1
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Tan K, Chen J, Kaku Y, Wang Y, Donius L, Khan RA, Li X, Richter H, Seaman MS, Walz T, Hwang W, Reinherz EL, Kim M. Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546734. [PMID: 37425731 PMCID: PMC10327024 DOI: 10.1101/2023.06.27.546734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Broadly neutralizing antibodies (bnAbs) against HIV-1 target conserved epitopes, thereby inhibiting viral entry. Yet surprisingly, those recognizing linear epitopes in the HIV-1 gp41 membrane proximal external region (MPER) are elicited neither by peptide nor protein scaffold vaccines. Here, we observe that while Abs generated by MPER/liposome vaccines may exhibit human bnAb-like paratopes, B-cell programming without constraints imposed by the gp160 ectodomain selects Abs unable to access the MPER within its native "crawlspace". During natural infection, the flexible hinge of IgG3 partially mitigates steric occlusion of less pliable IgG1 subclass Abs with identical MPER specificity, until affinity maturation refines entry mechanisms. The IgG3 subclass maintains B-cell competitiveness, exploiting bivalent ligation resulting from greater intramolecular Fab arm length, offsetting weak antibody affinity. These findings suggest future immunization strategies.
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2
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Panasiuk M, Chraniuk M, Zimmer K, Hovhannisyan L, Krapchev V, Peszyńska-Sularz G, Narajczyk M, Węsławski J, Konopacka A, Gromadzka B. Characterization of surface-exposed structural loops as insertion sites for foreign antigen delivery in calicivirus-derived VLP platform. Front Microbiol 2023; 14:1111947. [PMID: 36922971 PMCID: PMC10010390 DOI: 10.3389/fmicb.2023.1111947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/18/2023] [Indexed: 03/02/2023] Open
Abstract
Chimeric virus-like particles (cVLPs) show great potential in improving public health as they are safe and effective vaccine candidates. The capsid protein of caliciviruses has been described previously as a self-assembling, highly immunogenic delivery platform. The ability to significantly induce cellular and humoral immunity can be used to boost the immune response to low immunogenic foreign antigens displayed on the surface of VLPs. Capsid proteins of caliciviruses despite sequence differences share similar architecture with structural loops that can be genetically modified to present foreign epitopes on the surface of cVLPs. Here, based on the VP1 protein of norovirus (NoV), we investigated the impact of the localization of the epitope in different structural loops of the P domain on the immunogenicity of the presented epitope. In this study, three distinct loops of NoV VP1 protein were genetically modified to present a multivalent influenza virus epitope consisting of a tandem repeat of M2/NP epitopes. cVLPs presenting influenza virus-conserved epitopes in different localizations were produced in the insect cells and used to immunize BALB/c mice. Specific reaction to influenza epitopes was compared in sera from vaccinated mice to determine whether the localization of the foreign epitope has an impact on the immunogenicity.
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Affiliation(s)
- Mirosława Panasiuk
- Department of In Vitro Studies, Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland.,Nano Expo Sp z.o.o, Gdańsk, Poland.,Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Milena Chraniuk
- Department of In Vitro Studies, Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland.,Nano Expo Sp z.o.o, Gdańsk, Poland
| | - Karolina Zimmer
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.,Faculty of Health Sciences, Department of Biochemistry and Molecular Biology, University of Bielsko-Biala, Bielsko-Biala, Poland
| | - Lilit Hovhannisyan
- Department of In Vitro Studies, Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland
| | - Vasil Krapchev
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Grażyna Peszyńska-Sularz
- Tri-City Central Animal Laboratory Research and Service Center, Medical University of Gdańsk, Gdańsk, Poland
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Jan Węsławski
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.,Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Konopacka
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Beata Gromadzka
- Department of In Vitro Studies, Institute of Biotechnology and Molecular Medicine, Gdańsk, Poland.,Nano Expo Sp z.o.o, Gdańsk, Poland.,Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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3
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Structural Basis for Rabbit Hemorrhagic Disease Virus Antibody Specificity. J Virol 2022; 96:e0121722. [PMID: 36326275 PMCID: PMC9682983 DOI: 10.1128/jvi.01217-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Isolated RHDV antibodies have been used for decades to distinguish between antigenic variants, monitor temporal capsid evolution, and examine neutralizing capacities. In this study, we provided the structural basis for an RHDV GI.2 specific diagnostic antibody (2D9) binding and reveal that a small number of amino acid substitutions at the binding site could differentiate between RHDV GI.2 and GI.1b.
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4
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Hoffecker IT, Shaw A, Sorokina V, Smyrlaki I, Högberg B. Stochastic modeling of antibody binding predicts programmable migration on antigen patterns. NATURE COMPUTATIONAL SCIENCE 2022; 2:179-192. [PMID: 36311262 PMCID: PMC7613752 DOI: 10.1038/s43588-022-00218-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Viruses and bacteria commonly exhibit spatial repetition of surface molecules that directly interface with the host immune system. However the complex interaction of patterned surfaces with immune molecules containing multiple binding domains is poorly understood. We developed a pipeline for constructing mechanistic models of antibody interactions with patterned antigen substrates. Our framework relies on immobilized DNA origami nanostructures decorated with precisely placed antigens. The results revealed that antigen spacing is a spatial control parameter that can be tuned to influence antibody residence time and migration speed. The model predicts that gradients in antigen spacing can drive persistent, directed antibody migration in the direction of more stable spacing. These results depict antibody-antigen interactions as a computational system wherein antigen geometry constrains and potentially directs antibody movement. We propose that this form of molecular programmability could be exploited during co-evolution of pathogens and immune systems or in the design of molecular machines.
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Affiliation(s)
- Ian T. Hoffecker
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
- Dept. of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23a, 17165 Solna, Sweden
- ,
| | - Alan Shaw
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
- Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720-3220
| | - Viktoria Sorokina
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
| | - Ioanna Smyrlaki
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
| | - Björn Högberg
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
- ,
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5
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Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
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Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
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6
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Soler MA, Fortuna S. Influence of Linker Flexibility on the Binding Affinity of Bidentate Binders. J Phys Chem B 2017; 121:3918-3924. [PMID: 28379693 DOI: 10.1021/acs.jpcb.6b12627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design of responsive nanosensors typically relies on the availability of probes capable of capturing their target with high affinity and specificity. This can be achieved by coupling two or more binding units through a linker. In this work, we study the dependence on the binder architecture of the binding affinity between a target molecule and a semirigid bidentate binder. Using two different binder architectures, central-rigid and extreme-rigid, and modifying the length and the flexibility degree of the linker we generated 153 different architectures. We computed their dissociation free energies by means of Monte Carlo simulations and thermodynamic integration. We found that central-rigid bidentate binders are a poor choice, as they dissociate more easily than analogous fully flexible bidentate binders. On the other hand, molecular architectures presenting extreme-rigid units were shown effective for a wide range of set-ups.
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Affiliation(s)
- Miguel A Soler
- Molecular Nanotechnology for Life Science Applications Theory Group, Department of Medical and Biological Sciences, University of Udine , Udine, 33100, Italy.,SISSA , Via Bonomea 265, Trieste, Italy
| | - Sara Fortuna
- Molecular Nanotechnology for Life Science Applications Theory Group, Department of Medical and Biological Sciences, University of Udine , Udine, 33100, Italy.,SISSA , Via Bonomea 265, Trieste, Italy.,Center for Biomedical Sciences and Engineering, University of Nova Gorica , Nova Gorica, Goriška 5000, Slovenia
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7
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Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia. J Virol 2015; 89:12217-20. [PMID: 26378178 DOI: 10.1128/jvi.01937-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/10/2015] [Indexed: 11/20/2022] Open
Abstract
To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.
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8
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Jagusiak A, Konieczny L, Krol M, Marszalek P, Piekarska B, Piwowar P, Roterman I, Rybarska J, Stopa B, Zemanek G. Intramolecular immunological signal hypothesis revived--structural background of signalling revealed by using Congo Red as a specific tool. Mini Rev Med Chem 2015; 14:1104-13. [PMID: 25429660 PMCID: PMC4440395 DOI: 10.2174/1389557514666141127150803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 10/11/2014] [Accepted: 11/11/2014] [Indexed: 11/22/2022]
Abstract
Micellar structures formed by self-assembling Congo red molecules bind to proteins penetrating into functionrelated
unstable packing areas. Here, we have used Congo red - a supramolecular protein ligand to investigate how the
intramolecular structural changes that take place in antibodies following antigen binding lead to complement activation.
