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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; 64:4462-4474. [PMID: 38776464 DOI: 10.1021/acs.jcim.3c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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Bauernfeind C, Zettl I, Ivanova T, Goryainova O, Weijler AM, Pranz B, Drescher A, Focke-Tejkl M, Pavkov-Keller T, Eckl-Dorna J, Tillib SV, Flicker S. Trimeric Bet v 1-specific nanobodies cause strong suppression of IgE binding. Front Immunol 2024; 15:1343024. [PMID: 38784378 PMCID: PMC11112410 DOI: 10.3389/fimmu.2024.1343024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024] Open
Abstract
Background Around 20% of the population in Northern and Central Europe is affected by birch pollen allergy, with the major birch pollen allergen Bet v 1 as the main elicitor of allergic reactions. Together with its cross-reactive allergens from related trees and foods, Bet v 1 causes an impaired quality of life. Hence, new treatment strategies were elaborated, demonstrating the effectiveness of blocking IgG antibodies on Bet v 1-induced IgE-mediated reactions. A recent study provided evidence for the first time that Bet v 1-specific nanobodies reduce patients´ IgE binding to Bet v 1. In order to increase the potential to outcompete IgE recognition of Bet v 1 and to foster cross-reactivity and cross-protection, we developed Bet v 1-specific nanobody trimers and evaluated their capacity to suppress polyclonal IgE binding to corresponding allergens and allergen-induced basophil degranulation. Methods Nanobody trimers were engineered by adding isoleucine zippers, thus enabling trimeric formation. Trimers were analyzed for their cross-reactivity, binding kinetics to Bet v 1, and related allergens, and patients' IgE inhibition potential. Finally, their efficacy to prevent basophil degranulation was investigated. Results Trimers showed enhanced recognition of cross-reactive allergens and increased efficiency to reduce IgE-allergen binding compared to nanobody monomers. Furthermore, trimers displayed slow dissociation rates from allergens and suppressed allergen-induced mediator release. Conclusion We generated high-affine nanobody trimers that target Bet v 1 and related allergens. Trimers blocked IgE-allergen interaction by competing with IgE for allergen binding. They inhibited IgE-mediated release of biological mediators, demonstrating a promising potential to prevent allergic reactions caused by Bet v 1 and relatives.
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Affiliation(s)
- Clarissa Bauernfeind
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ines Zettl
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Tatiana Ivanova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Oksana Goryainova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Marianne Weijler
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Barbara Pranz
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Margarete Focke-Tejkl
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- BioHealth Field of Excellence, University of Graz, Graz, Austria
| | - Julia Eckl-Dorna
- Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Sergei V. Tillib
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sabine Flicker
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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Sharma E, Vitte J. A systematic review of allergen cross-reactivity: Translating basic concepts into clinical relevance. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100230. [PMID: 38524786 PMCID: PMC10959674 DOI: 10.1016/j.jacig.2024.100230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/29/2023] [Accepted: 01/03/2024] [Indexed: 03/26/2024]
Abstract
Access to the molecular culprits of allergic reactions allows for the leveraging of molecular allergology as a new precision medicine approach-one built on interdisciplinary, basic, and clinical knowledge. Molecular allergology relies on the use of allergen molecules as in vitro tools for the diagnosis and management of allergic patients. It complements the conventional approach based on skin and in vitro allergen extract testing. Major applications of molecular allergology comprise accurate identification of the offending allergen thanks to discrimination between genuine sensitization and allergen cross-reactivity, evaluation of potential severity, patient-tailored choice of the adequate allergen immunotherapy, and prediction of its expected efficacy and safety. Allergen cross-reactivity, defined as the recognition of 2 or more allergen molecules by antibodies or T cells of the same specificity, frequently interferes with allergen extract testing. At the mechanistic level, allergen cross-reactivity depends on the allergen, the host's immune response, and the context of their interaction. The multiplicity of allergen molecules and families adds further difficulty. Understanding allergen cross-reactivity at the immunologic level and translating it into a daily tool for the management of allergic patients is further complicated by the ever-increasing number of characterized allergenic molecules, the lack of dedicated resources, and the need for a personalized, patient-centered approach. Conversely, knowledge sharing paves the way for improved clinical use, innovative diagnostic tools, and further interdisciplinary research. Here, we aimed to provide a comprehensive and unbiased state-of-the art systematic review on allergen cross-reactivity. To optimize learning, we enhanced the review with basic, translational, and clinical definitions, clinical vignettes, and an overview of online allergen databases.
