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Leonard EK, Tomala J, Gould JR, Leff MI, Lin JX, Li P, Porter MJ, Johansen ER, Thompson L, Cao SD, Henclova T, Huliciak M, Vaněk O, Kovar M, Leonard WJ, Spangler JB. Engineered cytokine/antibody fusion proteins improve delivery of IL-2 to pro-inflammatory cells and promote antitumor activity. bioRxiv 2023:2023.05.03.539272. [PMID: 37205604 PMCID: PMC10187205 DOI: 10.1101/2023.05.03.539272] [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] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Progress in cytokine engineering is driving therapeutic translation by overcoming the inherent limitations of these proteins as drugs. The interleukin-2 (IL-2) cytokine harbors great promise as an immune stimulant for cancer treatment. However, the cytokine's concurrent activation of both pro-inflammatory immune effector cells and anti-inflammatory regulatory T cells, its toxicity at high doses, and its short serum half-life have limited clinical application. One promising approach to improve the selectivity, safety, and longevity of IL-2 is complexation with anti-IL-2 antibodies that bias the cytokine towards the activation of immune effector cells (i.e., effector T cells and natural killer cells). Although this strategy shows therapeutic potential in preclinical cancer models, clinical translation of a cytokine/antibody complex is complicated by challenges in formulating a multi-protein drug and concerns about complex stability. Here, we introduce a versatile approach to designing intramolecularly assembled single-agent fusion proteins (immunocytokines, ICs) comprising IL-2 and a biasing anti-IL-2 antibody that directs the cytokine's activities towards immune effector cells. We establish the optimal IC construction and further engineer the cytokine/antibody affinity to improve immune biasing function. We demonstrate that our IC preferentially activates and expands immune effector cells, leading to superior antitumor activity compared to natural IL-2 without inducing toxicities associated with IL-2 administration. Collectively, this work presents a roadmap for the design and translation of immunomodulatory cytokine/antibody fusion proteins.
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Affiliation(s)
- Elissa K. Leonard
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine; Baltimore, USA
| | - Jakub Tomala
- Institute of Biotechnology of the Academy of Sciences of the Czech Republic; Vestec, Czech Republic
| | - Joseph R. Gould
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine; Baltimore, USA
| | - Michael I. Leff
- Department of Biology, Johns Hopkins University; Baltimore, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health; Bethesda, USA
| | - Peng Li
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health; Bethesda, USA
| | | | - Eric R. Johansen
- Department of Chemistry, Johns Hopkins University; Baltimore, USA
| | - Ladaisha Thompson
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine; Baltimore, USA
| | - Shanelle D. Cao
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University School of Engineering; Baltimore, USA
| | - Tereza Henclova
- Institute of Biotechnology of the Academy of Sciences of the Czech Republic; Vestec, Czech Republic
| | - Maros Huliciak
- Institute of Biotechnology of the Academy of Sciences of the Czech Republic; Vestec, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University; Prague, Czech Republic
| | - Marek Kovar
- Laboratory of Tumor Immunology, Institute of Microbiology of the Academy of Sciences of the Czech Republic; Prague, Czech Republic
| | - Warren J. Leonard
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health; Bethesda, USA
| | - Jamie B. Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine; Baltimore, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University School of Engineering; Baltimore, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Oncology, Johns Hopkins University School of Medicine; Baltimore, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine; Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine; Baltimore, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine; Baltimore, USA
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Bláha J, Skálová T, Kalousková B, Skořepa O, Cmunt D, Grobárová V, Pazicky S, Poláchová E, Abreu C, Stránský J, Kovaľ T, Dušková J, Zhao Y, Harlos K, Hašek J, Dohnálek J, Vaněk O. Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse. Nat Commun 2022; 13:5022. [PMID: 36028489 PMCID: PMC9418145 DOI: 10.1038/s41467-022-32577-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/06/2021] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Signaling by the human C-type lectin-like receptor, natural killer (NK) cell inhibitory receptor NKR-P1, has a critical role in many immune-related diseases and cancer. C-type lectin-like receptors have weak affinities to their ligands; therefore, setting up a comprehensive model of NKR-P1-LLT1 interactions that considers the natural state of the receptor on the cell surface is necessary to understand its functions. Here we report the crystal structures of the NKR-P1 and NKR-P1:LLT1 complexes, which provides evidence that NKR-P1 forms homodimers in an unexpected arrangement to enable LLT1 binding in two modes, bridging two LLT1 molecules. These interaction clusters are suggestive of an inhibitory immune synapse. By observing the formation of these clusters in solution using SEC-SAXS analysis, by dSTORM super-resolution microscopy on the cell surface, and by following their role in receptor signaling with freshly isolated NK cells, we show that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling. In summary, our findings collectively support a model of NKR-P1:LLT1 clustering, which allows the interacting proteins to overcome weak ligand-receptor affinity and to trigger signal transduction upon cellular contact in the immune synapse. NKR-P1 is an inhibitory receptor on the surface of natural killer cells, and its engagement with the ligand LLT1 on activated monocytes and B cells triggers NK cell self-tolerance and other immunological processes. Here authors set up a comprehensive, structure-based model of NKR-P1-LLT1 interaction that involves NKR-P1 homodimer formation and subsequent bridging of two LLT1 molecules.
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Affiliation(s)
- Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic.,EMBL, Hamburg Unit c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Tereza Skálová
- Institute of Biotechnology, The Czech Academy of Sciences, BIOCEV Centre, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic.,Institute of Applied Physics - Biophysics group, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic
| | - Denis Cmunt
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic.,Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Chemin des Boveresses 155, 1066, Epalinges, Switzerland
| | - Valéria Grobárová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Samuel Pazicky
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic.,School of Biological Sciences, Nanyang Technological University, Nanyang Drive 60, 637551, Singapore, Singapore
| | - Edita Poláchová
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic
| | - Jan Stránský
- Institute of Biotechnology, The Czech Academy of Sciences, BIOCEV Centre, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Tomáš Kovaľ
- Institute of Biotechnology, The Czech Academy of Sciences, BIOCEV Centre, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Jarmila Dušková
- Institute of Biotechnology, The Czech Academy of Sciences, BIOCEV Centre, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN, Oxford, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN, Oxford, UK
| | - Jindřich Hašek
- Institute of Biotechnology, The Czech Academy of Sciences, BIOCEV Centre, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Jan Dohnálek
- Institute of Biotechnology, The Czech Academy of Sciences, BIOCEV Centre, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic.