According to our findings, Congo red binding significantly enhances the formation of antigen-antibody complexes. As a
result, even low-affinity transiently binding antibodies can participate in immune complexes in the presence of Congo
red, although immune complexes formed by these antibodies fail to trigger the complement cascade. This indicates that
binding of antibodies to the antigen may not, by itself, fulfill the necessary conditions to generate the signal which
triggers effector activity. These findings, together with the results of molecular dynamics simulation studies, enable us to
conclude that, apart from the necessary assembling of antibodies, intramolecular structural changes generated by
strains which associate high- affinity bivalent antibody fitting to antigen determinants are also required to cross the
complement activation threshold.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - G Zemanek
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Lazarza 16, 31- 530 Krakow, Poland..
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9
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Fleury MJJ, Nicol JTJ, Samimi M, Arnold F, Cazal R, Ballaire R, Mercey O, Gonneville H, Combelas N, Vautherot JF, Moreau T, Lorette G, Coursaget P, Touzé A. Identification of the neutralizing epitopes of Merkel cell polyomavirus major capsid protein within the BC and EF surface loops. PLoS One 2015; 10:e0121751. [PMID: 25812141 PMCID: PMC4374900 DOI: 10.1371/journal.pone.0121751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/04/2015] [Indexed: 11/19/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) is the first polyomavirus clearly associated with a human cancer, i.e. the Merkel cell carcinoma (MCC). Polyomaviruses are small naked DNA viruses that induce a robust polyclonal antibody response against the major capsid protein (VP1). However, the polyomavirus VP1 capsid protein epitopes have not been identified to date. The aim of this study was to identify the neutralizing epitopes of the MCPyV capsid. For this goal, four VP1 mutants were generated by insertional mutagenesis in the BC, DE, EF and HI loops between amino acids 88-89, 150-151, 189-190, and 296-297, respectively. The reactivity of these mutants and wild-type VLPs was then investigated with anti-VP1 monoclonal antibodies and anti-MCPyV positive human sera. The findings together suggest that immunodominant conformational neutralizing epitopes are present at the surface of the MCPyV VLPs and are clustered within BC and EF loops.
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Affiliation(s)
- Maxime J J Fleury
- L'UNAM Université, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA 3142, Université d'Angers, Angers, France
| | - Jérôme T J Nicol
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Mahtab Samimi
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France; CHRU de Tours-Hôpital Trousseau, Service de Dermatologie, Tours, France
| | - Françoise Arnold
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Raphael Cazal
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Raphaelle Ballaire
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Olivier Mercey
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Hélène Gonneville
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Nicolas Combelas
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | | | - Thierry Moreau
- UMR INSERM 1100, Mécanismes Protéolytiques dans l'Inflammation, Faculté de Médecine, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Gérard Lorette
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France; CHRU de Tours-Hôpital Trousseau, Service de Dermatologie, Tours, France
| | - Pierre Coursaget
- Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
| | - Antoine Touzé
- UMR INRA 1282, Virologie et Immunologie Moléculaire, Faculté des Sciences Pharmaceutiques, Université François Rabelais, PRES Centre-Val de Loire Université, Tours, France
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10
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Chaves RC, Teulon JM, Odorico M, Parot P, Chen SWW, Pellequer JL. Conformational dynamics of individual antibodies using computational docking and AFM. J Mol Recognit 2014; 26:596-604. [PMID: 24089367 DOI: 10.1002/jmr.2310] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/01/2013] [Accepted: 08/15/2013] [Indexed: 12/12/2022]
Abstract
Molecular recognition between a receptor and a ligand requires a certain level of flexibility in macromolecules. In this study, we aimed at analyzing the conformational variability of receptors portrayed by monoclonal antibodies that have been individually imaged using atomic force microscopy (AFM). Individual antibodies were chemically coupled to activated mica surface, and they have been imaged using AFM in ambient conditions. The resulting topographical surface of antibodies was used to assemble the three subunits constituting antibodies: two antigen-binding fragments and one crystallizable fragment using a surface-constrained computational docking approach. Reconstructed structures based on 10 individual topographical surfaces of antibodies are presented for which separation and relative orientation of the subunits were measured. When compared with three X-ray structures of antibodies present in the protein data bank database, results indicate that several arrangements of the reconstructed subunits are comparable with those of known structures. Nevertheless, no reconstructed structure superimposes adequately to any particular X-ray structure consequence of the antibody flexibility. We conclude that high-resolution AFM imaging with appropriate computational reconstruction tools is adapted to study the conformational dynamics of large individual macromolecules deposited on mica.
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Affiliation(s)
- Rui C Chaves
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207, Bagnols sur Cèze, France
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11
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Edeling MA, Austin SK, Shrestha B, Dowd KA, Mukherjee S, Nelson CA, Johnson S, Mabila MN, Christian EA, Rucker J, Pierson TC, Diamond MS, Fremont DH. Potent dengue virus neutralization by a therapeutic antibody with low monovalent affinity requires bivalent engagement. PLoS Pathog 2014; 10:e1004072. [PMID: 24743696 PMCID: PMC3990716 DOI: 10.1371/journal.ppat.1004072] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/03/2014] [Indexed: 01/07/2023] Open
Abstract
We recently described our most potently neutralizing monoclonal antibody, E106, which protected against lethal Dengue virus type 1 (DENV-1) infection in mice. To further understand its functional properties, we determined the crystal structure of E106 Fab in complex with domain III (DIII) of DENV-1 envelope (E) protein to 2.45 Å resolution. Analysis of the complex revealed a small antibody-antigen interface with the epitope on DIII composed of nine residues along the lateral ridge and A-strand regions. Despite strong virus neutralizing activity of E106 IgG at picomolar concentrations, E106 Fab exhibited a ∼20,000-fold decrease in virus neutralization and bound isolated DIII, E, or viral particles with only a micromolar monovalent affinity. In comparison, E106 IgG bound DENV-1 virions with nanomolar avidity. The E106 epitope appears readily accessible on virions, as neutralization was largely temperature-independent. Collectively, our data suggest that E106 neutralizes DENV-1 infection through bivalent engagement of adjacent DIII subunits on a single virion. The isolation of anti-flavivirus antibodies that require bivalent binding to inhibit infection efficiently may be a rare event due to the unique icosahedral arrangement of envelope proteins on the virion surface.
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Affiliation(s)
- Melissa A. Edeling
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - S. Kyle Austin
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bimmi Shrestha
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kimberly A. Dowd
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Swati Mukherjee
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher A. Nelson
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Syd Johnson
- MacroGenics, Rockville, Maryland, United States of America
| | - Manu N. Mabila
- Integral Molecular, Philadelphia, Pennsylvania, United States of America
| | | | - Joseph Rucker
- Integral Molecular, Philadelphia, Pennsylvania, United States of America
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael S. Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daved H. Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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12
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Understanding the role of cross-arm binding efficiency in the activity of monoclonal and multispecific therapeutic antibodies. Methods 2014; 65:95-104. [DOI: 10.1016/j.ymeth.2013.07.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 01/09/2023] Open
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13
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Wagstaffe SJ, Hill KE, Williams DW, Randle BJ, Thomas DW, Stephens P, Riley DJ. Bispecific antibody-mediated detection of the Staphylococcus aureus thermonuclease. Anal Chem 2012; 84:5876-84. [PMID: 22650421 DOI: 10.1021/ac203403d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a novel fluorescence-based immunoassay which enables qualitative detection of the Staphylococcus aureus Thermonuclease (TNase) enzyme, thus providing confirmation of the presence of the S. aureus bacterium in vitro. The biomedical problem of chronic wound healing and the continuing emergence of antibiotic-resistant species is addressed in the development of a detection system capable of the rapid, real-time assessment of bacterial load and diversity. The use of bispecific antibodies (BsAb) provides integration of the molecular detection and signal response components of a standard immunoassay due to steric hindrance-mediated release of prebound fluorescent reporter molecules upon specific binding of TNase to adjacent sites. Rhodamine and fluorescein-labeled hemocyanin from Megathura crenulata (KLH) were prepared as effective immunoconjugates containing a sensitive fluorescent reporter moiety. BsAb that both specifically quenched the fluorescence of the reporter conjugate and bound the TNase target antigen were produced using cell fusion techniques. Assays were then performed to analyze the properties attributable to the steric hindrance-mediated release of the fluorescent reporter molecules upon adjacent TNase binding. This was performed by monitoring the intensity of fluorescence emission of the immunogenic reporter conjugate released into an aqueous environment at 578 and 520 nm, respectively.
