1
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Schilling PE, Kontaxis G, Dragosits M, Schiestl RH, Becker CFW, Maier I. Mannosylated hemagglutinin peptides bind cyanovirin-N independent of disulfide-bonds in complementary binding sites. RSC Adv 2020; 10:11079-11087. [PMID: 35495330 PMCID: PMC9050506 DOI: 10.1039/d0ra01128b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/10/2020] [Indexed: 01/11/2023] Open
Abstract
Cyanovirin-N (CV-N) has been shown to reveal broad neutralizing activity against human immunodeficiency virus (HIV) and to specifically bind Manα(1→2)Manα units exposed on various glycoproteins of enveloped viruses, such as influenza hemagglutinin (HA) and Ebola glycoprotein. Chemically synthesized dimannosylated HA peptides bound domain-swapped and dimeric CV-N with either four disulfide-bonds (Cys–Cys), or three Cys–Cys bonds and an intact fold of the high-affinity binding site at an equilibrium dissociation constant KD of 10 μM. Cys–Cys mutagenesis with ion-pairing amino-acids glutamic acid and arginine was calculated by in silico structure-based protein design and allowed for recognizing dimannose and dimannosylated peptide binding to low-affinity binding sites (KD ≈ 11 μM for one C58–C73 bond, and binding to dimannosylated peptide). In comparison, binding to HA was achieved based on one ion-pairing C58E–C73R substitution at KD = 275 nM, and KD = 5 μM for two C58E–C73R substitutions. We were utilizing a triazole bioisostere linkage to form the respective mannosylated-derivative on the HA peptide sequence of residues glutamine, glycine, and glutamic acid. Thus, mono- and dimannosylated peptides with N-terminal cysteine facilitated site-specific interactions with HA peptides, mimicking a naturally found N-linked glycosylation site on the HA head domain. Di-mannosylated peptides reveal mannose binding to cyanovirin-N (CV-N) low-affinity binding sites.![]()
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Affiliation(s)
- Philipp E Schilling
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 A-1090 Vienna Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna Campus Vienna Bohrgasse 5 A-1030 Vienna Austria
| | - Martin Dragosits
- Department of Chemistry, Division of Biochemistry, University of Natural Resources and Life Sciences Muthgasse 18 A-1190 Vienna Austria
| | - Robert H Schiestl
- Department of Pathology and Laboratory Medicine, Geffen School of Medicine, University of California Los Angeles CA-90095 USA.,Department of Environmental Health Sciences, Fielding School of Public Health, University of California, Los Angeles 650 Charles E. Young Dr. South Los Angeles CA-90095 USA +1-310-267-2578 +1-310-267-2087
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 A-1090 Vienna Austria
| | - Irene Maier
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 A-1090 Vienna Austria.,Department of Environmental Health Sciences, Fielding School of Public Health, University of California, Los Angeles 650 Charles E. Young Dr. South Los Angeles CA-90095 USA +1-310-267-2578 +1-310-267-2087
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2
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Wang W, Hao D, Ge J, Zhao L, Huang Y, Zhu K, Wu X, Su Z, Yu R, Ma G. A minimalist peptide ligand for IgG by minimizing the binding domain of protein A. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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3
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Aretz J, Rademacher C. Ranking Hits From Saturation Transfer Difference Nuclear Magnetic Resonance-Based Fragment Screening. Front Chem 2019; 7:215. [PMID: 31032246 PMCID: PMC6473174 DOI: 10.3389/fchem.2019.00215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/19/2019] [Indexed: 12/24/2022] Open
Abstract
Fragment-based screening is an established route to identify low-molecular-weight molecules to generate high-affinity inhibitors in drug discovery. The affinities of these early hits from fragment screenings require a highly sensitive biophysical screening technique. Saturation transfer difference (STD) nuclear magnetic resonance (NMR) is one of the most popular methods owing to its high sensitivity for low-affinity ligands. It would be highly beneficial if rank-ordering of hits according to their affinity from an initial or counter-screen could be performed—a selection criterion found in the literature. We applied Complete Relaxation and Conformational Exchange Matrix (CORCEMA) theory adapted for saturation transfer (ST) measurements (CORCEMA-ST) calculations to predict STD NMR results from a large set of fragment/receptor pairs to investigate the boundaries under which the assumption holds true that a high STD effect can be applied to select for higher-affinity fragments. Overall, we come to the conclusion that this assumption is invalid.
