1
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Lachiondo-Ortega S, Rejano-Gordillo CM, Simon J, Lopitz-Otsoa F, C Delgado T, Mazan-Mamczarz K, Goikoetxea-Usandizaga N, Zapata-Pavas LE, García-Del Río A, Guerra P, Peña-Sanfélix P, Hermán-Sánchez N, Al-Abdulla R, Fernandez-Rodríguez C, Azkargorta M, Velázquez-Cruz A, Guyon J, Martín C, Zalamea JD, Egia-Mendikute L, Sanz-Parra A, Serrano-Maciá M, González-Recio I, Gonzalez-Lopez M, Martínez-Cruz LA, Pontisso P, Aransay AM, Barrio R, Sutherland JD, Abrescia NGA, Elortza F, Lujambio A, Banales JM, Luque RM, Gahete MD, Palazón A, Avila MA, G Marin JJ, De S, Daubon T, Díaz-Quintana A, Díaz-Moreno I, Gorospe M, Rodríguez MS, Martínez-Chantar ML. SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer. Cell Rep 2024; 43:113924. [PMID: 38507413 PMCID: PMC11025316 DOI: 10.1016/j.celrep.2024.113924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 08/08/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The posttranslational modification of proteins critically influences many biological processes and is a key mechanism that regulates the function of the RNA-binding protein Hu antigen R (HuR), a hub in liver cancer. Here, we show that HuR is SUMOylated in the tumor sections of patients with hepatocellular carcinoma in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum. Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs that modulates HuR binding affinity to its target RNAs, further modifying the transcriptomic profile toward hepatic tumor progression. Overall, SUMOylation constitutes a mechanism of HuR regulation that could be potentially exploited as a therapeutic strategy for liver cancer.
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Affiliation(s)
- Sofia Lachiondo-Ortega
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Claudia M Rejano-Gordillo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, University Institute of Biosanitary Research of Extremadura (INUBE), 06071 Badajoz, Spain; Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Jorge Simon
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Fernando Lopitz-Otsoa
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Teresa C Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - L Estefanía Zapata-Pavas
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Ana García-Del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Pietro Guerra
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Patricia Peña-Sanfélix
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Natalia Hermán-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Ruba Al-Abdulla
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Institute of Medical Biochemistry and Molecular Biology, University Medicine of Greifswald, 17475 Greifswald, Germany
| | - Carmen Fernandez-Rodríguez
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Joris Guyon
- University of Bordeaux, INSERM, BPH, U1219, 33000 Bordeaux, France; CHU de Bordeaux, Service de Pharmacologie Médicale, 33000 Bordeaux, France
| | - César Martín
- Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Juan Diego Zalamea
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Arantza Sanz-Parra
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patrizia Pontisso
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Ana M Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Félix Elortza
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Raúl M Luque
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Manuel D Gahete
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Asís Palazón
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Matias A Avila
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Hepatology Program, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM), Instituto de Investigación Biomédica de Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Thomas Daubon
- University of Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain.
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2
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Lete M, Hoffmann M, Schomann N, Martínez-Castillo A, Peccati F, Konietzny PB, Delgado S, Snyder NL, Jiménez-Oses G, Abrescia NGA, Ardá A, Hartmann L, Jiménez-Barbero J. Molecular Recognition of Glycan-Bearing Glycomacromolecules Presented at Membrane Surfaces by Lectins: An NMR View. ACS Omega 2023; 8:16883-16895. [PMID: 37214724 PMCID: PMC10193412 DOI: 10.1021/acsomega.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
Lectin-glycan interactions are at the heart of a multitude of biological events. Glycans are usually presented in a multivalent manner on the cell surface as part of the so-called glycocalyx, where they interact with other entities. This multivalent presentation allows us to overcome the typical low affinities found for individual glycan-lectin interactions. Indeed, the presentation of glycans may drastically impact their binding by lectins, highly affecting the corresponding binding affinity and even selectivity. In this context, we herein present the study of the interaction of a variety of homo- and heteromultivalent lactose-functionalized glycomacromolecules and their lipid conjugates with two human galectins. We have employed as ligands the glycomacromolecules, as well as liposomes decorated with those structures, to evaluate their interactions in a cell-mimicking environment. Key details of the interaction have been unravelled by NMR experiments, both from the ligand and receptor perspectives, complemented by cryo-electron microscopy methods and molecular dynamics simulations.
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Affiliation(s)
- Marta
G. Lete
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Miriam Hoffmann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Nils Schomann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Ane Martínez-Castillo
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Francesca Peccati
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Patrick B. Konietzny
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Sandra Delgado
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Nicole L. Snyder
- Department
of Chemistry, Davidson College, Davidson, North Carolina 28035, United States
| | - Gonzalo Jiménez-Oses
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
| | - Nicola G. A. Abrescia
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas, Instituto de Salud Carlos
III, Madrid 28029, Spain
| | - Ana Ardá
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
| | - Laura Hartmann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
- Department
of Organic and Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
- Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid 28029, Spain
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3
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Guerra GS, Barriales D, Lorenzo G, Moreno S, Anguita J, Brun A, Abrescia NGA. Immunization with a small fragment of the Schmallenberg virus nucleoprotein highly conserved across the Orthobunyaviruses of the Simbu serogroup reduces viremia in SBV challenged IFNAR -/- mice. Vaccine 2023; 41:3275-3284. [PMID: 37085455 DOI: 10.1016/j.vaccine.2023.04.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/23/2023]
Abstract
Schmallenberg Virus (SBV), an arbovirus from the Peribunyaviridae family and Orthobunyavirus genus, was discovered in late 2011 in Germany and has been circulating in Europe, Asia and Africa ever since. The virus causes a disease associated with ruminants that includes fever, fetal malformation, drop in milk production, diarrhoea and stillbirths, becoming a burden for small and large farms. Building on previous studies on SBV nucleoprotein (SBV-N) as a promising vaccine candidate, we have investigated the possible protein regions responsible for protection. Based on selective truncation of domains designed from the available crystal structure of the SBV-N, we identified both the N-terminal domain (N-term; Met1 - Thr133) and a smaller fragment within (C4; Met1 - Ala58) as vaccine prototypes. Two injections of the N-term and C4 polypeptides protected mice knockout for type I interferon (IFN) receptors (IFNAR-/-) challenged with virulent SBV, opposite to control groups that presented severe signs of morbidity and weight loss. Viremia analyses along with the presence of IFN-γ secreted from splenocytes re-stimulated with the N-terminal region of the protein corroborate that these two portions of SBV-N can be employed as subunit vaccines. Apart from both proteinaceous fragments being easily produced in bacterial cells, the C4 polypeptide shares a high sequence homology (∼87.1 %) with the corresponding region of nucleoproteins of several viruses of the Simbu serogroup, a group of Orthobunyaviruses that comprises SBV and veterinary pathogens like Akabane virus and human infecting viruses like Oropouche. Thus, we propose that this smaller fragment is better suited for vaccine nanoparticle formulation, and it paves the way to further research with other related Orthobunyaviruses.
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Affiliation(s)
- Gabriel Soares Guerra
- Structure and Cell Biology of Viruses Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain
| | - Diego Barriales
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | - Gema Lorenzo
- Animal Health Research Center (INIA-CISA/CSIC), 28130 Valdeolmos, Madrid, Spain
| | - Sandra Moreno
- Animal Health Research Center (INIA-CISA/CSIC), 28130 Valdeolmos, Madrid, Spain
| | - Juan Anguita
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia 48015, Spain
| | - Alejandro Brun
- Animal Health Research Center (INIA-CISA/CSIC), 28130 Valdeolmos, Madrid, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia 48015, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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4
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Romerio A, Gotri N, Franco AR, Artusa V, Shaik MM, Pasco ST, Atxabal U, Matamoros-Recio A, Mínguez-Toral M, Zalamea JD, Franconetti A, Abrescia NGA, Jimenez-Barbero J, Anguita J, Martín-Santamaría S, Peri F. New Glucosamine-Based TLR4 Agonists: Design, Synthesis, Mechanism of Action, and In Vivo Activity as Vaccine Adjuvants. J Med Chem 2023; 66:3010-3029. [PMID: 36728697 PMCID: PMC9969399 DOI: 10.1021/acs.jmedchem.2c01998] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We disclose here a panel of small-molecule TLR4 agonists (the FP20 series) whose structure is derived from previously developed TLR4 ligands (FP18 series). The new molecules have increased chemical stability and a shorter, more efficient, and scalable synthesis. The FP20 series showed selective activity as TLR4 agonists with a potency similar to FP18. Interestingly, despite the chemical similarity with the FP18 series, FP20 showed a different mechanism of action and immunofluorescence microscopy showed no NF-κB nor p-IRF-3 nuclear translocation but rather MAPK and NLRP3-dependent inflammasome activation. The computational studies related a 3D shape of FP20 series with agonist binding properties inside the MD-2 pocket. FP20 displayed a CMC value lower than 5 μM in water, and small unilamellar vesicle (SUV) formation was observed in the biological activity concentration range. FP20 showed no toxicity in mouse vaccination experiments with OVA antigen and induced IgG production, thus indicating a promising adjuvant activity.
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Affiliation(s)
- Alessio Romerio
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Nicole Gotri
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Ana Rita Franco
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Valentina Artusa
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Mohammed Monsoor Shaik
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Samuel T. Pasco
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Unai Atxabal
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Alejandra Matamoros-Recio
- Centro
de Investigaciones Biológicas Margarita Salas CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Marina Mínguez-Toral
- Centro
de Investigaciones Biológicas Margarita Salas CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Juan Diego Zalamea
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Antonio Franconetti
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G. A. Abrescia
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain,Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Jesus Jimenez-Barbero
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain,Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain,Department
of Organic Chemistry, II Faculty of Science and Technology, EHU-UPV, 48940 Leioa, Spain,Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
| | - Juan Anguita
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain,Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | | | - Francesco Peri
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy,
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5
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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6
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Arriaga I, Navarro A, Etxabe A, Trigueros C, Samulski RJ, Moullier P, François A, Abrescia NGA. Cellular and Structural Characterization of VP1 and VP2 Knockout Mutants of AAV3B Serotype and Implications for AAV Manufacturing. Hum Gene Ther 2022; 33:1142-1156. [PMID: 36082996 DOI: 10.1089/hum.2022.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AAV virion biology is still lacking a complete understanding of the role that the various structural subunits (VP1, 2, and 3) play in virus assembly, infectivity, and therapeutic delivery for clinical indications. In this study, we focus on the less studied adeno-associated virus AAV3B and generate a collection of AAV plasmid substrates that assemble virion particles deficient specifically in VP1, VP2, or VP1 and 2 structural subunits. Using a collection of biological and structural assays, we observed that virions devoid of VP1, VP2, or VP1 and 2 efficiently assembled virion particles, indistinguishable by cryoelectron microscopy (cryo-EM) from that of wild type (WT), but unique in virion transduction (WT > VP2 > VP1 > VP1 and 2 mutants). We also observed that the missing structural subunit was mostly compensated by additional VP3 protomers in the formed virion particle. Using cryo-EM analysis, virions fell into three classes, namely full, empty, and partially filled, based on comparison of density values within the capsid. Further, we characterize virions described as "broken" or "disassembled" particles, and provide structural information that supports the particle dissolution occurring through the two-fold symmetry sites. Finally, we highlight the unique value of employing cryo-EM as an essential tool for release criteria with respect to AAV manufacturing.
