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Tsuchida T, Susa K, Kibiki T, Tsuchiya T, Miyamoto K, In Y, Minoura K, Taniguchi T, Ishida T, Tomoo K. Structural study of the recognition mechanism of tau antibody Tau2r3 with the key sequence (VQIINK) in tau aggregation. Biochem Biophys Res Commun 2021; 585:36-41. [PMID: 34784549 DOI: 10.1016/j.bbrc.2021.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022]
Abstract
One of the histopathological features of Alzheimer's disease (AD) is higher order neurofibrillary tangles formed by abnormally aggregated tau protein. The sequence 275VQIINK280 in the microtubule-binding domain of tau plays a key role in tau aggregation. Therefore, an aggregation inhibitor targeting the VQIINK region in tau may be an effective therapeutic agent for AD. We have previously shown that the Fab domain (Fab2r3) of a tau antibody that recognizes the VQIINK sequence can inhibit tau aggregation, and we have determined the tertiary structure of the Fab2r3-VQIINK complex. In this report, we determined the tertiary structure of apo Fab2r3 and analyzed differences in the structures of apo Fab2r3 and Fab2r3-VQIINK to examine the ligand recognition mechanism of Fab2r3. In comparison with the Fab2r3-VQIINK structure, there were large differences in the arrangement of the constant and variable domains in apo Fab2r3. Remarkable structural changes were especially observed in the H3 and L3 loop regions of the complementarity determining regions (CDRs) in apo Fab2r3 and the Fab2r3-VQIINK complex. These structural differences in CDRs suggest that formation of hydrophobic pockets suitable for the antigen is important for antigen recognition by tau antibodies.
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Affiliation(s)
- Tomohiro Tsuchida
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kouki Susa
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Tomohiro Kibiki
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Takahiro Tsuchiya
- Department of Microbiology and Infection Control, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Katsushiro Miyamoto
- Department of Microbiology and Infection Control, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yasuko In
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Katsuhiko Minoura
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Taizo Taniguchi
- Pharma Crea Kobe Co. Ltd., Showajutaku・Fukumoto Bldg. 8F, 4-2-18, Hachimandori, Chuo-ku, Kobe, Hyogo, 651-0085, Japan
| | - Toshimasa Ishida
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Koji Tomoo
- Department of Physical Chemistry, Osaka Medical and Pharmaceutical University, 4-20-1, Nasahara, Takatsuki, Osaka, 569-1094, Japan.
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Human IgG1, IgG3, and IgG3 Hinge-Truncated Mutants Show Different Protection Capabilities against Meningococci Depending on the Target Antigen and Epitope Specificity. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2016; 23:698-706. [PMID: 27307451 DOI: 10.1128/cvi.00193-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/08/2016] [Indexed: 02/08/2023]
Abstract
We compared the bactericidal activity of recombinant sets of chimeric IgG monoclonal antibodies against two important outer membrane meningococcal vaccine antigens: PorA and factor H binding protein (FHbp). The sets contained human Fc portions from IgG1, IgG3, and two IgG3 mutants (IgG3m15 and IgGm17) with hinge regions of 15 and 17 amino acids encoded by hinge exons h2 and h1, respectively (human IgG3 has a hinge region of 62 amino acids encoded by hinge exons h1, h2, h3, and h4, while human IgG1 has a hinge region of only 15 amino acids encoded by one hinge exon) and mouse V regions. IgG1 showed higher bactericidal activity than IgG3 when directed against PorA (an abundant antigen), while IgG3 was more bactericidal than IgG1 when directed against FHbp (a sparsely and variably distributed antigen). On the other hand, the IgG3 hinge-truncated antibodies IgG3m15 and IgGm17 showed higher bactericidal activity than both IgG1 and IgG3 regardless of the target antigen. Thus, the Fc region of IgG3 antibodies appears to have an enhanced complement-activating function, independent of their long hinge region, compared to IgG1 antibodies. The greater activity of the truncated IgG3 hinge mutants indicates that the long hinge of IgG3 seems to downregulate through an unknown mechanism the inherent increased complement-activating capability of IgG3 Fc when the antibody binds to a sparse antigen.
