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Grifnée E, Kune C, Delvaux C, Tilmant T, Quinton L, Matagne A, Mazzucchelli G, Far J, De Pauw E. Investigation of Structure-Stabilizing Elements in Proteins by Ion Mobility Mass Spectrometry and Collision-Induced Unfolding. J Am Soc Mass Spectrom 2024. [PMID: 38660944 DOI: 10.1021/jasms.3c00398] [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] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A recently developed proteolytic reactor, designed for protein structural investigation, was coupled to ion mobility mass spectrometry to monitor collisional cross section (CCS) evolution of model proteins undergoing trypsin-mediated mono enzymatic digestion. As peptides are released during digestion, the CCS of the remaining protein structure may deviate from the classical 2/3 power of the CCS-mass relationship for spherical structures. The classical relationship between CCS and mass (CCS = A × M2/3) for spherical structures, assuming a globular shape in the gas phase, may deviate as stabilizing elements are lost during digestion. In addition, collision-induced unfolding (CIU) experiments on partially digested proteins provided insights into the CCS resilience in the gas phase to ion activation, potentially due to the presence of stabilizing elements. The study initially investigated a model peptide ModBea (3 kDa), assessing the impact of disulfide bridges on CCS resilience in both reduced and oxidized forms. Subsequently, β-lactoglobulin (2 disulfide bridges), calmodulin (Ca2+ coordination cation), and cytochrome c (heme) were selected to investigate the influence of common structuring elements on CCS resilience. CIU experiments probed the unfolding process, evaluating the effect of losing specific peptides on the energy landscapes of partially digested proteins. Comparisons of the TWCCSN2→He to trend curves describing the CCS/mass relationship revealed that proteins with structure-stabilizing elements consistently exhibit TWCCSN2→He and greater resilience toward CIU compared to proteins lacking these elements. The integration of online digestion, ion mobility, and CIU provides a valuable tool for identifying structuring elements in biopolymers in the gas phase.
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Affiliation(s)
- Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Thomas Tilmant
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Center for Protein Engineering, InBioS Research Unit, University of Liège, B-4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
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Frère JM, Verlaine O, Matagne A. The measurement of true initial rates is not always absolutely necessary to estimate enzyme kinetic parameters. Sci Rep 2023; 13:15053. [PMID: 37699921 PMCID: PMC10497622 DOI: 10.1038/s41598-023-41805-y] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
In the chapters dealing with enzyme reactions, the authors of all Biochemistry textbooks and of even more specialized texts consider that the characteristic parameters (kcat and Km) must be determined under initial or steady-state rate conditions. This implies the transformation of a very limited proportion of substrate (at most 10-20%) or a continuous recording of the product or substrate concentration vs. time. Both options can present practical difficulties. Is it possible to get around these very stringent conditions? Here we show that in the most favourable cases up to 70% of the substrate can be converted resulting in systematic errors on the parameters (that can easily be taken account of) if the simple Henri-Michaelis-Menten equation is utilised. Alternatively, the integrated form of the same equation directly yields excellent estimates of the same parameters. Our observations should greatly facilitate the task of researchers who study systems in which measurements of the reaction progress are painstaking or when substrate concentrations close to the detection limit must be used. The general conclusion is that it is not always absolutely necessary to determine initial or steady-state rates to obtain reliable estimations of the enzyme kinetic parameters..
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Affiliation(s)
- Jean-Marie Frère
- Enzymology and Protein Folding Laboratory, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
- Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
| | - Olivier Verlaine
- Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - André Matagne
- Enzymology and Protein Folding Laboratory, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
- Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
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Robert C, Kerff F, Bouillenne F, Gavage M, Vandevenne M, Filée P, Matagne A. Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition. J Biol Chem 2023; 299:102892. [PMID: 36642181 PMCID: PMC9929448 DOI: 10.1016/j.jbc.2023.102892] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) are secreted cytokines belonging to the transforming growth factor-β superfamily. New therapeutic approaches based on BMP activity, particularly for cartilage and bone repair, have sparked considerable interest; however, a lack of understanding of their interaction pathways and the side effects associated with their use as biopharmaceuticals have dampened initial enthusiasm. Here, we used BMP-2 as a model system to gain further insight into both the relationship between structure and function in BMPs and the principles that govern affinity for their cognate antagonist Noggin. We produced BMP-2 and Noggin as inclusion bodies in Escherichia coli and developed simple and efficient protocols for preparing pure and homogeneous (in terms of size distribution) solutions of the native dimeric forms of the two proteins. The identity and integrity of the proteins were confirmed using mass spectrometry. Additionally, several in vitro cell-based assays, including enzymatic measurements, RT-qPCR, and matrix staining, demonstrated their biological activity during cell chondrogenic and hypertrophic differentiation. Furthermore, we characterized the simple 1:1 noncovalent interaction between the two ligands (KDca. 0.4 nM) using bio-layer interferometry and solved the crystal structure of the complex using X-ray diffraction methods. We identified the residues and binding forces involved in the interaction between the two proteins. Finally, results obtained with the BMP-2 N102D mutant suggest that Noggin is remarkably flexible and able to accommodate major structural changes at the BMP-2 level. Altogether, our findings provide insights into BMP-2 activity and reveal the molecular details of its interaction with Noggin.
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Affiliation(s)
- Charly Robert
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium,Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Frédéric Kerff
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium,Biological Macromolecule Crystallography, University of Liège, Liège, Belgium
| | - Fabrice Bouillenne
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Maxime Gavage
- Analytical Laboratory, CER Groupe, rue du Point du Jour, Marloie, Belgium
| | - Marylène Vandevenne
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium,Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Patrice Filée
- Laboratory of immuno-biology, CER Groupe, Novalis Science Park, Aye, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium; Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium.
