W, Boominathan V, Chen YL, Biswal SL, Terlier T, McAndrews KM, Kalluri R. Single extracellular vesicle imaging and computational analysis identifies inherent architectural heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571132. [PMID: 38168235 PMCID: PMC10760062 DOI: 10.1101/2023.12.11.571132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Evaluating the heterogeneity of extracellular vesicles (EVs) is crucial for unraveling their complex actions and biodistribution. Here, we identify consistent architectural heterogeneity of EVs using cryogenic transmission electron microscopy (cryo-TEM) which has an inherent ability to image biological samples without harsh labeling methods and while preserving their native conformation. Imaging EVs isolated using different methodologies from distinct sources such as cancer cells, normal cells, and body fluids, we identify a structural atlas of their dominantly consistent shapes. We identify EV architectural attributes by utilizing a segmentation neural network model. In total, 7,576 individual EVs were imaged and quantified by our computational pipeline. Across all 7,576 independent EVs, the average eccentricity was 0.5366, and the average equivalent diameter was 132.43 nm. The architectural heterogeneity was consistent across all sources of EVs, independent of purification techniques, and compromised of single spherical (S. Spherical), rod-like or tubular, and double shapes. This study will serve as a reference foundation for high-resolution EV images and offer insights into their potential biological impact.
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3
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Brodmerkel MN, De Santis E, Caleman C, Marklund EG. Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration. Protein J 2023:10.1007/s10930-023-10110-y. [PMID: 37031302 DOI: 10.1007/s10930-023-10110-y] [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] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our findings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray diffraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
- Department of Physics and Astronomy, Uppsala University, 75120, Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120, Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden.
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4
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Boiko DA, Kashin AS, Sorokin VR, Agaev YV, Zaytsev RG, Ananikov VP. Analyzing ionic liquid systems using real-time electron microscopy and a computational framework combining deep learning and classic computer vision techniques. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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5
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Las Heras K, Royo F, Garcia-Vallicrosa C, Igartua M, Santos-Vizcaino E, Falcon-Perez JM, Hernandez RM. Extracellular vesicles from hair follicle-derived mesenchymal stromal cells: isolation, characterization and therapeutic potential for chronic wound healing. Stem Cell Res Ther 2022; 13:147. [PMID: 35395929 PMCID: PMC8994406 DOI: 10.1186/s13287-022-02824-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) and their extracellular vesicles (MSC-EVs) have demonstrated to elicit immunomodulatory and pro-regenerative properties that are beneficial for the treatment of chronic wounds. Thanks to different mediators, MSC-EVs have shown to play an important role in the proliferation, migration and cell survival of different skin cell populations. However, there is still a big bid to achieve the most effective, suitable and available source of MSC-EVs. METHODS We isolated, characterized and compared medium-large EVs (m-lEVs) and small EVs (sEVs) obtained from hair follicle-derived MSCs (HF-MSCs) against the gold standard in regenerative medicine, EVs isolated from adipose tissue-derived MSCs (AT-MSCs). RESULTS We demonstrated that HF-EVs, as well as AT-EVs, expressed typical MSC-EVs markers (CD9, CD44, CD63, CD81 and CD105) among other different functional markers. We showed that both cell types were able to increase human dermal fibroblasts (HDFs) proliferation and migration. Moreover, both MSC-EVs were able to increase angiogenesis in human umbilical vein endothelial cells (HUVECs) and protect HDFs exposed to a hyperglycemic environment from oxidative stress and cytotoxicity. CONCLUSIONS Taken together, HF-EVs demonstrated to exhibit comparable potential to that of AT-EVs as promising candidates in the treatment of chronic wounds.
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Affiliation(s)
- Kevin Las Heras
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy (UPV/EHU), 01006, Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain
| | - Félix Royo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Exosomes Laboratory, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), 28029, Madrid, Spain
| | - Clara Garcia-Vallicrosa
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Exosomes Laboratory, 48160, Derio, Spain
| | - Manoli Igartua
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy (UPV/EHU), 01006, Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain
| | - Edorta Santos-Vizcaino
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy (UPV/EHU), 01006, Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain
| | - Juan M Falcon-Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Exosomes Laboratory, 48160, Derio, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), 28029, Madrid, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| | - Rosa Maria Hernandez
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy (UPV/EHU), 01006, Vitoria-Gasteiz, Spain.
- Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain.
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain.
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Abstract
Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.
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Affiliation(s)
| | - Natalia Szulc
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
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Klaholz BP. Studying the Structural Organization of Polyribosomes with Alexander S. Spirin. BIOCHEMISTRY (MOSCOW) 2021; 86:1053-1059. [PMID: 34565311 DOI: 10.1134/s0006297921090030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
"Would it be possible to analyze molecular mechanisms and structural organisation of polyribosome assemblies using cryo electron tomography?" - we asked through a longstanding collaboration between my research group and that of Alexander S. Spirin. Indeed, it was: we found that double-row polyribosomes can have both circular and linear arrangements of their mRNA [Afonina, Z. A., et al. (2013) Biochemistry (Moscow)], we figured out how eukaryotic ribosomes assemble on an mRNA to form supramolecular left-handed helices [Myasnikov, A. G., et al. (2014) Nat. Commun.], that the circularization of polyribosomes is poly-A and cap-independent [Afonina, Z. A., et al. (2014) Nucleic Acids Res.], and that intermediary polyribosomes with open structures exist after a transition from a juvenile phase to strongly translating polysomes of medium size [Afonina, Z. A., et al. (2015) Nucleic Acids Res.] until they form densely packed helical structures with reduced activity. Our joint fruitful exchanges, hence, led to major advances in the field, which are reviewed here from a personal and historical perspective in memory of Alexander S. Spirin.