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Affiliation(s)
- Sarah J Wagstaffe
- Department of Materials, Imperial College London, London, United Kingdom
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14
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Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. Virology 2012; 431:40-9. [PMID: 22682774 DOI: 10.1016/j.virol.2012.05.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/21/2012] [Accepted: 05/07/2012] [Indexed: 11/22/2022]
Abstract
The use of adeno-associated virus (AAV) as a gene therapy vector is limited by the host neutralizing immune response. The cryo-electron microscopy (EM) structure at 8.5Å resolution is determined for a complex of AAV-2 with the Fab' fragment of monoclonal antibody (MAb) A20, the most extensively characterized AAV MAb. The binding footprint is determined through fitting the cryo-EM reconstruction with a homology model following sequencing of the variable domain, and provides a structural basis for integrating diverse prior epitope mappings. The footprint extends from the previously implicated plateau to the side of the spike, and into the conserved canyon, covering a larger area than anticipated. Comparison with structures of binding and non-binding serotypes indicates that recognition depends on a combination of subtle serotype-specific features. Separation of the neutralizing epitope from the heparan sulfate cell attachment site encourages attempts to develop immune-resistant vectors that can still bind to target cells.
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15
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Abrantes J, van der Loo W, Le Pendu J, Esteves PJ. Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review. Vet Res 2012; 43:12. [PMID: 22325049 PMCID: PMC3331820 DOI: 10.1186/1297-9716-43-12] [Citation(s) in RCA: 262] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 02/10/2012] [Indexed: 02/06/2023] Open
Abstract
Rabbit haemorrhagic disease virus (RHDV) is a calicivirus of the genus Lagovirus that causes rabbit haemorrhagic disease (RHD) in adult European rabbits (Oryctolagus cuniculus). First described in China in 1984, the virus rapidly spread worldwide and is nowadays considered as endemic in several countries. In Australia and New Zealand where rabbits are pests, RHDV was purposely introduced for rabbit biocontrol. Factors that may have precipitated RHD emergence remain unclear, but non-pathogenic strains seem to pre-date the appearance of the pathogenic strains suggesting a key role for the comprehension of the virus origins. All pathogenic strains are classified within one single serotype, but two subtypes are recognised, RHDV and RHDVa. RHD causes high mortality in both domestic and wild adult animals, with individuals succumbing between 48-72 h post-infection. No other species has been reported to be fatally susceptible to RHD. The disease is characterised by acute necrotising hepatitis, but haemorrhages may also be found in other organs, in particular the lungs, heart, and kidneys due to disseminated intravascular coagulation. Resistance to the disease might be explained in part by genetically determined absence or weak expression of attachment factors, but humoral immunity is also important. Disease control in rabbitries relies mainly on vaccination and biosecurity measures. Such measures are difficult to be implemented in wild populations. More recent research has indicated that RHDV might be used as a molecular tool for therapeutic applications. Although the study of RHDV and RHD has been hampered by the lack of an appropriate cell culture system for the virus, several aspects of the replication, epizootology, epidemiology and evolution have been disclosed. This review provides a broad coverage and description of the current knowledge on the disease and the virus.
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Affiliation(s)
- Joana Abrantes
- CIBIO/UP, Centro de Investigacao em Biodiversidade e Recursos Geneticos/Universidade do Porto, Campus Agrario de Vairao, 4485-661 Vairao, Portugal
- INSERM, U892, Université de Nantes, 44007 Nantes, France
| | - Wessel van der Loo
- CIBIO/UP, Centro de Investigacao em Biodiversidade e Recursos Geneticos/Universidade do Porto, Campus Agrario de Vairao, 4485-661 Vairao, Portugal
| | | | - Pedro J Esteves
- CIBIO/UP, Centro de Investigacao em Biodiversidade e Recursos Geneticos/Universidade do Porto, Campus Agrario de Vairao, 4485-661 Vairao, Portugal
- CITS, Centro de Investigacao em Tecnologias de Saude, CESPU, Gandra, Portugal
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16
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Harms BD, Kearns JD, Su SV, Kohli N, Nielsen UB, Schoeberl B. Optimizing properties of antireceptor antibodies using kinetic computational models and experiments. Methods Enzymol 2012; 502:67-87. [PMID: 22208982 DOI: 10.1016/b978-0-12-416039-2.00004-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Monoclonal antibodies are valuable as anticancer therapeutics because of their ability to selectively bind tumor-associated target proteins like receptor tyrosine kinases. Kinetic computational models that capture protein-protein interactions using mass action kinetics are a valuable tool for understanding the binding properties of monoclonal antibodies to their targets. Insights from the models can be used to explore different formats, to set antibody design specifications such as affinity and valence, and to predict potency. Antibody binding to target is driven by both intrinsic monovalent affinity and bivalent avidity. In this chapter, we describe a combined experimental and computational method of assessing the relative importance of these effects on observed drug potency. The method, which we call virtual flow cytometry (VFC), merges experimental measurements of monovalent antibody binding kinetics and affinity curves of antibody-antigen binding into a kinetic computational model of antibody-antigen interaction. The VFC method introduces a parameter χ, the avidity factor, which characterizes the ability of an antibody to cross-link its target through bivalent binding. This simple parameterization of antibody cross-linking allows the model to successfully describe and predict antibody binding curves across a wide variety of experimental conditions, including variations in target expression level and incubation time of antibody with target. We further demonstrate how computational models of antibody binding to cells can be used to predict target inhibition potency. Importantly, we demonstrate computationally that antibodies with high ability to cross-link antigen have significant potency advantages. We also present data suggesting that the parameter χ is a physical, epitope-dependent property of an antibody, and as a result propose that determination of antibody cross-linking and avidity should be incorporated into the screening of antibody panels for therapeutic development. Overall, our results suggest that antibody cross-linking, in addition to monovalent binding affinity, is a key design parameter of antibody performance.
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Affiliation(s)
- Brian D Harms
- Merrimack Pharmaceuticals, Cambridge, Massachusetts, USA
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17
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Hu Z, Tian X, Zhai Y, Xu W, Zheng D, Sun F. Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus. Protein Cell 2010; 1:48-58. [PMID: 21203997 DOI: 10.1007/s13238-010-0007-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 11/07/2009] [Indexed: 10/19/2022] Open
Abstract
Rabbit hemorrhagic disease was described in China in 1984 and can cause hemorrhagic necrosis of the liver within two or three days after infection. The etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the Caliciviridae family. Compared to other calicivirus, such as rNV and SMSV, the structure of Lagovirus members is not well characterized. In this report, structures of two types of wild RHDV particles, the intact virion and the core-like particle (CLP), were reconstructed by cryo-electron microscopy at 11 &0A and 17 &0A, respectively. This is the first time the 3D structure of wild caliciviruses CLP has been provided, and the 3D structure of intact RHDV virion is the highest resolution structure in Lagovirus. Comparison of the intact virion and CLP structures clearly indicated that CLP was produced from the intact virion with the protrusion dissociated. In contrast with the crystal structures of recombinant Norovirus and San Miguel sea lion virus, the capsomers of RHDV virion exhibited unique structural features and assembly modes. Both P1 and P2 subdomains have interactions inside the AB capsomer, while only P2 subdomains have interaction inside CC capsomer. The pseudo atomic models of RHDV capsomers were constructed by homology modeling and density map fitting, and the rotation of RHDV VP60 P domain with respect to its S domain, compared with SMSV, was observed. Collectively, our cryo-electron microscopic studies of RHDV provide close insight into the structure of Lagovirus, which is important for functional analysis and better vaccine development in the future.
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Affiliation(s)
- Zhongjun Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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18
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Abstract
The caliciviruses are by far the major cause of non-bacterial gastroenteritis, highly infectious, and have a rapid and severe onset of symptoms. Studies on this family of viruses have been hampered by the lack of animal model and tissue culture system. However, recent advances in protein expression systems and the development of a mouse norovirus animal model has led to rapid advances in our understanding of these viruses with regard to structure and the host immune response. Our current understanding of this important family of viruses is reviewed here.
