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Nault L, Taofifenua C, Anne A, Chovin A, Demaille C, Besong-Ndika J, Cardinale D, Carette N, Michon T, Walter J. Electrochemical atomic force microscopy imaging of redox-immunomarked proteins on native potyviruses: from subparticle to single-protein resolution. ACS NANO 2015; 9:4911-4924. [PMID: 25905663 DOI: 10.1021/acsnano.5b00952] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We show herein that electrochemical atomic force microscopy (AFM-SECM), operated in molecule touching (Mt) mode and combined with redox immunomarking, enables the in situ mapping of the distribution of proteins on individual virus particles and makes localization of individual viral proteins possible. Acquisition of a topography image allows isolated virus particles to be identified and structurally characterized, while simultaneous acquisition of a current image allows the sought after protein, marked by redox antibodies, to be selectively located. We concomitantly show that Mt/AFM-SECM, due to its single-particle resolution, can also uniquely reveal the way redox functionalization endowed to viral particles is distributed both statistically among the viruses and spatially over individual virus particles. This possibility makes Mt/AFM-SECM a unique tool for viral nanotechnology.
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Affiliation(s)
- Laurent Nault
- †Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, Sorbonne Paris Cité, Unité Mixte de Recherche Université, CNRS No 7591, Bâtiment Lavoisier, 15 rue Jean-Antoine de Baïf, 75205 Cedex 13 Paris, France
| | - Cécilia Taofifenua
- †Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, Sorbonne Paris Cité, Unité Mixte de Recherche Université, CNRS No 7591, Bâtiment Lavoisier, 15 rue Jean-Antoine de Baïf, 75205 Cedex 13 Paris, France
| | - Agnès Anne
- †Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, Sorbonne Paris Cité, Unité Mixte de Recherche Université, CNRS No 7591, Bâtiment Lavoisier, 15 rue Jean-Antoine de Baïf, 75205 Cedex 13 Paris, France
| | - Arnaud Chovin
- †Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, Sorbonne Paris Cité, Unité Mixte de Recherche Université, CNRS No 7591, Bâtiment Lavoisier, 15 rue Jean-Antoine de Baïf, 75205 Cedex 13 Paris, France
| | - Christophe Demaille
- †Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, Sorbonne Paris Cité, Unité Mixte de Recherche Université, CNRS No 7591, Bâtiment Lavoisier, 15 rue Jean-Antoine de Baïf, 75205 Cedex 13 Paris, France
| | - Jane Besong-Ndika
- ‡UMR 1332 Biologie du Fruit et Pathologie, INRA-Université Bordeaux 2, 71 av. Edouard Bourlaux, 20032-33882 Cedex Villenave d'Ornon, France
- §Department of Food and Environmental Sciences, University of Helsinki, Latokartanonkaari 11, FI-00014 Helsinki, Finland
| | - Daniela Cardinale
- ‡UMR 1332 Biologie du Fruit et Pathologie, INRA-Université Bordeaux 2, 71 av. Edouard Bourlaux, 20032-33882 Cedex Villenave d'Ornon, France
| | - Noëlle Carette
- ‡UMR 1332 Biologie du Fruit et Pathologie, INRA-Université Bordeaux 2, 71 av. Edouard Bourlaux, 20032-33882 Cedex Villenave d'Ornon, France
| | - Thierry Michon
- ‡UMR 1332 Biologie du Fruit et Pathologie, INRA-Université Bordeaux 2, 71 av. Edouard Bourlaux, 20032-33882 Cedex Villenave d'Ornon, France
| | - Jocelyne Walter
- ‡UMR 1332 Biologie du Fruit et Pathologie, INRA-Université Bordeaux 2, 71 av. Edouard Bourlaux, 20032-33882 Cedex Villenave d'Ornon, France
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Rehm P, Pick C, Borner J, Markl J, Burmester T. The diversity and evolution of chelicerate hemocyanins. BMC Evol Biol 2012; 12:19. [PMID: 22333134 PMCID: PMC3306762 DOI: 10.1186/1471-2148-12-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/14/2012] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Oxygen transport in the hemolymph of many arthropod species is facilitated by large copper-proteins referred to as hemocyanins. Arthropod hemocyanins are hexamers or oligomers of hexamers, which are characterized by a high O2 transport capacity and a high cooperativity, thereby enhancing O2 supply. Hemocyanin subunit sequences had been available from horseshoe crabs (Xiphosura) and various spiders (Araneae), but not from any other chelicerate taxon. To trace the evolution of hemocyanins and the emergence of the large hemocyanin oligomers, hemocyanin cDNA sequences were obtained from representatives of selected chelicerate classes. RESULTS Hemocyanin subunits from a sea spider, a scorpion, a whip scorpion and a whip spider were sequenced. Hemocyanin has been lost in Opiliones, Pseudoscorpiones, Solifugae and Acari, which may be explained by the evolution of trachea (i.e., taxon Apulmonata). Bayesian phylogenetic analysis was used to reconstruct the evolution of hemocyanin subunits and a relaxed molecular clock approach was applied to date the major events. While the sea spider has a simple hexameric hemocyanin, four distinct subunit types evolved before Xiphosura and Arachnida diverged around 470 Ma ago, suggesting the existence of a 4 × 6mer at that time. Subsequently, independent gene duplication events gave rise to the other distinct subunits in each of the 8 × 6mer hemocyanin of Xiphosura and the 4 × 6mer of Arachnida. The hemocyanin sequences were used to infer the evolutionary history of chelicerates. The phylogenetic trees support a basal position of Pycnogonida, a sister group relationship of Xiphosura and Arachnida, and a sister group relationship of the whip scorpions and the whip spiders. CONCLUSION Formation of a complex hemocyanin oligomer commenced early in the evolution of euchelicerates. A 4 × 6mer hemocyanin consisting of seven subunit types is conserved in most arachnids since more than 400 Ma, although some entelegyne spiders display selective subunit loss and independent oligomerization. Hemocyanins also turned out to be a good marker to trace chelicerate evolution, which is, however, limited by the loss of hemocyanin in some taxa. The molecular clock calculations were in excellent agreement with the fossil record, also demonstrating the applicability of hemocyanins for such approach.