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Affiliation(s)
- Iker Arriaga
- Structure and Cell Biology of Viruses Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | | | | | - R Jude Samulski
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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7
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Risueño C, Abrescia NGA, Coluzza I. Insights into Hepatitis C Virus E2 core Interactions with Human Cellular Receptor CD81 at Different pHs from Molecular Simulations. J Phys Chem B 2022; 126:8391-8403. [PMID: 36255318 DOI: 10.1021/acs.jpcb.2c04697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hepatitis C virus (HCV) is the second viral agent that causes the majority of chronic hepatic infections worldwide, following Hepatitis B virus (HBV) infection. HCV infection comprises several steps, from the attachment to the receptors to the delivery of the viral genetic material and replication inside the cells. Tetraspanin CD81 is a key entry factor for HCV as it accompanies the virus during attachment and internalization through clathrin-mediated endocytosis. HCV-CD81 binding takes place through the viral glycoprotein E2. We performed full-atom molecular dynamics simulations reproducing the pH conditions that occur during the viral attachment to the hepatocytes (pH 7.4) and internalization (pH 6.2-4.6). We observed that changing the pH from 7.4 to 6.2 triggers a large conformational change in the binding orientation between E2core (E2core corresponds to residues 412-645 of the viral glycoprotein E2) and CD81LEL (CD81LEL corresponds to residues 112-204 of CD81) that occurs even more rapidly at low pH 4.6. This pH-induced switching mechanism has never been observed before and could allow the virus particles to sense the right moment during the maturation of the endosome to start fusion.
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Affiliation(s)
- Cristina Risueño
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160, Spain.,Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, Donostia-San Sebastián 20014, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain.,Basque Foundation for Science, IKERBASQUE, Bilbao 48009, Spain
| | - Ivan Coluzza
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, Donostia-San Sebastián 20014, Spain.,Basque Foundation for Science, IKERBASQUE, Bilbao 48009, Spain.,Computational Biophysics Lab, Basque Center for Materials, Applications and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque Científico UPV/EHU Barrio Sarriena, Leioa 48940, Spain
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8
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Stagnoli S, Peccati F, Connell SR, Martinez-Castillo A, Charro D, Millet O, Bruzzone C, Palazon A, Ardá A, Jiménez-Barbero J, Ereño-Orbea J, Abrescia NGA, Jiménez-Osés G. Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods. Front Microbiol 2022; 13:870938. [PMID: 35495643 PMCID: PMC9053831 DOI: 10.3389/fmicb.2022.870938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Two years after its emergence, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several vaccines. The extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin converting enzyme 2 (ACE2) through its receptor binding domain (RBD), is the major target of neutralizing antibodies. Like to many other viral fusion proteins, the SARS-CoV-2 spike protein utilizes a glycan shield to thwart the host immune response. To grasp the influence of chemical signatures on carbohydrate mobility and reconcile the cryo-EM density of specific glycans we combined our cryo-EM map of the S ectodomain to 4.1 Å resolution, reconstructed from a limited number of particles, and all-atom molecular dynamics simulations. Chemical modifications modeled on representative glycans (defucosylation, sialylation and addition of terminal LacNAc units) show no significant influence on either protein shielding or glycan flexibility. By estimating at selected sites the local correlation between the full density map and atomic model-based maps derived from molecular dynamics simulations, we provide insight into the geometries of the α-Man-(1→3)-[α-Man-(1→6)-]-β-Man-(1→4)-β-GlcNAc(1→4)-β-GlcNAc core common to all N-glycosylation sites.
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Affiliation(s)
- Soledad Stagnoli
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Francesca Peccati
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Sean R. Connell
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Structural Biology Unit, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Martinez-Castillo
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Diego Charro
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Chiara Bruzzone
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Asis Palazon
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ana Ardá
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Jesús Jiménez-Barbero
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - June Ereño-Orbea
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Nicola G. A. Abrescia,
| | - Gonzalo Jiménez-Osés
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Gonzalo Jiménez-Osés,
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9
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Goikoetxea‐Usandizaga N, Serrano‐Maciá M, Delgado TC, Simón J, Fernández Ramos D, Barriales D, Cornide M, Jiménez M, Pérez‐Redondo M, Lachiondo‐Ortega S, Rodríguez‐Agudo R, Bizkarguenaga M, Zalamea JD, Pasco ST, Caballero‐Díaz D, Alfano B, Bravo M, González‐Recio I, Mercado‐Gómez M, Gil‐Pitarch C, Mabe J, Gracia‐Sancho J, Abecia L, Lorenzo Ó, Martín‐Sanz P, Abrescia NGA, Sabio G, Rincón M, Anguita J, Miñambres E, Martín C, Berenguer M, Fabregat I, Casado M, Peralta C, Varela‐Rey M, Martínez‐Chantar ML. Mitochondrial bioenergetics boost macrophage activation, promoting liver regeneration in metabolically compromised animals. Hepatology 2022; 75:550-566. [PMID: 34510498 PMCID: PMC9300136 DOI: 10.1002/hep.32149] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/11/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Hepatic ischemia-reperfusion injury (IRI) is the leading cause of early posttransplantation organ failure as mitochondrial respiration and ATP production are affected. A shortage of donors has extended liver donor criteria, including aged or steatotic livers, which are more susceptible to IRI. Given the lack of an effective treatment and the extensive transplantation waitlist, we aimed at characterizing the effects of an accelerated mitochondrial activity by silencing methylation-controlled J protein (MCJ) in three preclinical models of IRI and liver regeneration, focusing on metabolically compromised animal models. APPROACH AND RESULTS Wild-type (WT), MCJ knockout (KO), and Mcj silenced WT mice were subjected to 70% partial hepatectomy (Phx), prolonged IRI, and 70% Phx with IRI. Old and young mice with metabolic syndrome were also subjected to these procedures. Expression of MCJ, an endogenous negative regulator of mitochondrial respiration, increases in preclinical models of Phx with or without vascular occlusion and in donor livers. Mice lacking MCJ initiate liver regeneration 12 h faster than WT and show reduced ischemic injury and increased survival. MCJ knockdown enables a mitochondrial adaptation that restores the bioenergetic supply for enhanced regeneration and prevents cell death after IRI. Mechanistically, increased ATP secretion facilitates the early activation of Kupffer cells and production of TNF, IL-6, and heparin-binding EGF, accelerating the priming phase and the progression through G1 /S transition during liver regeneration. Therapeutic silencing of MCJ in 15-month-old mice and in mice fed a high-fat/high-fructose diet for 12 weeks improves mitochondrial respiration, reduces steatosis, and overcomes regenerative limitations. CONCLUSIONS Boosting mitochondrial activity by silencing MCJ could pave the way for a protective approach after major liver resection or IRI, especially in metabolically compromised, IRI-susceptible organs.
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Affiliation(s)
- Naroa Goikoetxea‐Usandizaga
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Marina Serrano‐Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Teresa C. Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Jorge Simón
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - David Fernández Ramos
- Precision Medicine and Liver Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain
| | - Diego Barriales
- Inflammation and Macrophage Plasticity LaboratoryCenter for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Maria E. Cornide
- Liver, Digestive System and Metabolism Department, Liver Transplantation and Graft Viability LabInstituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Mónica Jiménez
- Liver, Digestive System and Metabolism Department, Liver Transplantation and Graft Viability LabInstituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | | | - Sofia Lachiondo‐Ortega
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Rubén Rodríguez‐Agudo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Maider Bizkarguenaga
- Precision Medicine and Liver Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Juan Diego Zalamea
- Structure and Cell Biology of Viruses Lab Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Samuel T. Pasco
- Inflammation and Macrophage Plasticity LaboratoryCenter for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Daniel Caballero‐Díaz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain,TGF‐β and Cancer GroupOncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)Gran Via de L’HospitaletBarcelonaSpain
| | - Benedetta Alfano
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Miren Bravo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Irene González‐Recio
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Maria Mercado‐Gómez
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Clàudia Gil‐Pitarch
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain
| | - Jon Mabe
- Electronics and Communications Unit, IK4‐TeknikerEibarSpain
| | - Jordi Gracia‐Sancho
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain,Liver Vascular Biology Research GroupIDIBAPSBarcelonaSpain
| | - Leticia Abecia
- Inflammation and Macrophage Plasticity LaboratoryCenter for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain,Immunology, Microbiology and Parasitology Department, Medicine and Nursing FacultyUniversity of the Basque CountryLeioaSpain
| | - Óscar Lorenzo
- Laboratory of Diabetes and Vascular PathologyIIS‐Fundación Jiménez Díaz‐Universidad Autónoma de Madrid, Spanish Biomedical Research Centre on Diabetes and Associated Metabolic Disorders (CIBERDEM) NetworkMadridSpain
| | - Paloma Martín‐Sanz
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain,Cell Signalling and Metabolism DepartmentInstituto de Investigaciones Biomédicas “Alberto Sols,” CSIC‐UAMMadridSpain
| | - Nicola G. A. Abrescia
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain,Structure and Cell Biology of Viruses Lab Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain,IKERBASQUEBasque Foundation for ScienceBilbaoSpain
| | - Guadalupe Sabio
- Centro Nacional de Investigaciones CardiovascularesStress Kinases in Diabetes, Cancer and BiochemistryMadridSpain
| | - Mercedes Rincón
- Department of MedicineImmunobiology DivisionUniversity of VermontBurlingtonVermontUSA
| | - Juan Anguita
- Inflammation and Macrophage Plasticity LaboratoryCenter for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain,IKERBASQUEBasque Foundation for ScienceBilbaoSpain
| | - Eduardo Miñambres
- Transplant Coordination Unit, Marqués de Valdecilla University Hospital–IDIVAL, Cantabria UniversitySantanderSpain
| | - César Martín
- Biofisika Institute, Centro Superior de Investigaciones Científicas, and Department of Biochemisty, Faculty of Science and TechnologyUniversity of Basque CountryLeioaSpain
| | - Marina Berenguer
- Liver UnitHospital Universitario y Politécnico La FeValenciaSpain
| | - Isabel Fabregat
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain,TGF‐β and Cancer GroupOncobell ProgramBellvitge Biomedical Research Institute (IDIBELL)Gran Via de L’HospitaletBarcelonaSpain,Faculty of Medicine and Health SciencesUniversity of BarcelonaL’HospitaletBarcelonaSpain
| | - Marta Casado
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain,Experimental Metabolic Pathology DepartmentInstituto de Biomedicina de ValenciaIBV‐CSICValenciaSpain
| | - Carmen Peralta
- Liver, Digestive System and Metabolism Department, Liver Transplantation and Graft Viability LabInstituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Marta Varela‐Rey
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain
| | - María Luz Martínez‐Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceDerioSpain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Carlos III National Health InstituteMadridSpain
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10
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Duyvesteyn HME, Santos-Pérez I, Peccati F, Martinez-Castillo A, Walter TS, Reguera D, Goñi FM, Jiménez-Osés G, Oksanen HM, Stuart DI, Abrescia NGA. Bacteriophage PRD1 as a nanoscaffold for drug loading. Nanoscale 2021; 13:19875-19883. [PMID: 34851350 PMCID: PMC8667075 DOI: 10.1039/d1nr04153c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Viruses are very attractive biomaterials owing to their capability as nanocarriers of genetic material. Efforts have been made to functionalize self-assembling viral protein capsids on their exterior or interior to selectively take up different payloads. PRD1 is a double-stranded DNA bacteriophage comprising an icosahedral protein outer capsid and an inner lipidic vesicle. Here, we report the three-dimensional structure of PRD1 in complex with the antipsychotic drug chlorpromazine (CPZ) by cryo-electron microscopy. We show that the jellyrolls of the viral major capsid protein P3, protruding outwards from the capsid shell, serve as scaffolds for loading heterocyclic CPZ molecules. Additional X-ray studies and molecular dynamics simulations show the binding modes and organization of CPZ molecules when complexed with P3 only and onto the virion surface. Collectively, we provide a proof of concept for the possible use of the lattice-like organisation and the quasi-symmetric morphology of virus capsomers for loading heterocyclic drugs with defined properties.