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Affiliation(s)
- Jonas Aretz
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany
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4
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Sugawara K, Kadoya T, Kuramitz H. Magnetic beads modified with an electron-transfer carbohydrate-mimetic peptide for sensing of a galactose-dependent protein. Anal Chim Acta 2018; 1001:158-167. [PMID: 29291799 DOI: 10.1016/j.aca.2017.11.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/17/2022]
Abstract
For use in the voltammetric sensing of galactose-dependent proteins, we modified magnetic beads with a peptide that had both electroactive- and molecular recognition properties. The peptide consisted of a YXY sequence and behaved as an electron-transfer carbohydrate-mimetic peptide that would combine with proteins. With this tool, the protein could be detected via a label-free system. We synthesized several penta- and hexa-peptides with a cysteine residue on the C-terminals to examine the properties of peptides. These peptides contained amino acid residues (X) of alanine, serine, or tyrosine. The peptides were immobilized on magnetic beads via N-(8-maleimidocapryloxy) succinimide. Soybean agglutinin(SBA), the in vivo function of which has been well established in animals, was selected as a model protein. The protein was detected via the changes in electrode response due to the oxidation of tyrosine residues from the phenol group to quinone. As a result, SBA was selectively accumulated on the beads modified with YYYYC. The calibration curve of SBA was linear and ranged from 2.5 × 10-12 to 1.0 × 10-10 M. With this system, SBA was recovered in human serum at values that ranged from 98 to 103%. Furthermore, the beads with peptides were regenerated five times using a protein denaturant. Accordingly, this electrochemical system was simple and could be rapidly applied to the detection of galactose-recognition proteins.
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Affiliation(s)
| | | | - Hideki Kuramitz
- Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering for Research, University of Toyama, Toyama 930-8555, Japan
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5
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Calvanese L, Focà A, Sandomenico A, Focà G, Caporale A, Doti N, Iaccarino E, Leonardi A, D'Auria G, Ruvo M, Falcigno L. Structural insights into the interaction of a monoclonal antibody and Nodal peptides by STD-NMR spectroscopy. Bioorg Med Chem 2017; 25:6589-6596. [PMID: 29113739 DOI: 10.1016/j.bmc.2017.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/05/2017] [Accepted: 10/26/2017] [Indexed: 12/31/2022]
Abstract
Nodal is a growth factor expressed during early embryonic development, but reactivated in several advanced-stage cancers. Targeting of Nodal signaling, which occurs via the binding to Cripto-1 co-receptor, results in inhibition of cell aggressiveness and reduced tumor growth. The Nodal binding region to Cripto-1 was identified and targeted with a high affinity monoclonal antibody (3D1). By STD-NMR technique, we investigated the interaction of Nodal fragments with 3D1 with the aim to elucidate at atomic level the interaction surface. Data indicate with high accuracy the antibody-antigen contact atoms and confirm the information previously obtained by immune-enzymatic methods. Main residues contacted by 3D1 are P46, V47, E49 and E50, which belong to the Nodal loop involved in the interaction with the co-receptor.
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Affiliation(s)
- Luisa Calvanese
- CIRPeB, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Annalia Focà
- Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Annamaria Sandomenico
- CIRPeB, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy; Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Giuseppina Focà
- Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Andrea Caporale
- CIRPeB, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Emanuela Iaccarino
- DISTABIF, Università degli Studi della Campania "Lugi Vanvitelli", via Vivaldi, 43, 80100 Caserta, Italy
| | - Antonio Leonardi
- Dept. Medicina Molecolare e Biotecnologie Mediche, Università Federico II di Napoli, Naples, Italy
| | - Gabriella D'Auria
- CIRPeB, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy; Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy; Dept. of Pharmacy, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy
| | - Menotti Ruvo
- CIRPeB, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy; Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy.
| | - Lucia Falcigno
- CIRPeB, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy; Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, via Mezzocannone, 16, 80134 Napoli, Italy; Dept. of Pharmacy, University of Naples Federico II, via Mezzocannone, 16, 80134 Napoli, Italy.