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Affiliation(s)
| | - Joana Vitte
- Aix-Marseille University, MEPHI, IHU Méditerranée Infection, Marseille, France
- Desbrest Institute of Epidemiology and Public Health (IDESP), University of Montpellier, INSERM, Montpellier, France
- University of Reims Champagne-Ardenne, INSERM UMR-S 1250 P3CELL and University Hospital of Reims, Immunology Laboratory, Reims, France
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4
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Bartos A, Majak I, Leszczyńska J. Detection of Bet v 1 Homologous Proteins and Plant Profilins by Indirect ELISA. Methods Mol Biol 2024; 2717:305-310. [PMID: 37737993 DOI: 10.1007/978-1-0716-3453-0_20] [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] [Indexed: 09/23/2023]
Abstract
Allergies are an ever-increasing health problem in developed societies. Cross-allergies caused by panallergens are a particularly difficult issue. Proteins similar to the main birch pollen Bet v 1 allergen and profilin are some of the most common allergens. These proteins have a very conservative structure and are present in many distinct organisms. Hence, the knowledge of their natural occurrence is very important for the prevention of allergic reactions. The immunometric method is the most useful approach for determining these allergens. The requirement of reliability and simplicity is fulfilled by enzyme-linked immunosorbent assay (ELISA). In this chapter, detailed procedures are described for the determination of Bet v 1 homologous proteins and plant profilins with the use of indirect, noncompetitive ELISA.
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Affiliation(s)
- Adrian Bartos
- Department of Bioinorganic Chemistry, Faculty of Pharmacy, Medical University of Lodz, Lodz, Poland
| | - Iwona Majak
- Institute of Technology and Food Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Joanna Leszczyńska
- Institute of Natural Products and Cosmetics, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland.
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Khatri K, O'Malley A, Linn C, Kowal K, Chruszcz M. Role of Small Molecule Ligands in IgE-Mediated Allergy. Curr Allergy Asthma Rep 2023; 23:497-508. [PMID: 37351723 DOI: 10.1007/s11882-023-01100-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 06/24/2023]
Abstract
PURPOSE OF REVIEW A significant fraction of allergens bind small molecular ligands, and many of these compounds are classified as lipids. However, in most cases, we do not know the role that is played by the ligands in the allergic sensitization or allergic effector phases. RECENT FINDINGS More effort is dedicated toward identification of allergens' ligands. This resulted in identification of some lipidic compounds that can play active immunomodulatory roles or impact allergens' molecular and allergic properties. Four allergen families (lipocalins, NPC2, nsLTP, and PR-10) are among the best characterized in terms of their ligand-binding properties. Allergens from these four families are able to bind many chemically diverse molecules. These molecules can directly interact with human immune system and/or affect conformation and stability of allergens. While there is more data on the allergens and their small molecular ligands, we are just starting to understand their role in allergy.
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Affiliation(s)
- Kriti Khatri
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Andrea O'Malley
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Christina Linn
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA
| | - Krzysztof Kowal
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA.
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Gribkova I, Eliseev M, Khorosheva E, Remneva G, Borisenko O. The Study of Mineral Elements Participation in Brewing Products Foam Structure Formation. BIO WEB OF CONFERENCES 2023. [DOI: 10.1051/bioconf/20235703002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The article is devoted to the study of the metal ion’s role in the formation of the foam colloidal structure. The nitrogenous compounds prominent role as structuring compounds of the colloidal film on the carbon dioxide bubbles surface is noted. Based on the calculation of the correlation strength between beer samples organic compounds obtained based on light and dark malts, as well as barley and corn as unmalted raw materials, the effect of Ca, Mg, Mn, Co and Na mineral ions on the foam structure was evaluated. It was shown that Ca, Mg, Mn, Na, Co ions take part in the foam structure formation in conjunction with the grain raw materials thiol nitrogen, and Ca, Mg, Mn ions in conjunction with catechins of both grain and hop raw materials. High correlation coefficients between foam resistance and all ions (r-0.991÷0.998), foam resistance, catechins and Co ions (r 0.991), as well as foam resistance and Ca and Mg ions (r -0.987) ensure the elasticity of the foam structure colloidal film.