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Affiliation(s)
- Peter Rehm
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
| | - Christian Pick
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
| | - Janus Borner
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
| | - Jürgen Markl
- Institute of Zoology, Johannes Gutenberg University Mainz, D-55099 Mainz, Germany
| | - Thorsten Burmester
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
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Anne A, Chovin A, Demaille C, Lafouresse M. High-Resolution Mapping of Redox-Immunomarked Proteins Using Electrochemical–Atomic Force Microscopy in Molecule Touching Mode. Anal Chem 2011; 83:7924-32. [DOI: 10.1021/ac201907v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Agnès Anne
- Laboratoire d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Arnaud Chovin
- Laboratoire d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Christophe Demaille
- Laboratoire d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Manon Lafouresse
- Laboratoire d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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Rodriguez RD, Anne A, Cambril E, Demaille C. Optimized hand fabricated AFM probes for simultaneous topographical and electrochemical tapping mode imaging. Ultramicroscopy 2011; 111:973-81. [DOI: 10.1016/j.ultramic.2011.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 12/16/2010] [Accepted: 02/05/2011] [Indexed: 10/18/2022]
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Wilson JE. The use of monoclonal antibodies and limited proteolysis in elucidation of structure-function relationships in proteins. METHODS OF BIOCHEMICAL ANALYSIS 2006; 35:207-50. [PMID: 2002771 DOI: 10.1002/9780470110560.ch4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- J E Wilson
- Biochemistry Department, Michigan State University, East Lansing
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Anne A, Demaille C, Moiroux J. Elastic bounded diffusion and electron propagation: dynamics of the wiring of a self-assembly of immunoglobulins bearing terminally attached ferrocene poly(ethylene glycol) chains according to a spatially controlled organization. J Am Chem Soc 2001; 123:4817-25. [PMID: 11457292 DOI: 10.1021/ja004050f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular monolayers of immunoglobulins bearing terminally attached ferrocene poly(ethylene glycol) chains (IgG-PEG-Fc) were self-assembled at an electrode surface in a step-by-step manner involving antigen-antibody recognition reactions. The total number N of assembled IgG-PEG-Fc monolayers and the number of spacers n(i) separating two successive IgG-PEG-Fc monolayers were controlled and varied. Electron transport through the protein assembly involves the dynamics of the terminally attached PEG chains and isotopic electron exchange between ferrocene heads belonging to successive IgG-PEG-Fc monolayers. The model of elastic bounded diffusion enabled us to analyze quantitatively the dependence of the rate of electron transport on N, n(i), and the rate constant (k(e)) of isotopic electron exchange. Wiring of a molecular monolayer of redox enzyme is also quantitatively characterized.
