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Salvatti BA, Chagas MA, Fernandes PO, Ladeira YFX, Bozzi AS, Valadares VS, Valente AP, de Miranda AS, Rocha WR, Maltarollo VG, Moraes AH. Understanding the Enzyme ( S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. J Chem Inf Model 2024. [PMID: 38776464 DOI: 10.1021/acs.jcim.3c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.
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Affiliation(s)
- Brunno A Salvatti
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Marcelo A Chagas
- Departamento de Ciências Exatas, Universidade do Estado de Minas Gerais, João Monlevade, Minas Gerais 35930-314, Brazil
| | - Phillipe O Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Yan F X Ladeira
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Aline S Bozzi
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Veronica S Valadares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Amanda S de Miranda
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Willian R Rocha
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinicius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
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Valadares VS, Martins LC, Moraes AH, Cino EA. Characterization of the interaction between TcmN and product analogs. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Fernandes PO, Chagas MA, Rocha WR, Moraes AH. Non-structural protein 5 (NS5) as a target for antiviral development against established and emergent flaviviruses. Curr Opin Virol 2021; 50:30-39. [PMID: 34340199 DOI: 10.1016/j.coviro.2021.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 11/19/2022]
Abstract
Flaviviruses are among the most critical pathogens in tropical regions and cause a growing number of severe diseases in developing countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Among the ten proteins encoded in the flavivirus RNA, non-structural protein 5, NS5, is a promising drug target. NS5 plays a fundamental role in flavivirus replication, viral RNA methylation, RNA polymerization, and host immune system evasion. Most of the NS5 inhibitor candidates target NS5 active sites. However, the similarity of NS5 activity sites with human enzymes can cause side effects. Identifying new allosteric sites in NS5 can contribute enormously to antiviral development. The NS5 structural characterization enabled exploring new regions, such as the residues involved in MTase-RdRp interaction, NS5 oligomerization, and NS5 interaction with other viral and host-cell proteins. Targeting NS5 critical interactions might lead to new compounds and overcomes the toxicity of current NS5-inhibitor candidates.
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Affiliation(s)
- Philipe O Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Marcelo A Chagas
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Willian R Rocha
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil; Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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Valadares VS, Martins LC, Roman EA, Valente AP, Cino EA, Moraes AH. Conformational dynamics of Tetracenomycin aromatase/cyclase regulate polyketide binding and enzyme aggregation propensity. Biochim Biophys Acta Gen Subj 2021; 1865:129949. [PMID: 34139289 DOI: 10.1016/j.bbagen.2021.129949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The N-terminal domain of Tetracenomycin aromatase/cyclase (TcmN), an enzyme derived from Streptomyces glaucescens, is involved in polyketide cyclization, aromatization, and folding. Polyketides are a diverse class of secondary metabolites produced by certain groups of bacteria, fungi, and plants with various pharmaceutical applications. Examples include antibiotics, such as tetracycline, and anticancer drugs, such as doxorubicin. Because TcmN is a promising enzyme for in vitro production of polyketides, it is important to identify conditions that enhance its thermal resistance and optimize its function. METHODS TcmN unfolding, stability, and dynamics were evaluated by fluorescence spectroscopy, circular dichroism, nuclear magnetic resonance 15N relaxation experiments, and microsecond molecular dynamics (MD) simulations. RESULTS TcmN thermal resistance was enhanced at low protein and high salt concentrations, was pH-dependent, and denaturation was irreversible. Conformational dynamics on the μs-ms timescale were detected for residues in the substrate-binding cavity, and two predominant conformers representing opened and closed cavity states were observed in the MD simulations. CONCLUSION Based on the results, a mechanism was proposed in which the thermodynamics and kinetics of the TcmN conformational equilibrium modulate enzyme function by favoring ligand binding and avoiding aggregation. GENERAL SIGNIFICANCE Understanding the principles underlying TcmN stability and dynamics may help in designing mutants with optimal properties for biotechnological applications.