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Vaněk O, Kalousková B, Abreu C, Nejadebrahim S, Skořepa O. Natural killer cell-based strategies for immunotherapy of cancer. Adv Protein Chem Struct Biol 2022; 129:91-133. [PMID: 35305726 DOI: 10.1016/bs.apcsb.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Natural killer (NK) cells are a family of lymphocytes with a natural ability to kill infected, harmed, or malignantly transformed cells. As these cells are part of the innate immunity, the cytotoxic mechanisms are activated upon recognizing specific patterns without prior antigen sensitization. This recognition is crucial for NK cell function in the maintenance of homeostasis and immunosurveillance. NK cells not only act directly toward malignant cells but also participate in the complex immune response by producing cytokines or cross-talk with other immune cells. Cancer may be seen as a break of all immune defenses when malignant cells escape the immunity and invade surrounding tissues creating a microenvironment supporting tumor progression. This process may be reverted by intervening immune response with immunotherapy, which may restore immune recognition. NK cells are important effector cells for immunotherapy. They may be used for adoptive cell transfer, genetically modified with chimeric antigen receptors, or triggered with appropriate antibodies and other antibody-fragment-based recombinant therapeutic proteins tailored specifically for NK cell engagement. NK cell receptors, responsible for target recognition and activation of cytotoxic response, could also be targeted in immunotherapy, for example, by various bi-, tri-, or multi-specific fusion proteins designed to bridge the gap between tumor markers present on target cells and activation receptors expressed on NK cells. However, this kind of immunoactive therapeutics may be developed only with a deep functional and structural knowledge of NK cell receptor: ligand interactions. This review describes the recent developments in the fascinating protein-engineering field of NK cell immunotherapeutics.
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Affiliation(s)
- Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shiva Nejadebrahim
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
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4
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Remans K, Lebendiker M, Abreu C, Maffei M, Sellathurai S, May MM, Vaněk O, de Marco A. Protein purification strategies must consider downstream applications and individual biological characteristics. Microb Cell Fact 2022; 21:52. [PMID: 35392897 PMCID: PMC8991485 DOI: 10.1186/s12934-022-01778-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins are used as reagents in a broad range of scientific fields. The reliability and reproducibility of experimental data will largely depend on the quality of the (recombinant) proteins and, consequently, these should undergo thorough structural and functional controls. Depending on the downstream application and the biochemical characteristics of the protein, different sets of specific features will need to be checked. RESULTS A number of examples, representative of recurrent issues and previously published strategies, has been reported that illustrate real cases of recombinant protein production in which careful strategy design at the start of the project combined with quality controls throughout the production process was imperative to obtain high-quality samples compatible with the planned downstream applications. Some proteins possess intrinsic properties (e.g., prone to aggregation, rich in cysteines, or a high affinity for nucleic acids) that require certain precautions during the expression and purification process. For other proteins, the downstream application might demand specific conditions, such as for proteins intended for animal use that need to be endotoxin-free. CONCLUSIONS This review has been designed to act as a practical reference list for researchers who wish to produce and evaluate recombinant proteins with certain specific requirements or that need particular care for their preparation and storage.
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Affiliation(s)
- Kim Remans
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mario Lebendiker
- Protein Purification Facility, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Mariano Maffei
- Evvivax Biotech, Via di Castel Romano 100, 00128, Rome, Italy
| | | | - Marina M May
- AiCuris Anti-Infective Cures AG, Friedrich-Ebert-Str. 475, 42117, Wuppertal, Germany
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000, Rožna Dolina-Nova Gorica, Slovenia.
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5
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Kalousková B, Skořepa O, Cmunt D, Abreu C, Krejčová K, Bláha J, Sieglová I, Král V, Fábry M, Pola R, Pechar M, Vaněk O. Tumor Marker B7-H6 Bound to the Coiled Coil Peptide-Polymer Conjugate Enables Targeted Therapy by Activating Human Natural Killer Cells. Biomedicines 2021; 9:biomedicines9111597. [PMID: 34829829 PMCID: PMC8615638 DOI: 10.3390/biomedicines9111597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/02/2023] Open
Abstract
Targeted cancer immunotherapy is a promising tool for restoring immune surveillance and eradicating cancer cells. Hydrophilic polymers modified with coiled coil peptide tags can be used as universal carriers designed for cell-specific delivery of such biologically active proteins. Here, we describe the preparation of pHPMA-based copolymer conjugated with immunologically active protein B7-H6 via complementary coiled coil VAALEKE (peptide E) and VAALKEK (peptide K) sequences. Receptor B7-H6 was described as a binding partner of NKp30, and its expression has been proven for various tumor cell lines. The binding of B7-H6 to NKp30 activates NK cells and results in Fas ligand or granzyme-mediated apoptosis of target tumor cells. In this work, we optimized the expression of coiled coil tagged B7-H6, its ability to bind activating receptor NKp30 has been confirmed by isothermal titration calorimetry, and the binding stoichiometry of prepared chimeric biopolymer has been characterized by analytical ultracentrifugation. Furthermore, this coiled coil B7-H6-loaded polymer conjugate activates NK cells in vitro and, in combination with coiled coil scFv, enables their targeting towards a model tumor cell line. Prepared chimeric biopolymer represents a promising precursor for targeted cancer immunotherapy by activating the cytotoxic activity of natural killer cells.
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Affiliation(s)
- Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Denis Cmunt
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Kateřina Krejčová
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
| | - Irena Sieglová
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (I.S.); (V.K.); (M.F.)
| | - Vlastimil Král
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (I.S.); (V.K.); (M.F.)
| | - Milan Fábry
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (I.S.); (V.K.); (M.F.)
| | - Robert Pola
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 16206 Prague, Czech Republic; (R.P.); (M.P.)
| | - Michal Pechar
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 16206 Prague, Czech Republic; (R.P.); (M.P.)
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague, Czech Republic; (B.K.); (O.S.); (D.C.); (C.A.); (K.K.); (J.B.)
- Correspondence:
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6
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Anderluh M, Berti F, Bzducha‐Wróbel A, Chiodo F, Colombo C, Compostella F, Durlik K, Ferhati X, Holmdahl R, Jovanovic D, Kaca W, Lay L, Marinovic‐Cincovic M, Marradi M, Ozil M, Polito L, Reina‐Martin JJ, Reis CA, Sackstein R, Silipo A, Švajger U, Vaněk O, Yamamoto F, Richichi B, van Vliet SJ. Emerging glyco-based strategies to steer immune responses. FEBS J 2021; 288:4746-4772. [PMID: 33752265 PMCID: PMC8453523 DOI: 10.1111/febs.15830] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
Glycan structures are common posttranslational modifications of proteins, which serve multiple important structural roles (for instance in protein folding), but also are crucial participants in cell-cell communications and in the regulation of immune responses. Through the interaction with glycan-binding receptors, glycans are able to affect the activation status of antigen-presenting cells, leading either to induction of pro-inflammatory responses or to suppression of immunity and instigation of immune tolerance. This unique feature of glycans has attracted the interest and spurred collaborations of glyco-chemists and glyco-immunologists to develop glycan-based tools as potential therapeutic approaches in the fight against diseases such as cancer and autoimmune conditions. In this review, we highlight emerging advances in this field, and in particular, we discuss on how glycan-modified conjugates or glycoengineered cells can be employed as targeting devices to direct tumor antigens to lectin receptors on antigen-presenting cells, like dendritic cells. In addition, we address how glycan-based nanoparticles can act as delivery platforms to enhance immune responses. Finally, we discuss some of the latest developments in glycan-based therapies, including chimeric antigen receptor (CAR)-T cells to achieve targeting of tumor-associated glycan-specific epitopes, as well as the use of glycan moieties to suppress ongoing immune responses, especially in the context of autoimmunity.