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Affiliation(s)
- A Anne
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université--CNRS No 7591, Université de Paris 7--Denis Diderot, 2 place Jussieu, 75251 Paris Cedex 05, France
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Demaille C, Moiroux J. Sensing a Self-Assembled Protein Structure through Its Permeation by a Ferrocene Labeled Poly(ethylene glycol) Chain. J Phys Chem B 1999. [DOI: 10.1021/jp991748a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christophe Demaille
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université, CNRS No 7591, Université de Paris 7, Denis Diderot, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - Jacques Moiroux
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université, CNRS No 7591, Université de Paris 7, Denis Diderot, 2 Place Jussieu, 75251 Paris Cedex 05, France
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Anne A, Demaille C, Moiroux J. Elastic Bounded Diffusion. Dynamics of Ferrocene-Labeled Poly(ethylene glycol) Chains Terminally Attached to the Outermost Monolayer of Successively Self-Assembled Monolayers of Immunoglobulins. J Am Chem Soc 1999. [DOI: 10.1021/ja991780i] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Agnès Anne
- Contribution from the Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche UniversitéCNRS No 7591, Université de Paris 7, Denis Diderot, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Christophe Demaille
- Contribution from the Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche UniversitéCNRS No 7591, Université de Paris 7, Denis Diderot, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Jacques Moiroux
- Contribution from the Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche UniversitéCNRS No 7591, Université de Paris 7, Denis Diderot, 2 place Jussieu, 75251 Paris Cedex 05, France
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Miller KI, Cuff ME, Lang WF, Varga-Weisz P, Field KG, van Holde KE. Sequence of the Octopus dofleini hemocyanin subunit: structural and evolutionary implications. J Mol Biol 1998; 278:827-42. [PMID: 9614945 DOI: 10.1006/jmbi.1998.1648] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequencing of the subunit of the hemocyanin of Octopus dofleini has been completed from a cDNA library. This represents the first molluscan hemocyanin to be completely sequenced. The sequence determined is for one of the two distinguishable cDNAs which have been recognized for this protein. The protein subunit has 2896 amino acids and contains seven functional units, each carrying two sets of three invariant histidine residues constituting the binding sites (A and B) for two copper atoms. The accompanying paper identifies this site in the C-terminal functional unit (Odg). Differences in sequence for the two cDNAs, for the region in which both are available, are concentrated in the "linker regions" between functional units. The sequences of the seven units exhibit high similarity, averaging about 40% identity, with a concentration of conserved sequences in the region surrounding the copper binding sites. The sequences around the B-site show significant homology to the sequences of arthropod hemocyanins. Comparison of the functional unit sequences in terms of hydrophobicity and surface exposure profiles, as well as regions of probable secondary structure, indicate that all functional units probably have a common tertiary folding; the protein subunit is a string of similarly folded beads. A number of putative N-linked carbohydrate binding sites can be recognized in the sequence; one of these corresponds to the carbohydrate observed in the X-ray diffraction study of functional unit Odg as disclosed in the accompying paper. Phylogenetic analysis of the sequences of the O. dofleini functional units, and comparison with other available molluscan sequences indicates that the multi-domain subunit structure must have arisen over a relatively brief period, preceeding the differentiation of major molluscan types.
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Affiliation(s)
- K I Miller
- Department of Biochemistry and Biophysics, Oregon State University Corvallis 97331, USA
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Cuff ME, Miller KI, van Holde KE, Hendrickson WA. Crystal structure of a functional unit from Octopus hemocyanin. J Mol Biol 1998; 278:855-70. [PMID: 9614947 DOI: 10.1006/jmbi.1998.1647] [Citation(s) in RCA: 312] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hemocyanins are giant oxygen transport proteins found in many arthropods and molluscs. Freely dissolved in the hemolymph, they are multisubunit proteins that contain many copies of the active site, a copper atom pair that reversibly binds oxygen. Octopus hemocyanin is composed of ten subunits, each of which contain seven oxygen-binding "functional units". The carboxyl-terminal 47 kDa functional unit, Odg, is a proteolytic isolate that binds oxygen reversibly while exhibiting slight Bohr and magnesium ion effects. In this work we present the X-ray structure determination and analysis of Odg at 2.3 A resolution. Odg has two structural domains: a largely alpha-helical copper binding domain, and a five-stranded anti-parallel beta-sandwich with the jelly roll topology found in many viruses. Six histidine residues ligate the copper atoms, one of which is involved in a thioether bridge. The results show that the hemocyanin from the mollusc and that from the arthropod have distinct tertiary folds in addition to the long recognized differences in their quaternary structures. Nonetheless, a comparison of Octopus and horseshoe crab hemocyanin reveals a similar active site, in a striking example of perhaps both convergent and divergent evolution.
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Affiliation(s)
- M E Cuff
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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Taveau JC, Boisset N, Lamy J, Lambert O, Lamy JN. Three-dimensional reconstruction of Limulus polyphemus hemocyanin from cryoelectron microscopy. J Mol Biol 1997; 266:1002-15. [PMID: 9086277 DOI: 10.1006/jmbi.1996.0840] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Hemocyanin (Hc) the respiratory pigment of the horseshoe crab Limulus polyphemus (Lp) is composed of 48 approximately 75 kDa copper-containing subunits arranged in eight hexameric groups. In this study, we used the random conical tilt series method to do a three-dimensional (3D) reconstruction of Lp Hc observed in vitreous ice. This approach allowed the unambiguous determination of the handedness of the molecule. Lp Hc contains two superimposed 4 x 6mer structures possessing the same structural features as the other 4 x 6meric Hcs, namely flip and flop views and a rocking effect. Moreover, 3D fitting of the X-ray structure of subunit LpII with the reconstruction volume shows that the intra4 x 6meric contacts described in arthropod Hcs also occur within Limulus Hc. The two half-molecules composing the 8 x 6mer have their flop faces in contact (flop/flop association), the main links being formed by subunits LpIV. Model building shows that the flop/flop association is the only possible arrangement which allows the assembly of the whole particle. The two alternate constructions (flip/flop and flip/flip) are forbidden because of steric hindrance.