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Affiliation(s)
- Helen M E Duyvesteyn
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Isaac Santos-Pérez
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
| | - Francesca Peccati
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Ane Martinez-Castillo
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
| | - Thomas S Walter
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
| | - David Reguera
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Felix M Goñi
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) and Instituto Biofisika (CSIC, UPV/EHU), Leioa, Spain
| | - Gonzalo Jiménez-Osés
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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11
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Srivastava AD, Unione L, Bunyatov M, Gagarinov IA, Delgado S, Abrescia NGA, Ardá A, Boons GJ. Chemoenzymatic Synthesis of Complex N-Glycans of the Parasite S. mansoni to Examine the Importance of Epitope Presentation on DC-SIGN recognition. Angew Chem Int Ed Engl 2021; 60:19287-19296. [PMID: 34124805 PMCID: PMC8456914 DOI: 10.1002/anie.202105647] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/02/2021] [Indexed: 12/14/2022]
Abstract
The importance of multivalency for N-glycan-protein interactions has primarily been studied by attachment of minimal epitopes to artificial multivalent scaffold and not in the context of multi-antennary glycans. N-glycans can be modified by bisecting GlcNAc, core xylosides and fucosides, and extended N-acetyl lactosamine moieties. The impact of such modifications on glycan recognition are also not well understood. We describe here a chemoenzymatic methodology that can provide N-glycans expressed by the parasitic worm S. mansoni having unique epitopes at each antenna and containing core xyloside. NMR, computational and electron microscopy were employed to investigate recognition of the glycans by the human lectin DC-SIGN. It revealed that core xyloside does not influence terminal epitope recognition. The multi-antennary glycans bound with higher affinity to DC-SIGN compared to mono-valent counterparts, which was attributed to proximity-induced effective concentration. The multi-antennary glycans cross-linked DC-SIGN into a dense network, which likely is relevant for antigen uptake and intracellular routing.
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Affiliation(s)
- Apoorva D Srivastava
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Mehman Bunyatov
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Ivan A Gagarinov
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Sandra Delgado
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162, Derio, Bizkaia, Spain
| | - Nicola G A Abrescia
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Bizkaia, Spain
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Bizkaia, Spain
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.,Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.,Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
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12
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Srivastava AD, Unione L, Bunyatov M, Gagarinov IA, Delgado S, Abrescia NGA, Ardá A, Boons G. Chemoenzymatic Synthesis of Complex
N
‐Glycans of the Parasite
S. mansoni
to Examine the Importance of Epitope Presentation on DC‐SIGN recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Apoorva D. Srivastava
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Bijvoet Center for Biomolecular Research Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Bijvoet Center for Biomolecular Research Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Mehman Bunyatov
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Bijvoet Center for Biomolecular Research Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Ivan A. Gagarinov
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Bijvoet Center for Biomolecular Research Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Sandra Delgado
- Molecular Recognition and Host-Pathogen Interactions CIC bioGUNE, Basque Research and Technology Alliance, BRTA Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
| | - Nicola G. A. Abrescia
- Molecular Recognition and Host-Pathogen Interactions CIC bioGUNE, Basque Research and Technology Alliance, BRTA Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Bizkaia Spain
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions CIC bioGUNE, Basque Research and Technology Alliance, BRTA Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Bizkaia Spain
| | - Geert‐Jan Boons
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Bijvoet Center for Biomolecular Research Utrecht University Universiteitsweg 99 3584 CG Utrecht The Netherlands
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
- Department of Chemistry University of Georgia Athens GA 30602 USA
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13
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Bertuzzi S, Gimeno A, Martinez-Castillo A, Lete MG, Delgado S, Airoldi C, Rodrigues Tavares M, Bláhová M, Chytil P, Křen V, Abrescia NGA, Ardá A, Bojarová P, Jiménez-Barbero J. Cross-Linking Effects Dictate the Preference of Galectins to Bind LacNAc-Decorated HPMA Copolymers. Int J Mol Sci 2021; 22:ijms22116000. [PMID: 34206141 PMCID: PMC8199549 DOI: 10.3390/ijms22116000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/02/2023] Open
Abstract
The interaction of multi-LacNAc (Galβ1-4GlcNAc)-containing N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers with human galectin-1 (Gal-1) and the carbohydrate recognition domain (CRD) of human galectin-3 (Gal-3) was analyzed using NMR methods in addition to cryo-electron-microscopy and dynamic light scattering (DLS) experiments. The interaction with individual LacNAc-containing components of the polymer was studied for comparison purposes. For Gal-3 CRD, the NMR data suggest a canonical interaction of the individual small-molecule bi- and trivalent ligands with the lectin binding site and better affinity for the trivalent arrangement due to statistical effects. For the glycopolymers, the interaction was stronger, although no evidence for forming a large supramolecule was obtained. In contrast, for Gal-1, the results indicate the formation of large cross-linked supramolecules in the presence of multivalent LacNAc entities for both the individual building blocks and the polymers. Interestingly, the bivalent and trivalent presentation of LacNAc in the polymer did not produce such an increase, indicating that the multivalency provided by the polymer is sufficient for triggering an efficient binding between the glycopolymer and Gal-1. This hypothesis was further demonstrated by electron microscopy and DLS methods.
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Affiliation(s)
- Sara Bertuzzi
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- BioOrgNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Ana Gimeno
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Ane Martinez-Castillo
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Marta G. Lete
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Sandra Delgado
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Cristina Airoldi
- BioOrgNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Marina Rodrigues Tavares
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského Nám. 2, 16206 Prague, Czech Republic; (M.R.T.); (M.B.); (P.C.)
| | - Markéta Bláhová
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského Nám. 2, 16206 Prague, Czech Republic; (M.R.T.); (M.B.); (P.C.)
| | - Petr Chytil
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského Nám. 2, 16206 Prague, Czech Republic; (M.R.T.); (M.B.); (P.C.)
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic;
| | - Nicola G. A. Abrescia
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Pavla Bojarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic;
- Department of Health Care Disciplines and Population Protection, Faculty of Biomedical Engineering, Czech Technical University in Prague, Nám. Sítná, 27201 Kladno, Czech Republic
- Correspondence: (P.B.); (J.J.-B.)
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940 Leioa, Bizkaia, Spain
- Correspondence: (P.B.); (J.J.-B.)
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14
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Robakiewicz S, Bridot C, Serna S, Gimeno A, Echeverria B, Delgado S, Ruyck J, Semwal S, Charro D, Dansercoer A, Verstraete K, Azkargorta M, Noort K, Wilbers R, Savvides SN, Abrescia NGA, Arda A, Reichardt NC, Jiménez-Barbero J, Bouckaert J. Minimal epitope for Mannitou IgM on paucimannose-carrying glycoproteins. Glycobiology 2021; 31:1005-1017. [PMID: 33909073 DOI: 10.1093/glycob/cwab027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/03/2021] [Accepted: 03/30/2021] [Indexed: 11/14/2022] Open
Abstract
Paucimannosidic glycans are restricted to the core structure [Man1-3GlcNAc2Fuc0-1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal and liver cancer. Mannitou IgM is a murine monoclonal antibody that was previously shown to recognise Man3GlcNAc2 with an almost exclusive selectivity. Here, we have sought the definition of the minimal glycan epitope of Mannitou IgM, initiated by screening on a newly designed paucimannosidic glycan microarray. Among the best binders were Man3GlcNAc2 and its α1,6 core-fucosylated variant, Man3GlcNAc2Fuc1. Unexpectedly and in contrast to earlier findings, Man5GlcNAc2-type structures bind equally well and a large tolerance was observed for substitutions on the α1,6 arm. It was confirmed that any substitution on the single α1,3-linked mannose completely abolishes binding. Surface plasmon resonance for kinetic measurements of Mannitou IgM binding, either directly on the glycans or as presented on omega-1 and kappa-5 soluble egg antigens from the helminth parasite Schistosoma mansoni, showed submicromolar affinities. To characterize the epitope in greater and atomic detail, saturation transfer difference nuclear magnetic resonance spectroscopy was performed with the Mannitou antigen-binding fragment. The STD-NMR data demonstrated the strongest interactions with the aliphatic protons H1 and H2 of the α1-3-linked mannose, and weaker imprints on its H3, H4 and H5 protons. In conclusion, Mannitou IgM binding requires a non-substituted α1,3-linked mannose branch of paucimannose also on proteins, making it a highly specific tool for the distinction of concurrent human tumor-associated carbohydrate antigens.