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Affiliation(s)
- Veronica S Valadares
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luan C Martins
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ernesto A Roman
- Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana Paula Valente
- National Center of Nuclear Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elio A Cino
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Marques MA, Landim-Vieira M, Moraes AH, Sun B, Johnston JR, Dieseldorff Jones KM, Cino EA, Parvatiyar MS, Valera IC, Silva JL, Galkin VE, Chase PB, Kekenes-Huskey PM, de Oliveira GAP, Pinto JR. Anomalous structural dynamics of minimally frustrated residues in cardiac troponin C triggers hypertrophic cardiomyopathy. Chem Sci 2021; 12:7308-7323. [PMID: 34163821 PMCID: PMC8171346 DOI: 10.1039/d1sc01886h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022] Open
Abstract
Cardiac TnC (cTnC) is highly conserved among mammals, and genetic variants can result in disease by perturbing Ca2+-regulation of myocardial contraction. Here, we report the molecular basis of a human mutation in cTnC's αD-helix (TNNC1-p.C84Y) that impacts conformational dynamics of the D/E central-linker and sampling of discrete states in the N-domain, favoring the "primed" state associated with Ca2+ binding. We demonstrate cTnC's αD-helix normally functions as a central hub that controls minimally frustrated interactions, maintaining evolutionarily conserved rigidity of the N-domain. αD-helix perturbation remotely alters conformational dynamics of the N-domain, compromising its structural rigidity. Transgenic mice carrying this cTnC mutation exhibit altered dynamics of sarcomere function and hypertrophic cardiomyopathy. Together, our data suggest that disruption of evolutionary conserved molecular frustration networks by a myofilament protein mutation may ultimately compromise contractile performance and trigger hypertrophic cardiomyopathy.
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Affiliation(s)
- Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Adolfo H Moraes
- Department of Chemistry, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago Maywood IL USA
| | - Jamie R Johnston
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Karissa M Dieseldorff Jones
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Elio A Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Michelle S Parvatiyar
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Isela C Valera
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School Norfolk VA USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University Tallahassee FL USA
| | | | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
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Johnston JR, Landim-Vieira M, Marques MA, de Oliveira GAP, Gonzalez-Martinez D, Moraes AH, He H, Iqbal A, Wilnai Y, Birk E, Zucker N, Silva JL, Chase PB, Pinto JR. The intrinsically disordered C terminus of troponin T binds to troponin C to modulate myocardial force generation. J Biol Chem 2019; 294:20054-20069. [PMID: 31748410 PMCID: PMC6937556 DOI: 10.1074/jbc.ra119.011177] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
Aberrant regulation of myocardial force production represents an early biomechanical defect associated with sarcomeric cardiomyopathies, but the molecular mechanisms remain poorly defined. Here, we evaluated the pathogenicity of a previously unreported sarcomeric gene variant identified in a pediatric patient with sporadic dilated cardiomyopathy, and we determined a molecular mechanism. Trio whole-exome sequencing revealed a de novo missense variant in TNNC1 that encodes a p.I4M substitution in the N-terminal helix of cardiac troponin C (cTnC). Reconstitution of this human cTnC variant into permeabilized porcine cardiac muscle preparations significantly decreases the magnitude and rate of isometric force generation at physiological Ca2+-activation levels. Computational modeling suggests that this inhibitory effect can be explained by a decrease in the rates of cross-bridge attachment and detachment. For the first time, we show that cardiac troponin T (cTnT), in part through its intrinsically disordered C terminus, directly binds to WT cTnC, and we find that this cardiomyopathic variant displays tighter binding to cTnT. Steady-state fluorescence and NMR spectroscopy studies suggest that this variant propagates perturbations in cTnC structural dynamics to distal regions of the molecule. We propose that the intrinsically disordered C terminus of cTnT directly interacts with the regulatory N-domain of cTnC to allosterically modulate Ca2+ activation of force, perhaps by controlling the troponin I switching mechanism of striated muscle contraction. Alterations in cTnC-cTnT binding may compromise contractile performance and trigger pathological remodeling of the myocardium.