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Affiliation(s)
- J C Taveau
- Laboratoire des Protéines Complexes, Université de Tours and CNRS EP117, France
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12
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Affiliation(s)
- K E van Holde
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA
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Makino N, Ohnaka H. Role of oligomeric interactions in the cooperativity of crayfish hemocyanin. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1162:237-45. [PMID: 8457587 DOI: 10.1016/0167-4838(93)90287-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To examine the effect of interactions between the hexameric units in the dodecameric hemocyanin, crayfish (Procambarus clarki) hemocyanin was partially dissociated. Gel-filtration yielded fractions containing the undissociated dodecamer and a mixture of the hexamer and heptamer (referred to as 'half-dodecamer'). Their O2 equilibria were compared and were analyzed by curve fitting of cooperativity models. The partial dissociation of the dodecamer significantly lowered the cooperativity but little affected the O2 affinities. The O2 equilibrium of the half-dodecamer could be described by the two-state allosteric model of Monod-Wyman-Changeux on the assumption that the cooperative unit is composed of six subunits. We tested the applicability of allosteric models for the dodecamer that deal with the interactions between the hexamers. To reduce the arbitrariness of the fitting, we presumed that some parameters are equal to the two-state model parameters for the half-dodecamer. It was found that the 'nesting model', which assumes allosteric equilibria at two different hierarchical levels, could be applied successfully to the dodecamer.
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Affiliation(s)
- N Makino
- Institute of Basic Medical Sciences, University of Tsukuba, Ibaraki, Japan
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15
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Comparative electron microscopy and image analysis of oxy- and deoxy-hemocyanin from the spiny lobster Panulirus interruptus. Ultramicroscopy 1993. [DOI: 10.1016/0304-3991(93)90248-v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Maaroufi H, Lamy JN. The quaternary structure of Scorpio maurus hemocyanin: Comparison with Androctonus australis hemocyanin. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/0305-0491(93)90361-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Harris LJ, Larson SB, Hasel KW, Day J, Greenwood A, McPherson A. The three-dimensional structure of an intact monoclonal antibody for canine lymphoma. Nature 1992; 360:369-72. [PMID: 1448155 DOI: 10.1038/360369a0] [Citation(s) in RCA: 174] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystal structures of Fab antibody fragments determined by X-ray diffraction characteristically feature four-domain, beta-barrel arrangements. A human antibody Fc fragment has also been found to have four beta-barrel domains. The structures of a few intact antibodies have been solved: in two myeloma proteins, the flexible hinge regions that connect the Fc to the Fab segments were deleted so the molecules were non-functional, structurally restrained, T-shaped antibodies; a third antibody, Kol, had no hinge residues missing but the Fc region was sufficiently disordered that it was not possible to relate its disposition accurately with respect to the Fab components. Here we report the structure at 3.5 A resolution of an IgG2a antitumour monoclonal antibody which contains an intact hinge region and was solved in a triclinic crystal by molecular replacement using known Fc and Fab fragments. The antibody is asymmetric, reflecting its dynamic character. There are two local, apparently independent, dyads in the molecule. One relates the heavy chains in the Fc, the other relates the constant domains of the Fabs. The variable domains are not related by this 2-fold axis because of the different Fab elbow angles of 159 degrees and 143 degrees. The Fc has assumed an asymmetric, oblique orientation with respect to loosely tethered yet almost collinear Fabs. Our study enables the two antigen-binding segments as well as the Fc portion of a functional molecule to be visualized and illustrates the flexibility of these immune response proteins.
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Affiliation(s)
- L J Harris
- Department of Biochemistry, University of California Riverside 92521
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Frank J, Radermacher M. Three-dimensional reconstruction of single particles negatively stained or in vitreous ice. Ultramicroscopy 1992; 46:241-62. [PMID: 1336233 DOI: 10.1016/0304-3991(92)90018-f] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The random-conical reconstruction method has been highly successful in three-dimensional imaging of macromolecules under low-dose conditions. This article summarizes the different steps of this technique as applied to molecules prepared with negative staining or vitreous ice, and sketches out the current directions of development. We anticipate that by using new instrumental developments, transfer function correction and computational refinement techniques, a resolution in the range of 7-10 A could ultimately be achieved.