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Affiliation(s)
- Stefania Robakiewicz
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 du CNRS et Université de Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
| | - Clarisse Bridot
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 du CNRS et Université de Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
| | - Sonia Serna
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Ana Gimeno
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Begoña Echeverria
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Sandra Delgado
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Jérôme Ruyck
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 du CNRS et Université de Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
| | - Shubham Semwal
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 du CNRS et Université de Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
| | - Diego Charro
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Ann Dansercoer
- Unit for Structural Biology, VIB - UGent Center for Inflammation Research, Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Kenneth Verstraete
- Unit for Structural Biology, VIB - UGent Center for Inflammation Research, Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Mikel Azkargorta
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Kim Noort
- Laboratory of Nematology, Plant Science Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ruud Wilbers
- Laboratory of Nematology, Plant Science Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Savvas N Savvides
- Unit for Structural Biology, VIB - UGent Center for Inflammation Research, Department of Biochemistry and Microbiology, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Nicola G A Abrescia
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ana Arda
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Niels C Reichardt
- Glycotechnology Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Science and Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Julie Bouckaert
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 du CNRS et Université de Lille, 50 Avenue Halley, 59650 Villeneuve d'Ascq, France
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15
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Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Coelho H, Diniz A, Peccati F, Delgado S, Bosch A, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jiménez‐Osés G, Jiménez‐Barbero J, Ardá A, Ereño‐Orbea J. Structural Characterization of N-Linked Glycans in the Receptor Binding Domain of the SARS-CoV-2 Spike Protein and their Interactions with Human Lectins. Angew Chem Int Ed Engl 2020; 59:23763-23771. [PMID: 32915505 PMCID: PMC7894318 DOI: 10.1002/anie.202011015] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Indexed: 01/17/2023]
Abstract
The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human HEK293F cells have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures not found in previous MS-based analyses. The interaction of the RBD 13 C-labelled glycans with different human lectins, which are expressed in different organs and tissues that may be affected during the infection process, has also been evaluated by NMR. In particular, 15 N-labelled galectins (galectins-3, -7 and -8 N-terminal), Siglecs (Siglec-8, Siglec-10), and C-type lectins (DC-SIGN, MGL) have been employed. Complementary experiments from the glycoprotein perspective or from the lectin's point of view have permitted to disentangle the specific interacting epitopes in each case. Based on these findings, 3D models of the interacting complexes have been proposed.
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Affiliation(s)
- Maria Pia Lenza
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Iker Oyenarte
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Tammo Diercks
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Jon Imanol Quintana
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Ana Gimeno
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Helena Coelho
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Ana Diniz
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Francesca Peccati
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Sandra Delgado
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Alexandre Bosch
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Mikel Valle
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Oscar Millet
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Nicola G. A. Abrescia
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)Instituto de Salud Carlos IIIMadridSpain
| | - Asís Palazón
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
| | - Filipa Marcelo
- UCIBIOREQUIMTEDepartamento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa2829-516CaparicaPortugal
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - Jesús Jiménez‐Barbero
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
- Department of Organic Chemistry IIUniversity of the Basque CountryUPV/EHU48940LeioaSpain
| | - Ana Ardá
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
| | - June Ereño‐Orbea
- CIC bioGUNEBasque Research and Technology AllianceBRTABizkaia Technology Park48162DerioSpain
- Ikerbasque, Basque Foundation for Science48013BilbaoSpain
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16
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Boshra H, Lorenzo G, Charro D, Moreno S, Guerra GS, Sanchez I, Garrido JM, Geijo M, Brun A, Abrescia NGA. A novel Schmallenberg virus subunit vaccine candidate protects IFNAR -/- mice against virulent SBV challenge. Sci Rep 2020; 10:18725. [PMID: 33230115 PMCID: PMC7684302 DOI: 10.1038/s41598-020-73424-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 09/14/2020] [Indexed: 12/04/2022] Open
Abstract
Schmallenberg virus (SBV), an arthropod-transmitted pathogenic bunyavirus, continues to be a threat to the European livestock industry, causing morbidity and mortality among young ruminant livestock. Here, we describe a novel SBV subunit vaccine, based on bacterially expressed SBV nucleoprotein (SBV-N) administered with a veterinary-grade Saponin adjuvant. When assayed in an IFNAR-/- mouse model, SBV-N with Saponin induced strong non-neutralizing broadly virus-reactive antibodies, decreased clinical signs, as well as significantly reduced viremia. Vaccination assays also suggest that this level of immune protection is cell mediated, as evidenced by the lack of neutralizing antibodies, as well as interferon-γ secretion observed in vitro. Therefore, based on these results, bacterially expressed SBV-N, co-administered with veterinary-grade Saponin adjuvant may serve as a promising economical alternative to current SBV vaccines, and warrant further evaluation in large ruminant animal models. Moreover, we propose that this strategy may be applicable to other bunyaviruses.
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Affiliation(s)
- Hani Boshra
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Spain. .,Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Bât B43, avenue de Cureghem 6, 4000, Liège, Belgium.
| | - Gema Lorenzo
- Animal Health Research Center (INIA-CISA), 28130, Valdeolmos, Madrid, Spain
| | - Diego Charro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Spain
| | - Sandra Moreno
- Animal Health Research Center (INIA-CISA), 28130, Valdeolmos, Madrid, Spain
| | - Gabriel Soares Guerra
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Spain
| | - Isbene Sanchez
- Vacunek SL, Bizkaia Technology Park, 48160, Derio, Spain
| | - Joseba M Garrido
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Derio, Bizkaia, Spain
| | - Marivi Geijo
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Derio, Bizkaia, Spain
| | - Alejandro Brun
- Animal Health Research Center (INIA-CISA), 28130, Valdeolmos, Madrid, Spain
| | - Nicola G A Abrescia
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Spain. .,Basque Foundation for Science, IKERBASQUE, 48013, Bilbao, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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17
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Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Coelho H, Diniz A, Peccati F, Delgado S, Bosch A, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jiménez‐Osés G, Jiménez‐Barbero J, Ardá A, Ereño‐Orbea J. Structural Characterization of N‐Linked Glycans in the Receptor Binding Domain of the SARS‐CoV‐2 Spike Protein and their Interactions with Human Lectins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maria Pia Lenza
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Iker Oyenarte
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Tammo Diercks
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Jon Imanol Quintana
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Ana Gimeno
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Helena Coelho
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Ana Diniz
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Francesca Peccati
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Sandra Delgado
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Alexandre Bosch
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Mikel Valle
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Oscar Millet
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Nicola G. A. Abrescia
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) Instituto de Salud Carlos III Madrid Spain
| | - Asís Palazón
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
| | - Filipa Marcelo
- UCIBIO REQUIMTE Departamento de Química Faculdade de Ciências e Tecnologia Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Gonzalo Jiménez‐Osés
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - Jesús Jiménez‐Barbero
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Department of Organic Chemistry II University of the Basque Country UPV/EHU 48940 Leioa Spain
| | - Ana Ardá
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
| | - June Ereño‐Orbea
- CIC bioGUNE Basque Research and Technology Alliance BRTA Bizkaia Technology Park 48162 Derio Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
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18
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Andrés G, Charro D, Matamoros T, Dillard RS, Abrescia NGA. The cryo-EM structure of African swine fever virus unravels a unique architecture comprising two icosahedral protein capsids and two lipoprotein membranes. J Biol Chem 2020; 295:1-12. [PMID: 31649031 PMCID: PMC6952596 DOI: 10.1074/jbc.ac119.011196] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/22/2019] [Indexed: 11/06/2022] Open
Abstract
African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease currently present in many countries of Africa, Europe, and Asia. Despite intense research efforts, relevant gaps in the architecture of the infectious virus particle remain. Here, we used single-particle cryo-EM to analyze the three-dimensional structure of the mature ASFV particle. Our results show that the ASFV virion, with a radial diameter of ∼2,080 Å, encloses a genome-containing nucleoid surrounded by two distinct icosahedral protein capsids and two lipoprotein membranes. The outer capsid forms a hexagonal lattice (triangulation number T = 277) composed of 8,280 copies of the double jelly-roll major capsid protein (MCP) p72, arranged in trimers displaying a pseudo-hexameric morphology, and of 60 copies of a penton protein at the vertices. The inner protein layer, organized as a T = 19 capsid, confines the core shell, and it is composed of the mature products derived from the ASFV polyproteins pp220 and pp62. Also, an icosahedral membrane lies between the two protein layers, whereas a pleomorphic envelope wraps the outer capsid. This high-level organization confers to ASFV a unique architecture among the NCLDVs that likely reflects the complexity of its infection process and may help explain current challenges in controlling it.
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Affiliation(s)
- German Andrés
- Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Diego Charro
- Molecular Recognition and Host-Pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Tania Matamoros
- Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Rebecca S Dillard
- NeCEN, Institute of Biology Leiden, Leiden University, 2333_CC Leiden, Netherlands
| | - Nicola G A Abrescia
- Molecular Recognition and Host-Pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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19
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Santos-Pérez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA. Structural basis for assembly of vertical single β-barrel viruses. Nat Commun 2019; 10:1184. [PMID: 30862777 PMCID: PMC6414509 DOI: 10.1038/s41467-019-08927-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/08/2019] [Indexed: 11/10/2022] Open
Abstract
The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs. Here, the authors present the cryo-EM structures of two archaeal, halophilic, internal membrane-containing icosahedral viruses at 3.7 and 3.8 Å resolution, providing insights into the assembly process of these and related PRD1-adeno lineage viruses.
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Affiliation(s)
- Isaac Santos-Pérez
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - Diego Charro
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Gil-Carton
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Technology Park, 48160, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Technology Park, 48160, Derio, Spain
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Nicola G A Abrescia
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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20
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Kotecha A, Wang Q, Dong X, Ilca SL, Ondiviela M, Zihe R, Seago J, Charleston B, Fry EE, Abrescia NGA, Springer TA, Huiskonen JT, Stuart DI. Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus. Nat Commun 2017; 8:15408. [PMID: 28534487 PMCID: PMC5457520 DOI: 10.1038/ncomms15408] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/26/2017] [Indexed: 11/21/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role.
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Affiliation(s)
- Abhay Kotecha
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Quan Wang
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine and Division of Hematology, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Serban L. Ilca
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Marina Ondiviela
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
| | - Rao Zihe
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | | | | | - Elizabeth E. Fry
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Timothy A. Springer
- Program in Cellular and Molecular Medicine and Division of Hematology, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Juha T. Huiskonen
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - David I. Stuart
- Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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21
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Boshra HY, Charro D, Lorenzo G, Sánchez I, Lazaro B, Brun A, Abrescia NGA. DNA vaccination regimes against Schmallenberg virus infection in IFNAR -/- mice suggest two targets for immunization. Antiviral Res 2017; 141:107-115. [PMID: 28235558 DOI: 10.1016/j.antiviral.2017.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/04/2017] [Accepted: 02/20/2017] [Indexed: 11/19/2022]
Abstract
Schmallenberg virus (SBV) is an RNA virus of the Bunyaviridae family, genus Orthobunyavirus that infects wild and livestock species of ruminants. While inactivated and attenuated vaccines have been shown to prevent SBV infection, little is known about their mode of immunity; specifically, which components of the virus are responsible for inducing immunological responses in the host. As previous DNA vaccination experiments on other bunyaviruses have found that glycoproteins, as well as modified (i.e. ubiquitinated) nucleoproteins (N) can confer immunity against virulent viral challenge, constructs encoding for fragments of SBV glycoproteins GN and GC, as well as ubiquitinated and non-ubiquitinated N were cloned in mammalian expression vectors, and vaccinated intramuscularly in IFNAR-/- mice. Upon viral challenge with virulent SBV, disease progression was monitored. Both the ubiquitinated and non-ubiquitinated nucleoprotein candidates elicited high titers of antibodies against SBV, but only the non-ubiquitinated candidate induced statistically significant protection of the vaccinated mice from viral challenge. Another construct encoding for a putative ectodomain of glycoprotein GC (segment aa. 678-947) also reduced the SBV-viremia in mice after SBV challenge. When compared to other experimental groups, both the nucleoprotein and GC-ectodomain vaccinated groups displayed significantly reduced viremia, as well as exhibiting no clinical signs of SBV infection. These results show that both the nucleoprotein and the putative GC-ectodomain can serve as protective immunological targets against SBV infection, highlighting that viral glycoproteins, as well as nucleoproteins are potent targets in vaccination strategies against bunyaviruses.