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Affiliation(s)
- Umesh Katpally
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
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19
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Structural comparison of different antibodies interacting with parvovirus capsids. J Virol 2009; 83:5556-66. [PMID: 19321620 DOI: 10.1128/jvi.02532-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron microscopy (cryoEM) reconstruction to resolutions varying from 8.5 to 18 A. The crystal structure of one of the Fab molecules and the sequence of the variable domain for each of the Fab molecules have been determined. The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. Fitting of the Fab and virus structures into the cryoEM densities identified the footprints of each antibody on the viral surface. As anticipated from earlier analyses, the Fab binding sites are directed to two epitopes, A and B. The A site is on an exposed part of the surface near an icosahedral threefold axis, whereas the B site is about equidistant from the surrounding five-, three-, and twofold axes. One antibody directed to the A site binds CPV but not FPV. Two of the antibodies directed to the B site neutralize the virus as Fab fragments. The differences in antibody properties have been linked to the amino acids within the antibody footprints, the position of the binding site relative to the icosahedral symmetry elements, and the orientation of the Fab structure relative to the surface of the virus. Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations.
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20
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Leon JS, Souza M, Wang Q, Smith ER, Saif LJ, Moe CL. Immunology of Norovirus Infection. IMMUNITY AGAINST MUCOSAL PATHOGENS 2008. [PMCID: PMC7120028 DOI: 10.1007/978-1-4020-8412-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Noroviruses are the leading cause of epidemic non-bacterial gastroenteritis worldwide. Despite their discovery over three decades ago, little is known about the host immune response to norovirus infection. The purpose of this chapter is to review the field of norovirus immunology and discuss the contributions of outbreak investigations, human and animal challenge studies and population-based studies. This chapter will survey both humoral and cellular immunity as well as recent advances in norovirus vaccine development.
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21
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Structure of antibody-neutralized murine norovirus and unexpected differences from viruslike particles. J Virol 2007; 82:2079-88. [PMID: 18094184 DOI: 10.1128/jvi.02200-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Noroviruses (family Caliciviridae) are the major cause of epidemic nonbacterial gastroenteritis in humans, but the mechanism of antibody neutralization is unknown and no structure of an infectious virion has been reported. Murine norovirus (MNV) is the only norovirus that can be grown in tissue culture, studied in an animal model, and reverse engineered via an infectious clone and to which neutralizing antibodies have been isolated. Presented here are the cryoelectron microscopy structures of an MNV virion and the virion in complex with neutralizing Fab fragments. The most striking differences between MNV and previous calicivirus structures are that the protruding domain is lifted off the shell domain by approximately 16A and rotated approximately 40 degrees in a clockwise fashion and forms new interactions at the P1 base that create a cagelike structure engulfing the shell domains. Neutralizing Fab fragments cover the outer surface of each copy of the capsid protein P2 domains without causing any apparent conformational changes. These unique features of MNV suggest that at least some caliciviruses undergo a capsid maturation process akin to that observed with other plant and bacterial viruses.
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22
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Kaufmann B, López-Bueno A, Mateu MG, Chipman PR, Nelson CDS, Parrish CR, Almendral JM, Rossmann MG. Minute virus of mice, a parvovirus, in complex with the Fab fragment of a neutralizing monoclonal antibody. J Virol 2007; 81:9851-8. [PMID: 17626084 PMCID: PMC2045413 DOI: 10.1128/jvi.00775-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of virus-like particles of the lymphotropic, immunosuppressive strain of minute virus of mice (MVMi) in complex with the neutralizing Fab fragment of the mouse monoclonal antibody (MAb) B7 was determined by cryo-electron microscopy to 7-A resolution. The Fab molecule recognizes a conformational epitope at the vertex of a three-fold protrusion on the viral surface, thereby simultaneously engaging three symmetry-related viral proteins in binding. The location of the epitope close to the three-fold axis is consistent with the previous analysis of MVMi mutants able to escape from the B7 antibody. The binding site close to the symmetry axes sterically forbids the binding of more than one Fab molecule per spike. MAb as well as the Fab molecules inhibits the binding of the minute virus of mice (MVM) to permissive cells but can also neutralize MVM postattachment. This finding suggests that the interaction of B7 with three symmetry-related viral subunits at each spike hinders structural transitions in the viral capsid essential during viral entry.
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Affiliation(s)
- Bärbel Kaufmann
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA
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23
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Laurent S, Blondeau C, Belghazi M, Remy S, Esnault E, Rasschaert P, Rasschaert D. Sequential autoprocessing of Marek's disease herpesvirus protease differs from that of other herpesviruses. J Virol 2007; 81:6117-21. [PMID: 17376905 PMCID: PMC1900316 DOI: 10.1128/jvi.02679-06] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herpesviruses encode a unique serine protease essential for viral capsid maturation. This protease undergoes autoprocessing at two sites, R and M, at the consensus sequence (V, L, I)(P3)-X(P2)-A(P1)/S(P1') (where X is a polar amino acid). We observed complete autoprocessing at the R and M sites of Marek's disease virus (MDV) protease following production of the polyprotein in Escherichia coli. Site-directed mutagenesis confirmed the predicted sequence of the R and M sites, with the M site sequence being nonconsensual: M(P3)-N(P2)-A(P1)/S(P1'). Mutagenesis and expression kinetics studies suggested that the atypical MDV M site was cleaved exclusively by the processed short protease, a feature making MDV unique among herpesviruses.
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Affiliation(s)
- S Laurent
- Equipe Télomérase et Lymphome Viro-induit, UPR INRA 1282 IASP-213, INRA de Tours, 37380 Nouzilly, France.
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24
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Piekarska B, Drozd A, Konieczny L, Król M, Jurkowski W, Roterman I, Spólnik P, Stopa B, Rybarska J. The indirect generation of long-distance structural changes in antibodies upon their binding to antigen. Chem Biol Drug Des 2007; 68:276-83. [PMID: 17177888 DOI: 10.1111/j.1747-0285.2006.00448.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
An allosteric mechanism for the generation of long-distance structural alterations in Fab fragments of antibodies in immune complexes has been postulated and tested in theoretical and experimental analysis. The flexing and/or torsion-derived forces exerted on the elbow region in Fab arms of bivalent antibodies upon binding to antigen were assumed to drive the disruption of hydrogen bonds which stabilize N- and C-terminal chain fragments in V-domains. This allows an extra movement in the elbow followed by a relaxation in the Fab arm and may generate long-distance effects if, in particular, the structural changes are generated asymmetrically involving one chain of the Fab arm only. This mechanism was studied by simulation of molecular dynamics. The local instability in the area involving the site of packing of the N-terminal chain fragment allows penetration and binding of the supramolecular dye Congo red that hence becomes an indicator of the initiated relaxation process and is also the prospective ligand in studies of designing drugs. The susceptibility to dye binding was observed in complexation of bivalent antibodies only, supplying the evidence that constraints associating the interaction with randomly distributed antigenic determinants drive the local structural changes in the V-domain followed by long-distance effects.
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Affiliation(s)
- Barbara Piekarska
- Chair of Medical Biochemistry, Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland.
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25
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Chen R, Neill JD, Estes MK, Prasad BVV. X-ray structure of a native calicivirus: structural insights into antigenic diversity and host specificity. Proc Natl Acad Sci U S A 2006; 103:8048-53. [PMID: 16702551 PMCID: PMC1472427 DOI: 10.1073/pnas.0600421103] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Indexed: 11/18/2022] Open
Abstract
Caliciviruses, grouped into four genera, are important human and veterinary pathogens with a potential for zoonosis. In these viruses, capsid-related functions such as assembly, antigenicity, and receptor interactions are predominantly encoded in a single protein that forms an icosahedral capsid. Understanding of the immunologic functions and pathogenesis of human caliciviruses in the Norovirus and Sapovirus genera is hampered by the lack of a cell culture system or animal models. Much of our understanding of these viruses, including the structure, has depended on recombinant capsids. Here we report the atomic structure of a native calicivirus from the Vesivirus genus that exhibits a broad host range possibly including humans and map immunological function onto a calicivirus structure. The vesivirus structure, despite a similar architectural design as seen in the recombinant norovirus capsid, exhibits novel features and indicates how the unique modular organization of the capsid protein with interdomain flexibility, similar to an antibody structure with a hinge and an elbow, integrates capsid-related functions and facilitates strain diversity in caliciviruses. The internally located N-terminal arm participates in a novel network of interactions through domain swapping to assist the assembly of the shell domain into an icosahedral scaffold, from which the protruding domain emanates. Neutralization epitopes localize to three hypervariable loops in the distal portion of the protruding domain surrounding a region that exhibits host-specific conservation. These observations suggest a mechanism for antigenic diversity and host specificity in caliciviruses and provide a structural framework for vaccine development.