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Affiliation(s)
- J Frank
- Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany 12201-0509
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Markl J, Decker H. Molecular Structure of the Arthropod Hemocyanins. BLOOD AND TISSUE OXYGEN CARRIERS 1992. [DOI: 10.1007/978-3-642-76418-9_12] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lünsdorf H, Tiedge H. Immunoelectron microscopy of enzymes, multienzyme complexes, and selected other oligomeric proteins. ELECTRON MICROSCOPY REVIEWS 1992; 5:105-27. [PMID: 1730073 DOI: 10.1016/0892-0354(92)90007-d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The collective term "immunoelectron microscopy" subsumes a number of techniques in which the biological material is decorated with specific antibodies, prior to being visualized in the electron microscope. In this article, we have reviewed literature on immunoelectron microscopy that focusses on the analysis of the molecular architecture of proteins, in particular of enzymes and of multienzyme complexes. Molecular immunoelectron microscopy has been remarkably successful with multi-subunit enzymes of complex quaternary structures, and in many cases the data have been the basis for the eventual development of detailed three-dimensional molecular models. The elucidation of subunit composition and juxtaposition of a given enzyme, an important accomplishment in itself, has in turn stimulated and guided discussions on the catalytic mechanism; illustrative examples include F1 ATPase and citrate lyase, among others. Here we have chosen a variety of enzymes, multienzyme complexes, and non-enzymatic proteins to demonstrate the versatility of immunoelectron microscopy, to illustrate methodological prerequisites and limitations, and to discuss significance and implications of individual immunoelectron microscopy studies.
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Affiliation(s)
- H Lünsdorf
- Bereich Mikrobiologie, Gesellschaft für Biotechnologische Forschung, Braunschweig, Germany
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Herskovits TT, Hamilton MG. Higher order assemblies of molluscan hemocyanins. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1991; 99:19-34. [PMID: 1959327 DOI: 10.1016/0305-0491(91)90003-v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
1. The hemocyanins of the Fissurellidae, Naticidae and Melongenidae families of marine gastropods as well as some other molluscs including some members of the Opistobranchia and Bivalvia groups have hemocyanins which exist in solution as tri-decameric and mixed, multi-decameric aggregates characterized by sedimentation coefficients close to 100 S, 130 S, 150 S, 170 S and 200 S to 230 S. 2. The particle masses of the molluscan hemocyanins appear to be integral multiples close to 4.4 x 10(6) daltons. Thus, particle mass values of 4.47 x 10(6), 8.67 x 10(6) and 13.40 x 10(6) daltons were obtained for representative decameric, di-decameric, and tri-decameric components of Stenoplax conspicua, Fasciolaria tulipa and Euspira (Lunatia) heros hemocyanins. For Busycon contrarium, a gastropod with a mixed multidecameric hemocyanin, scanning transmission electron microscopic (STEM) measurements gave particle masses ranging from 8.89 x 10(6) and 13.20 x 10(6) for the di- and tri-decameric components to 38.87 x 10(6) and 43.40 x 10(6) daltons for highest nano- and deca-decameric aggregates. 3. The electron microscopic images of both uranyl acetate-stained and unstained specimens of hemocyanin aggregates indicate a non-random mode of assembly of the multi-decameric particles. This is most apparent from the electron micrographs of the moon snail hemocyanins. The tri-decameric and tetra-decameric particles seem to be assembled from a single di-decameric unit of the Mellema and Klug arrangement, with the collar ends facing outward, to which decameric units have been added from one or both ends, in a unidirectional tail-to-head to tail-to-collar manner. Consequently, all the aggregates including the higher, Melongenidae polymers have the appearance of closed cylinders terminating with the collar ends. 4. The radial distribution of the end-on views of the hemocyanin of the moon-snail Calinatioina oldroydii, show that the radial mass drops to zero at the center of the cylindrical particles consisting of one, two, or three decamers. This suggests that no caps are present at the ends of the hemocyanin particles which would inhibit or terminate their linear assembly. 5. The light-scattering behavior of B. contrarium and Marisa cornarietis hemocyanins examined as a function of increasing reagent concentration using the hydrophobic urea and Hofmeister salt series of reagents, show distinct aggregation and increase in molecular weights at low concentrations of reagent. Together with the stabilizing influence of Mg2+ and Ca2+ ions, this suggests polar and ionic stabilization of the inter-decameric contacts between the central di-decamers and the added decameric units of the higher aggregates of molluscan hemocyanins.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- T T Herskovits
- Department of Chemistry, Fordham University, Bronx, New York, NY 10458
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Boisset N, Taveau JC, Lamy J, Wagenknecht T, Radermacher M, Frank J. Three-dimensional reconstruction of native Androctonus australis hemocyanin. J Mol Biol 1990; 216:743-60. [PMID: 2258938 DOI: 10.1016/0022-2836(90)90396-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A sample of native 4 x 6-meric hemocyanin of Androctonus australis was negatively stained with the double-layer technique, and was observed by transmission electron microscopy under low-dose conditions with a 50 degree and 0 degree tilt. The three-dimensional reconstruction method from "Single-exposure, random conical tilt series" was then applied. Independent three-dimensional reconstructions were obtained from the top, side and 45 degree views. Despite a pronounced flattening effect, presumably due to the specimen preparation technique, the positions of the 24 subunits composing the oligomer were unequivocally determined. This experiment definitely solves the problem of the architectural organization of the subunits in the cheliceratan 4 x 6-meric hemocyanins. Moreover, distinction between the flip and flop faces and an attenuated rocking effect were observed.