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Affiliation(s)
- Hani Y Boshra
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Diego Charro
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | | | | | | | | | - Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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22
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Affiliation(s)
- Marta Ruiz-Guillen
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Cristian Smerdou
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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23
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Santos-Pérez I, Oksanen HM, Bamford DH, Goñi FM, Reguera D, Abrescia NGA. Membrane-assisted viral DNA ejection. Biochim Biophys Acta Gen Subj 2016; 1861:664-672. [PMID: 27993658 DOI: 10.1016/j.bbagen.2016.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 11/26/2022]
Abstract
Genome packaging and delivery are fundamental steps in the replication cycle of all viruses. Icosahedral viruses with linear double-stranded DNA (dsDNA) usually package their genome into a preformed, rigid procapsid using the power generated by a virus-encoded packaging ATPase. The pressure and stored energy due to this confinement of DNA at a high density is assumed to drive the initial stages of genome ejection. Membrane-containing icosahedral viruses, such as bacteriophage PRD1, present an additional architectural complexity by enclosing their genome within an internal membrane vesicle. Upon adsorption to a host cell, the PRD1 membrane remodels into a proteo-lipidic tube that provides a conduit for passage of the ejected linear dsDNA through the cell envelope. Based on volume analyses of PRD1 membrane vesicles captured by cryo-electron tomography and modeling of the elastic properties of the vesicle, we propose that the internal membrane makes a crucial and active contribution during infection by maintaining the driving force for DNA ejection and countering the internal turgor pressure of the host. These novel functions extend the role of the PRD1 viral membrane beyond tube formation or the mere physical confinement of the genome. The presence and assistance of an internal membrane might constitute a biological advantage that extends also to other viruses that package their linear dsDNA to high density within an internal vesicle.
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Affiliation(s)
- Isaac Santos-Pérez
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Hanna M Oksanen
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9B, 00014, Finland
| | - Dennis H Bamford
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9B, 00014, Finland
| | - Felix M Goñi
- Unidad de Biofísica (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain
| | - David Reguera
- Departament de Física de la Materia Condensada, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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24
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Affiliation(s)
- David I Stuart
- Instruct, Division of Structural Biology, the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, UK
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Nicola G A Abrescia
- Structural Biology Unit, CICbioGUNE, CIBERehd, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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25
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Ruiz-Guillen M, Gabev E, Quetglas JI, Casales E, Ballesteros-Briones MC, Poutou J, Aranda A, Martisova E, Bezunartea J, Ondiviela M, Prieto J, Hernandez-Alcoceba R, Abrescia NGA, Smerdou C. Capsid-deficient alphaviruses generate propagative infectious microvesicles at the plasma membrane. Cell Mol Life Sci 2016; 73:3897-916. [PMID: 27117550 PMCID: PMC7079800 DOI: 10.1007/s00018-016-2230-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/25/2022]
Abstract
Alphavirus budding is driven by interactions between nucleocapsids assembled in the cytoplasm and envelope proteins present at the plasma membrane. So far, the expression of capsid and envelope proteins in infected cells has been considered an absolute requirement for alphavirus budding and propagation. In the present study, we show that Semliki Forest virus and Sindbis virus lacking the capsid gene can propagate in mammalian and insect cells. This propagation is mediated by the release of infectious microvesicles (iMVs), which are pleomorphic and have a larger size and density than wild-type virus. iMVs, which contain viral RNA inside and viral envelope proteins on their surface, are released at the plasma membrane and infect cells using the endocytic pathway in a similar way to wild-type virus. iMVs are not pathogenic in immunocompetent mice when injected intravenously, but can infect different organs like lungs and heart. Finally, we also show that alphavirus genomes without capsid can mediate the propagation of heterologous genes, making these vectors potentially interesting for gene therapy or vaccination studies. The minimalist infectious system described in this study shows that a self-replicating RNA able to express membrane proteins with binding and fusion properties is able to propagate, providing some insights into virus evolution.
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Affiliation(s)
- Marta Ruiz-Guillen
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- 3P Biopharmaceuticals S.L., Noain, Spain
| | - Evgeni Gabev
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Jose I Quetglas
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Erkuden Casales
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | | | - Joanna Poutou
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Alejandro Aranda
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- UFR des Sciences de la Santé Simone Veil, 2 avenue de la Source de la Bievre, 78180, Montugny-le-Bretonneux, France
| | - Eva Martisova
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Jaione Bezunartea
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Experimental Ophthalmology Laboratory, School of Medicine, University of Navarra, Pamplona, Spain
| | - Marina Ondiviela
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain
| | - Jesus Prieto
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Liver Unit, Clinica Universitaria de Navarra, CIBERehd, Pamplona, Spain
| | - Ruben Hernandez-Alcoceba
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Cristian Smerdou
- Division of Gene Therapy, CIMA, University of Navarra, Pamplona, Spain.
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
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Gil-Carton D, Jaakkola ST, Charro D, Peralta B, Castaño-Díez D, Oksanen HM, Bamford DH, Abrescia NGA. Insight into the Assembly of Viruses with Vertical Single β-barrel Major Capsid Proteins. Structure 2015; 23:1866-1877. [PMID: 26320579 DOI: 10.1016/j.str.2015.07.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 02/02/2023]
Abstract
Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of life. Here, using biochemical and cryo-electron microscopy techniques, we solved the structure of euryarchaeal, halophilic, internal membrane-containing Haloarcula hispanica icosahedral virus 2 (HHIV-2). We show that the density of the two major capsid proteins (MCPs) recapitulates vertical single β-barrel proteins and that disulfide bridges stabilize the capsid. Below, ordered density is visible close to the membrane and at the five-fold vertices underneath the host-interacting vertex complex underpinning membrane-protein interactions. The HHIV-2 structure exemplifies the division of conserved architectural elements of a virion, such as the capsid, from those that evolve rapidly due to selective environmental pressure such as host-recognizing structures. We propose that in viruses with two vertical single β-barrel MCPs the vesicle is indispensable, and membrane-protein interactions serve as protein-railings for guiding the assembly.
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Affiliation(s)
- David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Salla T Jaakkola
- Department of Biosciences and Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014 Helsinki, Finland
| | - Diego Charro
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Bibiana Peralta
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - Daniel Castaño-Díez
- Scientific Computing Unit, Max-Planck Institute for Brain Research, 60438 Frankfurt, Germany
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014 Helsinki, Finland
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014 Helsinki, Finland
| | - Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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Azkargorta M, Wojtas MN, Abrescia NGA, Elortza F. Lysine methylation mapping of crenarchaeal DNA-directed RNA polymerases by collision-induced and electron-transfer dissociation mass spectrometry. J Proteome Res 2014; 13:2637-48. [PMID: 24625205 DOI: 10.1021/pr500084p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic machineries fundamental for information processing (e.g., transcription, replication, translation) in Archaea are simplified versions of their eukaryotic counterparts. This is clearly noticeable in the conservation of sequence and structure of corresponding enzymes (see for example the archaeal DNA-directed RNA polymerase (RNAP)). In Eukarya, post-translational modifications (PTMs) often serve as functional regulatory factors for various enzymes and complexes. Among the various PTMs, methylation and acetylation have been recently attracting most attention. Nevertheless, little is known about such PTMs in Archaea, and cross-methodological studies are scarce. We examined methylation and N-terminal acetylation of endogenously purified crenarchaeal RNA polymerase from Sulfolobus shibatae (Ssh) and Sulfolobus acidocaldarius (Sac). In-gel and in-solution protein digestion methods were combined with collision-induced dissociation (CID) and electron-transfer dissociation (ETD) mass spectrometry analysis. Overall, 20 and 26 methyl-lysines for S. shibatae and S. acidocaldarius were identified, respectively. Furthermore, two N-terminal acetylation sites for each of these organisms were assessed. As a result, we generated a high-confidence data set for the mapping of methylation and acetylation sites in both Sulfolobus species, allowing comparisons with the data previously obtained for RNAP from Sulfolobus solfataricus (Sso). We confirmed that all observed methyl-lysines are on the surface of the RNAP.
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Affiliation(s)
- Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, CIBERehd, 48160 Derio, Spain
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28
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Stuart DI, Abrescia NGA. From lows to highs: using low-resolution models to phase X-ray data. Acta Crystallogr D Biol Crystallogr 2013; 69:2257-65. [PMID: 24189238 PMCID: PMC3817700 DOI: 10.1107/s0907444913022336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/08/2013] [Indexed: 11/11/2022]
Abstract
The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ~13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.
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Affiliation(s)
- David I Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
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29
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Peralta B, Gil-Carton D, Castaño-Díez D, Bertin A, Boulogne C, Oksanen HM, Bamford DH, Abrescia NGA. Mechanism of membranous tunnelling nanotube formation in viral genome delivery. PLoS Biol 2013; 11:e1001667. [PMID: 24086111 PMCID: PMC3782422 DOI: 10.1371/journal.pbio.1001667] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 08/15/2013] [Indexed: 11/19/2022] Open
Abstract
In internal membrane-containing viruses, a lipid vesicle enclosed by the icosahedral capsid protects the genome. It has been postulated that this internal membrane is the genome delivery device of the virus. Viruses built with this architectural principle infect hosts in all three domains of cellular life. Here, using a combination of electron microscopy techniques, we investigate bacteriophage PRD1, the best understood model for such viruses, to unveil the mechanism behind the genome translocation across the cell envelope. To deliver its double-stranded DNA, the icosahedral protein-rich virus membrane transforms into a tubular structure protruding from one of the 12 vertices of the capsid. We suggest that this viral nanotube exits from the same vertex used for DNA packaging, which is biochemically distinct from the other 11. The tube crosses the capsid through an aperture corresponding to the loss of the peripentonal P3 major capsid protein trimers, penton protein P31 and membrane protein P16. The remodeling of the internal viral membrane is nucleated by changes in osmolarity and loss of capsid-membrane interactions as consequence of the de-capping of the vertices. This engages the polymerization of the tail tube, which is structured by membrane-associated proteins. We have observed that the proteo-lipidic tube in vivo can pierce the gram-negative bacterial cell envelope allowing the viral genome to be shuttled to the host cell. The internal diameter of the tube allows one double-stranded DNA chain to be translocated. We conclude that the assembly principles of the viral tunneling nanotube take advantage of proteo-lipid interactions that confer to the tail tube elastic, mechanical and functional properties employed also in other protein-membrane systems.