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Affiliation(s)
- Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, 67404, France. .,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, 67404, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, 67404, France.,Université de Strasbourg, Strasbourg, 67081, France
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8
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Rizzo J, Wong SSW, Gazi AD, Moyrand F, Chaze T, Commere P, Novault S, Matondo M, Péhau‐Arnaudet G, Reis FCG, Vos M, Alves LR, May RC, Nimrichter L, Rodrigues ML, Aimanianda V, Janbon G. Cryptococcus extracellular vesicles properties and their use as vaccine platforms. J Extracell Vesicles 2021; 10:e12129. [PMID: 34377375 PMCID: PMC8329992 DOI: 10.1002/jev2.12129] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Whereas extracellular vesicle (EV) research has become commonplace in different biomedical fields, this field of research is still in its infancy in mycology. Here we provide a robust set of data regarding the structural and compositional aspects of EVs isolated from the fungal pathogenic species Cryptococcus neoformans, C. deneoformans and C. deuterogattii. Using cutting-edge methodological approaches including cryogenic electron microscopy and cryogenic electron tomography, proteomics, and flow cytometry, we revisited cryptococcal EV features and suggest a new EV structural model, in which the vesicular lipid bilayer is covered by mannoprotein-based fibrillar decoration, bearing the capsule polysaccharide as its outer layer. About 10% of the EV population is devoid of fibrillar decoration, adding another aspect to EV diversity. By analysing EV protein cargo from the three species, we characterized the typical Cryptococcus EV proteome. It contains several membrane-bound protein families, including some Tsh proteins bearing a SUR7/PalI motif. The presence of known protective antigens on the surface of Cryptococcus EVs, resembling the morphology of encapsulated virus structures, suggested their potential as a vaccine. Indeed, mice immunized with EVs obtained from an acapsular C. neoformans mutant strain rendered a strong antibody response in mice and significantly prolonged their survival upon C. neoformans infection.
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Affiliation(s)
- Juliana Rizzo
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Sarah Sze Wah Wong
- Unité Mycologie Moléculaire, CNRS UMR2000Département de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Anastasia D. Gazi
- Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015ParisFrance
| | - Frédérique Moyrand
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Thibault Chaze
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Pierre‐Henri Commere
- Cytometry and BiomarkersCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Sophie Novault
- Cytometry and BiomarkersCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour la Biologie (MSBio), CNRS UMR 2000Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | - Gérard Péhau‐Arnaudet
- Ultrastructural Bio‐Imaging, UTechS UBI, CNRS UMR 3528Département de Biologie cellulaire et infection, Institut Pasteur, F‐75015ParisFrance
| | - Flavia C. G. Reis
- Instituto Carlos ChagasFundação Oswaldo Cruz (FIOCRUZ)CuritibaBrazil
- Centro de Desenvolvimento Tecnologico em Saude (CDTS‐Fiocruz)São PauloBrazil
| | - Matthijn Vos
- NanoImaging Core FacilityCentre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F‐75015ParisFrance
| | | | - Robin C. May
- Institute of Microbiology and Infection and School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG)Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Marcio L. Rodrigues
- Instituto Carlos ChagasFundação Oswaldo Cruz (FIOCRUZ)CuritibaBrazil
- Instituto de Microbiologia Paulo de Góes (IMPG)Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Vishukumar Aimanianda
- Unité Mycologie Moléculaire, CNRS UMR2000Département de Mycologie, Institut Pasteur, F‐75015ParisFrance
| | - Guilhem Janbon
- Unité Biologie des ARN des Pathogènes FongiquesDépartement de Mycologie, Institut Pasteur, F‐75015ParisFrance
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9
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Bordanaba-Florit G, Royo F, Kruglik SG, Falcón-Pérez JM. Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles. Nat Protoc 2021; 16:3163-3185. [PMID: 34135505 DOI: 10.1038/s41596-021-00551-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.
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Affiliation(s)
- Guillermo Bordanaba-Florit
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - Félix Royo
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Paris, France
| | - Juan M Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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10
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Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PLoS Biol 2021; 19:e3001207. [PMID: 33909605 PMCID: PMC8110273 DOI: 10.1371/journal.pbio.3001207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 05/10/2021] [Accepted: 03/26/2021] [Indexed: 12/27/2022] Open
Abstract
Missense variants are present amongst the healthy population, but some of them are causative of human diseases. A classification of variants associated with “healthy” or “diseased” states is therefore not always straightforward. A deeper understanding of the nature of missense variants in health and disease, the cellular processes they may affect, and the general molecular principles which underlie these differences is essential to offer mechanistic explanations of the true impact of pathogenic variants. Here, we have formalised a statistical framework which enables robust probabilistic quantification of variant enrichment across full-length proteins, their domains, and 3D structure-defined regions. Using this framework, we validate and extend previously reported trends of variant enrichment in different protein structural regions (surface/core/interface). By examining the association of variant enrichment with available functional pathways and transcriptomic and proteomic (protein half-life, thermal stability, abundance) data, we have mined a rich set of molecular features which distinguish between pathogenic and population variants: Pathogenic variants mainly affect proteins involved in cell proliferation and nucleotide processing and are enriched in more abundant proteins. Additionally, rare population variants display features closer to common than pathogenic variants. We validate the association between these molecular features and variant pathogenicity by comparing against existing in silico variant impact annotations. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants and provides the rationale to prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. The ZoomVar database, which we created for this study, is available at fraternalilab.kcl.ac.uk/ZoomVar. It allows users to programmatically annotate missense variants with protein structural information and to calculate variant enrichment in different protein structural regions. How do can one improve the classification of genetic variants as harmful or harmless? This study uses a robust statistical analysis to exploit the interplay between protein structure, proteomic measurements and functional pathways to enable better discrimination between missense variants in health and disease.