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7
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Gribkova I, Eliseev M, Zakharov M, Kosareva O, Zakharova V. Developing colloidal structure of beer by grain organic compounds. FOODS AND RAW MATERIALS 2022. [DOI: 10.21603/2308-4057-2022-2-538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The present article introduces the problem of determining the general structure of beer as a complex system of related biomolecules. The objective was to establish the correlation of various quantities of organic compounds in beer formulation.
The research featured samples of filtered pasteurized beer obtained from a retail chain shop in Moscow (Russia). The experiment relied on standard research methods, including instrumental methods of analysis, e.g., high-performance liquid chromatography (HPLC). The obtained experimental data underwent a statistical analysis using the Statistica software (StatSoft, 2016).
The research established the correlation between the type of grain (barley or wheat malt) and the content of organic compounds, e.g., β-glucan, polyphenols, soluble nitrogen, etc. The research also revealed some patterns in the distribution of proteins, which served as a framework for the system of organic compounds. The distribution of thiol proteins proved to depend on the dissolution degree of the grain and was different in barley light, barley dark, and wheat malt samples. The fraction distribution of β-glucan depended on the color of the malt. In light beer samples, it concentrated in high- and medium-molecular fractions of nitrogenous substances, in dark beer – in low-molecular fractions (≤ 63%). Initial wort density and alcohol content affected the amount of catechins and total polyphenols. Nitrogenous compounds depended on the color, initial extract, and alcohol content.
The nitrogenous structure and other organic compounds of beer proved to depend on protein substances. The research also revealed a number of factors that affected the fraction distribution of biomolecules in different beer sorts.
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Affiliation(s)
- Irina Gribkova
- All-Russian Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | | | - Maxim Zakharov
- All-Russian Research Institute of Brewing, Non-Alcoholic and Wine Industry
| | - Olga Kosareva
- Moscow University for Industry and Finance “Synergy”
| | - Varvara Zakharova
- All-Russian Research Institute of Brewing, Non-Alcoholic and Wine Industry
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Führer S, Unterhauser J, Zeindl R, Eidelpes R, Fernández-Quintero ML, Liedl KR, Tollinger M. The Structural Flexibility of PR-10 Food Allergens. Int J Mol Sci 2022; 23:ijms23158252. [PMID: 35897827 PMCID: PMC9330593 DOI: 10.3390/ijms23158252] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/18/2022] Open
Abstract
PR-10 proteins constitute a major cause of food allergic reactions. Birch-pollen-related food allergies are triggered by the immunologic cross-reactivity of IgE antibodies with structurally homologous PR-10 proteins that are present in birch pollen and various food sources. While the three-dimensional structures of PR-10 food allergens have been characterized in detail, only a few experimental studies have addressed the structural flexibility of these proteins. In this study, we analyze the millisecond-timescale structural flexibility of thirteen PR-10 proteins from prevalent plant food sources by NMR relaxation-dispersion spectroscopy, in a comparative manner. We show that all the allergens in this study have inherently flexible protein backbones in solution, yet the extent of the structural flexibility appears to be strikingly protein-specific (but not food-source-specific). Above-average flexibility is present in the two short helices, α1 and α2, which form a V-shaped support for the long C-terminal helix α3, and shape the internal ligand-binding cavity, which is characteristic for PR-10 proteins. An in-depth analysis of the NMR relaxation-dispersion data for the PR-10 allergen from peanut reveals the presence of at least two subglobal conformational transitions on the millisecond timescale, which may be related to the release of bound low-molecular-weight ligands from the internal cavity.
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Affiliation(s)
- Sebastian Führer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Jana Unterhauser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Reiner Eidelpes
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
| | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (M.L.F.-Q.); (K.R.L.)