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Affiliation(s)
- Bibiana Peralta
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio, Spain
| | | | - Daniel Castaño-Díez
- Center for Cellular Imaging and Nano-Analitics (C-CINA) Biozentrum, University of Basel, Basel, Switzerland
| | - Aurelie Bertin
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université de Paris–Sud, Orsay, France
| | - Claire Boulogne
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université de Paris–Sud, Orsay, France
| | - Hanna M. Oksanen
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail:
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Roversi P, Ondiviela M, Abrescia NGA. Structural comparison of the head-subdomain of human CD81 large extra-cellular loop. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313097286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
A virus particle must work as a safe box for protecting its genome, but at the same time it has to undergo dramatic conformational changes in order to preserve itself by propagating in a cell infection. Thus, viruses are miniaturized wonders whose structural complexity requires them to be investigated by a combination of different techniques that can tackle both static and dynamic processes. In this chapter we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy have been and can be combined with other techniques to determine the structure of complex viruses. The power of these hybrid method approaches are revealed through the various examples provided.
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Affiliation(s)
- Daniel Badia-Martinez
- Structural Biology Unit, CICbioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
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Wojtas MN, Abrescia NGA. Soaking of DNA into crystals of archaeal RNA polymerase achieved by desalting in droplets. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1134-8. [PMID: 22949213 PMCID: PMC3433216 DOI: 10.1107/s1744309112033507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/24/2012] [Indexed: 11/06/2023]
Abstract
Transcription is a fundamental process across the three domains of life and is carried out by multi-subunit enzymatic DNA-directed RNA polymerases (RNAPs). The interaction of RNAP with nucleic acids is tightly controlled for precise and processive RNA synthesis. Whilst a wealth of structural information has been gathered on the eukaryotic Pol II in complex with DNA/RNA, no information exists on its ancestral counterpart archaeal RNAP. Thus, in order to extend knowledge of the archaeal transcriptional apparatus, crystallization of Sulfolobus shibatae RNAP (molecular mass of ~400 kDa) with DNA fragments was pursued. To achieve this goal, crystal growth was first optimized using a nanoseeding technique. An ad hoc soaking protocol was then put into place, which consisted of gently exchanging the high-salt buffer used for apo-RNAP crystal growth into a low-salt buffer necessary for DNA binding to RNAP. Of the various crystals screened, one diffracted to 4.3 Å resolution and structural analysis showed the presence of bound DNA [Wojtas et al. (2012). Nucleic Acids Res. 40, doi:10.1093/nar/gks692].
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Affiliation(s)
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NGA. Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic Acids Res 2012; 40:9941-52. [PMID: 22848102 PMCID: PMC3479171 DOI: 10.1093/nar/gks692] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP–DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP–DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP–DNA interaction.
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Abstract
Is it possible to meaningfully comprehend the diversity of the viral world? We propose that it is. This is based on the observation that, although there is immense genomic variation, every infective virion is restricted by strict constraints in structure space (i.e., there are a limited number of ways to fold a protein chain, and only a small subset of these have the potential to construct a virion, the hallmark of a virus). We have previously suggested the use of structure for the higher-order classification of viruses, where genomic similarities are no longer observable. Here, we summarize the arguments behind this proposal, describe the current status of structural work, highlighting its power to infer common ancestry, and discuss the limitations and obstacles ahead of us. We also reflect on the future opportunities for a more concerted effort to provide high-throughput methods to facilitate the large-scale sampling of the virosphere.
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El Omari K, Dhaliwal B, Ren J, Abrescia NGA, Lockyer M, Powell KL, Hawkins AR, Stammers DK. Structures of respiratory syncytial virus nucleocapsid protein from two crystal forms: details of potential packing interactions in the native helical form. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1179-83. [PMID: 22102022 DOI: 10.1107/s1744309111029228] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/19/2011] [Indexed: 11/10/2022]
Abstract
Respiratory syncytial virus (RSV) is a frequent cause of respiratory illness in infants, but there is currently no vaccine nor effective drug treatment against this virus. The RSV RNA genome is encapsidated and protected by a nucleocapsid protein; this RNA-nucleocapsid complex serves as a template for viral replication. Interest in the nucleocapsid protein has increased owing to its recent identification as the target site for novel anti-RSV compounds. The crystal structure of human respiratory syncytial virus nucleocapsid (HRSVN) was determined to 3.6 Å resolution from two crystal forms belonging to space groups P2(1)2(1)2(1) and P1, with one and four decameric rings per asymmetric unit, respectively. In contrast to a previous structure of HRSVN, the addition of phosphoprotein was not required to obtain diffraction-quality crystals. The HRSVN structures reported here, although similar to the recently published structure, present different molecular packing which may have some biological implications. The positions of the monomers are slightly shifted in the decamer, confirming the adaptability of the ring structure. The details of the inter-ring contacts in one crystal form revealed here suggest a basis for helical packing and that the stabilization of native HRSVN is via mainly ionic interactions.
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Affiliation(s)
- K El Omari
- Division of Structural Biology and Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
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Abrescia NGA, Grimes JM, Oksanen HM, Bamford JKH, Bamford DH, Stuart DI. The use of low-resolution phasing followed by phase extension from 7.6 to 2.5 Å resolution with noncrystallographic symmetry to solve the structure of a bacteriophage capsid protein. Acta Crystallogr D Biol Crystallogr 2011; 67:228-32. [PMID: 21358054 DOI: 10.1107/s0907444911002277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 01/14/2011] [Indexed: 11/10/2022]
Abstract
P2, the major capsid protein of bacteriophage PM2, adopts the double β-barrel fold characteristic of the PRD1-adenoviral lineage. The 2.5 Å resolution X-ray data obtained by analysis of the two major lattices of a multiple crystal of P2 were phased by molecular replacement, using as a search model structure factors to 7.6 Å resolution obtained from electron density cut from the map of the entire PM2 virion. Phase extension to 2.5 Å resolution used solely sixfold cycling averaging and solvent flattening. This represents an atypical example of an oligomeric protein for which the structure has been determined at high resolution by bootstrapping from low-resolution initial phases.
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Affiliation(s)
- Nicola G A Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain
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37
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Graham SC, Bahar MW, Cooray S, Chen RAJ, Whalen DM, Abrescia NGA, Alderton D, Owens RJ, Stuart DI, Smith GL, Grimes JM. Vaccinia virus proteins A52 and B14 Share a Bcl-2-like fold but have evolved to inhibit NF-kappaB rather than apoptosis. PLoS Pathog 2008; 4:e1000128. [PMID: 18704168 PMCID: PMC2494871 DOI: 10.1371/journal.ppat.1000128] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 07/17/2008] [Indexed: 12/18/2022] Open
Abstract
Vaccinia virus (VACV), the prototype poxvirus, encodes numerous proteins that modulate the host response to infection. Two such proteins, B14 and A52, act inside infected cells to inhibit activation of NF-kappaB, thereby blocking the production of pro-inflammatory cytokines. We have solved the crystal structures of A52 and B14 at 1.9 A and 2.7 A resolution, respectively. Strikingly, both these proteins adopt a Bcl-2-like fold despite sharing no significant sequence similarity with other viral or cellular Bcl-2-like proteins. Unlike cellular and viral Bcl-2-like proteins described previously, A52 and B14 lack a surface groove for binding BH3 peptides from pro-apoptotic Bcl-2-like proteins and they do not modulate apoptosis. Structure-based phylogenetic analysis of 32 cellular and viral Bcl-2-like protein structures reveals that A52 and B14 are more closely related to each other and to VACV N1 and myxoma virus M11 than they are to other viral or cellular Bcl-2-like proteins. This suggests that a progenitor poxvirus acquired a gene encoding a Bcl-2-like protein and, over the course of evolution, gene duplication events have allowed the virus to exploit this Bcl-2 scaffold for interfering with distinct host signalling pathways.
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Affiliation(s)
- Stephen C. Graham
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mohammad W. Bahar
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Samantha Cooray
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Ron A.-J. Chen
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Daniel M. Whalen
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicola G. A. Abrescia
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David Alderton
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Raymond J. Owens
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David I. Stuart
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Geoffrey L. Smith
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Jonathan M. Grimes
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Graham SC, Bahar MW, Abrescia NGA, Smith GL, Stuart DI, Grimes JM. Structure of CrmE, a Virus-encoded Tumour Necrosis Factor Receptor. J Mol Biol 2007; 372:660-71. [PMID: 17681535 DOI: 10.1016/j.jmb.2007.06.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 06/18/2007] [Accepted: 06/28/2007] [Indexed: 11/17/2022]
Abstract
Vaccinia virus (VACV), the smallpox vaccine, encodes many proteins that subvert the host immune response. One of these, cytokine response modifier E (CrmE), is secreted by infected cells and protects these cells from apoptotic challenge by tumour necrosis factor alpha (TNFalpha). We have expressed recombinant CrmE from VACV strain Lister in Escherichia coli, shown that the purified protein is monomeric in solution and competent to bind TNFalpha, and solved the structure to 2.0 A resolution. This is the first structure of a virus-encoded tumour necrosis factor receptor (TNFR). CrmE shares significant sequence similarity with mammalian type 2 TNF receptors (TNFSFR1B, p75; TNFR type 2). The structure confirms that CrmE adopts the canonical TNFR fold but only one of the two "ligand-binding" loops of TNFRSF1A is conserved in CrmE, suggesting a mechanism for the higher affinity of poxvirus TNFRs for TNFalpha over lymphotoxin-alpha. The roles of dimerisation and pre-ligand-assembly domains (PLADs) in poxvirus and mammalian TNFR activity are discussed.
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MESH Headings
- Amino Acid Sequence
- Crystallography, X-Ray
- Humans
- Hydrophobic and Hydrophilic Interactions
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Receptors, Tumor Necrosis Factor/chemistry
- Receptors, Tumor Necrosis Factor/isolation & purification
- Receptors, Tumor Necrosis Factor/metabolism
- Receptors, Tumor Necrosis Factor, Type I/chemistry
- Receptors, Tumor Necrosis Factor, Type I/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Tumor Necrosis Factor-alpha/isolation & purification
- Tumor Necrosis Factor-alpha/metabolism
- Vaccinia virus/chemistry
- Viral Proteins/chemistry
- Viral Proteins/isolation & purification
- Viral Proteins/metabolism
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Affiliation(s)
- Stephen C Graham
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Oxford Protein Production Facility Roosevelt Drive, Headington, Oxford OX3 7BN, UK
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Cooray S, Bahar MW, Abrescia NGA, McVey CE, Bartlett NW, Chen RAJ, Stuart DI, Grimes JM, Smith GL. Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein. J Gen Virol 2007; 88:1656-1666. [PMID: 17485524 PMCID: PMC2885619 DOI: 10.1099/vir.0.82772-0] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Vaccinia virus (VACV) encodes many immunomodulatory proteins, including inhibitors of apoptosis and modulators of innate immune signalling. VACV protein N1 is an intracellular homodimer that contributes to virus virulence and was reported to inhibit nuclear factor (NF)-κB signalling. However, analysis of NF-κB signalling in cells infected with recombinant viruses with or without the N1L gene showed no difference in NF-κB-dependent gene expression. Given that N1 promotes virus virulence, other possible functions of N1 were investigated and this revealed that N1 is an inhibitor of apoptosis in cells transfected with the N1L gene and in the context of VACV infection. In support of this finding virally expressed N1 co-precipitated with endogenous pro-apoptotic Bcl-2 proteins Bid, Bad and Bax as well as with Bad and Bax expressed by transfection. In addition, the crystal structure of N1 was solved to 2.9 Å resolution (0.29 nm). Remarkably, although N1 shows no sequence similarity to cellular proteins, its three-dimensional structure closely resembles Bcl-xL and other members of the Bcl-2 protein family. The structure also reveals that N1 has a constitutively open surface groove similar to the grooves of other anti-apoptotic Bcl-2 proteins, which bind the BH3 motifs of pro-apoptotic Bcl-2 family members. Molecular modelling of BH3 peptides into the N1 surface groove, together with analysis of their physico-chemical properties, suggests a mechanism for the specificity of peptide recognition. This study illustrates the importance of the evolutionary conservation of structure, rather than sequence, in protein function and reveals a novel anti-apoptotic protein from orthopoxviruses.