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Affiliation(s)
- Rong Chen
- *Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - John D. Neill
- National Animal Disease Center, Agriculture Research Service, U.S. Department of Agriculture, Ames, IA 50010
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030; and
| | - B. V. Venkataram Prasad
- *Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030; and
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26
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Fleury MJJ, Touzé A, Alvarez E, Carpentier G, Clavel C, Vautherot JF, Coursaget P. Identification of type-specific and cross-reactive neutralizing conformational epitopes on the major capsid protein of human papillomavirus type 31. Arch Virol 2006; 151:1511-23. [PMID: 16508703 PMCID: PMC7086758 DOI: 10.1007/s00705-006-0734-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 01/25/2006] [Indexed: 11/11/2022]
Abstract
The majority of the neutralizing epitopes of papillomaviruses (PV) are conformation-specific and have not been fully characterised. Studies have, to date, been limited to a few HPV types only. We analysed the epitopes on the major capsid protein (L1) of Human papillomavirus (HPV) type 31 using monoclonal antibodies (MAbs) generated against HPV-31 virus-like particles (VLPs). The type-specific MAbs against HPV-31 were all found to be neutralizing and recognized conformation-dependent epitopes. Two other MAbs directed against a conformational epitope were found to be cross-reactive with other HPV types, and one of them was found to be cross-neutralizing. Cross-reactive antibodies were further investigated using wild-type HPV-16 L1 VLPs and two mutants. The results obtained suggested the existence of a cross-neutralizing conformational epitope at the N-terminal part of the FG loop of the major capsid protein, and the other four cross-reactive MAbs recognized epitopes also located at the N-terminal part of the FG loop.
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Affiliation(s)
- M J J Fleury
- INSERM U618, Université François Rabelais, Tours, France
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27
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Greig SL, Berriman JA, O'Brien JA, Taylor JA, Bellamy AR, Yeager MJ, Mitra AK. Structural determinants of rotavirus subgroup specificity mapped by cryo-electron microscopy. J Mol Biol 2005; 356:209-21. [PMID: 16359700 DOI: 10.1016/j.jmb.2005.11.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 11/10/2005] [Accepted: 11/15/2005] [Indexed: 11/30/2022]
Abstract
The rotavirus double-layered particle (DLP) is a molecular machine that transcribes 11 genomic segments of double-stranded RNA into full-length mRNA segments during viral replication. DLPs from the human Wa strain of virus, belonging to subgroup II (SG II), possess a significantly reduced level of transcriptase activity compared to bovine UK DLPs that belong to subgroup I (SG I). Cryo-electron microscopy and icosahedral image analysis was used to define the structural basis for this difference in transcriptase activity and to derive three-dimensional density maps of bovine UK and human Wa DLPs at 26 angstroms and 28 angstroms resolution, respectively. The two rotavirus strains had the same diameter, T = 13 l icosahedral lattice symmetry and size of the VP6 trimers on the surface of the DLPs. However, the Wa particles displayed a remarkable absence of VP6 trimers surrounding each 5-fold vertex position. To further explore these structural differences, three-dimensional reconstructions were generated of DLPs decorated with Fab fragments derived from subgroup-specific monoclonal antibodies. The X-ray structures of VP6 and a generic Fab fragment were then docked into the cryo-electron microscopy density maps, which allowed us to propose at "pseudo-atomic" resolution the locations of the amino acid residues defining the subgroup-specific epitopes. Our results demonstrate a correlation between the structure of the VP6 layer and the transcriptase activity of the particles, and suggest that the stability of VP6 trimers, specifically those at the icosahedral 5-fold axes, may be critical for mRNA synthesis. Thus, subgroup specificity of rotavirus may reflect differences in the architecture of the double-layered particle, with resultant consequences for viral mRNA synthesis.
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Affiliation(s)
- Sarah L Greig
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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28
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Randle BJ, Scoltock SJ, Scott DK. Integrating molecular detection and response to create self-signalling antibodies. Biochem Biophys Res Commun 2004; 324:504-10. [PMID: 15474456 DOI: 10.1016/j.bbrc.2004.09.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Indexed: 11/17/2022]
Abstract
Monoclonal antibodies are reproducible, specific, and cost-effective molecular probes; use outside the laboratory is, however, restricted by technical limitations. Addressing these constraints, the first self-signalling antibodies are now described, where specific antigen binding causes release of bound reporter from bispecific antibodies (BsAb) to generate a detectable signal. The report examines the concept that two different antibody binding sites in close proximity can promote interaction between molecules recognised by these sites, generating a signal by molecular crowding. Signal strength is found to increase with increasing homogeneity for a BsAb reactive with multimeric surfactant antigen; signal response is linear for a BsAb reactive with univalent small analyte deoxypyridinoline. Self-signalling is consistent with intramolecular steric hindrance. This is the first report detailing integration of two different functions, molecular detection and signal response, into BsAbs and with detection of large and small analytes, has generic application to antibody-based systems.
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Affiliation(s)
- Beverley J Randle
- Antibody Research Laboratory, Division of Obstetrics, Department of Clinical Sciences at South Bristol, St. Michael's Hospital, University of Bristol, Bristol BS2 8EG, United Kingdom
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29
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Chen R, Neill JD, Noel JS, Hutson AM, Glass RI, Estes MK, Prasad BVV. Inter- and intragenus structural variations in caliciviruses and their functional implications. J Virol 2004; 78:6469-79. [PMID: 15163740 PMCID: PMC416503 DOI: 10.1128/jvi.78.12.6469-6479.2004] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The family Caliciviridae is divided into four genera and consists of single-stranded RNA viruses with hosts ranging from humans to a wide variety of animals. Human caliciviruses are the major cause of outbreaks of acute nonbacterial gastroenteritis, whereas animal caliciviruses cause various host-dependent illnesses with a documented potential for zoonoses. To investigate inter- and intragenus structural variations and to provide a better understanding of the structural basis of host specificity and strain diversity, we performed structural studies of the recombinant capsid of Grimsby virus, the recombinant capsid of Parkville virus, and San Miguel sea lion virus serotype 4 (SMSV4), which are representative of the genera Norovirus (genogroup 2), Sapovirus, and Vesivirus, respectively. A comparative analysis of these structures was performed with that of the recombinant capsid of Norwalk virus, a prototype member of Norovirus genogroup 1. Although these capsids share a common architectural framework of 90 dimers of the capsid protein arranged on a T=3 icosahedral lattice with a modular domain organization of the subunit consisting of a shell (S) domain and a protrusion (P) domain, they exhibit distinct differences. The distally located P2 subdomain of P shows the most prominent differences both in shape and in size, in accordance with the observed sequence variability. Another major difference is in the relative orientation between the S and P domains, particularly between those of noroviruses and other caliciviruses. Despite being a human pathogen, the Parkville virus capsid shows more structural similarity to SMSV4, an animal calicivirus, suggesting a closer relationship between sapoviruses and animal caliciviruses. These comparative structural studies of caliciviruses provide a functional rationale for the unique modular domain organization of the capsid protein with an embedded flexibility reminiscent of an antibody structure. The highly conserved S domain functions to provide an icosahedral scaffold; the hypervariable P2 subdomain may function as a replaceable module to confer host specificity and strain diversity; and the P1 subdomain, located between S and P2, provides additional fine-tuning to position the P2 subdomain.