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Affiliation(s)
- Marko Anderluh
- Chair of Pharmaceutical ChemistryFaculty of PharmacyUniversity of LjubljanaSlovenia
| | | | - Anna Bzducha‐Wróbel
- Department of Biotechnology and Food MicrobiologyWarsaw University of Life Sciences‐SGGWPoland
| | - Fabrizio Chiodo
- Department of Molecular Cell Biology and ImmunologyCancer Center AmsterdamAmsterdam Infection and Immunity InstituteAmsterdam UMCVrije Universiteit AmsterdamNetherlands
| | - Cinzia Colombo
- Department of Chemistry and CRC Materiali Polimerici (LaMPo)University of MilanItaly
| | - Federica Compostella
- Department of Medical Biotechnology and Translational MedicineUniversity of MilanItaly
| | - Katarzyna Durlik
- Department of Microbiology and ParasitologyJan Kochanowski UniversityKielcePoland
| | - Xhenti Ferhati
- Department of Chemistry ‘Ugo Schiff’University of FlorenceFlorenceItaly
| | - Rikard Holmdahl
- Division of Medical Inflammation ResearchDepartment of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Dragana Jovanovic
- Vinča Institute of Nuclear Sciences ‐ National Institute of the Republic of SerbiaUniversity of BelgradeSerbia
| | - Wieslaw Kaca
- Department of Microbiology and ParasitologyJan Kochanowski UniversityKielcePoland
| | - Luigi Lay
- Department of Chemistry and CRC Materiali Polimerici (LaMPo)University of MilanItaly
| | - Milena Marinovic‐Cincovic
- Vinča Institute of Nuclear Sciences ‐ National Institute of the Republic of SerbiaUniversity of BelgradeSerbia
| | - Marco Marradi
- Department of Chemistry ‘Ugo Schiff’University of FlorenceFlorenceItaly
| | - Musa Ozil
- Department of ChemistryFaculty of Arts and SciencesRecep Tayyip Erdogan University RizeTurkey
| | | | | | - Celso A. Reis
- I3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyInstituto de Ciências Biomédicas Abel SalazarUniversity of PortoPortugal
| | - Robert Sackstein
- Department of Translational Medicinethe Translational Glycobiology InstituteHerbert Wertheim College of MedicineFlorida International UniversityMiamiFLUSA
| | - Alba Silipo
- Department of Chemical SciencesUniversity of Naples Federico IIComplesso Universitario Monte Sant’AngeloNapoliItaly
| | - Urban Švajger
- Blood Transfusion Center of SloveniaLjubljanaSlovenia
| | - Ondřej Vaněk
- Department of BiochemistryFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Fumiichiro Yamamoto
- Immunohematology & Glycobiology LaboratoryJosep Carreras Leukaemia Research InstituteBadalonaSpain
| | - Barbara Richichi
- Department of Chemistry ‘Ugo Schiff’University of FlorenceFlorenceItaly
| | - Sandra J. van Vliet
- Department of Molecular Cell Biology and ImmunologyCancer Center AmsterdamAmsterdam Infection and Immunity InstituteAmsterdam UMCVrije Universiteit AmsterdamNetherlands
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7
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Anderluh M, Berti F, Bzducha-Wróbel A, Chiodo F, Colombo C, Compostella F, Durlik K, Ferhati X, Holmdahl R, Jovanovic D, Kaca W, Lay L, Marinovic-Cincovic M, Marradi M, Ozil M, Polito L, Reina JJ, Reis CA, Sackstein R, Silipo A, Švajger U, Vaněk O, Yamamoto F, Richichi B, van Vliet SJ. Recent advances on smart glycoconjugate vaccines in infections and cancer. FEBS J 2021; 289:4251-4303. [PMID: 33934527 PMCID: PMC9542079 DOI: 10.1111/febs.15909] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/09/2021] [Accepted: 04/30/2021] [Indexed: 01/01/2023]
Abstract
Vaccination is one of the greatest achievements in biomedical research preventing death and morbidity in many infectious diseases through the induction of pathogen-specific humoral and cellular immune responses. Currently, no effective vaccines are available for pathogens with a highly variable antigenic load, such as the human immunodeficiency virus or to induce cellular T-cell immunity in the fight against cancer. The recent SARS-CoV-2 outbreak has reinforced the relevance of designing smart therapeutic vaccine modalities to ensure public health. Indeed, academic and private companies have ongoing joint efforts to develop novel vaccine prototypes for this virus. Many pathogens are covered by a dense glycan-coat, which form an attractive target for vaccine development. Moreover, many tumor types are characterized by altered glycosylation profiles that are known as "tumor-associated carbohydrate antigens". Unfortunately, glycans do not provoke a vigorous immune response and generally serve as T-cell-independent antigens, not eliciting protective immunoglobulin G responses nor inducing immunological memory. A close and continuous crosstalk between glycochemists and glycoimmunologists is essential for the successful development of efficient immune modulators. It is clear that this is a key point for the discovery of novel approaches, which could significantly improve our understanding of the immune system. In this review, we discuss the latest advancements in development of vaccines against glycan epitopes to gain selective immune responses and to provide an overview on the role of different immunogenic constructs in improving glycovaccine efficacy.
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Affiliation(s)
- Marko Anderluh
- Faculty of Pharmacy, Faculty of Pharmacy, Chair of Pharmaceutical Chemistry, University of Ljubljana, Slovenia
| | | | - Anna Bzducha-Wróbel
- Department of Biotechnology and Food Microbiology, Warsaw University of Life Sciences-SGGW, Warszawa, Poland
| | - Fabrizio Chiodo
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,Institute of Biomolecular Chemistry (ICB), Italian National Research Council (CNR), Pozzuoli, Italy
| | - Cinzia Colombo
- Department of Chemistry and CRC Materiali Polimerici (LaMPo), University of Milan, Italy
| | - Federica Compostella
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milano, Italy
| | - Katarzyna Durlik
- Department of Microbiology and Parasitology, Jan Kochanowski University, Kielce, Poland
| | - Xhenti Ferhati
- Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Dragana Jovanovic
- Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Serbia
| | - Wieslaw Kaca
- Department of Microbiology and Parasitology, Jan Kochanowski University, Kielce, Poland
| | - Luigi Lay
- Department of Chemistry and CRC Materiali Polimerici (LaMPo), University of Milan, Italy
| | - Milena Marinovic-Cincovic
- Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Serbia
| | - Marco Marradi
- Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Musa Ozil
- Faculty of Arts and Sciences, Department of Chemistry, Recep Tayyip Erdogan University, Rize, Turkey
| | - Laura Polito
- National Research Council, CNR-SCITEC, Milan, Italy
| | - Josè Juan Reina
- Departamento de Química Orgánica, Universidad de Málaga-IBIMA, Spain.,Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, Málaga, Spain
| | - Celso A Reis
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Portugal
| | - Robert Sackstein
- Department of Translational Medicine, Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Napoli, Italy
| | - Urban Švajger
- Blood Transfusion Center of Slovenia, Ljubljana, Slovenia
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Fumiichiro Yamamoto
- Immunohematology & Glycobiology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Barbara Richichi
- Department of Chemistry 'Ugo Schiff', University of Florence, Sesto Fiorentino, Italy
| | - Sandra J van Vliet
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
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8
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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9
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Vaněk O, Celadova P, Skořepa O, Bláha J, Kalousková B, Dvorská A, Poláchová E, Pucholtová H, Kavan D, Pompach P, Hofbauerová K, Kopecký V, Mesci A, Voigt S, Carlyle JR. Publisher Correction: Production of recombinant soluble dimeric C-type lectin-like receptors of rat natural killer cells. Sci Rep 2020; 10:2828. [PMID: 32054978 PMCID: PMC7018945 DOI: 10.1038/s41598-020-59778-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic.