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Affiliation(s)
- Jamie R Johnston
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Mayra A Marques
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - David Gonzalez-Martinez
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Huan He
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
| | - Anwar Iqbal
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Yael Wilnai
- Department of Pediatrics, Dana-Dwek ChildrenγÇÖs Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel 6423906
| | - Einat Birk
- Department of Cardiology, Schneider ChildrenγÇÖs Medical Center, Tel Aviv University, Petah Tikva, Israel 4920235
| | - Nili Zucker
- Department of Cardiology, Schneider ChildrenγÇÖs Medical Center, Tel Aviv University, Petah Tikva, Israel 4920235
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Jose Renato Pinto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
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Marques MA, de Oliveira GA, Moraes AH, Landim-Vieira M, Jones KD, Cino EA, Chase PB, Silva JL, Pinto JR. Dynamic and Structural Allosteric Events between the D/E Linker and N-Domain of Cardiac Troponin C Reveal a Novel Mechanism for Cardiac Muscle Regulation. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Valadares VS, Martins LC, Tannus LG, Moraes AH, Cino EA. Characterization of Conformational Diversity, Stability, and Catalytic Activity of TcmN, an Enzyme Involved in Antibiotic Biosynthesis. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Moraes AH, Asam C, Almeida FCL, Wallner M, Ferreira F, Valente AP. Structural basis for cross-reactivity and conformation fluctuation of the major beech pollen allergen Fag s 1. Sci Rep 2018; 8:10512. [PMID: 30002383 PMCID: PMC6043577 DOI: 10.1038/s41598-018-28358-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Fag s 1 is a member of the Pathogen Related protein family 10 (PR-10) and can elicit cross-reaction with IgE antibodies produced against the birch pollen allergen Bet v 1. The Nuclear Magnetic Resonance (NMR) structure of Fag s 1 is presented along with its dynamic properties. It shares 66% identity with Bet v 1 and exhibits the expected three α-helices and seven β-sheets arranged as a semi-beta barrel and exposing the residues mapped as the Bet v 1 IgE epitope. The structural dynamics of Fag s 1 were monitored on the fast and intermediate timescales, using relaxation rates. The complex dynamics of Fag s 1 are closely related to the internal cavity, and they modulate IgE and ligand binding.
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Affiliation(s)
- Adolfo H Moraes
- Chemistry Department, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Claudia Asam
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Fabio C L Almeida
- National NMR Center, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michael Wallner
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Ana Paula Valente
- National NMR Center, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Veltri T, de Oliveira GAP, Bienkiewicz EA, Palhano FL, Marques MDA, Moraes AH, Silva JL, Sorenson MM, Pinto JR. Amide hydrogens reveal a temperature-dependent structural transition that enhances site-II Ca 2+-binding affinity in a C-domain mutant of cardiac troponin C. Sci Rep 2017; 7:691. [PMID: 28386062 PMCID: PMC5429600 DOI: 10.1038/s41598-017-00777-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/14/2017] [Indexed: 01/07/2023] Open
Abstract
The hypertrophic cardiomyopathy-associated mutant D145E, in cardiac troponin C (cTnC) C-domain, causes generalised instability at multiple sites in the isolated protein. As a result, structure and function of the mutant are more susceptible to higher temperatures. Above 25 °C there are large, progressive increases in N-domain Ca2+-binding affinity for D145E but only small changes for the wild-type protein. NMR-derived backbone amide temperature coefficients for many residues show a sharp transition above 30–40 °C, indicating a temperature-dependent conformational change that is most prominent around the mutated EF-hand IV, as well as throughout the C-domain. Smaller, isolated changes occur in the N-domain. Cardiac skinned fibres reconstituted with D145E are more sensitive to Ca2+ than fibres reconstituted with wild-type, and this defect is amplified near body-temperature. We speculate that the D145E mutation destabilises the native conformation of EF-hand IV, leading to a transient unfolding and dissociation of helix H that becomes more prominent at higher temperatures. This creates exposed hydrophobic surfaces that may be capable of binding unnaturally to a variety of targets, possibly including the N-domain of cTnC when it is in its open Ca2+-saturated state. This would constitute a potential route for propagating signals from one end of TnC to the other.
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Affiliation(s)
- Tiago Veltri
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.,Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas F° 373, Cidade Universitária, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ewa A Bienkiewicz
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA
| | - Fernando L Palhano
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas F° 373, Cidade Universitária, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Mayra de A Marques
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adolfo H Moraes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martha M Sorenson
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas F° 373, Cidade Universitária, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.