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Liang Y, Guttman M, Davenport TM, Hu SL, Lee KK. Probing the Impact of Local Structural Dynamics of Conformational Epitopes on Antibody Recognition. Biochemistry 2016; 55:2197-213. [PMID: 27003615 PMCID: PMC5479570 DOI: 10.1021/acs.biochem.5b01354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Antibody-antigen interactions are governed by recognition of specific residues and structural complementarity between the antigen epitope and antibody paratope. While X-ray crystallography has provided detailed insights into static conformations of antibody-antigen complexes, factors such as conformational flexibility and dynamics, which are not readily apparent in the structures, can also have an impact on the binding event. Here we investigate the contribution of dynamics in the HIV-1 gp120 glycoprotein to antibody recognition of conserved conformational epitopes, including the CD4- and coreceptor-binding sites, and an inner domain site that is targeted by ADCC-active antibodies. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) was used to measure local structural dynamics across a panel of variable loop truncation mutants of HIV-1 gp120, including full-length gp120, ΔV3, ΔV1/V2, and extended core, which includes ΔV1/V2 and V3 loop truncations. CD4-bound full-length gp120 was also examined as a reference state. HDX-MS revealed a clear trend toward an increased level of order of the conserved subunit core resulting from loop truncation. Combined with biolayer interferometry and enzyme-linked immunosorbent assay measurements of antibody-antigen binding, we demonstrate that an increased level of ordering of the subunit core was associated with better recognition by an array of antibodies targeting complex conformational epitopes. These results provide detailed insight into the influence of structural dynamics on antibody-antigen interactions and suggest the importance of characterizing the structural stability of vaccine candidates to improve antibody recognition of complex epitopes.
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Affiliation(s)
- Yu Liang
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Thaddeus M. Davenport
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Shiu-Lok Hu
- Department of Pharmaceutics, University of Washington, Seattle, Washington 98195, United States
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Aakeröy CB, Smith M, Desper J. Finding a single-molecule receptor for citramalic acid through supramolecular chelation. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have demonstrated that the tritopic hydrogen-bond acceptor 1,3,5-(5,6-dimethylbenzimidazol-1-yl)-2,4,6-trimethylbenzene can act as a perfectly complementary receptor for citramalic acid. The solid-state structure of the cocrystal of the two components show that they form 1:1 pairs where each pair is held together by three near-linear O–H···N hydrogen bonds in a converging manner. The conformational flexibility of both species is apparently no hindrance to the formation of discrete dimeric “cups” wherein each species presents three hydrogen-bond donors/acceptors in a face-to-face orientation.
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Affiliation(s)
- Christer B. Aakeröy
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Michelle Smith
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - John Desper
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
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5
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Peri C, Gagni P, Combi F, Gori A, Chiari M, Longhi R, Cretich M, Colombo G. Rational epitope design for protein targeting. ACS Chem Biol 2013; 8:397-404. [PMID: 23138758 DOI: 10.1021/cb300487u] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a new multidisciplinary strategy integrating computational biology with high-throughput microarray analysis aimed to translate molecular understanding of protein-antibody recognition into the design of efficient and selective protein-based analytical and diagnostic tools. The structures of two proteins with different folds and secondary structure contents, namely, the beta-barrel FABP and the α-helical S100B, were used as the basis for the prediction and design of potential antibody-binding epitopes using the recently developed MLCE computational method. Starting from the idea that the structure, dynamics, and stability of a protein-antigen play a key role in the interaction with antibodies, MLCE integrates the analysis of the dynamical and energetic properties of proteins to identify nonoptimized, low-intensity energetic interaction-networks on the surface of the isolated antigens, which correspond to substructures that can aptly be recognized by a binding partner. The identified epitopes were next synthesized as free peptides and used to elicit specific antibodies in rabbits. Importantly, the resulting antibodies were proven to specifically and selectively recognize the original, full-length proteins in microarray-based tests. Competition experiments further demonstrated the specificity of the molecular recognition between the target immobilized proteins and the generated antibodies. Our integrated computational and microarray-based results demonstrate the possibility to rationally discover and design synthetic epitopes able to elicit antibodies specific for full-length proteins starting only from three-dimensional structural information on the target. We discuss implications for diagnosis and vaccine development purposes.