| | - Petra Celadova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic.,EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603, Hamburg, Germany
| | - Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Anna Dvorská
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Edita Poláchová
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Helena Pucholtová
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Daniel Kavan
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic.,Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Petr Pompach
- Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Kateřina Hofbauerová
- Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic.,Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Vladimír Kopecký
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic
| | - Aruz Mesci
- Department of Immunology, University of Toronto, 1 King's College Circle, M5S 1A8, Toronto, ON, Canada
| | - Sebastian Voigt
- Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - James R Carlyle
- Department of Immunology, University of Toronto, 1 King's College Circle, M5S 1A8, Toronto, ON, Canada
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10
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Skalova T, Bláha J, Stránský J, Koval T, Dušková J, Zhao Y, Harlos K, Vaněk O, Dohnálek J. Structure of human natural killer cell receptor NKR-P1 in complex with its ligand LLT1. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318091775] [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: 11/11/2022] Open
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11
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Škerlová J, Bláha J, Pachl P, Hofbauerová K, Kukačka Z, Man P, Pompach P, Novák P, Otwinowski Z, Brynda J, Vaněk O, Řezáčová P. Crystal structure of native β‐
N
‐acetylhexosaminidase isolated from
Aspergillus oryzae
sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J 2017; 285:580-598. [DOI: 10.1111/febs.14360] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/03/2017] [Accepted: 12/08/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Jana Škerlová
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics The Czech Academy of Sciences Prague Czech Republic
| | - Jan Bláha
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
| | - Kateřina Hofbauerová
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
- Institute of Physics Faculty of Mathematics and Physics Charles University Prague Czech Republic
| | - Zdeněk Kukačka
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | - Petr Man
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | - Petr Pompach
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | - Petr Novák
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
- Institute of Microbiology The Czech Academy of Sciences Prague Czech Republic
| | | | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics The Czech Academy of Sciences Prague Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry The Czech Academy of Sciences Prague Czech Republic
- Institute of Molecular Genetics The Czech Academy of Sciences Prague Czech Republic
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12
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Bláha J, Kalousková B, Skořepa O, Pažický S, Novák P, Vaněk O. High-level expression and purification of soluble form of human natural killer cell receptor NKR-P1 in HEK293S GnTI - cells. Protein Expr Purif 2017; 140:36-43. [PMID: 28757467 DOI: 10.1016/j.pep.2017.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 05/29/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 02/09/2023]
Abstract
Human natural killer receptor protein 1 (NKR-P1, CD161, gene klrb1) is a C-type lectin-like receptor of natural killer (NK) cells responsible for recognition of its cognate protein ligand lectin-like transcript 1 (LLT1). NKR-P1 is the single human orthologue of the prototypical rodent NKR-P1 receptors. Naturally, human NKR-P1 is expressed on the surface of NK cells, where it serves as inhibitory receptor; and on T and NKT cells functioning as co-stimulatory receptor promoting secretion of IFNγ. Most notably, it is expressed on Th17 and Tc17 lymphocytes where presumably promotes targeting into LLT1 expressing immunologically privileged niches. We tested effect of different protein tags (SUMO, TRX, GST, MsyB) on expression of soluble NKR-P1 in E. coli. Then we optimized the expression construct of soluble NKR-P1 by preparing a library of expression constructs in pOPING vector containing the extracellular lectin-like domain with different length of the putative N-terminal stalk region and tested its expression in Sf9 and HEK293 cells. Finally, a high-level expression of soluble NKR-P1 was achieved by stable expression in suspension-adapted HEK293S GnTI- cells utilizing pOPINGTTneo expression vector. Purified soluble NKR-P1 is homogeneous, deglycosylatable, crystallizable and monomeric in solution, as shown by size-exclusion chromatography, multi-angle light scattering and analytical ultracentrifugation.
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Affiliation(s)
- Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Samuel Pažický
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Petr Novák
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic; Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic.
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13
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Skálová T, Bláha J, Harlos K, Dušková J, Koval' T, Stránský J, Hašek J, Vaněk O, Dohnálek J. Changes of LLT1, a ligand for human NKR-P1, with varied glycosylation and crystallization conditions. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316094936] [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: 11/10/2022] Open
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14
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Stranava M, Martínek V, Man P, Fojtikova V, Kavan D, Vaněk O, Shimizu T, Martinkova M. Structural characterization of the heme-based oxygen sensor, AfGcHK, its interactions with the cognate response regulator, and their combined mechanism of action in a bacterial two-component signaling system. Proteins 2016; 84:1375-89. [PMID: 27273553 DOI: 10.1002/prot.25083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 03/11/2016] [Revised: 05/19/2016] [Accepted: 05/30/2016] [Indexed: 01/11/2023]
Abstract
The oxygen sensor histidine kinase AfGcHK from the bacterium Anaeromyxobacter sp. Fw 109-5 forms a two-component signal transduction system together with its cognate response regulator (RR). The binding of oxygen to the heme iron of its N-terminal sensor domain causes the C-terminal kinase domain of AfGcHK to autophosphorylate at His183 and then transfer this phosphate to Asp52 or Asp169 of the RR protein. Analytical ultracentrifugation revealed that AfGcHK and the RR protein form a complex with 2:1 stoichiometry. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) suggested that the most flexible part of the whole AfGcHK protein is a loop that connects the two domains and that the heme distal side of AfGcHK, which is responsible for oxygen binding, is the only flexible part of the sensor domain. HDX-MS studies on the AfGcHK:RR complex also showed that the N-side of the H9 helix in the dimerization domain of the AfGcHK kinase domain interacts with the helix H1 and the β-strand B2 area of the RR protein's Rec1 domain, and that the C-side of the H8 helix region in the dimerization domain of the AfGcHK protein interacts mostly with the helix H5 and β-strand B6 area of the Rec1 domain. The Rec1 domain containing the phosphorylable Asp52 of the RR protein probably has a significantly higher affinity for AfGcHK than the Rec2 domain. We speculate that phosphorylation at Asp52 changes the overall structure of RR such that the Rec2 area containing the second phosphorylation site (Asp169) can also interact with AfGcHK. Proteins 2016; 84:1375-1389. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Martin Stranava
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic
| | - Václav Martínek
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic.,Department of Chemical Education, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic
| | - Petr Man
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic.,Laboratory of Structure Biology and Cell Signalling, BioCeV - Institute of Microbiology, Czech Academy of Sciences, V.V.I, Prumyslova 595, Vestec, Czech Republic
| | - Veronika Fojtikova
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic
| | - Daniel Kavan
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic.,Laboratory of Structure Biology and Cell Signalling, BioCeV - Institute of Microbiology, Czech Academy of Sciences, V.V.I, Prumyslova 595, Vestec, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic
| | - Marketa Martinkova
- Department of Biochemistry, Charles University in Prague, Hlavova (Albertov) 2030-8, Prague 2, Czech Republic.