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Affiliation(s)
- Rong Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Alkek Building N410, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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30
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Dimmock NJ, Hardy SA. Valency of antibody binding to virions and its determination by surface plasmon resonance. Rev Med Virol 2004; 14:123-35. [PMID: 15027004 DOI: 10.1002/rmv.419] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
All IgGs are homobivalent, but their ability to bind bivalently to the surface of a virus particle depends mainly on a favourable spacing of cognate epitopes and the angle that the FAb arm makes with the virus surface. If the angle of binding forces the second FAb arm to point into solution, monovalent binding is inevitable. This IgG will have the same affinity as its FAb, will be less stably bound than if it were bound bivalently, cannot cross-link epitopes on the surface of a virion, and cannot neutralise by cross-linking surface proteins. However, at moderate IgG concentrations, monovalently bound IgG can reduce infectivity by aggregating virions, a phenomenon that cannot occur with IgG bound bivalently. This review describes how surface plasmon resonance can be used to determine the valency of IgG binding to enveloped and non-enveloped virus particles, and discusses the implications of this new methodology.
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Affiliation(s)
- Nigel J Dimmock
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
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31
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Bárcena J, Verdaguer N, Roca R, Morales M, Angulo I, Risco C, Carrascosa JL, Torres JM, Castón JR. The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid. Virology 2004; 322:118-34. [PMID: 15063122 DOI: 10.1016/j.virol.2004.01.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 01/16/2004] [Accepted: 01/19/2004] [Indexed: 11/22/2022]
Abstract
To function adequately, many if not all proteins involved in macromolecular assemblies show conformational polymorphism as an intrinsic feature. This general strategy has been described for many essential cellular processes. Here we describe this structural polymorphism in a viral protein, the coat protein of Rabbit hemorrhagic disease virus (RHDV), which is required during virus capsid assembly. By combining genetic, structure modeling, and cryo-electron microscopy and image processing analysis, we have established the mechanism that allows RHDV coat protein to switch among quasi-equivalent conformational states to achieve the appropriate curvature for the formation of a closed shell. The RHDV capsid structure is based on a T = 3 lattice, containing 180 copies of identical subunits, similar to those of other caliciviruses. The quasi-equivalent interactions between the coat proteins are achieved by the N-terminal region of a subset of subunits, which faces the inner surface of the capsid shell. Mutant coat protein lacking this N-terminal sequence assembles into T = 1 capsids. Our results suggest that the polymorphism of the RHDV T = 3 capsid might bear resemblance to that of plant virus T = 3 capsids.
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Affiliation(s)
- Juan Bárcena
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130, Madrid, Spain
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32
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Affiliation(s)
- Thomas J Smith
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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33
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Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B. Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain lambda. Biopolymers 2003; 69:189-200. [PMID: 12767122 DOI: 10.1002/bip.10355] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The role of the N-terminal polypeptide fragment of the immunoglobulin l-chain in V domain packing stability, and the flexibility of the whole chain was approached by molecular dynamics simulation. The observations were supported by experimental analysis. The N-terminal polypeptide fragment appeared to be the low-stability packing element in the V domain. At moderately elevated temperature it may be replaced at its packing locus by Congo red and then removed by proteolysis. After removal of Congo red by adsorption to (diethylamino)ethyl (DEAE) cellulose, the stability of complete L chain and of L chain devoid of the N-terminal polypeptide fragment were compared. The results indicated that the N-terminal polypeptide fragment plays an essential role in the stability of the V domain. Its removal makes the domain accessible for ANS and Congo red dye binding without heating. The decreased domain stability was registered in particular as increased root mean square (RMS) fluctuation and higher susceptibility to proteolytic attack. The long-range effect was most clearly manifested at 340 K as independent V and C domain fluctuation in the l-chain devoid of the N-terminal polypeptide fragment. This is likely due to the lack of direct connections between the N- and C-termini of the V domain polypeptide. In a complete V domain the connection involves residues 8-12 and 106-110 in particular. Partial or complete disruption of this connection increases the freedom of V domain rotation, while its increased cohesion strengthens the coupling of the V and C domains, making the whole L chain less flexible.
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Affiliation(s)
- Marcin Król
- Department of Biostatistics and Medical Informatics, Collegium Medicum, Jagiellonian University, 17 Kopernika St, Kraków, 31-501 Poland
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34
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Chen R, Neill JD, Prasad BVV. Crystallization and preliminary crystallographic analysis of San Miguel sea lion virus: an animal calicivirus. J Struct Biol 2003; 141:143-8. [PMID: 12615540 DOI: 10.1016/s1047-8477(02)00583-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Caliciviridae is a family of nonenveloped, icosahedral, positive-sense single-stranded RNA viruses. This family of viruses consists of both animal and human pathogens. Adapting human caliciviruses to cell culture has not been successful, whereas some animal caliciviruses, including San Miguel sea lion virus, have been successfully propagated in vitro. Here we report the crystallization of San Miguel sea lion virus serotype 4 (SMSV4) and the preliminary X-ray crystallographic analysis of the crystals. SMSV4 have been crystallized using the hanging-drop method. These crystals diffracted to approximately 3A resolution using a synchrotron radiation source. A single crystal under cryo-conditions yielded a complete set of diffraction data. Data processing of the diffraction patterns showed that SMSV crystals belong to I23 space group with cell dimensions a=b=c=457 A. The crystallographic asymmetric unit includes five icosahedral asymmetric units, each consisting of three capsid protein subunits. In the space group I23, given the icosahedral symmetry and the size of the virus particle, the location of the particle is constrained to be at the point where the crystallographic 2- and 3-fold axes intersect. The orientation of the virus particle in the unit cell was ascertained by self-rotation function calculations.
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Affiliation(s)
- Rong Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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35
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Gilbert RJ, Grimes JM, Stuart DI. Hybrid vigor: hybrid methods in viral structure determination. ADVANCES IN PROTEIN CHEMISTRY 2003; 64:37-91. [PMID: 13677045 DOI: 10.1016/s0065-3233(03)01002-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Affiliation(s)
- Robert J Gilbert
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
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36
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Kortt AA, Dolezal O, Power BE, Hudson PJ. Dimeric and trimeric antibodies: high avidity scFvs for cancer targeting. BIOMOLECULAR ENGINEERING 2001; 18:95-108. [PMID: 11566601 DOI: 10.1016/s1389-0344(01)00090-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recombinant antibody fragments can be engineered to assemble into stable multimeric oligomers of high binding avidity and specificity to a wide range of target antigens and haptens. This review describes the design and expression of diabodies (dimers), triabodies (trimers) and tetrabodies (tetramers). In particular we discuss the role of linker length between V-domains and the orientation of the V-domains to direct the formation of either diabodies (60 kDa), triabodies (90 kDa) or tetrabodies (120 kDa), and how the size, flexibility and valency of each molecules is suited to different applications for in vivo imaging and therapy. Single chain Fv antibody fragments joined by polypeptide linkers of at least 12 residues irrespective of V-domains orientation predominantly form monomers with varying amounts of dimer and higher molecular mass oligomers in equilibrium. A scFv molecule with a linker of 3-12 residues cannot fold into a functional Fv domain and instead associates with a second scFv molecule to form a bivalent dimer (diabody, approximately 60 kDa). Reducing the linker length below three residues can force scFv association into trimers (triabodies, approximately 90 kDa) or tetramers ( approximately 120 kDa) depending on linker length, composition and V-domain orientation. A particular advantage for tumour targeting is that molecules of 60-100 kDa have increased tumour penetration and fast clearance rates compared with the parent Ig (150 kDa). We highlight a number of cancer-targeting scFv diabodies that have undergone successful pre-clinical trials for in vivo stability and efficacy. We also briefly review the design of multi-specific Fv modules suited to cross-link two or more different target antigens. Bi-specific diabodies formed by association of different scFv molecules have been designed as cross-linking reagents for T-cell recruitment into tumours (immunotherapy), viral retargeting (gene therapy) and as red blood cell agglutination reagents (immunodiagnostics). The more challenging trispecific multimers (triabodies) remain to be described.
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Affiliation(s)
- A A Kortt
- CSIRO Health Science and Nutrition, 343 Royal Parade, Vic. 3052, Parkville, Australia.