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Affiliation(s)
- Samantha Cooray
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Mohammad W. Bahar
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Nicola G. A. Abrescia
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Colin E. McVey
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Nathan W. Bartlett
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Ron A.-J. Chen
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - David I. Stuart
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jonathan M. Grimes
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Geoffrey L. Smith
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
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Jovanovic J, Takagi J, Choulier L, Abrescia NGA, Stuart DI, van der Merwe PA, Mardon HJ, Handford PA. αVβ6 Is a Novel Receptor for Human Fibrillin-1. J Biol Chem 2007; 282:6743-51. [PMID: 17158881 DOI: 10.1074/jbc.m607008200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human fibrillin-1, the major structural protein of connective tissue 10-12 nm microfibrils, contains multiple calcium binding epidermal growth factor-like domains interspersed with transforming growth factor beta-binding protein-like (TB) domains. TB4 contains a flexible RGD loop that mediates cell adhesion via alphaVbeta3 and alpha5beta1 integrins. This study identifies integrin alphaVbeta6 as a novel cellular receptor for fibrillin-1 with a K(d) of approximately 0.45 mum. Analyses of this interaction by surface plasmon resonance and immunocytochemistry reveal different module requirements for alphaVbeta6 activation compared with those of alphaVbeta3, suggesting that a covalent linkage of an N-terminal calcium binding epidermal growth factor-like domain to TB4 can modulate alphaV integrin binding specificity. Furthermore, our data suggest alpha5beta1 is a low affinity fibrillin-1 receptor (K(d) > 1 mum), thus providing a molecular explanation for the different alpha5beta1 distribution patterns seen when human keratinocytes and fibroblasts are plated on recombinant fibrillin fragments versus those derived from the physiological ligand fibronectin. Non-focal contact distribution of alpha5beta1 suggests that its engagement by fibrillin-1 may elicit a lesser degree and/or different type of intracellular signaling compared with that seen with a high affinity ligand.
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Affiliation(s)
- Jelena Jovanovic
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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41
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Burman A, Clark S, Abrescia NGA, Fry EE, Stuart DI, Jackson T. Specificity of the VP1 GH loop of Foot-and-Mouth Disease virus for alphav integrins. J Virol 2006; 80:9798-810. [PMID: 16973584 PMCID: PMC1617245 DOI: 10.1128/jvi.00577-06] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) can use a number of integrins as receptors to initiate infection. Attachment to the integrin is mediated by a highly conserved arginine-glycine-aspartic acid (RGD) tripeptide located on the GH loop of VP1. Other residues of this loop are also conserved and may contribute to integrin binding. In this study we have used a 17-mer peptide, whose sequence corresponds to the GH loop of VP1 of type O FMDV, as a competitor of integrin-mediated virus binding and infection. Alanine substitution through this peptide identified the leucines at the first and fourth positions following RGD (RGD+1 and RGD+4 sites) as key for inhibition of virus binding and infection mediated by alphavbeta6 or alphavbeta8 but not for inhibition of virus binding to alphavbeta3. We also show that FMDV peptides containing either methionine or arginine at the RGD+1 site, which reflects the natural sequence variation seen across the FMDV serotypes, are effective inhibitors for alphavbeta6. In contrast, although RGDM-containing peptides were effective for alphavbeta8, RGDR-containing peptides were not. These observations were confirmed by showing that a virus containing an RGDR motif uses alphavbeta8 less efficiently than alphavbeta6 as a receptor for infection. Finally, evidence is presented that shows alphavbeta3 to be a poor receptor for infection by type O FMDV. Taken together, our data suggest that the integrin binding loop of FMDV has most likely evolved for binding to alphavbeta6 with a higher affinity than to alphavbeta3 and alphavbeta8.
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Affiliation(s)
- Alison Burman
- Division of Microbiology, Institute for Animal Health, Pirbright, Surrey, GU24 ONF, United Kingdom
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42
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Abrescia NGA, Kivelä HM, Grimes JM, Bamford JKH, Bamford DH, Stuart DI. Preliminary crystallographic analysis of the major capsid protein P2 of the lipid-containing bacteriophage PM2. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:762-5. [PMID: 16511151 PMCID: PMC1952355 DOI: 10.1107/s174430910502141x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 07/05/2005] [Indexed: 11/10/2022]
Abstract
PM2 (Corticoviridae) is a dsDNA bacteriophage which contains a lipid membrane beneath its icosahedral capsid. In this respect it resembles bacteriophage PRD1 (Tectiviridae), although it is not known whether the similarity extends to the detailed molecular architecture of the virus, for instance the fold of the major coat protein P2. Structural analysis of PM2 has been initiated and virus-derived P2 has been crystallized by sitting-nanodrop vapour diffusion. Crystals of P2 have been obtained in space group P2(1)2(1)2, with two trimers in the asymmetric unit and unit-cell parameters a = 171.1, b = 78.7, c = 130.1 A. The crystals diffract to 4 A resolution at the ESRF BM14 beamline (Grenoble, France) and the orientation of the non-crystallographic threefold axes, the spatial relationship between the two trimers and the packing of the trimers within the unit cell have been determined. The trimers form tightly packed layers consistent with the crystal morphology, possibly recapitulating aspects of the arrangement of subunits in the virus.
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Affiliation(s)
- Nicola G. A. Abrescia
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
| | - Hanna M. Kivelä
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland
| | - Jonathan M. Grimes
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
| | - Jaana K. H. Bamford
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
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Ferris NP, Abrescia NGA, Stuart DI, Jackson T, Burman A, King DP, Paton DJ. Utility of recombinant integrin alpha v beta6 as a capture reagent in immunoassays for the diagnosis of foot-and-mouth disease. J Virol Methods 2005; 127:69-79. [PMID: 15893568 DOI: 10.1016/j.jviromet.2005.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Revised: 02/21/2005] [Accepted: 02/22/2005] [Indexed: 11/23/2022]
Abstract
Recombinant integrin alpha v beta6 was evaluated as a capture ligand in a sandwich ELISA for the detection and serotyping of foot-and-mouth disease (FMD) virus. Our routinely applied method employs seven serotype-specific rabbit polyclonal antibodies as capture ligands and seven serotype-specific guinea pig polyclonal antibodies as detecting reagents. The recombinant integrin bound FMD virus of all seven serotypes but not that of another vesicular disease, swine vesicular disease (SVD). Considerable heterotypic cross-reactions were evident when using the integrin capture ligand in combination with guinea pig detecting antibodies but totally type-specific reactions resulted when serotype-specific monoclonal antibodies (mabs) were used instead of the guinea pig reagents. The specificity of reaction of the integrin capture/mab detector combination was superior to that of our routinely employed rabbit/guinea pig ELISA and offers an improvement for test interpretation. As a universal trapping reagent for all FMD virus serotypes the alpha v beta6 recombinant protein also has the potential for application in other test procedures for viral identification (e.g. pen-side chromatographic strip-tests, biosensors, immunocapture RT-PCR, antigenic characterization procedures and monoclonal antibody profiling of emerging field virus strains) and in antibody detection assays employed for the diagnosis of FMD.
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Affiliation(s)
- Nigel P Ferris
- Institute for Animal Health, Pirbright Laboratory, Woking, Surrey GU24 0NF, UK.
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Cockburn JJB, Abrescia NGA, Grimes JM, Sutton GC, Diprose JM, Benevides JM, Thomas GJ, Bamford JKH, Bamford DH, Stuart DI. Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 2004; 432:122-5. [PMID: 15525993 DOI: 10.1038/nature03053] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 09/21/2004] [Indexed: 11/09/2022]
Abstract
Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 A resolution by cryo-electron microscopy and image reconstruction, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 A resolution, allows the first detailed analysis of a membrane-containing virus. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.
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Affiliation(s)
- Joseph J B Cockburn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK
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Abrescia NGA, Cockburn JJB, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martín C, Burnett RM, Stuart DI, Bamford DH, Bamford JKH. Insights into assembly from structural analysis of bacteriophage PRD1. Nature 2004; 432:68-74. [PMID: 15525981 DOI: 10.1038/nature03056] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 09/21/2004] [Indexed: 11/09/2022]
Abstract
The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have specialist roles in controlling virus assembly. The linearly extended P30 appears to nucleate the formation of the icosahedral facets (composed of trimers of the major capsid protein, P3) and acts as a molecular tape-measure, defining the size of the virus and cementing the facets together. Pentamers of P31 form the vertex base, interlocking with subunits of P3 and interacting with the membrane protein P16. The architectural similarities with adenovirus and one of the largest known virus particles PBCV-1 support the notion that the mechanism of assembly of PRD1 is scaleable and applies across the major viral lineage formed by these viruses.
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Affiliation(s)
- Nicola G A Abrescia
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK
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Abrescia NGA, González C, Gouyette C, Subirana JA. X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA. Biochemistry 2004; 43:4092-100. [PMID: 15065851 DOI: 10.1021/bi0355140] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA.
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Affiliation(s)
- Nicola G A Abrescia
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Av. Diagonal 647, E-08028 Barcelona, Spain.
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47
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Abstract
The structure of a new form of duplex DNA, the antiparallel Hoogsteen duplex, is studied in polyd(AT) sequences by means of state-of-the-art molecular dynamics simulations in aqueous solution. The structure, which was found to be stable in all of the simulations, has many similarities with the standard Watson-Crick duplex in terms of general structure, flexibility, and molecular recognition patterns. Accurate MM-PB/SA (and MM-GB/SA) analysis shows that the new structure has an effective energy similar to that of the B-type duplex, while it is slightly disfavored by intramolecular entropic considerations. Overall, MD simulations strongly suggest that the antiparallel Hoogsteen duplex is an accessible structure for a polyd(AT) sequence, which might compete under proper experimental conditions with normal B-DNA. MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved.