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Affiliation(s)
- Claudio Peri
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Paola Gagni
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Fabio Combi
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Alessandro Gori
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Marcella Chiari
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Renato Longhi
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Marina Cretich
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Isituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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Blackler RJ, Müller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV. A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity. Biochemistry 2011; 50:3357-68. [DOI: 10.1021/bi101886v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan J. Blackler
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Sven Müller-Loennies
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Cory L. Brooks
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Dylan W. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Lore Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Helmut Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Stephen V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
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7
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Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J 2010; 98:1966-75. [PMID: 20441761 DOI: 10.1016/j.bpj.2010.01.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/08/2010] [Accepted: 01/11/2010] [Indexed: 02/02/2023] Open
Abstract
An increasing number of functional studies of proteins have shown that sequence and structural similarities alone may not be sufficient for reliable prediction of their interaction properties. This is particularly true for proteins recognizing specific antibodies, where the prediction of antibody-binding sites, called epitopes, has proven challenging. The antibody-binding properties of an antigen depend on its structure and related dynamics. Aiming to predict the antibody-binding regions of a protein, we investigate a new approach based on the integrated analysis of the dynamical and energetic properties of antigens, to identify nonoptimized, low-intensity energetic interaction networks in the protein structure isolated in solution. The method is based on the idea that recognition sites may correspond to localized regions with low-intensity energetic couplings with the rest of the protein, which allows them to undergo conformational changes, to be recognized by a binding partner, and to tolerate mutations with minimal energetic expense. Upon analyzing the results on isolated proteins and benchmarking against antibody complexes, it is found that the method successfully identifies binding sites located on the protein surface that are accessible to putative binding partners. The combination of dynamics and energetics can thus discriminate between epitopes and other substructures based only on physical properties. We discuss implications for vaccine design.
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Chi SW, Kim J, Yi GS, Hong HJ, Ryu SE. Broadly neutralizing anti-HBV antibody binds to non-epitope regions of preS1. FEBS Lett 2009; 583:3095-100. [DOI: 10.1016/j.febslet.2009.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/18/2009] [Accepted: 08/18/2009] [Indexed: 12/25/2022]
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9
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Kügler M, Stein C, Schwenkert M, Saul D, Vockentanz L, Huber T, Wetzel SK, Scholz O, Plückthun A, Honegger A, Fey GH. Stabilization and humanization of a single-chain Fv antibody fragment specific for human lymphocyte antigen CD19 by designed point mutations and CDR-grafting onto a human framework. Protein Eng Des Sel 2009; 22:135-47. [DOI: 10.1093/protein/gzn079] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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10
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Amela I, Cedano J, Querol E. Pathogen proteins eliciting antibodies do not share epitopes with host proteins: a bioinformatics approach. PLoS One 2007; 2:e512. [PMID: 17551592 PMCID: PMC1885212 DOI: 10.1371/journal.pone.0000512] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 05/04/2007] [Indexed: 12/20/2022] Open
Abstract
The best way to prevent diseases caused by pathogens is by the use of vaccines. The advent of genomics enables genome-wide searches of new vaccine candidates, called reverse vaccinology. The most common strategy to apply reverse vaccinology is by designing subunit recombinant vaccines, which usually generate an humoral immune response due to B-cell epitopes in proteins. A major problem for this strategy is the identification of protective immunogenic proteins from the surfome of the pathogen. Epitope mimicry may lead to auto-immune phenomena related to several human diseases. A sequence-based computational analysis has been carried out applying the BLASTP algorithm. Therefore, two huge databases have been created, one with the most complete and current linear B-cell epitopes, and the other one with the surface-protein sequences of the main human respiratory bacterial pathogens. We found that none of the 7353 linear B-cell epitopes analysed shares any sequence identity region with human proteins capable of generating antibodies, and that only 1% of the 2175 exposed proteins analysed contain a stretch of shared sequence with the human proteome. These findings suggest the existence of a mechanism to avoid autoimmunity. We also propose a strategy for corroborating or warning about the viability of a protein linear B-cell epitope as a putative vaccine candidate in a reverse vaccinology study; so, epitopes without any sequence identity with human proteins should be very good vaccine candidates, and the other way around.