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15
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Doležal M, Zábranský A, Dostál J, Vaněk O, Brynda J, Lepšík M, Hadravová R, Pichová I. Myristoylation drives dimerization of matrix protein from mouse mammary tumor virus. Retrovirology 2016; 13:2. [PMID: 26728401 PMCID: PMC4700671 DOI: 10.1186/s12977-015-0235-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 07/23/2015] [Accepted: 12/22/2015] [Indexed: 11/25/2022] Open
Abstract
Background Myristoylation of the matrix (MA) domain mediates the transport and binding of Gag polyproteins to the plasma membrane (PM) and is required for the assembly of most retroviruses. In betaretroviruses, which assemble immature particles in the cytoplasm, myristoylation is dispensable for assembly but is crucial for particle transport to the PM. Oligomerization of HIV-1 MA stimulates the transition of the myristoyl group from a sequestered to an exposed conformation, which is more accessible for membrane binding. However, for other retroviruses, the effect of MA oligomerization on myristoyl group exposure has not been thoroughly investigated. Results Here, we demonstrate that MA from the betaretrovirus mouse mammary tumor virus (MMTV) forms dimers in solution and that this process is stimulated by its myristoylation. The crystal structure of N-myristoylated MMTV MA, determined at 1.57 Å resolution, revealed that the myristoyl groups are buried in a hydrophobic pocket at the dimer interface and contribute to dimer formation. Interestingly, the myristoyl groups in the dimer are mutually swapped to achieve energetically stable binding, as documented by molecular dynamics modeling. Mutations within the myristoyl binding site resulted in reduced MA dimerization and extracellular particle release. Conclusions Based on our experimental, structural, and computational data, we propose a model for dimerization of MMTV MA in which myristoyl groups stimulate the interaction between MA molecules. Moreover, dimer-forming MA molecules adopt a sequestered conformation with their myristoyl groups entirely buried within the interaction interface. Although this differs from the current model proposed for lentiviruses, in which oligomerization of MA triggers exposure of myristoyl group, it appears convenient for intracellular assembly, which involves no apparent membrane interaction and allows the myristoyl group to be sequestered during oligomerization. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0235-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michal Doležal
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
| | - Aleš Zábranský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
| | - Jiří Dostál
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 40, Prague, Czech Republic.
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
| | - Romana Hadravová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic.
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16
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Vaněk O, Bláha J, Pachl P, Novák P. High-density transfection is superior for production of readily crystallizable glycoproteins in suspension adapted HEK293S GnTI −cells: a case study of human lymphocyte receptor LLT1. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315096680] [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: 11/10/2022] Open
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17
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Skálová T, Bláha J, Harlos K, Dušková J, Koval' T, Stránský J, Hašek J, Vaněk O, Dohnálek J. Human LLT1, a ligand for NKR-P1, and its variability under various conditions. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315095959] [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: 11/10/2022] Open
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18
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Machová I, Snášel J, Dostál J, Brynda J, Fanfrlík J, Singh M, Tarábek J, Vaněk O, Bednárová L, Pichová I. Structural and functional studies of phosphoenolpyruvate carboxykinase from Mycobacterium tuberculosis. PLoS One 2015; 10:e0120682. [PMID: 25798914 PMCID: PMC4370629 DOI: 10.1371/journal.pone.0120682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/05/2015] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis, the second leading infectious disease killer after HIV, remains a top public health priority. The causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), which can cause both acute and clinically latent infections, reprograms metabolism in response to the host niche. Phosphoenolpyruvate carboxykinase (Pck) is the enzyme at the center of the phosphoenolpyruvate-pyruvate-oxaloacetate node, which is involved in regulating the carbon flow distribution to catabolism, anabolism, or respiration in different states of Mtb infection. Under standard growth conditions, Mtb Pck is associated with gluconeogenesis and catalyzes the metal-dependent formation of phosphoenolpyruvate. In non-replicating Mtb, Pck can catalyze anaplerotic biosynthesis of oxaloacetate. Here, we present insights into the regulation of Mtb Pck activity by divalent cations. Through analysis of the X-ray structure of Pck-GDP and Pck-GDP-Mn2+ complexes, mutational analysis of the GDP binding site, and quantum mechanical (QM)-based analysis, we explored the structural determinants of efficient Mtb Pck catalysis. We demonstrate that Mtb Pck requires presence of Mn2+ and Mg2+ cations for efficient catalysis of gluconeogenic and anaplerotic reactions. The anaplerotic reaction, which preferably functions in reducing conditions that are characteristic for slowed or stopped Mtb replication, is also effectively activated by Fe2+ in the presence of Mn2+ or Mg2+ cations. In contrast, simultaneous presence of Fe2+ and Mn2+ or Mg2+ inhibits the gluconeogenic reaction. These results suggest that inorganic ions can contribute to regulation of central carbon metabolism by influencing the activity of Pck. Furthermore, the X-ray structure determination, biochemical characterization, and QM analysis of Pck mutants confirmed the important role of the Phe triad for proper binding of the GDP-Mn2+ complex in the nucleotide binding site and efficient catalysis of the anaplerotic reaction.
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Affiliation(s)
- Iva Machová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Snášel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jiří Dostál
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Mahavir Singh
- LIONEX diagnostics & Therapeutics, Braunschweig, Germany
| | - Ján Tarábek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Sciences, Charles University in Prague, Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- * E-mail:
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19
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Skálová T, Bláha J, Harlos K, Dušková J, Koval’ T, Stránský J, Hašek J, Vaněk O, Dohnálek J. Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states. Acta Crystallogr D Biol Crystallogr 2015; 71:578-91. [PMID: 25760607 PMCID: PMC4356368 DOI: 10.1107/s1399004714027928] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/22/2014] [Indexed: 12/03/2022]
Abstract
Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, gene KLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the first N-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5 glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.