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11
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Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg 2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps. Acta Crystallogr D Struct Biol 2021; 77:534-539. [PMID: 33825713 PMCID: PMC8025889 DOI: 10.1107/s2059798321001893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
Cryo electron microscopy (cryo-EM) can produce maps of macromolecules that have resolutions that are sufficiently high that structural details such as chemical modifications, water molecules and bound metal ions can be discerned. However, those accustomed to interpreting the electron-density maps of macromolecules produced by X-ray crystallography need to be careful when assigning features such as these in cryo-EM maps because cations, for example, interact far more strongly with electrons than they do with X-rays. Using simulated electrostatic potential (ESP) maps as a tool led us to re-examine a recent cryo-EM map of the human ribosome, and we realized that some of the ESP peaks originally identified as novel groups covalently bonded to the N7, O6 or O4 atoms of several guanines, adenines or uridines, respectively, in this structure are likely to instead represent Mg2+ ions coordinated to these atoms, which provide only partial charge compensation compared with Mg2+ ions located next to phosphate groups. In addition, direct evidence is provided for a variation in the level of 2'-O ribose methylation of nucleotides in the human ribosome. ESP maps can thus help in identifying ions next to nucleotide bases, i.e. at positions that can be difficult to address in cryo-EM maps due to charge effects, which are specifically encountered in cryo-EM. This work is particularly relevant to nucleoprotein complexes and shows that it is important to consider charge effects when interpreting cryo-EM maps, thus opening possibilities for localizing charges in structures that may be relevant for enzymatic mechanisms and drug interactions.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - S. Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 Rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Peter B. Moore
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Bruno P. Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 Rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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12
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Tang X, Wippel HH, Chavez JD, Bruce JE. Crosslinking mass spectrometry: A link between structural biology and systems biology. Protein Sci 2021; 30:773-784. [PMID: 33594738 DOI: 10.1002/pro.4045] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
Protein structure underpins functional roles in all biological processes; therefore, improved understanding of protein structures is of fundamental importance in nearly all biological and biomedical research areas. Traditional techniques such as X-ray crystallography and more recently, cryo-EM, can reveal structural features on isolated proteins/protein complexes at atomic resolution level and have become indispensable tools for structural biology. Crosslinking mass spectrometry (XL-MS), on the other hand, is an emerging technique capable of capturing transient and dynamic information on protein interactions and assemblies in their native environment. The combination of XL-MS with traditional techniques holds potential for bridging the gap between structural biology and systems biology approaches. Such a combination will enable visualization of protein structures and interactions within the crowded macromolecular environment in living systems that can dramatically increase understanding of biological functions. In this review, we first discuss general strategies of XL-MS and then survey recent examples to show how qualitative and quantitative XL-MS studies can be integrated with available protein structural data to better understand biological function at systems level.
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Affiliation(s)
- Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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13
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Birnie A, Dekker C. Genome-in-a-Box: Building a Chromosome from the Bottom Up. ACS NANO 2021; 15:111-124. [PMID: 33347266 PMCID: PMC7844827 DOI: 10.1021/acsnano.0c07397] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/16/2020] [Indexed: 05/24/2023]
Abstract
Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce "genome-in-a-box" (GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.
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Affiliation(s)
- Anthony Birnie
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli
Institute of Nanoscience Delft, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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14
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Andronov L, Vonesch JL, Klaholz BP. Practical Aspects of Super-Resolution Imaging and Segmentation of Macromolecular Complexes by dSTORM. Methods Mol Biol 2021; 2247:271-286. [PMID: 33301123 DOI: 10.1007/978-1-0716-1126-5_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Super-resolution fluorescence microscopy allows imaging macromolecular complexes down to the nanoscopic scale and thus is a great tool to combine and integrate cellular imaging in the native cellular environment with structural analysis by X-ray crystallography or high-resolution cryo electron microscopy or tomography. Here we describe practical aspects of SMLM imaging by dSTORM, from the initial sample preparation using mounting media, antibodies and fluorescent markers, the experimental setup for data acquisition including multi-color colocalization and 3D data acquisition, and finally tips and clues on advanced data processing that includes image reconstruction and data segmentation using 2D or 3D clustering methods. This approach opens the path toward multi-resolution integration in cellular structural biology.
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Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France
| | - Jean-Luc Vonesch
- Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France.
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15
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Abstract
Microphysiological systems (MPS), often referred to as "organ-on-chips," are microfluidic-based in vitro models that aim to recapitulate the dynamic chemical and mechanical microenvironment of living organs. MPS promise to bridge the gap between in vitro and in vivo models and ultimately improve the translation from preclinical animal studies to clinical trials. However, despite the explosion of interest in this area in recent years, and the obvious rewards for such models that could improve R&D efficiency and reduce drug attrition in the clinic, the pharmaceutical industry has been slow to fully adopt this technology. The ability to extract robust, quantitative information from MPS at scale is a key requirement if these models are to impact drug discovery and the subsequent drug development process. Microscopy imaging remains a core technology that enables the capture of information at the single-cell level and with subcellular resolution. Furthermore, such imaging techniques can be automated, increasing throughput and enabling compound screening. In this review, we discuss a range of imaging techniques that have been applied to MPS of varying focus, such as organoids and organ-chip-type models. We outline the opportunities these technologies can bring in terms of understanding mechanistic biology, but also how they could be used in higher-throughput screens, widening the scope of their impact in drug discovery. We discuss the associated challenges of imaging these complex models and the steps required to enable full exploitation. Finally, we discuss the requirements for MPS, if they are to be applied at a scale necessary to support drug discovery projects.
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Affiliation(s)
- Samantha Peel
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Mark Jackman
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
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16
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Basanta B, Chowdhury S, Lander GC, Grotjahn DA. A guided approach for subtomogram averaging of challenging macromolecular assemblies. J Struct Biol X 2020; 4:100041. [PMID: 33319208 PMCID: PMC7724198 DOI: 10.1016/j.yjsbx.2020.100041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/13/2020] [Accepted: 11/18/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Saikat Chowdhury
- Department of Biochemistry and Cell Biology, 144 Center for Molecular Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
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17
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Wang L, Kruse H, Sobolev OV, Moriarty NW, Waller MP, Afonine PV, Biczysko M. Real-space quantum-based refinement for cryo-EM: Q|R#3. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1184-1191. [PMID: 33263324 DOI: 10.1107/s2059798320013194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/29/2020] [Indexed: 11/10/2022]
Abstract
Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.