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Affiliation(s)
- Isaac Amela
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Cedano
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- * To whom correspondence should be addressed. E-mail:
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11
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Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B, Spólnik P. Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction. Proteins 2006; 59:545-54. [PMID: 15778960 DOI: 10.1002/prot.20434] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It was shown experimentally that binding of a micelle composed of Congo red molecules to immunological complexes leads to the enhanced stability of the latter, and simultaneously prevents binding of a complement molecule (C1q). The dye binds in a cavity created by the removal of N-terminal polypeptide chain, as observed experimentally in a model system-immunoglobulin G (IgG) light chain dimer. Molecular Dynamics (MD) simulations of three forms of IgG light chain dimer, with and without the dye, were performed to investigate the role of N-terminal fragment and self-assembled ligand in coupling between V and C domains. Root-mean-square distance (RMSD) time profiles show that removal of N-terminal fragment leads to destabilization of V domain. A micelle composed of four self-assembled dye molecules stabilizes and fixes the domain. Analysis of root-mean-square fluctuation (RMSF) values and dynamic cross-correlation matrices (DCCM) reveals that removal of N-terminal fragment results in complete decoupling between V and C domains. Binding of self-assembled Congo red molecules improves the coupling, albeit slightly. The disruption of a small beta-sheet composed of N- and C-terminal fragments of the domain (NC sheet) is the most likely reason for the decoupling. Self-assembled ligand, bound in the place originally occupied by N-terminal fragment, is not able to take over the function of the beta-sheet. Lack of correlation of motions between residues in V and C domains denotes that light chain-Congo red complexes have hampered ability to transmit conformational changes between domains. This is a likely explanation of the lack of complement binding by immunological complexes, which bind Congo red, and supports the idea that the NC sheet is the key structural fragment taking part in immunological signal transduction.
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Affiliation(s)
- Marcin Król
- Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kraków, Poland.
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12
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Vidarsson G, Overbeeke N, Stemerding AM, van den Dobbelsteen G, van Ulsen P, van der Ley P, Kilian M, van de Winkel JGJ. Working mechanism of immunoglobulin A1 (IgA1) protease: cleavage of IgA1 antibody to Neisseria meningitidis PorA requires de novo synthesis of IgA1 Protease. Infect Immun 2005; 73:6721-6. [PMID: 16177349 PMCID: PMC1230903 DOI: 10.1128/iai.73.10.6721-6726.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neisseria meningitidis secretes a protease that specifically cleaves the hinge region of immunoglobulin A1 (IgA1), releasing the effector (Fc) domain of IgA1 from the antigen binding (Fab) determinants. Theoretically, the remaining Fab fragments can block pathogen receptors or toxins and still provide protection. Here, we describe binding of V-gene-matched human IgA1 and IgA2 to PorA of strain H44/76. On live meningococci, efficient cleavage of IgA1, but not cleavage of IgA2, was observed, and up to approximately 80% of the IgA1 Fc tails were lost from the meningococcal surface within 30 min. No cleavage of IgA1 was found on an isogenic H44/76 strain lacking IgA1 protease. Furthermore, our data indicate that PorA-bound IgA1 is masked by the serogroup B polysaccharide capsule, rendering the IgA1 less accessible to degradation by secreted IgA1 protease present in the bacterial surroundings. Experiments with protein synthesis inhibitors showed that de novo production of IgA1 protease was responsible for cleavage of PorA-bound IgA1 on encapsulated bacteria. Finally, our data suggest that cleavage of IgA1 by IgA1 protease releases a significant proportion of Fab fragments from the bacterium, probably as a result of their reduced avidity compared to that of whole antibodies.
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Affiliation(s)
- Gestur Vidarsson
- Immunotherapy Laboratory, Department of Immunology, University Medical Center Utrecht (UMCU), The Netherlands.