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Affiliation(s)
- Tereza Skálová
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic
| | - Karl Harlos
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jarmila Dušková
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Tomáš Koval’
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
| | - Jan Stránský
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jindřich Hašek
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic
| | - Jan Dohnálek
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
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20
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Michálková Z, Komárek M, Šillerová H, Della Puppa L, Joussein E, Bordas F, Vaněk A, Vaněk O, Ettler V. Evaluating the potential of three Fe- and Mn-(nano)oxides for the stabilization of Cd, Cu and Pb in contaminated soils. J Environ Manage 2014; 146:226-234. [PMID: 25178528 DOI: 10.1016/j.jenvman.2014.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 08/01/2014] [Accepted: 08/06/2014] [Indexed: 06/03/2023]
Abstract
The potential of three Fe- and Mn-(nano)oxides for stabilizing Cd, Cu and Pb in contaminated soils was investigated using batch and column experiments, adsorption tests and tests of soil microbial activity. A novel synthetic amorphous Mn oxide (AMO), which was recently proposed as a stabilizing amendment, proved to be the most efficient in decreasing the mobility of the studied metals compared to nano-maghemite and nano-magnetite. Its application resulted in significant decreases of exchangeable metal fractions (92%, 92% and 93% decreases of Cd, Cu and Pb concentrations, respectively). The adsorption capacity of the AMO was an order of magnitude higher than those recorded for the other amendments. It was also the most efficient treatment for reducing Cu concentrations in the soil solution. No negative effects on soil microorganisms were recorded. On the other hand, the AMO was able to dissolve soil organic matter to some extent.
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Affiliation(s)
- Zuzana Michálková
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 21, Czech Republic.
| | - Michael Komárek
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 21, Czech Republic.
| | - Hana Šillerová
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 21, Czech Republic.
| | - Loïc Della Puppa
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 21, Czech Republic; Groupement de Recherche Eau Sol Environnement, Université de Limoges, 123 Avenue Albert Thomas, Limoges 87060, France.
| | - Emmanuel Joussein
- Groupement de Recherche Eau Sol Environnement, Université de Limoges, 123 Avenue Albert Thomas, Limoges 87060, France.
| | - François Bordas
- Groupement de Recherche Eau Sol Environnement, Université de Limoges, 123 Avenue Albert Thomas, Limoges 87060, France.
| | - Aleš Vaněk
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 21, Czech Republic.
| | - Ondřej Vaněk
- Faculty of Science, Charles University in Prague, Albertov 6, Prague 2, 128 40, Czech Republic.
| | - Vojtěch Ettler
- Faculty of Science, Charles University in Prague, Albertov 6, Prague 2, 128 40, Czech Republic.
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21
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Skálová T, Kotýnková K, Vaněk O, Dušková J, Hašek J, Koval' T, Kolenko P, Stránský J, Fejfarová K, Dohnálek J. Structure of mouse Clr-g, a CTL ligand for NK receptor NKR-P1F. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314097459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Natural killer (NK) cells are large granular lymphocytes with innate immune reaction against tumor cells or cells affected by viral infection. They have a variety of receptors on their surface which mediate contact with cells tested by NK cells. Using X-ray crystallography, we determined a structure of an extracellular part of mouse C-type lectin related protein g (Clr-g, [1], PDB code 3RS1), a ligand for NK receptor NKR-P1F. The ligand and the receptor are both of C-type lectin like fold and this is the first determined structure of a CTL ligand of an NK receptor. The protein was produced in E. coli. The rod-like crystals appeared by spontaneous crystallization of the pure protein (2.5 mg/ml) on tube walls. Diffraction data of the vitrified crystal were measured at synchrotron BessyII of HZB in Berlin and were processed up to 1.95 Å. The protein was found in the form of dimers similar to that of CD69. The N-terminus of the chain (residues Met, Asn, Lys) is in the crystal bound to a neighbor dimer and shows thus that binding of a peptide to mouse Clr-g is possible, although not expected or confirmed by other experiments known to us. A model of interaction of Clr-g with NKR-P1F was designed based on electrostatic complementarity of both molecules. This work was supported by the Czech Science Foundation (grant No. P302/11/0855), Ministry of Education, Youth and Sports of the Czech Republic (grant No. LG14009) and by the project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.
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22
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Kovalová A, Ledvina M, Šaman D, Zyka D, Kubíčková M, Žídek L, Sklenář V, Pompach P, Kavan D, Bílý J, Vaněk O, Kubínková Z, Libigerová M, Ivanová L, Antolíková M, Mrázek H, Rozbeský D, Hofbauerová K, Křen V, Bezouška K. Retraction: Synthetic N-Acetyl- d-glucosamine Based Fully Branched Tetrasaccharide, a Mimetic of the Endogenous Ligand for CD69, Activates CD69 + Killer Lymphocytes upon Dimerization via a Hydrophilic Flexible Linker. J Med Chem 2014; 57:5477. [DOI: 10.1021/jm5007726] [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: 11/29/2022]
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23
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Pechar M, Pola R, Laga R, Braunová A, Filippov SK, Bogomolova A, Bednárová L, Vaněk O, Ulbrich K. Coiled Coil Peptides and Polymer–Peptide Conjugates: Synthesis, Self-Assembly, Characterization and Potential in Drug Delivery Systems. Biomacromolecules 2014; 15:2590-9. [DOI: 10.1021/bm500436p] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Michal Pechar
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
| | - Robert Pola
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
| | - Richard Laga
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
| | - Alena Braunová
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
| | - Sergey K. Filippov
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
| | - Anna Bogomolova
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Ondřej Vaněk
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague 2, Czech Republic
| | - Karel Ulbrich
- Institute
of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 16206 Prague 6, Czech Republic
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24
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Kavan D, Kubíčková M, Bílý J, Vaněk O, Hofbauerová K, Mrázek H, Rozbeský D, Bojarová P, Křen V, Žídek L, Sklenář V, Bezouška K. Retraction of Cooperation between Subunits Is Essential for High-Affinity Binding of N-Acetyl- d-hexosamines to Dimeric Soluble and Dimeric Cellular Forms of Human CD69. Biochemistry 2014; 53:2864. [DOI: 10.1021/bi500367g] [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: 11/29/2022]
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25
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Renaudet O, Křenek K, Bossu I, Dumy P, Kádek A, Adámek D, Vaněk O, Kavan D, Gažák R, Šulc M, Bezouška K, Křen V. Retraction of "Synthesis of multivalent glycoconjugates containing the immunoactive LELTE peptide: effect of glycosylation on cellular activation and natural killing by human peripheral blood mononuclear cells". J Am Chem Soc 2014; 136:1156. [PMID: 24400684 DOI: 10.1021/ja4081277] [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: 11/28/2022]
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26
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Vaněk O, Illéš D, Zawadová D, Bláha J, Veselá AB, Martínková L. Recombinant fungal nitrilases - effect of reduction on their structure and function. Acta Crystallogr A 2013. [DOI: 10.1107/s010876731309689x] [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: 11/10/2022] Open
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27
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Bláha J, Veselá AB, Illéš D, Martínková L, Vaněk O. Crystallization of arylacetonitrilase from Arthoderma benhamie. Acta Crystallogr A 2013. [DOI: 10.1107/s010876731309692x] [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: 11/10/2022] Open
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28
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Ryšlavá H, Doubnerová V, Kavan D, Vaněk O. Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 2013; 92:80-109. [PMID: 23603109 DOI: 10.1016/j.jprot.2013.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/22/2022]
Abstract
The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12840 Prague 2, Czech Republic.