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6
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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7
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Gauthier C, Chassagne P, Theillet FX, Guerreiro C, Thouron F, Nato F, Delepierre M, Sansonetti PJ, Phalipon A, Mulard LA. Non-stoichiometric O-acetylation of Shigella flexneri 2a O-specific polysaccharide: synthesis and antigenicity. Org Biomol Chem 2016; 12:4218-32. [PMID: 24836582 DOI: 10.1039/c3ob42586j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic functional mimics of the O-antigen from Shigella flexneri 2a are seen as promising vaccine components against endemic shigellosis. Herein, the influence of the polysaccharide non-stoichiometric di-O-acetylation on antigenicity is addressed for the first time. Three decasaccharides, representing relevant internal mono- and di-O-acetylation profiles of the O-antigen, were synthesized from a pivotal protected decasaccharide designed to tailor late stage site-selective O-acetylation. The latter was obtained via a convergent route involving the imidate glycosylation chemistry. Binding studies to five protective mIgGs showed that none of the acetates adds significantly to broad antibody recognition. Yet, one of the five antibodies had a unique pattern of binding. With IC50 in the micromolar to submicromolar range mIgG F22-4 exemplifies a remarkable tight binding antibody against diversely O-acetylated and non-O-acetylated fragments of a neutral polysaccharide of medical importance.
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Affiliation(s)
- Charles Gauthier
- Institut Pasteur, Chimie des Biomolécules, Dépt de Biologie Structurale et Chimie, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.
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8
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Marchetti R, Dillon MJ, Burtnick MN, Hubbard MA, Kenfack MT, Blériot Y, Gauthier C, Brett PJ, AuCoin DP, Lanzetta R, Silipo A, Molinaro A. Burkholderia pseudomallei Capsular Polysaccharide Recognition by a Monoclonal Antibody Reveals Key Details toward a Biodefense Vaccine and Diagnostics against Melioidosis. ACS Chem Biol 2015. [PMID: 26198038 DOI: 10.1021/acschembio.5b00502] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Burkholderia pseudomallei is the bacterium responsible for melioidosis, an infectious disease with high mortality rates. Since melioidosis is a significant public health concern in endemic regions and the organism is currently classified as a potential biothreat agent, the development of effective vaccines and rapid diagnostics is a priority. The capsular polysaccharide (CPS) expressed by B. pseudomallei is a highly conserved virulence factor and a protective antigen. Because of this, CPS is considered an attractive antigen for use in the development of both vaccines and diagnostics. In the present study, we describe the interactions of CPS with the murine monoclonal antibody (mAb) 4C4 using a multidisciplinary approach including organic synthesis, molecular biology techniques, surface plasmon resonance, and nuclear magnetic spectroscopy. Using these methods, we determined the mode of binding between mAb 4C4 and native CPS or ad hoc synthesized capsular polysaccharide fragments. Interestingly, we demonstrated that the O-acetyl moiety of CPS is essential for the interaction of the CPS epitope with mAb 4C4. Collectively, our results provide important insights into the structural features of B. pseudomallei CPS that enable antibody recognition that may help the rational design of CPS-based vaccine candidates. In addition, our findings confirm that the mAb 4C4 is suitable for use in an antibody-based detection assay for diagnosis of B. pseudomallei infections.