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37
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Affiliation(s)
- P J Klasse
- Imperial College School of Medicine, Jefferiss Research Trust Laboratories, Wright-Fleming Institute, St. Mary's Hospital, Norfolk Place, London W2 1PG, UK
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38
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Smith TJ. Antibody interactions with rhinovirus: lessons for mechanisms of neutralization and the role of immunity in viral evolution. Curr Top Microbiol Immunol 2001; 260:1-28. [PMID: 11443870 DOI: 10.1007/978-3-662-05783-4_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- T J Smith
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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39
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Affiliation(s)
- E Hewat
- Institut de Biologie Structurale J-P Ebel, 41 Avenue rue Jules Horowitz, 38027, Grenoble, France
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40
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Matsuura Y, Tohya Y, Mochizuki M, Takase K, Sugimura T. Identification of conformational neutralizing epitopes on the capsid protein of canine calicivirus. J Gen Virol 2001; 82:1695-1702. [PMID: 11413381 DOI: 10.1099/0022-1317-82-7-1695] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two neutralizing monoclonal antibodies (MAbs) against canine calicivirus (CaCV), which has a distinct antigenicity from feline calicivirus (FCV), were obtained. Both MAbs recognized conformational epitopes on the capsid protein of CaCV and were used to identify these epitopes. Neutralization-resistant variants of CaCV were selected in the presence of individual MAbs in a cell culture. Cross-neutralization tests using the variants indicated that the MAbs recognized functionally independent epitopes on the capsid protein. Recombinantly expressed ORF2 products (capsid precursors) of the variants showed no reactivity to the MAbs used for the selection, suggesting that the resistance was induced by a failing in binding of the MAbs to the variant capsid proteins. Several nucleotide changes resulting in amino acid substitutions in the capsid protein were found by sequence analysis. Reactivities of the MAbs to the revertant ORF2 products produced from each variant ORF2 by site-directed mutagenesis identified a single amino acid substitution in each variant capsid protein responsible for the failure of MAb binding. The amino acid residues related to forming the conformational neutralizing epitopes were located in regions equivalent to the 5' and 3' hypervariable regions of the FCV capsid protein, where antigenic sites were demonstrated in previous studies. The recombinant ORF2 products expressed in bacteria failed to induce neutralizing antibody, suggesting that neutralizing antibodies were only generated when properly folded capsid protein was used as an antigen. In CaCV, the conformational epitopes may play a more important role in neutralization than do linear epitopes.
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Affiliation(s)
- Yuichi Matsuura
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan1
| | - Yukinobu Tohya
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan2
| | - Masami Mochizuki
- Laboratory of Clinical Microbiology, Kyoritsu Shoji Corporation, 1-12-4 Kudan-Kita, Chiyoda-ku, Tokyo 102-0073, Japan3
| | - Kozo Takase
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan1
| | - Takaaki Sugimura
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan1
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41
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42
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Thouvenin E, Schoehn G, Rey F, Petitpas I, Mathieu M, Vaney MC, Cohen J, Kohli E, Pothier P, Hewat E. Antibody inhibition of the transcriptase activity of the rotavirus DLP: a structural view. J Mol Biol 2001; 307:161-72. [PMID: 11243811 DOI: 10.1006/jmbi.2000.4479] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
On entering the host cell the rotavirus virion loses its outer shell to become a double-layered particle (DLP). The DLP then transcribes the 11 segments of its dsRNA genome using its own transcriptase complex, and the mature mRNA emerges along the 5-fold axis. In order to better understand the transcription mechanism and the role of VP6 in transcription we have studied three monoclonal antibodies against VP6: RV-238 which inhibits the transcriptase activity of the DLP; and RV-133 and RV-138 which have no effect on transcription. The structures obtained by cryo-electron microscopy of the DLP/Fab complexes and by X-ray crystallography of the VP6 trimer and the VP6/Fab-238 complex have been combined to give pseudo-atomic structures. Steric hindrance between the Fabs results in limited Fab occupancy. In particular, there are on average only three of a possible five Fabs-238 which point towards the 5-fold axis. Thus, Fabs-238 are not in a position to block the exiting mRNA, nor is there any visible conformational change in VP6 on antibody binding at a resolution of 23 A. However, the epitope of the inhibiting antibody involves two VP6 monomers, whereas, those of the non-inhibiting antibodies have an epitope on only one VP6. Thus, the inhibition of transcription may be a result of inhibition of a possible change in the VP6 conformation associated with the transcription of mRNA.
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Affiliation(s)
- E Thouvenin
- Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble, France
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43
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Todorovska A, Roovers RC, Dolezal O, Kortt AA, Hoogenboom HR, Hudson PJ. Design and application of diabodies, triabodies and tetrabodies for cancer targeting. J Immunol Methods 2001; 248:47-66. [PMID: 11223068 DOI: 10.1016/s0022-1759(00)00342-2] [Citation(s) in RCA: 188] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Multivalent recombinant antibody fragments provide high binding avidity and unique specificity to a wide range of target antigens and haptens. This review describes the design and expression of diabodies, triabodies and tetrabodies using examples of scFv molecules that target viruses (influenza neuraminidase) and cancer (Ep-CAM; epithelial cell adhesion molecule). We discuss the preferred choice of linker length between V-domains to direct the formation of either diabodies (60 kDa), triabodies (90 kDa) or tetrabodies (120 kDa), each with size, flexibility and valency suited to different applications for in vivo imaging and therapy. The increased binding valency of these scFv multimers results in high avidity (low off-rates). A particular advantage for tumour targeting is that molecules of 60-100 kDa have increased tumour penetration and fast clearance rates compared to the parent Ig (150 kDa). We highlight a number of cancer-targeting scFv multimers that have recently successfully undergone pre-clinical trials for in vivo stability and efficacy. We also review the design of multi-specific Fv modules suited to cross-link two or more different target antigens. These bi- and tri-specific multimers can be formed by association of different scFv molecules and, in the first examples, have been designed as cross-linking reagents for T-cell recruitment into tumours (immunotherapy), viral retargeting (gene therapy) and as red blood cell agglutination reagents (immunodiagnostics).
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Affiliation(s)
- A Todorovska
- CSIRO Health Science and Nutrition and CRC for Diagnostic Technologies, 343 Royal Parade, Victoria 3052, Parkville, Australia
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44
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Okun VM, Moser R, Ronacher B, Kenndler E, Blaas D. VLDL receptor fragments of different lengths bind to human rhinovirus HRV2 with different stoichiometry. An analysis of virus-receptor complexes by capillary electrophoresis. J Biol Chem 2001; 276:1057-62. [PMID: 11054420 DOI: 10.1074/jbc.m008039200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The formation of complexes between the minor receptor group human rhinovirus HRV2 and two recombinant soluble receptor fragments derived from the human very low density lipoprotein receptor (VLDLR) and containing ligand-binding repeats 1-3 (MBP.VLDLR(1-3)) or 1-8 (MBP.VLDLR(1-8)) fused to the carboxyl terminus of the maltose-binding protein was analyzed by affinity capillary electrophoresis. At low molar ratios of receptor/virus, the peaks corresponding to substoichiometric complexes were broad indicating heterogeneity. When the receptors were present in molar excess with respect to the virus, the peaks were sharp, suggesting saturation of all binding sites. For the determination of the stoichiometry, constant amounts of receptor were incubated with increasing amounts of virus, and the peak areas corresponding to free receptor were measured and plotted versus total virus concentration. Extrapolation of the linear part of the resulting curve to zero concentration of free receptor enabled quantitation of the molar ratios of the components present in the complex. Using this method, we determined that about 60 molecules of MBP.VLDLR(1-3) but only about 30 molecules of MBP.VLDLR(1-8) were bound per virion.