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29
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Skálová T, Kotýnková K, Dušková J, Hašek J, Koval T, Kolenko P, Novák P, Man P, Hanč P, Vaněk O, Bezouška K, Dohnálek J. Mouse Clr-g, a ligand for NK cell activation receptor NKR-P1F: crystal structure and biophysical properties. J Immunol 2012; 189:4881-9. [PMID: 23071282 DOI: 10.4049/jimmunol.1200880] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Interactions between C-type lectin-like NK cell receptors and their protein ligands form one of the key recognition mechanisms of the innate immune system that is involved in the elimination of cells that have been malignantly transformed, virally infected, or stressed by chemotherapy or other factors. We determined an x-ray structure for the extracellular domain of mouse C-type lectin related (Clr) protein g, a ligand for the activation receptor NKR-P1F. Clr-g forms dimers in the crystal structure resembling those of human CD69. This newly reported structure, together with the previously determined structure of mouse receptor NKR-P1A, allowed the modeling and calculations of electrostatic profiles for other closely related receptors and ligands. Despite the high similarity among Clr-g, Clr-b, and human CD69, these molecules have fundamentally different electrostatics, with distinct polarization of Clr-g. The electrostatic profile of NKR-P1F is complementary to that of Clr-g, which suggests a plausible interaction mechanism based on contacts between surface sites of opposite potential.
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Affiliation(s)
- Tereza Skálová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, vvi, 16206 Praha 6, Czech Republic.
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30
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Grave L, Tůmová L, Mrázek H, Kavan D, Chmelík J, Vaněk O, Novák P, Bezouška K. Preparation of soluble isotopically labeled NKp30, a human natural cytotoxicity receptor, for structural studies using NMR. Protein Expr Purif 2012; 86:142-50. [PMID: 23059620 DOI: 10.1016/j.pep.2012.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 09/26/2012] [Accepted: 09/28/2012] [Indexed: 02/07/2023]
Abstract
Using a codon-optimized gene fragment, we report remarkable yields for extracellular domain of human NK cell receptor (NKp30ex) when produced on M9 minimal medium, even with low (2g/L) glucose concentration. The yields were identical using media containing (15)NH(4)Cl or (15)NH(4)Cl in combination with all-(13)C-d-glucose allowing to produce homogenous soluble monomeric NKp30 in several formats needed for advanced NMR studies. Our optimized protocol now allows to produce routinely 10mg batches of these NKp30ex proteins per 1L of M9 production medium in four working days. The purity and identity of the produced proteins were checked by SDS-PAGE, MALDI MS peptide mapping, and high resolution ion cyclotron resonance MS. Analytical ultracentrifugation confirmed the monomeric status of the produced proteins. Long-term stability of the produced protein proved to be very good allowing its use for NMR studies using elevated temperatures. These studies should reveal further details of the interaction of NKp30 with several of its ligands including target cell surface proteins and heparin-derived oligosaccharides.
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Affiliation(s)
- Lena Grave
- Department of Biochemistry, Charles University Prague, Praha, Czech Republic
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31
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Mrázek H, Benada O, Man P, Vaněk O, Křen V, Bezouška K, Weignerová L. Facile production of Aspergillus niger α- N -acetylgalactosaminidase in yeast. Protein Expr Purif 2012; 81:106-114. [DOI: 10.1016/j.pep.2011.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/26/2011] [Accepted: 09/19/2011] [Indexed: 11/28/2022]
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32
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Kolenko P, Rozbeský D, Vaněk O, Bezouška K, Hašek J, Dohnálek J. Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1519-23. [PMID: 22139156 PMCID: PMC3232129 DOI: 10.1107/s1744309111046203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 11/02/2011] [Indexed: 11/11/2022]
Abstract
The structure of the H107R variant of the extracellular domain of the mouse natural killer cell receptor NKR-P1A has been determined by X-ray diffraction at 2.3 Å resolution from a merohedrally twinned crystal. Unlike the structure of the wild-type receptor in space group I4(1)22 with a single chain per asymmetric unit, the crystals of the variant belonged to space group I4(1) with a dimer in the asymmetric unit. Different degrees of merohedral twinning were detected in five data sets collected from different crystals. The mutation does not have a significant impact on the overall structure, but led to the binding of an additional phosphate ion at the interface of the molecules.
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Affiliation(s)
- Petr Kolenko
- Institute of Macromolecular Chemistry AS CR, vvi, Prague, Czech Republic.
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33
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Pechar M, Pola R, Laga R, Ulbrich K, Bednárová L, Maloň P, Sieglová I, Král V, Fábry M, Vaněk O. Coiled Coil Peptides as Universal Linkers for the Attachment of Recombinant Proteins to Polymer Therapeutics. Biomacromolecules 2011; 12:3645-55. [DOI: 10.1021/bm200897b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Michal Pechar
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Robert Pola
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Richard Laga
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Karel Ulbrich
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovskeho nam. 2, 162 06, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Petr Maloň
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague 6, Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague 6, Czech Republic
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34
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Ryšlavá H, Kalendová A, Doubnerová V, Skočdopol P, Kumar V, Kukačka Z, Pompach P, Vaněk O, Slámová K, Bojarová P, Kulik N, Ettrich R, Křen V, Bezouška K. Enzymatic characterization and molecular modeling of an evolutionarily interesting fungal β-N-acetylhexosaminidase. FEBS J 2011; 278:2469-84. [DOI: 10.1111/j.1742-4658.2011.08173.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kolenko P, Rozbeský D, Vaněk O, Kopecký V, Hofbauerová K, Novák P, Pompach P, Hašek J, Skálová T, Bezouška K, Dohnálek J. Molecular architecture of mouse activating NKR-P1 receptors. J Struct Biol 2011; 175:434-41. [PMID: 21600988 DOI: 10.1016/j.jsb.2011.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/28/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
Receptors belonging to NKR-P1 family and their specific Clr ligands form an alternative missing self recognition system critical in immunity against tumors and viruses, elimination of tumor cells subjected to genotoxic stress, activation of T cell dependent immune response, and hypertension. The three-dimensional structure of the extracellular domain of the mouse natural killer (NK) cell receptor mNKR-P1Aex has been determined by X-ray diffraction. The core of the C-type lectin domain (CTLD) is homologous to the other CTLD receptors whereas one quarter of the domain forms an extended loop interacting tightly with a neighboring loop in the crystal. This domain swapping mechanism results in a compact interaction interface. A second dimerization interface resembles the known arrangement of other CTLD NK receptors. A functional dimeric form of the receptor is suggested, with the loop, evolutionarily conserved within this family, proposed to participate in interactions with ligands.