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Affiliation(s)
- Lum Wang
- International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Oleg V Sobolev
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mark P Waller
- Pending AI Pty Ltd, iAccelerat, Innovation Campus, North Wollongong, NSW 2500, Australia
| | - Pavel V Afonine
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Malgorzata Biczysko
- International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
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18
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Murin CD. Considerations of Antibody Geometric Constraints on NK Cell Antibody Dependent Cellular Cytotoxicity. Front Immunol 2020; 11:1635. [PMID: 32849559 PMCID: PMC7406664 DOI: 10.3389/fimmu.2020.01635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
It has been well-established that antibody isotype, glycosylation, and epitope all play roles in the process of antibody dependent cellular cytotoxicity (ADCC). For natural killer (NK) cells, these phenotypes are linked to cellular activation through interaction with the IgG receptor FcγRIIIa, a single pass transmembrane receptor that participates in cytoplasmic signaling complexes. Therefore, it has been hypothesized that there may be underlying spatial and geometric principles that guide proper assembly of an activation complex within the NK cell immune synapse. Further, synergy of antibody phenotypic properties as well as allosteric changes upon antigen binding may also play an as-of-yet unknown role in ADCC. Understanding these facets, however, remains hampered by difficulties associated with studying immune synapse dynamics using classical approaches. In this review, I will discuss relevant NK cell biology related to ADCC, including the structural biology of Fc gamma receptors, and how the dynamics of the NK cell immune synapse are being studied using innovative microscopy techniques. I will provide examples from the literature demonstrating the effects of spatial and geometric constraints on the T cell receptor complex and how this relates to intracellular signaling and the molecular nature of lymphocyte activation complexes, including those of NK cells. Finally, I will examine how the integration of high-throughput and "omics" technologies will influence basic NK cell biology research moving forward. Overall, the goal of this review is to lay a basis for understanding the development of drugs and therapeutic antibodies aimed at augmenting appropriate NK cell ADCC activity in patients being treated for a wide range of illnesses.
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Affiliation(s)
- Charles D. Murin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, United States
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19
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Dodd T, Yan C, Ivanov I. Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy. J Chem Inf Model 2020; 60:2470-2483. [PMID: 32202798 DOI: 10.1021/acs.jcim.0c00087] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in cryoelectron microscopy (cryo-EM) have revolutionized the structural investigation of large macromolecular assemblies. In this review, we first provide a broad overview of modeling methods used for flexible fitting of molecular models into cryo-EM density maps. We give special attention to approaches rooted in molecular simulations-atomistic molecular dynamics and Monte Carlo. Concise descriptions of the methods are given along with discussion of their advantages, limitations, and most popular alternatives. We also describe recent extensions of the widely used molecular dynamics flexible fitting (MDFF) method and discuss how different model-building techniques could be incorporated into new hybrid modeling schemes and simulation workflows. Finally, we provide two illustrative examples of model-building and refinement strategies employing MDFF, cascade MDFF, and RosettaCM. These examples come from recent cryo-EM studies that elucidated transcription preinitiation complexes and shed light on the functional roles of these assemblies in gene expression and gene regulation.
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Affiliation(s)
- Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
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20
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Müh F, Zouni A. Structural basis of light-harvesting in the photosystem II core complex. Protein Sci 2020; 29:1090-1119. [PMID: 32067287 PMCID: PMC7184784 DOI: 10.1002/pro.3841] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.
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Affiliation(s)
- Frank Müh
- Department of Theoretical Biophysics, Institute for Theoretical Physics, Johannes Kepler University Linz, Linz, Austria
| | - Athina Zouni
- Humboldt-Universität zu Berlin, Institute for Biology, Biophysics of Photosynthesis, Berlin, Germany
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21
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Emelyanov A, Shtam T, Kamyshinsky R, Garaeva L, Verlov N, Miliukhina I, Kudrevatykh A, Gavrilov G, Zabrodskaya Y, Pchelina S, Konevega A. Cryo-electron microscopy of extracellular vesicles from cerebrospinal fluid. PLoS One 2020; 15:e0227949. [PMID: 31999742 PMCID: PMC6991974 DOI: 10.1371/journal.pone.0227949] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are membrane-enclosed vesicles which play important role for cell communication and physiology. EVs are found in many human biological fluids, including blood, breast milk, urine, cerebrospinal fluid (CSF), ejaculate, saliva etc. These nano-sized vesicles contain proteins, mRNAs, microRNAs, non-coding RNAs and lipids that are derived from producing cells. EVs deliver complex sets of biological information to recipient cells thereby modulating their behaviors by their molecular cargo. In this way EVs are involved in the pathological development and progression of many human disorders, including neurodegenerative diseases. In this study EVs purified by ultracentrifugation from CSF of patients with Parkinson's disease (PD) and individuals of the comparison group were characterized using nanoparticle tracking analysis, flow cytometry and cryo-electron microscopy. Vesicular size and the presence of exosomal marker CD9 on the surface provided evidence that most of the EVs were exosome-like vesicles. Cryo-electron microscopy allowed us to visualize a large spectrum of extracellular vesicles of various size and morphology with lipid bilayers and vesicular internal structures. Thus, we described the diversity and new characteristics of the vesicles from CSF suggesting that subpopulations of EVs with different and specific functions may exist.
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Affiliation(s)
- Anton Emelyanov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Tatiana Shtam
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Roman Kamyshinsky
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | - Luiza Garaeva
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Nikolai Verlov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Irina Miliukhina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
- Institute of Experimental Medicine, St. Petersburg, Russia
| | - Anastasia Kudrevatykh
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
- Institute of Experimental Medicine, St. Petersburg, Russia
| | - Gaspar Gavrilov
- S.M. Kirov Saint-Petersburg Military Medical Academy, St. Petersburg, Russia
| | - Yulia Zabrodskaya
- Polenov Neurosurgical Institute–Branch of National Almazov Medical Research Centre, St. Petersburg, Russia
| | - Sofya Pchelina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Institute of Experimental Medicine, St. Petersburg, Russia
| | - Andrey Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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22
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Detrimental and protective action of microglial extracellular vesicles on myelin lesions: astrocyte involvement in remyelination failure. Acta Neuropathol 2019; 138:987-1012. [PMID: 31363836 PMCID: PMC6851224 DOI: 10.1007/s00401-019-02049-1] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022]
Abstract
Microglia are highly plastic immune cells which exist in a continuum of activation states. By shaping the function of oligodendrocyte precursor cells (OPCs), the brain cells which differentiate to myelin-forming cells, microglia participate in both myelin injury and remyelination during multiple sclerosis. However, the mode(s) of action of microglia in supporting or inhibiting myelin repair is still largely unclear. Here, we analysed the effects of extracellular vesicles (EVs) produced in vitro by either pro-inflammatory or pro-regenerative microglia on OPCs at demyelinated lesions caused by lysolecithin injection in the mouse corpus callosum. Immunolabelling for myelin proteins and electron microscopy showed that EVs released by pro-inflammatory microglia blocked remyelination, whereas EVs produced by microglia co-cultured with immunosuppressive mesenchymal stem cells promoted OPC recruitment and myelin repair. The molecular mechanisms responsible for the harmful and beneficial EV actions were dissected in primary OPC cultures. By exposing OPCs, cultured either alone or with astrocytes, to inflammatory EVs, we observed a blockade of OPC maturation only in the presence of astrocytes, implicating these cells in remyelination failure. Biochemical fractionation revealed that astrocytes may be converted into harmful cells by the inflammatory EV cargo, as indicated by immunohistochemical and qPCR analyses, whereas surface lipid components of EVs promote OPC migration and/or differentiation, linking EV lipids to myelin repair. Although the mechanisms through which the lipid species enhance OPC maturation still remain to be fully defined, we provide the first demonstration that vesicular sphingosine 1 phosphate stimulates OPC migration, the first fundamental step in myelin repair. From this study, microglial EVs emerge as multimodal and multitarget signalling mediators able to influence both OPCs and astrocytes around myelin lesions, which may be exploited to develop novel approaches for myelin repair not only in multiple sclerosis, but also in neurological and neuropsychiatric diseases characterized by demyelination.