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Affiliation(s)
- N Boisset
- Laboratoire de Biochimie Fondamentale and URA, 1334 CNRS, Tours, France
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Abstract
In order to study proteins that do not occur in two- or three-dimensionally ordered form, one may take two different approaches: either search for conditions that induce the formation of crystals, and proceed with the established methods of X-ray or electron crystallography, or attempt to study the molecules in the form of single particles with the EM. Although many proteins have been successfully crystallized, and some general recipes for inducing ordered arrangement have been found (Mannella, 1984; Uzgiris & Kornberg, 1983), there exists a large number of proteins and protein assemblies that have resisted such attempts for a long time. Furthermore, there are macromolecular assemblies, associated with membranes and engaged in switching or gating, whose function is tied to their occurrence in isolated form, and hence are best studied without extraction from the membrane. For these reasons, the single-particle approach to the study of macromolecular structure (Franket al.1978, 1981; Radermacheret al.1987a, b; for recent reviews, see Franket al.1985, 1988e; Frank, 1989) has found numerous applications after initial technical and conceptual hurdles were overcome. Although atomic resolution cannot be achieved with this approach for a variety of reasons, a quantitative description of architecture on the quaternary level is nevertheless possible, as exemplified in the 3D studies of ribosomal particles (overviews, see Franket al.1988a) and, most recently, the junctional channel complex (Wagenknechtet al.1989a).
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Affiliation(s)
- J Frank
- Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany 12201-0509
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Lamy J, Billiald P, Taveau JC, Boisset N, Motta G, Lamy J. Topological mapping of 13 epitopes on a subunit of Androctonus australis hemocyanin. J Struct Biol 1990; 103:64-74. [PMID: 1697760 DOI: 10.1016/1047-8477(90)90087-s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A topological localization of epitopes on the surface of the Aa6 subunit of Androctonus australis hemocyanin has been carried out. First, immunocomplex strings composed of native hemocyanin and monoclonal antibodies were examined in the electron microscope and submitted to an image processing by correspondence analysis. The average images were then compared to a three-dimensional model of the 24-mer suggesting that 11 of the 13 epitopes are located in three zones of the subunit surface. Second, the overlaps between the epitopes were then studied by polyacrylamide gel electrophoresis, competitive binding inhibition, and immunoelectron microscopy. Four groups of epitopes were identified. One group was capable of binding exclusively to the free subunit. The other three groups were identical to those found in immunoelectron microscopy. The data are consistent with the existence of a small number of immunodominant regions on the surface of the Aa6 subunit.
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Affiliation(s)
- J Lamy
- Laboratoire de Biochimie, Faculté de Pharmacie, Université François Rabelais, CNRS URA 1334, 37042 Tours, France
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Wade RH, Taveau JC, Lamy JN. Concerning the axial rotational flexibility of the Fab regions of immunoglobulin G. J Mol Biol 1989; 206:349-56. [PMID: 2716050 DOI: 10.1016/0022-2836(89)90484-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
By electron microscopy, we have observed immunocomplexes with both negative stain and in amorphous ice using monoclonal antibodies directed against one of the 24 subunits of scorpion haemocyanin. A copy of this subunit occurs at each of the corners of the square-shaped haemocyanin molecule. Three distinct orientations of adjacent haemocyanin molecules may be observed in immunocomplex pairs or chains using both the above-mentioned methods. These observations, coupled with low-resolution computer simulations of immunocomplex formation, argue strongly in favour of the existence of a considerable degree of rotational flexibility within the IgG molecule and around the long axis of the Fab arms, as was suggested by previous observations with negative stain. We find that the arms can rotate by up to 180 degrees with respect to the Fc region.
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Affiliation(s)
- R H Wade
- Laboratoire de Biologie Structurale, LBio-Département de Recherche Fondamentale, CENG, Grenoble, France
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27
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Subunit-specific monoclonal antibodies to tarantula hemocyanin, and a common epitope shared with calliphorin. J Comp Physiol B 1989. [DOI: 10.1007/bf00691734] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Miller KI, van Holde KE, Toumadje A, Johnson WC, Lamy J. Structure and function of the carboxyl-terminal oxygen-binding domain from the subunit of Octopus dofleini hemocyanin. Biochemistry 1988; 27:7282-8. [PMID: 3207676 DOI: 10.1021/bi00419a016] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The C-terminal domain, Od-1, of the 7-domain subunit of Octopus dofleini hemocyanin has been prepared by partial trypsinolysis followed by ion-exchange chromatography. It binds oxygen reversibly and is homogeneous in molecular weight. Its physical properties have been compared with those of the subunit. The domain molecular weight is found by sedimentation equilibrium to be 4.7 X 10(4), in excellent agreement with the result recently obtained in our laboratory from cDNA sequencing of this domain [Lang, W. H. (1988) Biochemistry (preceding paper in this issue)]. It has a sedimentation coefficient of 3.8 S. Both the molecular weight and sedimentation coefficient are consistent with the domain constituting approximately one-seventh of the Mr 3.5 X 10(5) subunit. Its amino acid composition and carbohydrate content differ significantly from that of the whole subunit, confirming the heterogeneity in domains previously established on an immunological basis. Circular dichroism predicts similar secondary structure for the domain and subunit. The domain does not self-associate in the presence of Mg2+ but does bind to the whole molecule in a ratio of approximately 1 domain/subunit. The oxygen affinity of this domain is quite low. It shows intrinsic magnesium and Bohr effects similar to those of the whole molecule but of greatly reduced magnitude.