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Affiliation(s)
- Petr Kolenko
- Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 16206 Prague 6, Czech Republic
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Vaněk O, Brynda J, Hofbauerová K, Kukačka Z, Pachl P, Bezouška K, Řezáčová P. Crystallization and diffraction analysis of β-N-acetylhexosaminidase from Aspergillus oryzae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:498-503. [PMID: 21505251 PMCID: PMC3080160 DOI: 10.1107/s1744309111004945] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 02/09/2011] [Indexed: 11/10/2022]
Abstract
Fungal β-N-acetylhexosaminidases are enzymes that are used in the chemoenzymatic synthesis of biologically interesting oligosaccharides. The enzyme from Aspergillus oryzae was produced and purified from its natural source and crystallized using the hanging-drop vapour-diffusion method. Diffraction data from two crystal forms (primitive monoclinic and primitive tetragonal) were collected to resolutions of 3.2 and 2.4 Å, respectively. Electrophoretic and quantitative N-terminal protein-sequencing analyses confirmed that the crystals are formed by a complete biologically active enzyme consisting of a glycosylated catalytic unit and a noncovalently attached propeptide.
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Affiliation(s)
- Ondřej Vaněk
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Kateřina Hofbauerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague, Czech Republic
| | - Petr Pachl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Karel Bezouška
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague, Czech Republic
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Rozbeský D, Kavan D, Chmelík J, Novák P, Vaněk O, Bezouška K. High-level expression of soluble form of mouse natural killer cell receptor NKR-P1C(B6) in Escherichia coli. Protein Expr Purif 2011; 77:178-84. [PMID: 21284957 DOI: 10.1016/j.pep.2011.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Revised: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
Abstract
Mouse NKR-P1C(B6) receptor corresponding to NK1.1 alloantigen is one of the most widespread surface markers of mouse NK and NKT cells in C57BL/6 mice detected by monoclonal antibody PK136. Although functional studies revealed the ability of this receptor to activate both natural killing and production of cytokines upon antibody crosslinking, the ligand for NKR-P1C(B6) remains unknown. In order to initiate ligand identification, structural studies, and epitope mapping experiments, we developed a simple and efficient expression and purification protocol allowing to produce large amounts of pure soluble monomeric mouse NKR-P1C(B6). Our protein encompassed approximately half of the stalk region and the entire C-terminal globular ligand binding domain. The identity of protein that was devoid of N-terminal initiation methionine and had all three expected disulfides closed was confirmed using high resolution ion cyclotron resonance mass spectrometry. Protein produced into inclusion bodies in Escherichia coli was efficiently refolded into a unique three dimensional structure as confirmed by NMR using (1)H-(15)N-HSQC spectra of uniformly labeled protein. The exceptional purity of the protein should allow its crystallization and detailed structural investigations, and is a prerequisite for its use as a probe in ligand identification and antibody epitope mapping experiments.
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Affiliation(s)
- Daniel Rozbeský
- Department of Biochemistry, Charles University in Prague, CZ-12840 Prague 2, Czech Republic
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Kaplan O, Bezouška K, Plíhal O, Ettrich R, Kulik N, Vaněk O, Kavan D, Benada O, Malandra A, Sveda O, Veselá AB, Rinágelová A, Slámová K, Cantarella M, Felsberg J, Dušková J, Dohnálek J, Kotik M, Křen V, Martínková L. Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10. BMC Biotechnol 2011; 11:2. [PMID: 21210990 PMCID: PMC3023689 DOI: 10.1186/1472-6750-11-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [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: 02/23/2010] [Accepted: 01/06/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Nitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult. RESULTS A nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzyme's native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn₃₅₆) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp₂₉₈-Val₃₁₃ peptide was shortened to Asp₂₉₈-Arg₃₁₀ in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution. CONCLUSIONS The nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.
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Affiliation(s)
- Ondřej Kaplan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Sovová Z, Kopecký V, Pazderka T, Hofbauerová K, Rozbeský D, Vaněk O, Bezouška K, Ettrich R. Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity. J Mol Model 2010; 17:1353-70. [PMID: 20839018 DOI: 10.1007/s00894-010-0837-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Accepted: 08/24/2010] [Indexed: 11/29/2022]
Abstract
Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refined homology models are generated for the C-type lectin-like extracellular domains of rat NKR-P1A and NKR-P1B, mouse NKR-P1A, NKR-P1C, NKR-P1F, and NKR-P1G, and human NKR-P1 receptors. Experimental data on secondary structure, tertiary interactions, and thermal transitions are acquired for four of the proteins using Raman and infrared spectroscopy. The experimental and modeling results are in agreement with respect to the overall structures of the NKR-P1 receptor domains, while suggesting functionally significant local differences among species and isoforms. Two sequence regions that are conserved in all analyzed NKR-P1 receptors do not correspond to conserved structural elements as might be expected, but are represented by loop regions, one of which is arranged differently in the constructed models. This region displays high flexibility but is anchored by conserved sequences, suggesting that its position relative to the rest of the domain might be variable. This loop may contribute to ligand-binding specificity via a coupled conformational transition.
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Affiliation(s)
- Zofie Sovová
- Laboratory of Structural Biology, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, Nové Hrady, Czech Republic
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Renaudet O, Křenek K, Bossu I, Dumy P, Kádek A, Adámek D, Vaněk O, Kavan D, Gažák R, Šulc M, Bezouška K, Křen V. Synthesis of Multivalent Glycoconjugates Containing the Immunoactive LELTE Peptide: Effect of Glycosylation on Cellular Activation and Natural Killing by Human Peripheral Blood Mononuclear Cells. J Am Chem Soc 2010; 132:6800-8. [DOI: 10.1021/ja101296t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olivier Renaudet
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Karel Křenek
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Isabelle Bossu
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Pascal Dumy
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Alan Kádek
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - David Adámek
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Ondřej Vaněk
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Daniel Kavan
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Radek Gažák
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Miroslav Šulc
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Karel Bezouška
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
| | - Vladimír Křen
- Département de Chimie Moléculaire, UMR CNRS 5250 and ICMG FR 2607, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic, and Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-12840 Praha 2, Czech Republic
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Kavan D, Kubíčková M, Bílý J, Vaněk O, Hofbauerová K, Mrázek H, Rozbeský D, Bojarová P, Křen V, Žídek L, Sklenář V, Bezouška K. Cooperation between Subunits Is Essential for High-Affinity Binding of N-Acetyl-d-hexosamines to Dimeric Soluble and Dimeric Cellular Forms of Human CD69. Biochemistry 2010; 49:4060-7. [DOI: 10.1021/bi100181a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Kavan
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Monika Kubíčková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Jan Bílý
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Kateřina Hofbauerová
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Hynek Mrázek
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Daniel Rozbeský
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Pavla Bojarová
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Vladimír Sklenář
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Karel Bezouška
- Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic
- Institute of Microbiology v.v.i., Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
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Vaněk O, Nálezková M, Kavan D, Borovičková I, Pompach P, Novák P, Kumar V, Vannucci L, Hudeček J, Hofbauerová K, Kopecký Jr V, Brynda J, Kolenko P, Dohnálek J, Kadeřávek P, Chmelík J, Gorčík L, Žídek L, Sklenář V, Bezouška K. Soluble recombinant CD69 receptors optimized to have an exceptional physical and chemical stability display prolonged circulation and remain intact in the blood of mice. FEBS J 2008; 275:5589-606. [DOI: 10.1111/j.1742-4658.2008.06683.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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