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de Oliveira GA, Marques MA, Cordeiro Y, Schuabb C, Moraes AH, Winter R, Oschkinat H, Foguel D, de Freitas MS, Silva JL. Structural Basis for the Dissociation of Alpha-Synuclein Fibrils Triggered by Pressure Perturbation of the Hydrophobic Core. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Marques MA, Pinto JR, Moraes AH, Iqbal A, de Magalhães MT, Monteiro J, Pedrote MM, Sorenson MM, Silva JL, de Oliveira GA. Allosteric Transmission Along a Loosely Structured Backbone Allows a Cardiac Troponin C Mutant to Function with only One Ca 2+ ion. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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13
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Marques MDA, Pinto JR, Moraes AH, Iqbal A, de Magalhães MTQ, Monteiro J, Pedrote MM, Sorenson MM, Silva JL, de Oliveira GAP. Allosteric Transmission along a Loosely Structured Backbone Allows a Cardiac Troponin C Mutant to Function with Only One Ca 2+ Ion. J Biol Chem 2017; 292:2379-2394. [PMID: 28049727 DOI: 10.1074/jbc.m116.765362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/28/2016] [Indexed: 01/19/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is one of the most common cardiomyopathies and a major cause of sudden death in young athletes. The Ca2+ sensor of the sarcomere, cardiac troponin C (cTnC), plays an important role in regulating muscle contraction. Although several cardiomyopathy-causing mutations have been identified in cTnC, the limited information about their structural defects has been mapped to the HCM phenotype. Here, we used high-resolution electron-spray ionization mass spectrometry (ESI-MS), Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG-RD), and affinity measurements of cTnC for the thin filament in reconstituted papillary muscles to provide evidence of an allosteric mechanism in mutant cTnC that may play a role to the HCM phenotype. We showed that the D145E mutation leads to altered dynamics on a μs-ms time scale and deactivates both of the divalent cation-binding sites of the cTnC C-domain. CPMG-RD captured a low populated protein-folding conformation triggered by the Glu-145 replacement of Asp. Paradoxically, although D145E C-domain was unable to bind Ca2+, these changes along its backbone allowed it to attach more firmly to thin filaments than the wild-type isoform, providing evidence for an allosteric response of the Ca2+-binding site II in the N-domain. Our findings explain how the effects of an HCM mutation in the C-domain reflect up into the N-domain to cause an increase of Ca2+ affinity in site II, thus opening up new insights into the HCM phenotype.
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Affiliation(s)
- Mayra de A Marques
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Jose Renato Pinto
- the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32304
| | - Adolfo H Moraes
- the Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil, and
| | - Anwar Iqbal
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Mariana T Q de Magalhães
- the Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Jamila Monteiro
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Murilo M Pedrote
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Martha M Sorenson
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Jerson L Silva
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil,
| | - Guilherme A P de Oliveira
- From the Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil,
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Moraes AH, Asam C, Batista A, Almeida FCL, Wallner M, Ferreira F, Valente AP. 1H, 13C and 15N resonance assignments and second structure information of Fag s 1: Fagales allergen from Fagus sylvatica. Biomol NMR Assign 2016; 10:45-48. [PMID: 26289775 PMCID: PMC5689376 DOI: 10.1007/s12104-015-9634-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/14/2015] [Indexed: 06/04/2023]
Abstract
Fagales allergens belonging to the Bet v 1 family account responsible for the majority of spring pollinosis in the temperate climate zones in the Northern hemisphere. Among them, Fag s 1 from beech pollen is an important trigger of Fagales pollen associated allergic reactions. The protein shares high similarity with birch pollen Bet v 1, the best-characterized member of this allergen family. Of note, recent work on Bet v 1 and its homologues found in Fagales pollen demonstrated that not all allergenic members of this family have the capacity to induce allergic sensitization. Fag s 1 was shown to bind pre-existing IgE antibodies most likely primarily directed against other members of this multi-allergen family. Therefore, it is especially interesting to compare the structures of Bet v 1-like pollen allergens, which have the potential to induce allergic sensitization with allergens that are mainly cross-reactive. This in the end will help to identify allergy eliciting molecular pattern on Bet v 1-like allergens. In this work, we report the (1)H, (15)N and (13)C NMR assignment of beech pollen Fag s 1 as well as the secondary structure information based on backbone chemical shifts.