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Affiliation(s)
- Roberta Marchetti
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
| | - Michael J. Dillon
- Department
of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada 89557, United States
| | - Mary N. Burtnick
- Department
of Microbiology and Immunology, University of South Alabama, Mobile, Alabama 36688, United States
| | - Mark A. Hubbard
- Department
of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada 89557, United States
| | - Marielle Tamigney Kenfack
- Université de Poitiers, Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073 Poitiers Cedex-9, France
| | - Yves Blériot
- Université de Poitiers, Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073 Poitiers Cedex-9, France
| | - Charles Gauthier
- Université de Poitiers, Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073 Poitiers Cedex-9, France
| | - Paul J. Brett
- Department
of Microbiology and Immunology, University of South Alabama, Mobile, Alabama 36688, United States
| | - David P. AuCoin
- Department
of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada 89557, United States
| | - Rosa Lanzetta
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
| | - Alba Silipo
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
| | - Antonio Molinaro
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
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9
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Aguirre C, Cala O, Krimm I. Overview of Probing Protein‐Ligand Interactions Using NMR. ACTA ACUST UNITED AC 2015; 81:17.18.1-17.18.24. [DOI: 10.1002/0471140864.ps1718s81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Olivier Cala
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
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10
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Marchetti R, Molinaro A, Silipo A. NMR as a Tool to Unveil the Molecular Basis of Glycan-mediated Host–Pathogen Interactions. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nature of the relationship between microbes and hosts spans the broad spectrum from beneficial (symbiosis) to pathogenic (disease); one of the key factors determining the establishment of any type of host–microbe interaction is the pattern of glycoconjugates exposed on cell surfaces, many known as virulence factors since they are pivotal for adhesion to host tissue, immunoevasion and immunosuppression, causing disease in the host. The recognition of these pathogen glycostructures by specific host receptors is an important means of immune defense. In this context, NMR represents a valuable tool to investigate the conformational properties of both host/pathogen signaling molecules and to disclose their interaction at a molecular level. This chapter provides an overview of several protein–carbohydrate interaction systems studied by NMR, and their implications in human and plant diseases.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
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11
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Studies of a murine monoclonal antibody directed against DARC: reappraisal of its specificity. PLoS One 2015; 10:e0116472. [PMID: 25706384 PMCID: PMC4338028 DOI: 10.1371/journal.pone.0116472] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/09/2014] [Indexed: 12/29/2022] Open
Abstract
Duffy Antigen Receptor for Chemokines (DARC) plays multiple roles in human health as a blood group antigen, a receptor for chemokines and the only known receptor for Plasmodium vivax merozoites. It is the target of the murine anti-Fy6 monoclonal antibody 2C3 which binds to the first extracellular domain (ECD1), but exact nature of the recognized epitope was a subject of contradictory reports. Here, using a set of complex experiments which include expression of DARC with amino acid substitutions within the Fy6 epitope in E. coli and K562 cells, ELISA, surface plasmon resonance (SPR) and flow cytometry, we have resolved discrepancies between previously published reports and show that the basic epitope recognized by 2C3 antibody is 22FEDVW26, with 22F and 26W being the most important residues. In addition, we demonstrated that 30Y plays an auxiliary role in binding, particularly when the residue is sulfated. The STD-NMR studies performed using 2C3-derived Fab and synthetic peptide corroborated most of these results, and together with the molecular modelling suggested that 25V is not involved in direct interactions with the antibody, but determines folding of the epitope backbone.
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12
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Hayafune M, Berisio R, Marchetti R, Silipo A, Kayama M, Desaki Y, Arima S, Squeglia F, Ruggiero A, Tokuyasu K, Molinaro A, Kaku H, Shibuya N. Chitin-induced activation of immune signaling by the rice receptor CEBiP relies on a unique sandwich-type dimerization. Proc Natl Acad Sci U S A 2014; 111:E404-13. [PMID: 24395781 PMCID: PMC3903257 DOI: 10.1073/pnas.1312099111] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Perception of microbe-associated molecular patterns (MAMPs) through pattern recognition receptors (PRRs) triggers various defense responses in plants. This MAMP-triggered immunity plays a major role in the plant resistance against various pathogens. To clarify the molecular basis of the specific recognition of chitin oligosaccharides by the rice PRR, CEBiP (chitin-elicitor binding protein), as well as the formation and activation of the receptor complex, biochemical, NMR spectroscopic, and computational studies were performed. Deletion and domain-swapping experiments showed that the central lysine motif in the ectodomain of CEBiP is essential for the binding of chitin oligosaccharides. Epitope mapping by NMR spectroscopy indicated the preferential binding of longer-chain chitin oligosaccharides, such as heptamer-octamer, to CEBiP, and also the importance of N-acetyl groups for the binding. Molecular modeling/docking studies clarified the molecular interaction between CEBiP and chitin oligosaccharides and indicated the importance of Ile122 in the central lysine motif region for ligand binding, a notion supported by site-directed mutagenesis. Based on these results, it was indicated that two CEBiP molecules simultaneously bind to one chitin oligosaccharide from the opposite side, resulting in the dimerization of CEBiP. The model was further supported by the observations that the addition of (GlcNAc)8 induced dimerization of the ectodomain of CEBiP in vitro, and the dimerization and (GlcNAc)8-induced reactive oxygen generation were also inhibited by a unique oligosaccharide, (GlcNβ1,4GlcNAc)4, which is supposed to have N-acetyl groups only on one side of the molecule. Based on these observations, we proposed a hypothetical model for the ligand-induced activation of a receptor complex, involving both CEBiP and Oryza sativa chitin-elicitor receptor kinase-1.