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13
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Oomen CJ, Hoogerhout P, Kuipers B, Vidarsson G, van Alphen L, Gros P. Crystal Structure of an Anti-meningococcal Subtype P1.4 PorA Antibody Provides Basis for Peptide–Vaccine Design. J Mol Biol 2005; 351:1070-80. [PMID: 16038932 DOI: 10.1016/j.jmb.2005.06.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 06/23/2005] [Accepted: 06/27/2005] [Indexed: 10/25/2022]
Abstract
In various western countries, subtype P1.4 of Neisseria meningitidis serogroup B causes the greatest incidence of meningococcal disease. To investigate the molecular recognition of this subtype, we crystallised a peptide (P1HVVVNNKVATH(P11)), corresponding to the subtype P1.4 epitope sequence of outer membrane protein PorA, in complex with a Fab fragment of the bactericidal antibody MN20B9.34 directed against this epitope. Structure determination at 1.95 A resolution revealed a unique complex of one P1.4 antigen peptide bound to two identical Fab fragments. One Fab recognises the putative epitope residues in a 2:2 type I beta-turn at residues P5NNKV(P8), whereas the other Fab binds the C-terminal residues of the peptide that we consider a crystallisation artefact. Interestingly, recognition of the P1.4 epitope peptide is mediated almost exclusively through the complementarity-determining regions of the heavy chain. We exploited the observed turn conformation for designing conformationally restricted cyclic peptides for use as a peptide vaccine. The conformational stability of the two peptide designs was assessed by molecular dynamics simulations. Unlike the linear peptide, both cyclic peptides, conjugated to tetanus toxoid as a carrier protein, elicited antibody responses in mice that recognised meningococci of subtype P1.7-2,4. Serum bactericidal assays showed that some, but not all, of the sera induced with the cyclic peptide conjugates could activate the complement system with titres that were very high compared to the titres induced by complete PorA protein in its native conformation administered in outer membrane vesicles.
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Affiliation(s)
- Clasien J Oomen
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Raats J, van Bree N, van Woezik J, Pruijn G. Generating recombinant anti-idiotypic antibodies for the detection of haptens in solution. J Immunoassay Immunochem 2004; 24:115-46. [PMID: 12778968 DOI: 10.1081/ias-120020081] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A new method is described for generating recombinant human and chicken antibody fragments for accurate quantification of haptens in solution. The chemistry of labelling small molecules has always been a problem in the development of immunoassays. Here, we describe a specific panning procedure that enables the selection of recombinant anti-idiotypic phage antibodies that bind to hapten binding molecules (e.g., antibodies) in the absence of the hapten, but are displaced in a highly specific and concentration dependent manner, in the presence of the hapten. The major advantage of such a detection system is that there is no need to label the hapten or to covalently attach it to a solid phase. In this study we demonstrate, using cortisol and aldosterone as model haptens, that the recombinant antibody phage display technology offers great possibilities to generate recombinant anti-idiotypic antibodies. Furthermore, we show that such antibodies can be used successfully to design highly sensitive immunoassays for the quantification of small molecules.
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Affiliation(s)
- Jos Raats
- Department of Biochemistry, University of Nijmegen, Nijmegen, The Netherlands.
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15
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Michaelsen TE, Ihle Ø, Beckstrøm KJ, Herstad TK, Kolberg J, Høiby EA, Aase A. Construction and functional activities of chimeric mouse-human immunoglobulin G and immunoglobulin M antibodies against the Neisseria meningitidis PorA P1.7 and P1.16 epitopes. Infect Immun 2003; 71:5714-23. [PMID: 14500492 PMCID: PMC201080 DOI: 10.1128/iai.71.10.5714-5723.2003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We studied the in vitro protective activities of human immunoglobulin G1 (IgG1), IgG3, and IgM antibodies against group B meningococci by constructing sets of chimeric mouse-human antibodies (chIgG1, chIgG3, and chIgM, respectively) with identical binding regions against the P1.7 and P1.16 epitopes on PorA. This was done by cloning the V genes of three mouse hybridoma antibodies and subsequently transfecting vectors containing the homologous heavy- and light-chain genes into NSO cells. Cell clones secreting intact human chIgG1, chIgG3, or chIgM antibodies originating from three parent mouse antibodies were isolated. The functional affinities appeared to be similar for all human isotypes and surprisingly also for the pentameric chIgM antibody. chIgG1 exhibited greater serum bactericidal activity (SBA) than chIgG3, while chIgG3 was more efficient in inducing a respiratory burst (RB) associated with opsonophagocytosis than chIgG1 was. On the other hand, chIgM exhibited SBA similar to that of chIgG1, but it exhibited much higher RB activity than chIgG3 and chIgG1 exhibited. The antibodies against the P1.16 epitope were more efficient in terms of SBA than the antibodies against the P1.7 epitope were; thus, 10- to 40-fold-lower concentrations of antibodies against P1.16 than of antibodies against P1.7 were needed to induce SBA. On the other hand, antibodies against these epitopes were equally effective in inducing RB. Our results revealed differences in the functional activities of human chIgG1, chIgG3, and chIgM antibodies against meningococci, which might influence their protective effects against meningococcal disease.