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23
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Special Issue: The Actin-Myosin Interaction in Muscle: Background and Overview. Int J Mol Sci 2019; 20:ijms20225715. [PMID: 31739584 PMCID: PMC6887992 DOI: 10.3390/ijms20225715] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
Muscular contraction is a fundamental phenomenon in all animals; without it life as we know it would be impossible. The basic mechanism in muscle, including heart muscle, involves the interaction of the protein filaments myosin and actin. Motility in all cells is also partly based on similar interactions of actin filaments with non-muscle myosins. Early studies of muscle contraction have informed later studies of these cellular actin-myosin systems. In muscles, projections on the myosin filaments, the so-called myosin heads or cross-bridges, interact with the nearby actin filaments and, in a mechanism powered by ATP-hydrolysis, they move the actin filaments past them in a kind of cyclic rowing action to produce the macroscopic muscular movements of which we are all aware. In this special issue the papers and reviews address different aspects of the actin-myosin interaction in muscle as studied by a plethora of complementary techniques. The present overview provides a brief and elementary introduction to muscle structure and function and the techniques used to study it. It goes on to give more detailed descriptions of what is known about muscle components and the cross-bridge cycle using structural biology techniques, particularly protein crystallography, electron microscopy and X-ray diffraction. It then has a quick look at muscle mechanics and it summarises what can be learnt about how muscle works based on the other studies covered in the different papers in the special issue. A picture emerges of the main molecular steps involved in the force-producing process; steps that are also likely to be seen in non-muscle myosin interactions with cellular actin filaments. Finally, the remarkable advances made in studying the effects of mutations in the contractile assembly in causing specific muscle diseases, particularly those in heart muscle, are outlined and discussed.
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24
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Klaholz BP. Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis. Acta Crystallogr D Struct Biol 2019; 75:878-881. [PMID: 31588919 PMCID: PMC6778849 DOI: 10.1107/s2059798319013391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/30/2019] [Indexed: 01/05/2023] Open
Abstract
In structural biology, deriving and refining atomic models into maps obtained from X-ray crystallography or cryo electron microscopy (cryo-EM) is essential for the detailed interpretation of a structure and its functional implications through interactions so that for example hydrogen bonds, drug specificity and associated molecular mechanisms can be analysed. This commentary summarizes the latest features of the Phenix software and also highlights the fact that cryo-EM increasingly contributes to data depositions in the PDB and EMDB.
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Affiliation(s)
- Bruno P. Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch 67404, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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25
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Guo J, Larabell CA. Soft X-ray tomography: virtual sculptures from cell cultures. Curr Opin Struct Biol 2019; 58:324-332. [PMID: 31495562 PMCID: PMC6791522 DOI: 10.1016/j.sbi.2019.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Cellular complexity is represented best in high-spatial resolution, three-dimensional (3D) reconstructions. Soft X-ray tomography (SXT) generates detailed volumetric reconstructions of cells preserved in a near-to-native, frozen-hydrated state. SXT is broadly applicable and can image specimens ranging from bacteria to large mammalian cells. As a reference, we summarize light and electron microscopic methods. We then present an overview of SXT and discuss its role in cellular imaging. We detail the methods used to image biological specimens and present recent highlights that illustrate the capabilities of the technique. We conclude by discussing correlative imaging, specifically the combination of SXT and fluorescence microscopy performed on the same specimen. This correlated approach combines the structural morphology of a cell with its physiological characteristics to build a deeply informative composite view.
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Affiliation(s)
- Jessica Guo
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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26
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Andronov L, Michalon J, Ouararhni K, Orlov I, Hamiche A, Vonesch JL, Klaholz BP. 3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. Bioinformatics 2019; 34:3004-3012. [PMID: 29635310 DOI: 10.1093/bioinformatics/bty200] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/02/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Single-molecule localization microscopy (SMLM) can play an important role in integrated structural biology approaches to identify, localize and determine the 3D structure of cellular structures. While many tools exist for the 3D analysis and visualization of crystal or cryo-EM structures little exists for 3D SMLM data, which can provide unique insights but are particularly challenging to analyze in three dimensions especially in a dense cellular context. Results We developed 3DClusterViSu, a method based on 3D Voronoi tessellations that allows local density estimation, segmentation and quantification of 3D SMLM data and visualization of protein clusters within a 3D tool. We show its robust performance on microtubules and histone proteins H2B and CENP-A with distinct spatial distributions. 3DClusterViSu will favor multi-scale and multi-resolution synergies to allow integrating molecular and cellular levels in the analysis of macromolecular complexes. Availability and impementation 3DClusterViSu is available under http://cbi-dev.igbmc.fr/cbi/voronoi3D. Supplementary information Supplementary figures are available at Bioinformatics online.