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Affiliation(s)
- A H Moraes
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C Asam
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, University of Salzburg, Salzburg, Austria
| | - A Batista
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C L Almeida
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Wallner
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, University of Salzburg, Salzburg, Austria
| | - F Ferreira
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, University of Salzburg, Salzburg, Austria
| | - A P Valente
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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15
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Bublin M, Kostadinova M, Fuchs JE, Ackerbauer D, Moraes AH, Almeida FCL, Lengger N, Hafner C, Ebner C, Radauer C, Liedl KR, Valente AP, Breiteneder H. A Cross-Reactive Human Single-Chain Antibody for Detection of Major Fish Allergens, Parvalbumins, and Identification of a Major IgE-Binding Epitope. PLoS One 2015; 10:e0142625. [PMID: 26579717 PMCID: PMC4651496 DOI: 10.1371/journal.pone.0142625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/23/2015] [Indexed: 11/19/2022] Open
Abstract
Fish allergy is associated with moderate to severe IgE-mediated reactions to the calcium binding parvalbumins present in fish muscle. Allergy to multiple fish species is caused by parvalbumin-specific cross-reactive IgE recognizing conserved epitopes. In this study, we aimed to produce cross-reactive single chain variable fragment (scFv) antibodies for the detection of parvalbumins in fish extracts and the identification of IgE epitopes. Parvalbumin-specific phage clones were isolated from the human ETH-2 phage display library by three rounds of biopanning either against cod parvalbumin or by sequential biopanning against cod (Gad m 1), carp (Cyp c 1) and rainbow trout (Onc m 1) parvalbumins. While biopanning against Gad m 1 resulted in the selection of clones specific exclusively for Gad m 1, the second approach resulted in the selection of clones cross-reacting with all three parvalbumins. Two clones, scFv-gco9 recognizing all three parvalbumins, and scFv-goo8 recognizing only Gad m 1 were expressed in the E. coli non-suppressor strain HB2151 and purified from the periplasm. scFv-gco9 showed highly selective binding to parvalbumins in processed fish products such as breaded cod sticks, fried carp and smoked trout in Western blots. In addition, the scFv-gco9-AP produced as alkaline phosphatase fusion protein, allowed a single-step detection of the parvalbumins. In competitive ELISA, scFv-gco9 was able to inhibit binding of IgE from fish allergic patients’ sera to all three β-parvalbumins by up to 80%, whereas inhibition by scFv-goo8 was up to 20%. 1H/15N HSQC NMR analysis of the rGad m 1:scFv-gco9 complex showed participation of amino acid residues conserved among these three parvalbumins explaining their cross-reactivity on a molecular level. In this study, we have demonstrated an approach for the selection of cross-reactive parvalbumin-specific antibodies that can be used for allergen detection and for mapping of conserved epitopes.
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Affiliation(s)
- Merima Bublin
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
- * E-mail:
| | - Maria Kostadinova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Daniela Ackerbauer
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Adolfo H. Moraes
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C. L. Almeida
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nina Lengger
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Christine Hafner
- Karl Landsteiner Institute for Dermatological Research, St. Pölten, Austria, Department of Dermatology, Karl Landsteiner University for Medical Sciences, St.Pölten, Austria
| | | | - Christian Radauer
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heimo Breiteneder
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
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16
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Asam C, Batista AL, Moraes AH, de Paula VS, Almeida FCL, Aglas L, Kitzmüller C, Bohle B, Ebner C, Ferreira F, Wallner M, Valente AP. Bet v 1--a Trojan horse for small ligands boosting allergic sensitization? Clin Exp Allergy 2015; 44:1083-93. [PMID: 24979350 DOI: 10.1111/cea.12361] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 04/28/2014] [Accepted: 05/31/2014] [Indexed: 01/23/2023]
Abstract
BACKGROUND Birch pollen allergy represents the main cause of winter and spring pollinosis in the temperate climate zone of the northern hemisphere and sensitization towards Bet v 1, the major birch pollen allergen, affects over 100 million allergic patients. The major birch pollen allergen Bet v 1 has been described as promiscuous acceptor for a wide variety of hydrophobic ligands. OBJECTIVE In search of intrinsic properties of Bet v 1, which account responsible for the high allergenic potential of the protein, we thought to investigate the effects of ligand-binding on immunogenic as well as allergenic properties. METHODS As surrogate ligand of Bet v 1 sodium deoxycholate (DOC) was selected. Recombinant and natural Bet v 1 were characterised physico-chemically as well as immunologically in the presence or absence of DOC, and an animal model of allergic sensitization was established. Moreover, human IgE binding to Bet v 1 was analysed by nuclear magnetic resonance (NMR) spectroscopy. RESULTS Ligand-binding had an overall stabilizing effect on Bet v 1. This translated in a Th2 skewing of the immune response in a mouse model. Analyses of human IgE binding on Bet v 1 in mediator release assays revealed that ligand-bound allergen-induced degranulation at lower concentrations; however, in basophil activation tests with human basophils ligand-binding did not show this effect. For the first time, human IgE epitopes on Bet v 1 were determined using antibodies isolated from patients' sera. The IgE epitope mapping of Bet v 1 demonstrated the presence of multiple binding regions. CONCLUSIONS AND CLINICAL RELEVANCE Deoxycholate binding stabilizes conformational IgE epitopes on Bet v 1; however, the epitopes themselves remain unaltered. Therefore, we speculate that humans are exposed to both ligand-bound and free Bet v 1 during sensitization, disclosing the ligand-binding cavity of the allergen as key structural element.