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Affiliation(s)
- K I Miller
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331
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Billiald P, Lamy J, Taveau JC, Motta G, Lamy J. Mapping of six epitopes on haemocyanin subunit Aa 6 by immunoelectron microscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 175:423-31. [PMID: 2456929 DOI: 10.1111/j.1432-1033.1988.tb14212.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Monoclonal antibodies directed against the haemocyanin of the scorpion Androctonus australis were raised in order to map antigenic determinants (epitopes). The method of mapping employed in this study is molecular immunoelectron microscopy. It consists of a direct electron microscopic observation of antigenic molecules labelled with monoclonal antibodies. The epitopes are then localized in a small region of the external surface of the antigenic molecule whose architecture and quaternary structure are well known. Six monoclonal antibodies have been selected and epitopes have been circumscribed within a small area of one subunit among the 24 subunits composing the whole antigenic molecule.
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Affiliation(s)
- P Billiald
- Laboratoire de Biochimie Fondamentale, Faculté de Pharmacie, Tours, France
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Frank J, Bretaudiere JP, Carazo JM, Verschoor A, Wagenknecht T. Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli. J Microsc 1988; 150:99-115. [PMID: 3045323 DOI: 10.1111/j.1365-2818.1988.tb04602.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Images of macromolecules obtained in the electron microscope are subjected to correspondence analysis. The structure inherent in the data in the resulting low-dimensional factor space is characterized by a mixed classification method which combines the dynamic clouds clustering technique with hierarchical ascendant classification (HAC). For our data, the rejection of marginal clusters obtained by dynamic clouds clustering appears as a crucial prerequisite for a stable performance of HAC. The method is applied to two sets of 204 and 177 images that show the 70S ribosome of Escherichia coli, in the range of overlap views as defined by A. Verschoor and co-workers, and to two sets of 480 and 496 images of the 50S subunit of E. coli depleted of L7/L12 proteins in the well-defined crown view. Reproducible classes are obtained, which are characterized by images reconstituted from factorial coordinates. These classes appear to be related to different orientations on the specimen grid (in the case of the 70S particle) and to different conformational states (50S subunit).
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Affiliation(s)
- J Frank
- New York State Department of Health, Albany 12201
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The quaternary structure of four crustacean two-hexameric hemocyanins: immunocorrelation, stoichiometry, reassembly and topology of individual subunits. J Comp Physiol B 1988. [DOI: 10.1007/bf00695326] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Makino N, Kimura S. Subunits of Panulirus japonicus hemocyanin. 1. Isolation and properties. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 173:423-30. [PMID: 3360019 DOI: 10.1111/j.1432-1033.1988.tb14016.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Structural and functional diversities of the subunits of Panulirus japonicus (spiny lobster) hemocyanin were investigated. The hemocyanin mostly exists as a hexamer in the native state. It was found that the hemocyanin is composed of three major subunits (Ib, II and III) and one minor subunit (Ia), which differ in N-terminal sequence. In the dissociated state, the major subunits (Ib, II and III) showed no or very small Bohr effects. The O2 affinity of the subunit III was about three times as high as those of the other two. The subunits could be reassociated into homogeneous and heterogeneous hexamers, which exhibited the cooperativity in O2 binding. The homohexamers were similar to each other in O2 affinity and the Bohr effect, though some differences were observed in the magnitude of the cooperativity. In particular, the subunit II homohexamer exhibited a high cooperativity, which was comparable to that of the native protein. The heterohexamers showed slightly higher O2 affinities and slightly lower cooperativity, as compared with the parent homohexamers. It was concluded that there is no essential difference among the three major subunits of P. japonicus hemocyanin in the O2 binding and assembly properties.