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Affiliation(s)
- Terje E Michaelsen
- Division of Infectious Disease Control, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403 Oslo, Norway.
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Drogari-Apiranthitou M, Kuijper EJ, Dekker N, Dankert J. Complement activation and formation of the membrane attack complex on serogroup B Neisseria meningitidis in the presence or absence of serum bactericidal activity. Infect Immun 2002; 70:3752-8. [PMID: 12065518 PMCID: PMC128098 DOI: 10.1128/iai.70.7.3752-3758.2002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Encapsulated meningococci are complement sensitive only in the presence of bactericidal antibodies by yet-unexplored mechanisms. The objective of this study was to investigate the involvement of major bacterial surface constituents on complement activation and membrane attack complex (MAC) formation on serogroup B meningococci in the presence or absence of antibody-dependent serum bactericidal activity (SBA). The strains used were the encapsulated H44/76, five of its variants differing in capsulation and expression of the class 1 porin (PorA), and its lipopolysaccharide (LPS)-deficient isogenic mutant (LPS(-)) pLAK33. Two normal sera, one with high SBA (SBA(+)) and one with no bactericidal activity (SBA(-)) against H44/76 as well as an a-gamma-globulinemic serum were used for sensibilization of the bacteria. C3b and iC3b deposition on H44/76, its unencapsulated variant v24, and pLAK33 was similar in SBA(+) and SBA(-) serum, and no difference was present between the strains. MAC deposition on H44/76 was higher in SBA(+) serum than in SBA(-) serum and the a-gamma-globulinemic serum. The amounts of C3b on H44/76, v24, and pLAK33 in the a-gamma-globulinemic serum were also not different, indicating immunoglobulin G (IgG)- and LPS-independent complement activation. H44/76 PorA(+) and its PorA(-) variant and the v24 PorA(+) and its PorA(-) variant incubated in SBA(-) serum induced comparable amounts of MAC, despite their different serum sensitivities. Complement formation on the surface of the bacteria occurred almost exclusively via the classical pathway, but the considerable amounts of Bb measured in the serum indicated alternative pathway activation in the fluid phase. We conclude that complement deposition on meningococci is, for the most part, independent of classical pathway IgG and is not influenced by the presence of PorA or LPS on the meningococcal surface. Addition of an anti-PorA chimeric antibody to the nonbactericidal normal serum, while promoting a dose-related bacterial lysis, did not influence the amounts of C3b, iC3b, and MAC formed on the bacterial surface. These findings support the hypothesis that proper MAC insertion rather than the quantity of MAC formed on the bacterial surface is of importance for efficient lysis of meningococci.
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Affiliation(s)
- M Drogari-Apiranthitou
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.