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Affiliation(s)
- Masahiro Hayafune
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Alba Silipo
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Miyu Kayama
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Sakiko Arima
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Ken Tokuyasu
- Food Resource Division, National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Antonio Molinaro
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
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13
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Poulin MB, Shi Y, Protsko C, Dalrymple SA, Sanders DAR, Pinto BM, Lowary TL. Specificity of a UDP-GalNAc pyranose-furanose mutase: a potential therapeutic target for Campylobacter jejuni infections. Chembiochem 2013; 15:47-56. [PMID: 24302429 DOI: 10.1002/cbic.201300653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Indexed: 12/23/2022]
Abstract
Pyranose-furanose mutases are essential enzymes in the life cycle of a number of microorganisms, but are absent in mammalian systems, and hence represent novel targets for drug development. To date, all such mutases show preferential recognition of a single substrate (e.g., UDP-Gal). We report here the detailed structural characterization of the first bifunctional pyranose-furanose mutase, which recognizes both UDP-Gal and UDP-GalNAc. The enzyme under investigation (cjUNGM) is involved in the biosynthesis of capsular polysaccharides (CPSs) in Campylobacter jejuni 11168. These CPSs are known virulence factors that are required for adhesion and invasion of human epithelial cells. Using a combination of UV/visible spectroscopy, X-ray crystallography, saturation transfer difference NMR spectroscopy, molecular dynamics and CORCEMA-ST calculations, we have characterized the binding of the enzyme to both UDP-Galp and UDP-GalpNAc, and compared these interactions with those of a homologous monofunctional mutase enzyme from E. coli (ecUGM). These studies reveal that two arginines in cjUNGM, Arg59 and Arg168, play critical roles in the catalytic mechanism of the enzyme and in controlling its specificity to ultimately lead to a GalfNAc-containing CPS. In ecUGM, these arginines are replaced with histidine and lysine, respectively, and this results in an enzyme that is selective for UDP-Gal. We propose that these changes in amino acids allow C. jejuni 11168 to produce suitable quantities of the sugar nucleotide substrate required for the assembly of a CPS containing GalfNAc, which is essential for viability.
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Affiliation(s)
- Myles B Poulin
- Alberta Glycomics Centre and Department of Chemistry, The University of Alberta, Gunning-Lemieux Chemistry Centre, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 (Canada)
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del Carmen Fernández-Alonso M, Díaz D, Berbis MÁ, Marcelo F, Cañada J, Jiménez-Barbero J. Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design. Curr Protein Pept Sci 2013; 13:816-30. [PMID: 23305367 PMCID: PMC3706953 DOI: 10.2174/138920312804871175] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/12/2012] [Accepted: 07/25/2012] [Indexed: 02/04/2023]
Abstract
Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.
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Abstract
The recent introduction of saturation transfer difference (STD) NMR has increased the tools for the study of protein–carbohydrate complexes. This is useful when it is combined with transfer nuclear Overhauser enhancement spectroscopy (NOESY) measurement, or when it is interpreted using the expected calculated values of transference, yielding additional, very valuable information for the study of this type of complex. The objective of this work is to cover the advances of the STD technique as exemplified by the investigations of DC-SIGN (dendritic cell-specific ICAM-3 grabbing non-integrin) recognition by simple carbohydrates or mimics of them, based on structures containing a terminal mannose or fucose. We also will discuss the methods for quantification of the STD values based on the initial growing rates with the saturation time.
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Marchetti R, Canales A, Lanzetta R, Nilsson I, Vogel C, Reed DE, AuCoin DP, Jiménez-Barbero J, Molinaro A, Silipo A. Unraveling the Interaction between the LPS O-Antigen ofBurkholderia anthinaand the 5D8 Monoclonal Antibody by Using a Multidisciplinary Chemical Approach, with Synthesis, NMR, and Molecular Modeling Methods. Chembiochem 2013; 14:1485-93. [DOI: 10.1002/cbic.201300225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Indexed: 11/11/2022]
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Molecular dynamics simulations of carbohydrate-mimetic haptens in complex with a complementary anti-carbohydrate antibody. Carbohydr Res 2012; 358:89-95. [DOI: 10.1016/j.carres.2012.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/22/2012] [Accepted: 05/28/2012] [Indexed: 11/30/2022]
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