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Affiliation(s)
- V M Okun
- Institute of Medical Biochemistry, Vienna Biocenter, University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
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45
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El Mehdaoui S, Touzé A, Laurent S, Sizaret PY, Rasschaert D, Coursaget P. Gene transfer using recombinant rabbit hemorrhagic disease virus capsids with genetically modified DNA encapsidation capacity by addition of packaging sequences from the L1 or L2 protein of human papillomavirus type 16. J Virol 2000; 74:10332-40. [PMID: 11044077 PMCID: PMC110907 DOI: 10.1128/jvi.74.22.10332-10340.2000] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to produce gene transfer vectors consisting of plasmid DNA packaged into virus-like particles (VLPs) with different cell tropisms. For this purpose, we have fused the N-terminally truncated VP60 capsid protein of the rabbit hemorrhagic disease virus (RHDV) with sequences which are expected to be sufficient to confer DNA packaging and gene transfer properties to the chimeric VLPs. Each of the two putative DNA-binding sequences of major L1 and minor L2 capsid proteins of human papillomavirus type 16 (HPV-16) were fused at the N terminus of the truncated VP60 protein. The two recombinant chimeric proteins expressed in insect cells self-assembled into VLPs similar in size and appearance to authentic RHDV virions. The chimeric proteins had acquired the ability to bind DNA. The two chimeric VLPs were therefore able to package plasmid DNA. However, only the chimeric VLPs containing the DNA packaging signal of the L1 protein were able efficiently to transfer genes into Cos-7 cells at a rate similar to that observed with papillomavirus L1 VLPs. It was possible to transfect only a very limited number of RK13 rabbit cells with the chimeric RHDV capsids containing the L2-binding sequence. The chimeric RHDV capsids containing the L1-binding sequence transfer genes into rabbit and hare cells at a higher rate than do HPV-16 L1 VLPs. However, no gene transfer was observed in human cell lines. The findings of this study demonstrate that the insertion of a DNA packaging sequence into a VLP which is not able to encapsidate DNA transforms this capsid into an artificial virus that could be used as a gene transfer vector. This possibility opens the way to designing new vectors with different cell tropisms by inserting such DNA packaging sequences into the major capsid proteins of other viruses.
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Affiliation(s)
- S El Mehdaoui
- Laboratoire de Virologie Moléculaire, EMI-U Protéases et Vectorisation No. 00-10 and USC INRA, Faculté des Sciences Pharmaceutiques, Tours, France
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46
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Dorange F, El Mehdaoui S, Pichon C, Coursaget P, Vautherot JF. Marek's disease virus (MDV) homologues of herpes simplex virus type 1 UL49 (VP22) and UL48 (VP16) genes: high-level expression and characterization of MDV-1 VP22 and VP16. J Gen Virol 2000; 81:2219-2230. [PMID: 10950980 DOI: 10.1099/0022-1317-81-9-2219] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genes UL49 and UL48 of Marek's disease virus 1 (MDV-1) strain RB1B, encoding the respective homologues of herpes simplex virus type 1 (HSV-1) genes VP22 and VP16, were cloned into a baculovirus vector. Seven anti-VP22 MAbs and one anti-VP16 MAb were generated and used to identify the tegument proteins in cells infected lytically with MDV-1. The two genes are known to be transcribed as a single bicistronic transcript, and the detection of only one of the two proteins (VP22) in MSB-1 lymphoma and in chicken embryo skin cells infected with MDV-1 prompted the study of the transcription/translation of the UL49-48 sequence in an in vivo and in vitro expression system. VP16 was expressed in vitro at detectable levels, whereas it could only be detected at a lower level in a more controlled environment. It was demonstrated that VP22 is phosphorylated in insect cells and possesses the remarkable property of being imported into all cells in a monolayer. VP22 localized rapidly and efficiently to nuclei, like its HSV-1 counterpart. The DNA-binding property of VP22 is also reported and a part of the region responsible for this activity was identified between aa 16 and 37 in the N-terminal region of the protein.
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Affiliation(s)
- Fabien Dorange
- Laboratoire de Virologie Moléculaire, Station de Pathologie Aviaire et de Parasitologie, Centre INRA de Tours, 37380 Nouzilly, France1
| | - Slimane El Mehdaoui
- Laboratoire de Virologie Moléculaire, INSERM EMIV-00-10, Faculté des Sciences Pharmaceutiques 'Philippe Maupas', 37200 Tours, France2
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, Glycobiologie, CNRS UPR4301 et Université d'Orleans, rue Charles-Sadron, F-45071 Orleans Cedex 02, France3
| | - Pierre Coursaget
- Laboratoire de Virologie Moléculaire, INSERM EMIV-00-10, Faculté des Sciences Pharmaceutiques 'Philippe Maupas', 37200 Tours, France2
| | - Jean-François Vautherot
- Laboratoire de Virologie Moléculaire, Station de Pathologie Aviaire et de Parasitologie, Centre INRA de Tours, 37380 Nouzilly, France1
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47
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Venkataram Prasad BV, Hardy ME, Estes MK. Structural studies of recombinant Norwalk capsids. J Infect Dis 2000; 181 Suppl 2:S317-21. [PMID: 10804144 DOI: 10.1086/315576] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Norwalk virus is the major cause of epidemic viral gastroenteritis in humans. Attempts to grow this human virus in laboratory cell lines have been unsuccessful; however, the Norwalk virus capsid protein, when expressed in insect cells infected with a recombinant baculovirus, spontaneously assembles into virus-like particles. The x-ray crystallographic structure of these recombinant Norwalk particles has been determined to 3.4 A, using a 22-A electron cryomicroscopy structure as a phasing model. The recombinant capsids, 380 A in diameter, exhibit a T=3 icosahedral symmetry. The capsid is formed by 90 dimers of the capsid protein, each of which forms an arch-like capsomere. The capsid protein has two distinct domains-a shell (S) and a protruding (P) domain-that are connected by a flexible hinge. Although the S domain has a classical beta-sandwich fold, the structure of the P domain is unlike any other viral protein. One of the subdomains in the P domain formed by the most variable part of the sequence is located at the exterior of the capsid.
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Affiliation(s)
- B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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48
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Abstract
Multivalent recombinant antibody fragments provide high binding avidity and unique specificity to a wide range of target antigens and haptens. This review describes how careful choice of linker length between V-domains creates new types of Fv modules with size, flexibility and valency suited to in vivo imaging and therapy. Further, we review the design of multi-specific Fv modules suited to cross-linking target antigens for cell-recruitment, viral delivery and immunodiagnostics. Single chain Fv antibody fragments (scFvs) are predominantly monomeric when the V(H) and V(L) domains are joined by polypeptide linkers of at least 12 residues. An scFv molecule with a linker of 3 to 12 residues cannot fold into a functional Fv domain and instead associates with a second scFv molecule to form a bivalent dimer (diabody, approximately 60 kDa). Reducing the linker length below three residues can force scFv association into trimers (triabodies, approximately 90 kDa) or tetramers ( approximately 120 KDa) depending on linker length, composition and V-domain orientation. The increased binding valency in these scFv multimers results in high avidity (long off-rates). A particular advantage for tumor targeting is that molecules of approximately 60-100 kDa have increased tumor penetration and fast clearance rates compared to the parent Ig. A number of cancer-targeting scFv multimers have recently undergone pre-clinical evaluation for in vivo stability and efficacy. Bi- and tri-specific multimers can be formed by association of different scFv molecules and, in the first examples, have been designed as cross-linking reagents for T-cell recruitment into tumors (immunotherapy) and as red blood cell agglutination reagents (immunodiagnostics).
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Affiliation(s)
- P J Hudson
- CSIRO Molecular Science and CRC for Diagnostic Technologies, 343 Royal Parade, Parkville, Victoria, 3052, Australia.
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49
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Xing L, Kato K, Li T, Takeda N, Miyamura T, Hammar L, Cheng RH. Recombinant hepatitis E capsid protein self-assembles into a dual-domain T = 1 particle presenting native virus epitopes. Virology 1999; 265:35-45. [PMID: 10603315 DOI: 10.1006/viro.1999.0005] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The three-dimensional structure of a self-assembled, recombinant hepatitis E virus particle has been solved to 22-A resolution by cryo-electron microscopy and three-dimensional image reconstruction. The single subunit of 50 kDa is derived from a truncated version of the open reading frame-2 gene of the virus expressed in a baculovirus system. This is the first structure of a T = 1 particle with protruding dimers at the icosahedral two-fold axes solved by cryo-electron microscopy. The protein shell of these hollow particles extends from a radius of 50 A outward to a radius of 135 A. In the reconstruction, the capsid is dominated by dimers that define the 30 morphological units. The outer domain of the homodimer forms a protrusion, which corresponds to the spike-like density seen in the cryo-electron micrograph. This particle retains native virus epitopes, suggesting its potential value as a vaccine.
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Affiliation(s)
- L Xing
- Department of Biosciences at Novum, Karolinska Institute, Huddinge, 14157, Sweden
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Baker TS, Olson NH, Fuller SD. Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev 1999; 63:862-922, table of contents. [PMID: 10585969 PMCID: PMC98980 DOI: 10.1128/mmbr.63.4.862-922.1999] [Citation(s) in RCA: 367] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-A) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical.
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Affiliation(s)
- T S Baker
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
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