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (M.L.F.-Q.); (K.R.L.)
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (S.F.); (J.U.); (R.Z.); (R.E.)
- Correspondence: ; Tel.: +43-512-504-57730
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Suanno C, Aloisi I, Parrotta L, Fernández-González D, Del Duca S. Allergenic risk assessment of urban parks: Towards a standard index. ENVIRONMENTAL RESEARCH 2021; 200:111436. [PMID: 34087192 DOI: 10.1016/j.envres.2021.111436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Allergenicity indices are a powerful tool to assess the health hazard posed by urban parks to pollen allergic subjects. Nonetheless, only few indices have been developed and applied to urban vegetation in the last decade, and they were never compared nor standardised over the same dataset. To address this issue, in this paper the two best-known allergenicity indices, the Urban Green Zones Allergenicity Index (IUGZA) and the Specific Allergenicity Index (SAI), have been calculated for the same park (the Botanical Garden of Bologna), collecting vegetation data through both systematic sampling and arboreal census. The results obtained with the two data collection methods were comparable for both indices, indicating systematic sampling as a reliable approximation of the total census. Besides, the allergenic risk resulted moderate to high according to SAI, and very low according to IUGZA. Since SAI does not consider the total volume of the vegetation, it was deemed less reliable than IUGZA in evaluating the allergenicity of an enclosed green space.
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Affiliation(s)
- Chiara Suanno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Iris Aloisi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - Luigi Parrotta
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Delia Fernández-González
- Institute of Atmospheric Sciences and Climate, ISAC-CNR, Via Piero Gobetti 101, 40129 Bologna, Italy; Department Biodiversity and Environmental Management, University of León, 24071, Callejón Campus Vegazana, s/n, 24007 León, Spain
| | - Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
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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] [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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11
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Führer S, Kamenik AS, Zeindl R, Nothegger B, Hofer F, Reider N, Liedl KR, Tollinger M. Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens. Sci Rep 2021; 11:4173. [PMID: 33603065 PMCID: PMC7892832 DOI: 10.1038/s41598-021-83705-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/05/2021] [Indexed: 11/09/2022] Open
Abstract
A major proportion of allergic reactions to hazelnuts (Corylus avellana) are caused by immunologic cross-reactivity of IgE antibodies to pathogenesis-related class 10 (PR-10) proteins. Intriguingly, the four known isoforms of the hazelnut PR-10 allergen Cor a 1, denoted as Cor a 1.0401-Cor a 1.0404, share sequence identities exceeding 97% but possess different immunologic properties. In this work we describe the NMR solution structures of these proteins and provide an in-depth study of their biophysical properties. Despite sharing highly similar three-dimensional structures, the four isoforms exhibit remarkable differences regarding structural flexibility, hydrogen bonding and thermal stability. Our experimental data reveal an inverse relation between structural flexibility and IgE-binding in ELISA experiments, with the most flexible isoform having the lowest IgE-binding potential, while the isoform with the most rigid backbone scaffold displays the highest immunologic reactivity. These results point towards a significant entropic contribution to the process of antibody binding.
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Affiliation(s)
- Sebastian Führer
- grid.5771.40000 0001 2151 8122Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Anna S. Kamenik
- grid.5771.40000 0001 2151 8122Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ricarda Zeindl
- grid.5771.40000 0001 2151 8122Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bettina Nothegger
- grid.5361.10000 0000 8853 2677Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Florian Hofer
- grid.5771.40000 0001 2151 8122Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Norbert Reider
- grid.5361.10000 0000 8853 2677Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- grid.5771.40000 0001 2151 8122Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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12
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Tiered approach for the identification of Mal d 1 reduced, well tolerated apple genotypes. Sci Rep 2020; 10:9144. [PMID: 32499528 PMCID: PMC7272412 DOI: 10.1038/s41598-020-66051-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
A rising proportion of the world population suffers from food-related allergies, including incompatibilities to apples. Although several allergenic proteins have been found in apples, the most important proteins that cause allergic reactions to apples in Central-Northern Europe, and North America are the Mal d 1 proteins, which are homologues of the birch pollen allergen Bet v 1. As the demand for hypoallergenic fruits is constantly increasing, we selected apple genotypes with a low total content of Mal d 1 by enzyme-linked immunosorbent assay analysis from segregating populations and tested the tolerability of these fruits through a human provocation study. This tiered approach, which exploited the natural diversity of apples, led to the identification of fruits, which were tolerated by allergic patients. In addition, we found a significant correlation (coefficient >0.76) between the total Mal d 1 content and flavan-3-ol amount and show that the isoform composition of the Mal d 1 proteins, which was determined by LC-MS/MS has a decisive effect on the tolerability of apple genotypes. The approach presented can be applied to other types of fruit and to other allergenic proteins. Therefore, the strategy can be used to reduce the allergen content of other plant foods, thereby improving food safety for allergy subjects.