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Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jonathan Michalon
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ali Hamiche
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean-Luc Vonesch
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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27
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Rivera-Calzada A, Carroni M. Editorial: Technical Advances in Cryo-Electron Microscopy. Front Mol Biosci 2019; 6:72. [PMID: 31508425 PMCID: PMC6713907 DOI: 10.3389/fmolb.2019.00072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/07/2019] [Indexed: 11/13/2022] Open
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28
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Cryo-SOFI enabling low-dose super-resolution correlative light and electron cryo-microscopy. Proc Natl Acad Sci U S A 2019; 116:4804-4809. [PMID: 30808803 PMCID: PMC6421404 DOI: 10.1073/pnas.1810690116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Correlative light and electron cryo-microscopy (cryo-CLEM) combines information from the specific labeling of fluorescence cryo-microscopy (cryo-FM) with the high resolution in environmental context of electron cryo-microscopy (cryo-EM). Exploiting super-resolution methods for cryo-FM is advantageous, as it enables the identification of rare events within the environmental background of cryo-EM at a sensitivity and resolution beyond that of conventional methods. However, due to the need for relatively high laser intensities, current super-resolution cryo-CLEM methods require cryo-protectants or support films which can severely reduce image quality in cryo-EM and are not compatible with many samples, such as mammalian cells. Here, we introduce cryogenic super-resolution optical fluctuation imaging (cryo-SOFI), a low-dose super-resolution imaging scheme based on the SOFI principle. As cryo-SOFI does not require special sample preparation, it is fully compatible with conventional cryo-EM specimens, and importantly, it does not affect the quality of cryo-EM imaging. By applying cryo-SOFI to a variety of biological application examples, we demonstrate resolutions up to ∼135 nm, an improvement of up to three times compared with conventional cryo-FM, while maintaining the specimen in a vitrified state for subsequent cryo-EM. Cryo-SOFI presents a general solution to the problem of specimen devitrification in super-resolution cryo-CLEM. It does not require a complex optical setup and can easily be implemented in any existing cryo-FM system.
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29
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Chiang CY, Chen C. Toward characterizing extracellular vesicles at a single-particle level. J Biomed Sci 2019; 26:9. [PMID: 30646920 PMCID: PMC6332877 DOI: 10.1186/s12929-019-0502-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/09/2019] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membrane-bound vesicles that serve a means of cell-cell communication. Studying EVs at a single-particle level is important because EVs are inherently heterogeneous. Novel micro- and nanotechnological tools have open opportunities for realizing single-EV measurements exploiting their biochemical, electrical, mechanical, and/or optical properties. This review summarizes the recent development of technologies toward sorting and analyzing single EVs. Sorting EVs into a more homogeneous subset relaxes the sensitivity and throughput required on the EV detection, and hence related techniques are also included in this review. These exciting technologies are on the rise and will expand our understanding of EVs and their applications in the near future.
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Affiliation(s)
- Chun-Yi Chiang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chihchen Chen
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
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30
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Visualizing the Role of 2'-OH rRNA Methylations in the Human Ribosome Structure. Biomolecules 2018; 8:biom8040125. [PMID: 30366442 PMCID: PMC6316459 DOI: 10.3390/biom8040125] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/10/2018] [Accepted: 10/18/2018] [Indexed: 01/17/2023] Open
Abstract
Chemical modifications of RNA have recently gained new attention in biological sciences. They occur notably on messenger RNA (mRNA) and ribosomal RNA (rRNA) and are important for various cellular functions, but their molecular mechanism of action is yet to be understood in detail. Ribosomes are large ribonucleoprotein assemblies, which synthesize proteins in all organisms. Human ribosomes, for example, carry more than 200 modified nucleotides, which are introduced during biogenesis. Chemically modified nucleotides may appear to be only scarcely different from canonical nucleotides, but modifications such as methylations can in fact modulate their chemical and topological properties in the RNA and alter or modulate the overall translation efficiency of the ribosomes resulting in dysfunction of the translation machinery. Recent functional analysis and high-resolution ribosome structures have revealed a large repertoire of modification sites comprising different modification types. In this review, we focus on 2′-O-methylations (2′-O-Me) and discuss the structural insights gained through our recent cryo electron microscopy (cryo-EM) high-resolution structural analysis of the human ribosome, such as their locations and their influence on the secondary and tertiary structures of human rRNAs. The detailed analysis presented here reveals that ribose conformations of the rRNA backbone differ when the 2′-OH hydroxyl position is methylated, with 3′-endo conformations being the default and the 2′-endo conformations being characteristic in that the associated base is flipped-out. We compare currently known 2′-O-Me sites in human rRNAs evaluated using RiboMethSeq and cryo-EM structural analysis and discuss their involvement in several human diseases.
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31
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The Structural and Functional Organization of Ribosomal Compartment in the Cell: A Mystery or a Reality? Trends Biochem Sci 2018; 43:938-950. [PMID: 30337135 DOI: 10.1016/j.tibs.2018.09.017] [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: 04/27/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/23/2022]
Abstract
Great progress has been made toward solving the atomic structure of the ribosome, which is the main biosynthetic machine in cells, but we still do not have a full picture of exactly how cellular ribosomes function. Based on the analysis of crystallographic and electron microscopy data, we propose a basic model of the structural organization of ribosomes into a compartment. This compartment is regularly formed by arrays of ribosomal tetramers made up of two dimers that are actually facing in opposite directions. The compartment functions as the main 'factory' for the production of cellular proteins. The model is consistent with the existing biochemical and genetic data. We also consider the functional connections of such a compartment with cellular transcription and ribosomal biogenesis.
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32
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Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D Struct Biol 2018; 74:814-840. [PMID: 30198894 PMCID: PMC6130467 DOI: 10.1107/s2059798318009324] [Citation(s) in RCA: 450] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 06/27/2018] [Indexed: 11/25/2022] Open
Abstract
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.
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Affiliation(s)
- Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai, 200444, People’s Republic of China
| | - Bruno P. Klaholz
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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33
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Neumann P, Dickmanns A, Ficner R. Validating Resolution Revolution. Structure 2018; 26:785-795.e4. [PMID: 29606592 DOI: 10.1016/j.str.2018.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022]
Abstract
Recent advances in instrumentation and image-processing software have resulted in a resolution revolution in cryo-electron microscopy (cryo-EM) and a surge in the popularity of this technique. However, despite technical progress and hundreds of structures determined so far, development of standards assessing the agreement between the cryo-EM map and the respective model has fallen behind. Here we establish a validation procedure evaluating this agreement and applied it to a set of 565 cryo-EM structures. Analysis of the results revealed that three-quarters of the validated structures exhibit moderate or low agreement between the map and the corresponding model, mostly due to limited structural features possessed by these maps. Model re-refinement significantly improved the agreement for only one-fifth of the structures, reaffirming the necessity to re-evaluate map resolution. The presented procedure provides an approach to re-estimate the resolution of cryo-EM map areas interpreted by the model.