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17
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Fischer MJ, Kuipers C, Hofkes RP, Hofmeyer LJ, Moret EE, de Mol NJ. Exploring computational lead optimisation with affinity constants obtained by surface plasmon resonance for the interaction of PorA epitope peptides with antibody against Neisseria meningitidis. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1568:205-15. [PMID: 11786227 DOI: 10.1016/s0304-4165(01)00215-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
LUDI is a program used for de novo structure-based design of ligands and can predict binding of ligands quantitatively using a scoring function. Here we evaluate LUDI in a lead optimisation study with ligands for the antibody MN12H2, that has been raised against outer membrane protein PorA epitope P1.16 of Neisseria meningitidis. The ligands were synthetic peptides that are derived from the smallest binding epitope (182)DTNNN(186). LUDI's fragment building rules are used for the proposal of new peptide-ligands for MN12H2 and were focused on replacements of Asp(186) in the epitope. Accordingly, a series of peptides was synthesised with isosteric mutations. The interaction of the peptides with MN12H2 was analysed with a surface plasmon resonance competition assay yielding equilibrium binding constants in solution (K(S)). The binding affinity seems to be largely determined by entropy, and the side chain of Asn(186) is sensitive for charge, inversion, hydrophobicity and size. Head-to-tail cyclisation of the peptide in a nine-amino-acid ring gives little reduction in affinity. It is concluded that the scoring function of LUDI does not help in optimisation of the peptide lead for MN12H2 binding. Other more elaborate molecular mechanics calculations show similar results. This implies that our current knowledge of molecular recognition is insufficient for explaining a case of peptide-protein binding, where the design process requires subtle changes in structure (from lead finding to lead optimisation).
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Affiliation(s)
- M J Fischer
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Faculty of Pharmacy, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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18
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Vidarsson G, van Der Pol WL, van Den Elsen JM, Vilé H, Jansen M, Duijs J, Morton HC, Boel E, Daha MR, Corthésy B, van De Winkel JG. Activity of human IgG and IgA subclasses in immune defense against Neisseria meningitidis serogroup B. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 166:6250-6. [PMID: 11342648 DOI: 10.4049/jimmunol.166.10.6250] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Both IgG and IgA Abs have been implicated in host defense against bacterial infections, although their relative contributions remain unclear. We generated a unique panel of human chimeric Abs of all human IgG and IgA subclasses with identical V genes against porin A, a major subcapsular protein Ag of Neisseria meningitidis and a vaccine candidate. Chimeric Abs were produced in baby hamster kidney cells, and IgA-producing clones were cotransfected with human J chain and/or human secretory component. Although IgG (isotypes IgG1-3) mediated efficient complement-dependent lysis, IgA was unable to. However, IgA proved equally active to IgG in stimulating polymorphonuclear leukocyte respiratory burst. Remarkably, although porin-specific monomeric, dimeric, and polymeric IgA triggered efficient phagocytosis, secretory IgA did not. These studies reveal unique and nonoverlapping roles for IgG and IgA Abs in defense against meningococcal infections.
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Affiliation(s)
- G Vidarsson
- Department of Immunology, Medarex Europe, Genmab, and Eijkman-Winkler Institute for Microbiology, Infectious Diseases and Inflammation, University Medical Center Utrecht, Utrecht, The Netherlands
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19
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Wang J, Jarvis GA, Achtman M, Rosenqvist E, Michaelsen TE, Aase A, Griffiss JM. Functional activities and immunoglobulin variable regions of human and murine monoclonal antibodies specific for the P1.7 PorA protein loop of Neisseria meningitidis. Infect Immun 2000; 68:1871-8. [PMID: 10722576 PMCID: PMC97360 DOI: 10.1128/iai.68.4.1871-1878.2000] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The meningococcal PorA protein is considered a promising vaccine candidate. Although much is understood regarding the structure of PorA proteins, little is known about the structure-function relationships of PorA antibodies. The aim of this study was to compare the functional and molecular characteristics of a human monoclonal antibody (MAb) and three murine MAbs specific for the PorA P1.7 serosubtype. Murine MAbs 207,B-4 (immunoglobulin G2a [IgG2a]) and MN14C11.6 (IgG2a) were both bactericidal and opsonophagocytic for P1.7-expressing meningococci, whereas human MAb SS269 (IgG3) and murine MAb 208,D-5 (IgA) initiated neither effector function. Epitope mapping with synthetic peptides revealed that MAbs 207,B-4 and 208,D-5 recognized the sequence ASGQ, which is the same specificity motif that a previous study had established for SS269 and MN14C11.6. Nucleotide and amino acid sequence analyses of the variable regions of the four MAbs showed that the SS269 V(H) region belonged to the VH3 family and was approximately 70% homologous to those of the murine MAbs which were all from the 7183 family, whereas the SS269 V(L) region belonged to the Vlambda1-b family and was less than 40% homologous to those of the murine MAbs which were all members of the Vkappa1 family. The Fab fragment of SS269 was cloned and expressed in Escherichia coli and was shown by enzyme-linked immunosorbent assay analyses to bind as well as intact SS269 MAb to P1.7,16 serosubtype group B strain 44/76. We conclude that distinct differences exist in the effector function activities and variable region gene sequences of human and murine P1.7-specific MAbs despite their recognition of similar epitopes.