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13
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Aglas L, Soh WT, Kraiem A, Wenger M, Brandstetter H, Ferreira F. Ligand Binding of PR-10 Proteins with a Particular Focus on the Bet v 1 Allergen Family. Curr Allergy Asthma Rep 2020; 20:25. [PMID: 32430735 PMCID: PMC7237532 DOI: 10.1007/s11882-020-00918-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Purpose of Review Pathogenesis-related class 10 (PR-10) proteins are highly conserved plant proteins, which are induced in response to abiotic and biotic stress factors. To date, no unique biological function could be assigned to them. Rather a more general role of PR-10 in plant development and defense mechanisms has been proposed. In addition, some PR-10 proteins act as allergens by triggering allergic symptoms in sensitized individuals. Regardless of the diversity of reported activities, all PR-10 proteins share a common fold characterized by a solvent-accessible hydrophobic cavity, which serves as a binding site for a myriad of small-molecule ligands, mostly phytohormones and flavonoids. Recent Findings Most of available data relate to the ligand binding activity of allergenic PR-10, particularly for those belonging to Bet v 1 family of allergens. Bet v 1 and its homologues were shown to bind flavonoids with high affinity, but the specificity appears to differ between homologues from different species. The flavonoid Q3O-(Glc)-Gal was shown to specifically bind to hazelnut Cor a 1 but not to Bet v 1. Similarly, Q3OS bound only to the major isoform Bet v 1.0101 and not to other closely related isoforms. In contrast, Bet v 1 and hazelnut Cor a 1 showed very similar binding behavior towards other flavonoids such as quercetin, genistein, apigenin, daidzein, and resveratrol. Summary Recent research findings highlighted the importance of more precise knowledge of ligand binding for understanding the functional diversification of PR-10 proteins.
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Affiliation(s)
- Lorenz Aglas
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria.,Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Amin Kraiem
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Mario Wenger
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Fatima Ferreira
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria.
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14
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Kamenik AS, Hofer F, Handle PH, Liedl KR. Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1. Front Mol Biosci 2020; 7:18. [PMID: 32154264 PMCID: PMC7045072 DOI: 10.3389/fmolb.2020.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Proteolytic susceptibility during endolysosomal degradation is decisive for allergic sensitization. In the major birch pollen allergen Bet v 1 most protease cleavage sites are located within its secondary structure elements, which are inherently inaccessible to proteases. The allergen thus must unfold locally, exposing the cleavage sites to become susceptible to proteolysis. Hence, allergen cleavage rates are presumed to be linked to their fold stability, i.e., unfolding probability. Yet, these locally unfolded structures have neither been captured in experiment nor simulation due to limitations in resolution and sampling time, respectively. Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of Bet v 1a and two variants with higher and lower cleavage rates. Already at the nanosecond-timescale we observe a significantly higher flexibility for the destabilized variant compared to Bet v 1a and the proteolytically stabilized mutant. Estimating the thermodynamics and kinetics of local unfolding around an initial cleavage site, we find that the Bet v 1 variant with the highest cleavage rate also shows the highest probability for local unfolding. For the stabilized mutant on the other hand we only find minimal unfolding probability. These results strengthen the link between the conformational dynamics of allergen proteins and their stability during endolysosomal degradation. The presented approach further allows atomistic insights in the conformational ensemble of allergen proteins and provides probability estimates below experimental detection limits.
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Affiliation(s)
| | | | | | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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