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Affiliation(s)
- Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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34
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Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Nucleic Acids Res 2018; 46:2624-2635. [PMID: 29309709 PMCID: PMC5861428 DOI: 10.1093/nar/gkx1292] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/13/2017] [Accepted: 12/28/2017] [Indexed: 12/13/2022] Open
Abstract
Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3-6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5'-GNGACCC-3' consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab-RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography.
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Affiliation(s)
- Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Marcel Dupont
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Stormy Ruiz
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Lucas J Bailey
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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35
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Stephens R, Lim K, Portela M, Kvansakul M, Humbert PO, Richardson HE. The Scribble Cell Polarity Module in the Regulation of Cell Signaling in Tissue Development and Tumorigenesis. J Mol Biol 2018; 430:3585-3612. [PMID: 29409995 DOI: 10.1016/j.jmb.2018.01.011] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 01/22/2023]
Abstract
The Scribble cell polarity module, comprising Scribbled (Scrib), Discs-large (Dlg) and Lethal-2-giant larvae (Lgl), has a tumor suppressive role in mammalian epithelial cancers. The Scribble module proteins play key functions in the establishment and maintenance of different modes of cell polarity, as well as in the control of tissue growth, differentiation and directed cell migration, and therefore are major regulators of tissue development and homeostasis. Whilst molecular details are known regarding the roles of Scribble module proteins in cell polarity regulation, their precise mode of action in the regulation of other key cellular processes remains enigmatic. An accumulating body of evidence indicates that Scribble module proteins play scaffolding roles in the control of various signaling pathways, which are linked to the control of tissue growth, differentiation and cell migration. Multiple Scrib, Dlg and Lgl interacting proteins have been discovered, which are involved in diverse processes, however many function in the regulation of cellular signaling. Herein, we review the components of the Scrib, Dlg and Lgl protein interactomes, and focus on the mechanism by which they regulate cellular signaling pathways in metazoans, and how their disruption leads to cancer.
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Affiliation(s)
- Rebecca Stephens
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Krystle Lim
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Marta Portela
- Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute (CSIC), Avenida Doctor Arce, 37, Madrid 28002, Spain
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Patrick O Humbert
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Helena E Richardson
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Anatomy & Neurobiology, University of Melbourne, Melbourne, Victoria 3010, Australia.
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36
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Fraternali F. [Protein-protein interacting networks, their structures and disease-related mutations]. Biol Aujourdhui 2018; 211:223-228. [PMID: 29412132 DOI: 10.1051/jbio/2017031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Indexed: 11/14/2022]
Abstract
In recent years, the comparison of protein interactomes has identified conserved modules, that could represent functional nuclei with a common ancestry. Within this context, recent analyses of protein-protein interacting networks have led to a debate on the influence of the experimental method on the quality and biological pertinence of these data. It is crucial to understand the measure in which divergence between networks of different species reflect sampling biases in respective experimental methods, as opposed to topological features dictated by biological functionality. This aspect requires novel, precise and practical mathematical tools, to quantify and compare high resolution networks. To this end, we have studied the relationship between pools of aleatory graphs and real biological signalization networks, while stressing the number of graph cycles in the networks, which represent complexes in experimental protein interactomes. By combining methods for graph and algorithm dynamics to count the loops, we evaluate the relative importance of the loops in biological networks in comparison with network analyses.
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Affiliation(s)
- Franca Fraternali
- Randall Division of Cellular and Molecular Biology, King's College, London, UK
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37
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Goud B, Louvard D. [Cell complexity should be placed at the heart of cancer research]. Med Sci (Paris) 2018; 34:63-71. [PMID: 29384098 DOI: 10.1051/medsci/20183401015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetic and most likely epigenetic alterations occurring during tumor progression and metastatic process lead to a broad deregulation of major cellular functions. However, the molecular mechanisms involved are still poorly understood. To understand them, the cell, the basic unit of life, remains more than ever the essential level to integrate the functional impact of genetics and epigenetics processes in the light of the global economy of the normal and cancerous cell, and of its interactions with its microenvironment.
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Affiliation(s)
- Bruno Goud
- Institut Curie, université de recherche Paris sciences et lettres (PSL), CNRS, UMR 144, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - Daniel Louvard
- Institut Curie, université de recherche Paris sciences et lettres (PSL), CNRS, UMR 144, 26, rue d'Ulm, 75248 Paris Cedex 05, France
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38
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Laddach A, Ng JCF, Chung SS, Fraternali F. Genetic variants and protein-protein interactions: a multidimensional network-centric view. Curr Opin Struct Biol 2018; 50:82-90. [PMID: 29306755 DOI: 10.1016/j.sbi.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/18/2023]
Abstract
We review recent progress in the mapping of genetic variants to proteins, in the context of their interactions, as measured from experiments and/or computational predictions. Such variants can impact on the molecular mechanisms underlying an interaction and its stability. We highlight recent work which relies on the effective use of protein-protein interaction networks (PPINs), integrated with 3D structural information, for evaluating disease-associated variants. Furthermore, we discuss how the integration of multiple layers of biological information, in the context of PPINs, can improve the interpretation of genetic variants and inspire new therapeutic strategies.
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Affiliation(s)
- Anna Laddach
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Joseph Chi-Fung Ng
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Sun Sook Chung
- Randall Division of Cell and Molecular Biophysics, King's College London, UK; Department of Haematological Medicine, King's College London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, UK.