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Affiliation(s)
- J Wang
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
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20
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van Den Elsen JM, Kuntz DA, Hoedemaeker FJ, Rose DR. Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein. Proc Natl Acad Sci U S A 1999; 96:13679-84. [PMID: 10570132 PMCID: PMC24124 DOI: 10.1073/pnas.96.24.13679] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ABC transporter, P-glycoprotein, is an integral membrane protein that mediates the ATP-driven efflux of drugs from multidrug-resistant cancer and HIV-infected cells. Anti-P-glycoprotein antibody C219 binds to both of the ATP-binding regions of P-glycoprotein and has been shown to inhibit its ATPase activity and drug binding capacity. C219 has been widely used in a clinical setting as a tumor marker, but recent observations of cross-reactivity with other proteins, including the c-erbB2 protein in breast cancer cells, impose potential limitations in detecting P-glycoprotein. We have determined the crystal structure at a resolution of 2.4 A of the variable fragment of C219 in complex with an epitope peptide derived from the nucleotide binding domain of P-glycoprotein. The 14-residue peptide adopts an amphipathic alpha-helical conformation, a secondary structure not previously observed in structures of antibody-peptide complexes. Together with available biochemical data, the crystal structure of the C219-peptide complex indicates the molecular basis of the cross-reactivity of C219 with non-multidrug resistance-associated proteins. Alignment of the C219 epitope with the recent crystal structure of the ATP-binding subunit of histidine permease suggests a structural basis for the inhibition of the ATP and drug binding capacity of P-glycoprotein by C219. The results provide a rationale for the development of C219 mutants with improved specificity and affinity that could be useful in antibody-based P-glycoprotein detection and therapy in multidrug resistant cancers.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/chemistry
- ATP Binding Cassette Transporter, Subfamily B, Member 1/immunology
- Amino Acid Sequence
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Crystallography, X-Ray
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Immunoglobulin Fragments/chemistry
- Immunoglobulin Fragments/immunology
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Protein Conformation
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Affiliation(s)
- J M van Den Elsen
- Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto M5G 2M9, Ontario, Canada
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Derrick JP, Maiden MC, Feavers IM. Crystal structure of an Fab fragment in complex with a meningococcal serosubtype antigen and a protein G domain. J Mol Biol 1999; 293:81-91. [PMID: 10512717 DOI: 10.1006/jmbi.1999.3144] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many pathogens present highly variable surface proteins to their host as a means of evading immune responses. The structure of a peptide antigen corresponding to the subtype P1.7 variant of the porin PorA from the human pathogen Neisseria meningitidis was determined by solution of the X-ray crystal structure of the ternary complex of the peptide (ANGGASGQVK) in complex with a Fab fragment and a domain from streptococcal protein G to 1.95 A resolution. The peptide adopted a beta-hairpin structure with a type I beta-turn between residues Gly4P and Gly7P, the conformation of the peptide being further stabilised by a pair of hydrogen bonds from the side-chain of Asn2P to main-chain atoms in Val9P. The antigen binding site within the Fab formed a distinct crevice lined by a high proportion of apolar amino acids. Recognition was supplemented by hydrogen bonds from heavy chain residues Thr50H, Asp95H, Leu97H and Tyr100H to main-chain and side-chain atoms in the peptide. Complementarity-determining region (CDR) 3 of the heavy chain was responsible for approximately 50 % of the buried surface area formed by peptide-Fab binding, with the remainder made up from CDRs 1 and 3 of the light chain and CDRs 1 and 2 of the heavy chain. Knowledge of the structures of variable surface antigens such as PorA is an essential prerequisite to a molecular understanding of antigenic variation and its implications for vaccine design.
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Affiliation(s)
- J P Derrick
- Department of Biomolecular Sciences, UMIST, Manchester, M60 1QD, UK.
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