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Affiliation(s)
- N Makino
- Division of Biochemistry, University of Tsukuba, Japan
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Herskovits TT. Recent aspects of the subunit organization and dissociation of hemocyanins. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1988; 91:597-611. [PMID: 3066572 DOI: 10.1016/0305-0491(88)90179-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
1. The hemocyanins of the arthropod phylum are built of multiples of hexamers consisting of 1,2,4,6 and 8 of such basic assemblies. Their molecular weights range from about 0.45 x 10(6) to 3.9 x 10(6) daltons. The basic hexameric unit consists of bean-shaped monomers organized in the form of two layers of trimers placed on top of one another. The subunits are heterogeneous, in most cases consisting of four or more electrophoretically different polypeptide chains. 2. Molluscan hemocyanins have an entirely different structure and pattern of assembly from the arthropodan hemocyanins. The basic assembly of the molluscan hemocyanins are decamers organized in the form of right-handed cylinders approximately 300 A in diameter and 140-190 A in height. Different species have one, two and sometimes more than two such assemblies forming correspondingly longer cylindrical particles with molecular weights ranging from about 3.3 x 10(6) to 13 x 10(6) daltons. Cephalopod and chiton hemocyanins consist of single decameric particles, while gastropods have hemocyanins organized of di-decamers or higher assemblies. The subunits of these hemocyanins are elongated protein chains with seven or eight folded globular domains, each housing a binuclear copper center capable of binding and delivering oxygen. 3. The dissociation behavior of the arthropod hemocyanin hexamers and di-hexamers with the hydrophobic urea series of reagents suggest polar and ionic interactions as the main sources of stabilization of the hexamers and the hexamer to hexamer contacts within the di-hexamers. 4. Dissociation studies with the same urea probes with the molluscan hemocyanins, however, suggest a different pattern of stabilization. The stabilization of the decamer to decamer contacts within the gastropod di-decamers appear to be predominantly polar and ionic with relatively few hydrophobic interaction sites. The dimer contacts within the decamers and the monomer to monomer contacts within the dimers observed in the octopus and chiton hemocyanins appear to be predominantly hydrophobic in nature. 5. The urea and the pH dissociation profiles of the single decameric assemblies of some of the octopus and chiton hemocyanins investigated by light-scattering molecular weight methods, have been fitted using either a two-species, decamer to dimer and decamer to monomer scheme of subunit dissociation or a three-species, decamer to dimer to monomer scheme of dissociation.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- T T Herskovits
- Department of Chemistry, Fordham University, Bronx, NY 10458
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Boisset N, Frank J, Taveau JC, Billiald P, Motta G, Lamy J, Sizaret PY, Lamy J. Intramolecular localization of epitopes within an oligomeric protein by immunoelectron microscopy and image processing. Proteins 1988; 3:161-83. [PMID: 2474818 DOI: 10.1002/prot.340030305] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Three epitopes have been localized by immunoelectron microscopy on subunit Aa6 of the 4 x 6-meric hemocyanin of the scorpion Androctonus australis. Soluble immunocomplexes composed of monoclonal antibodies and of native hemocyanin were purified, negatively stained with uranyle acetate by the single-layer technique, and examined under the electron microscope (EM). The molecule images were digitized, aligned, and submitted to correspondence analysis according to the method of Van Heel and Frank (Ultramicroscopy 6:187-194, 1981). A high-precision localization of the attachment point of the Fab arm to the antigen was achieved through a careful analysis of the average images. This method easily allowed the discrimination of epitopes located in different domains (Mr 20 kDa) of the same subunit. Nonoverlapping epitopes located in the same structural domain of subunit Aa6 could be distinguished by the stain exclusion patterns of their Fab arms. The method is general and may be used for epitope mapping in any antigen producing definite EM views.
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Affiliation(s)
- N Boisset
- Laboratoire de Biochimie, Faculté de Pharmacie, Université François Rabelais, Tours, France
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Bretaudiere JP, Frank J. Reconstitution of molecule images analysed by correspondence analysis: a tool for structural interpretation. J Microsc 1986; 144:1-14. [PMID: 3632765 DOI: 10.1111/j.1365-2818.1986.tb04669.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Correspondence analysis is gaining increasing importance in the analysis of electron micrographs of macromolecules. Partial or complete reconstitution of images from their factorial representations is introduced as a useful tool in interpreting variational patterns and tracing their physical origin. The value of image reconstitution is demonstrated with two examples, one using a set of model images and the other a set of images of a haemocyanin molecule assembly product.
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Motta G, Locker D. Detection of antibody-secreting hybridomas with diazobenzyloxymethyl paper. Methods Enzymol 1986; 121:491-7. [PMID: 3523127 DOI: 10.1016/0076-6879(86)21049-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Abstract
Erythrocruorins are giant extracellular respiratory proteins found freely dissolved in the blood of annelids. We present here results from our ultracentrifugation, electron microscopy, spectroscopy, and diffraction experiments on these erythrocruorins. These data are rationalized in terms of a three-dimensional model of the quaternary structure. The proposed structure is arranged in a hierarchy of symmetry. The implications of this structure for the assembly process are considered with special attention to uniqueness and self-limitation. The hypothesis is consistent with observations not used in its construction and it serves as a working hypothesis to focus further experimentation.
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