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39
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Barbet-Massin E, van der Sluis E, Musial J, Beckmann R, Reif B. Reconstitution of Isotopically Labeled Ribosomal Protein L29 in the 50S Large Ribosomal Subunit for Solution-State and Solid-State NMR. Methods Mol Biol 2018; 1764:87-100. [PMID: 29605910 DOI: 10.1007/978-1-4939-7759-8_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) has recently emerged as a method of choice to study structural and dynamic properties of large biomolecular complexes at atomic resolution. Indeed, recent technological and methodological developments have enabled the study of ever more complex systems in the solid-state. However, to explore multicomponent protein complexes by NMR, specific labeling schemes need to be developed that are dependent on the biological question to be answered. We show here how to reconstitute an isotopically labeled protein within the unlabeled 50S or 70S ribosomal subunit. In particular, we focus on the 63-residue ribosomal protein L29 (~7 kDa), which is located at the exit of the tunnel of the large 50S ribosomal subunit (~1.5 MDa). The aim of this work is the preparation of a suitable sample to investigate allosteric conformational changes in a ribosomal protein that are induced by the nascent polypeptide chain and that trigger the interaction with different chaperones (e.g., trigger factor or SRP).
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Affiliation(s)
- Emeline Barbet-Massin
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Garching, Germany.,Dynamic Biosensors, Planegg, Germany
| | - Eli van der Sluis
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Bionanoscience, Faculty of Applied Sciences, TU Delft, Delft, The Netherlands
| | - Joanna Musial
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Garching, Germany. .,Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz-Zentrum München (HMGU), Neuherberg, Germany.
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40
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von Loeffelholz O, Natchiar SK, Djabeur N, Myasnikov AG, Kratzat H, Ménétret JF, Hazemann I, Klaholz BP. Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes. Curr Opin Struct Biol 2017; 46:140-148. [PMID: 28850874 DOI: 10.1016/j.sbi.2017.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/23/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
Cryo electron microscopy (cryo-EM) historically has had a strong impact on the structural and mechanistic analysis of protein synthesis by the prokaryotic and eukaryotic ribosomes. Vice versa, studying ribosomes has helped moving forwards many methodological aspects in single particle cryo-EM, at the level of automated data collection and image processing including advanced techniques for particle sorting to address structural and compositional heterogeneity. Here we review some of the latest ribosome structures, where cryo-EM allowed gaining unprecedented insights based on 3D structure sorting with focused classification and refinement methods helping to reach local resolution levels better than 3Å. Such high-resolution features now enable the analysis of drug interactions with RNA and protein side-chains including even the visualization of chemical modifications of the ribosomal RNA. These advances represent a major breakthrough in structural biology and show the strong potential of cryo-EM beyond the ribosome field including for structure-based drug design.
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Affiliation(s)
- Ottilie von Loeffelholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France. mailto:
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41
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Klaholz BP. The Ribosome Holds the RNA Polymerase on Track in Bacteria. Trends Biochem Sci 2017; 42:686-689. [PMID: 28801047 DOI: 10.1016/j.tibs.2017.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
The central dogma of molecular biology comprises two fundamental mechanistic steps of gene expression (transcription and translation), which, in bacteria, are coupled. A recent study provides structural insights into a supercomplex between the RNA polymerase and the ribosome, thus highlighting the synergy between two key macromolecular machineries in the cell.
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Affiliation(s)
- Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.
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42
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Plitzko JM, Schuler B, Selenko P. Structural Biology outside the box-inside the cell. Curr Opin Struct Biol 2017; 46:110-121. [PMID: 28735108 DOI: 10.1016/j.sbi.2017.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/17/2017] [Accepted: 06/23/2017] [Indexed: 01/11/2023]
Abstract
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
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Affiliation(s)
- Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philipp Selenko
- Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Laboratory, Robert-Roessle Strasse 10, D-13125 Berlin, Germany.
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43
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Studying structure and function of spliceosomal helicases. Methods 2017; 125:63-69. [PMID: 28668587 DOI: 10.1016/j.ymeth.2017.06.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 12/27/2022] Open
Abstract
The splicing of eukaryotic precursor mRNAs requires the activity of at least three DEAD-box helicases, one Ski2-like helicase and four DEAH-box helicases. High resolution structures for five of these spliceosomal helicases were obtained by means of X-ray crystallography. Additional low resolution structural information could be derived from single particle cryo electron microscopy and small angle X-ray scattering. The functional characterization includes biochemical methods to measure the ATPase and helicase activities. This review gives an overview on the techniques used to gain insights in to the structure and function of spliceosomal helicases.
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44
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Zabeo D, Cvjetkovic A, Lässer C, Schorb M, Lötvall J, Höög JL. Exosomes purified from a single cell type have diverse morphology. J Extracell Vesicles 2017; 6:1329476. [PMID: 28717422 PMCID: PMC5505001 DOI: 10.1080/20013078.2017.1329476] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are produced by all known organisms and are important for cell communication and physiology. Great morphological diversity has been described regarding EVs found in body fluids such as blood plasma, breast milk, and ejaculate. However, a detailed morphological analysis has never been performed on exosomes when purified from a single cell type. In this study we analysed and quantified, via multiple electron microscopy techniques, the morphology of exosomes purified from the human mast cell line HMC-1. The results revealed a wide diversity in exosome morphology, suggesting that subpopulations of exosomes with different and specific functions may exist. Our findings imply that a new, more efficient way of defining exosome subpopulations is necessary. A system was proposed where exosomes were classified into nine different categories according to their size and shape. Three additional morphological features were also found in exosomes regardless of their morphological classification. These findings show that exosomes purified from a single cell line are also morphologically diverse, similar to previous observations for EVs in body fluids. This knowledge can help to improve the interpretation of experimental results and widen our general understanding of the biological functions of exosomes.
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Affiliation(s)
- Davide Zabeo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Cecilia Lässer
- Krefting Research Center, University of Gothenburg, Gothenburg, Sweden
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratories, Heidelberg, Germany
| | - Jan Lötvall
- Krefting Research Center, University of Gothenburg, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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45
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Vénien-Bryan C, Li Z, Vuillard L, Boutin JA. Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery. Acta Crystallogr F Struct Biol Commun 2017; 73:174-183. [PMID: 28368275 PMCID: PMC5379166 DOI: 10.1107/s2053230x17003740] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/08/2017] [Indexed: 02/06/2023] Open
Abstract
The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.
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Affiliation(s)
- Catherine Vénien-Bryan
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, UPMC, IRD, MNHN, 4 Place Jussieu, 75005 Paris, France
| | - Zhuolun Li
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, UPMC, IRD, MNHN, 4 Place Jussieu, 75005 Paris, France
| | - Laurent Vuillard
- Chimie des Protéines, Pôle d’Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean Albert Boutin
- Pôle d’Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
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