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Affiliation(s)
- C Asam
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, University of Salzburg, Salzburg, Austria
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Moraes AH, Ackerbauer D, Kostadinova M, Bublin M, de Oliveira GA, Ferreira F, Almeida FCL, Breiteneder H, Valente AP. Solution and high-pressure NMR studies of the structure, dynamics, and stability of the cross-reactive allergenic cod parvalbumin Gad m 1. Proteins 2014; 82:3032-42. [PMID: 25116395 DOI: 10.1002/prot.24664] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/03/2014] [Accepted: 08/06/2014] [Indexed: 02/02/2023]
Abstract
Beta-parvalbumins from different fish species have been identified as the main elicitors of IgE-mediated reactions in fish-allergic individuals. Here, we report for the first time the NMR determination of the structure and dynamics of the major Atlantic cod (Gadus morhua) allergen Gad m 1 and compare them with other known parvalbumins. Although the Gad m 1 structure and accessibility of putative IgE epitopes are similar to parvalbumins in mackerel and carp, the charge distribution at the putative epitopes is different. The determination of the Gad m 1 structure contributes to a better understanding of cross-reactivity among fish parvalbumins. In addition, the high-pressure NMR and temperature variation experiments revealed the important contribution of the AB motif and other regions to the protein folding. This structural information could assist the future identification of hot spots for targeted mutations to develop hypoallergenic Ca(2+) -free forms for potential use in immunotherapy.
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Affiliation(s)
- Adolfo H Moraes
- Department of Structural Biology, Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance, Federal University of Rio de Janeiro, Brazil
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18
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Moraes AH, Ackerbauer D, Kostadinova M, Bublin M, Ferreira F, Almeida FCL, Breiteneder H, Valente AP. ¹H, ¹³C and ¹⁵N resonance assignments and second structure information of Gad m 1: a β-parvalbumin allergen from Atlantic cod (Gadus morhua). Biomol NMR Assign 2013; 7:133-136. [PMID: 22585088 DOI: 10.1007/s12104-012-9393-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 05/03/2012] [Indexed: 05/31/2023]
Abstract
Gad m 1 is the major allergen from Atlantic cod. It belongs to β-parvalbumin protein family and is characterized by the presence of two calcium-binding sites so called EF-hand motifs. β-Parvalbumins such as Gad m 1 are the most important fish allergens and their high cross-reactivity is the cause of the observed polysensitization to various fish species in allergic patients. Despite extensive efforts, the complete elucidation of β-parvalbumin-IgE complexes has not been achieved yet. Allergen structural studies are essential for the development of novel immunotherapy strategies, including vaccination with hypoallergenic derivatives and chimeric molecules. Here, we report for the first time the NMR study of a β-parvalbumin: Gad m 1. This report includes: (1)H, (13)C and (15)N resonance assignments of Gad m 1 as well as the second structure information based on the (13)C chemical shifts.
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Affiliation(s)
- A H Moraes
- Centro Nacional de Ressonância Magnética, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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