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Affiliation(s)
- Elena Cubero
- Molecular Modeling & Bioinformatic Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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Abrescia NGA, Subirana JA. When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice. Acta Crystallogr D Biol Crystallogr 2002; 58:2205-8. [PMID: 12454502 DOI: 10.1107/s0907444902015500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2002] [Accepted: 08/27/2002] [Indexed: 11/10/2022]
Abstract
The d(ApTpApTpApT) deoxyhexanucleotide packs in two different lattice systems: monoclinic and hexagonal. In this study, it is shown that in the hexagonal crystals twinning and pseudosymmetry coexist. The presence of both components resulted in a puzzling space-group determination. Only when a correct model became available [Hoogsteen-DNA; Abrescia et al. (2002), Proc. Natl Acad. Sci. USA, 99, 2806-2811] was it possible to discriminate between twinning and pseudosymmetry. Here, the steps that led to a correct space-group assignment and to the solution of the oligonucleotide structure in the hexagonal lattice by molecular replacement are described.
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Affiliation(s)
- Nicola G A Abrescia
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Avenida Diagonal 647, E-080028 Barcelona, Spain.
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Abrescia NGA, Thompson A, Huynh-Dinh T, Subirana JA. Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing. Proc Natl Acad Sci U S A 2002; 99:2806-11. [PMID: 11880632 PMCID: PMC122429 DOI: 10.1073/pnas.052675499] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We report here an alternative double-helical structure of the DNA molecule. It has been found in the d(ATA(Br)UAT) and d(ATATAT) sequences by single-crystal x-ray crystallography. This sequence is found not only in TATA boxes, but also in other regulatory regions of DNA. Bases of the two antiparallel strands form Hoogsteen pairs, with adenines in the syn conformation. The structure is related neither to those found in triple helices nor to parallel DNA duplexes. Its conformational parameters are very similar to those of duplex DNA in the B form. Both forms may coexist under physiological conditions, although the Hoogsteen pairing greatly influences the recognition sites on DNA. Our results demonstrate that an alternative to the classical B-DNA double helix is possible.
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Affiliation(s)
- Nicola G A Abrescia
- Departament d'Enginyeria Quimica, Universitat Politècnica de Catalunya, Avga Diagonal 647, E-08028 Barcelona, Spain
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50
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Manoj N, Srinivas VR, Surolia A, Vijayan M, Suguna K, Ravishankar R, Suguna K, Surolia A, Vijayan M, Schwarzenbacher R, Zeth K, Diederichs, Kostner GM, Gries A, Laggner P, Prassl R, Madhusudan, Akamine P, Xuong NH, Taylor SS, Sagar MB, Ravishankar R, Saikrishnan K, Roy S, Purnapatre K, Handa P, Varshney U, Vijayan M, Biswal BK, Sukumar N, Vijayan M, Rao JKM, Johnson A, Pattabhi V, Krishna SS, Sastri M, Savithri HS, Murthy MRN, Pillai B, Kannan, Hosur MV, Kumar M, Patwardhan S, Kannan KK, Hosur MV, Padmanabhaa B, Sasaki-Sugio S, Nukaga M, Matsuzaki T, Karthikevan S, Sharma S, Sharma AK, Paramasivam M, Kumar P, Khan JA, Yadav S, Srinivasan A, Singh TP, Gourinath S, Alam N, Srintvasan A, Singh TP, Chandra V, Kaur P, Betzel C, Singh TP, Ghosh S, Bera AK, Bhattacharya S, Chakraborty S, Pal AK, Mukhopadhyay BP, Dey I, Haldar U, Baneriee A, Sevcik J, Solovicova A, Sekar K, Sundaralingam M, Betzel C, Genov N, Singh TP, Liang DC, Jiang T, Zhang JP, Chang WR, Jahnke W, Blommers M, Panchal SC, Hosur RV, Pillay B, Hosur MV, Mathur P, Srivatsun S, Joshi RM, Jaganathan NR, Chauhan VS, Atreya HS, Sahu SC, Chary KVR, Ponce-Homos JE, Parisi M, Capurro C, Toriano R, Ready LG, Jones LR, Thomas DD, Tashmukhamedov BA, Sagdullaev BT, Usmanov PB, Govil G, Mauricio AC, Heitzmann D, Warth R, Bleich M, Greger R, Ferreira KTG, Ferreira HG, Zagoory O, Alfahel E, Parola AH, Adjadj E, Priel Z, Hama-Inaba H, Wang R, Choi K, Nakajima T, Haginoya K, Mori M, Ohyama H, Yukawa O, Hayata I, Quinjou É, Joshi NB, Kannurpatti SK, Joshi PG, Sinha M, Shen X, Hu T, Bei L, Knetsch MLW, Schäfers N, Manstein DJ, Izadi-Pruneyre N, Sandblom J, Galvanovskis J, Pologea-Moraru R, Kovacs E, Savopol T, Dinu A, Sanghvi SH, Mishra KP, Jazbinšek V, Thiel G, Blouquit Y, Müller W, Wübeller G, Tronteli Z, Fajmut L, Marhl M, Brumen M, Volotovski ID, Sokolovski SG, Knight MR, Vasil’ev AN, Mispelter J, Chalyi AV, Sharma P, Steinbach PJ, Sharma M, Amin ND, Barchir J, Albers RW, Pant HC, Balasubramanyam M, Condrescu M, Heyd B, Reeves JP, Gardner JP, Monajembashi S, Pilarczyk G, Greulich KO, Kovacs E, El-Refaei FM, Talaat MM, El-Awadi AI, Ali FM, Lerat G, Tahradník I, Pavelková J, Zahradniková A, Zhorov BS, Ananthanaravanan VS, Michailov MC, Neu E, Seidenbusch W, Gornik E, Martin D, Milnard P, Welscher U, Weiss DG, Pattnaik BR, Jellali A, Forster V, Hicks D, Sahel J, Dreyfus H, Picaud S, Wang HW, Desmadreil M, Sui SF, Luther PK, Barry J, Morris E, Squire J, Sundari CS, Balasubramanian D, Veluraia K, Christlet THT, Suresh MX, Lin Y, Berry H, Pelta J, Lairez D, Laretta-Garde V, Krilov D, Stojanović N, Herak JN, Jasuja R, Ivanova M, Mirchev R, Rao BDN, Ferrone FA, Stopar D, Spruijt RB, Wolfs CJAM, Hemminga MA, Arcovito G, De Spirito M, Sui SF, Wang HW, Agrawal RK, Raghunathan V, Heagle AB, Penczek P, Grassucci R, Frank J, Sharma MR, Jeyakumar LH, Fleischer S, Wagenknecht T, Knupp C, Munro PMG, Chau MH, Luther PK, Ezra E, Squire JM, Ichihara K, Kitazawa H, Iguchi Y, Hotani H, Itoh TJ, Pifat G, Kveder M, Rao BDN, Pečar S, Schara M, Nair D, Singh K, Rao KVS, Salunke DM, Kaur K, Jain D, Sundaravadivel B, Goel M, Pesais P, Salunke DM, Kovalenko EI, Semenkova GN, Cherenkevich SN, Lakshmanan T, Sriram D, Srinivasan S, Loganathan D, Ramalingam TS, Lebrón JA, Srivastava S, Bjorkman PJ, Singh AK, Gayatri TN, Jain D, Kaur K, Sundaravadivel B, Salunke DM, Caffarena ER, Grigera JR, Bisch PM, Coutinho E, Kiessling V, Fromherz P, Rao KN, Gaikwad SM, Khan MI, Suresh CG, Kaliannan P, Gromiha MM, Elanthiraiyan M, Chadha K, Saran A, Payne J, Ambrus JL, Nair MPN, Nair MPN, Mahajan S, Chadha KC, Hewitt R, Schwartz SA, Bourguignon J, Faure M, Sapico LF, Cohen-Addad C, Neuburger M, Ober R, Sieker L, Macherel D, Douce R, Gurumurthy DS, Velmurugan S, Lobo Z, Srivastava S, Gesme J, Phadke RS, Govil G, Desai P, Coutinho E, Guseinova IM, Suleimanov SY, Zulfugarov IS, Novruzova SN, Aliev JA, Ismayilov MA, Lijima H, Savchenko TV, Alieva DR, Ilík P, Kouřil R, Bartošková H, Nauš J, Gaikwad JU, Thomas S, Vidyasagar PB, Garab G, Paxton R, Simidjiev I, Rajagopal S, Várkonyi Z, Stoylova S, Cseh Z, Papp E, Mustárdy L, Holzenburg A, Bruder R, Genick UK, Srikrishnan T, Woo TT, Millar DP, Gerwert K, Getzoff ED, Jávorfí T, Garab G, Naqvi KR, Kalimullah M, Gaikwad J, Thomas S, Grace CR, Semwal M, Vidyasagar PB, Kouril R, Ilik P, Naus M, Pomozi I, Horváth G, Wehner R, Bernard GD, Damjanović A, Nagenagowda G, Ritz T, Schulten K, Jushuo W, Jixiu S, Yandao G, Tingyun K, Nanming Z, Freiberg A, Timpmann K, Ruus R, Lynn AM, Woodbury NW, Nemtseva EV, Kudryasheva NS, Sizykh AG, Shikhov VN, Nesterenko TV, Tikhomirov AA, Forti G, Finazzi G, Furia A, Cowsik SM, Barbagallo RP, Forti G, Iskenderova S, Agalarov R, Gasanov R, Osamu M, Nobuhiro GO, Soni RK, Ramrakhiani M, Yagi H, Sahu SC, Tozawa K, Sekino N, Iwabuchi T, Yoshida M, Akutsu H, Avetisyan AV, Kaulen AD, Skulachev VP, Feniouk BA, Breyton C, Chauhan S, Kühlbrandt W, Assarsson M, Gräslund A, Zsiros O, Horváth G, Mustárdy L, Libisch B, Gombos Z, Budagovskaya NV, Kudryasheva N, Bhattacharya A, Harada E, Fukuoka Y, Ohmura T, Fukunishi A, Kawai G, Watanabe K, Akutsu H, Derganc J, Božič B, Svetina S, Chary KVR, Žekš B, Hoh JFY, Li ZB, Rossmanith GH, de Beer EL, Treijtel BW, Frederix PLTM, Blangè T, Hénon S, Galtet F, Govil G, Laurent V, Planus E, Isabey D, Rath LS, Dash PK, Raval MK, Ramakrishnan C, Balaram R, Randic M, Basak SC, Kumar A, Vracko M, Nandy A, Amic D, Beslo D, Nikolic S, Trinajstic N, Walahaw J, Woolfson DN, Lensink MFJ, Berendsen HJC, Pellecchia M, Reddy BVB, Shindylov IN, Bourne PE, Donnamaria MC, de Xammar Oro J, Grigera JR, Neagu M, Neagu A, Praprotnik M, Janežič D, Zuiderweg ERP, Mark P, Nilsson L, Martorana V, Bulone D, Fata LL, Manno M, Biagio PLS, Dardenne LE, Werneck AS, Neto MDO, Kawano K, Bisch PM, Kannan N, Vishveshwara S, Christlet THT, Veluraja K, Grunwald GD, Balaban AT, Basak K, Gute BD, Mills D, Aizawa T, Opitz D, Balasubramanian K, Mihalas GI, Lungeanu D, Macovievici G, Gruia R, Neagu M, Cortez-Maghelly C, Dalcin B, Passos EP, 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