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Tomasi L, Thiriard A, Heyndrickx L, Georges D, Van den Wijngaert S, Olislagers V, Sharma S, Matagne A, Ackerman ME, Ariën KK, Goetghebuer T, Marchant A. Younger Children Develop Higher Effector Antibody Responses to SARS-CoV-2 Infection. Open Forum Infect Dis 2022; 9:ofac554. [PMCID: PMC9709628 DOI: 10.1093/ofid/ofac554] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022] Open
Abstract
Abstract
Background
The basis of the less severe clinical presentation of coronavirus disease 2019 (COVID-19) in children as compared with adults remains incompletely understood. Studies have suggested that a more potent boosting of immunity to endemic common cold coronaviruses (HCoVs) may protect children.
Methods
To test this hypothesis, we conducted a detailed analysis of antibodies induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children aged 2 months to 14 years.
Results
Younger children had higher titers of antibodies to SARS-CoV-2 receptor binding domain (RBD), S1 but not S2 domain, and total spike (S) protein, higher avidity RBD immunoglobulin G, and higher titers of neutralizing and complement-activating antibodies as compared with older children. In contrast, older children had higher titers of antibodies to HCoVs, which correlated with antibodies to the SARS-CoV-2 S2 domain but not with neutralizing or complement-activating antibodies.
Conclusions
These results reveal a unique capacity of young children to develop effector antibody responses to SARS-CoV-2 infection independently of their immunity to HCoVs.
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Affiliation(s)
- Lisa Tomasi
- Pediatric Department, Saint-Pierre Hospital , Brussels , Belgium
| | - Anais Thiriard
- Institute for Medical Immunology, and ULB-Center for Research in Immunology, Université Libre de Bruxelles , Charleroi , Belgium
| | - Leo Heyndrickx
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp , Antwerp , Belgium
| | - Daphnée Georges
- Institute for Medical Immunology, and ULB-Center for Research in Immunology, Université Libre de Bruxelles , Charleroi , Belgium
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège , Liège , Belgium
| | | | - Véronique Olislagers
- Institute for Medical Immunology, and ULB-Center for Research in Immunology, Université Libre de Bruxelles , Charleroi , Belgium
| | - Shilpee Sharma
- Institute for Medical Immunology, and ULB-Center for Research in Immunology, Université Libre de Bruxelles , Charleroi , Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège , Liège , Belgium
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College , Hanover, New Hampshire , USA
| | - Kevin K Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp , Antwerp , Belgium
- Department of Biomedical Sciences, University of Antwerp , Antwerp , Belgium
| | - Tessa Goetghebuer
- Pediatric Department, Saint-Pierre Hospital , Brussels , Belgium
- Institute for Medical Immunology, and ULB-Center for Research in Immunology, Université Libre de Bruxelles , Charleroi , Belgium
| | - Arnaud Marchant
- Institute for Medical Immunology, and ULB-Center for Research in Immunology, Université Libre de Bruxelles , Charleroi , Belgium
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Pannus P, Neven KY, De Craeye S, Heyndrickx L, Vande Kerckhove S, Georges D, Michiels J, Francotte A, Van Den Bulcke M, Zrein M, Van Gucht S, Schmickler MN, Verbrugghe M, Matagne A, Thomas I, Dierick K, Weiner JA, Ackerman ME, Goriely S, Goossens ME, Ariën KK, Desombere I, Marchant A. Poor Antibody Response to BioNTech/Pfizer Coronavirus Disease 2019 Vaccination in Severe Acute Respiratory Syndrome Coronavirus 2-Naive Residents of Nursing Homes. Clin Infect Dis 2022; 75:e695-e704. [PMID: 34864935 PMCID: PMC8690239 DOI: 10.1093/cid/ciab998] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Residents of nursing homes (NHs) are at high risk of coronavirus disease 2019 (COVID-19)-related disease and death and may respond poorly to vaccination because of old age and frequent comorbid conditions. METHODS Seventy-eight residents and 106 staff members, naive to infection or previously infected with severe acute respiratory syndrome coronavirus (SARS-CoV-2), were recruited in NHs in Belgium before immunization with 2 doses of 30 µg BNT162b2 messenger RNA (mRNA) vaccine at days 0 and 21. Binding antibodies (Abs) to SARS-CoV-2 receptor-binding domain (RBD), spike domains S1 and S2, RBD Ab avidity, and neutralizing Abs against SARS-CoV-2 wild type and B.1.351 were assessed at days 0, 21, 28, and 49. RESULTS SARS-CoV-2-naive residents had lower Ab responses to BNT162b2 mRNA vaccination than naive staff. These poor responses involved lower levels of immunoglobulin (Ig) G to all spike domains, lower avidity of RBD IgG, and lower levels of Abs neutralizing the vaccine strain. No naive residents had detectable neutralizing Abs to the B.1.351 variant. In contrast, SARS-CoV-2-infected residents had high responses to mRNA vaccination, with Ab levels comparable to those in infected staff. Cluster analysis revealed that poor vaccine responders included not only naive residents but also naive staff, emphasizing the heterogeneity of responses to mRNA vaccination in the general population. CONCLUSIONS The poor Ab responses to mRNA vaccination observed in infection-naive NH residents and in some naive staff members suggest suboptimal protection against breakthrough infection, especially with variants of concern. These data support the administration of a third dose of mRNA vaccine to further improve protection of NH residents against COVID-19.
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Affiliation(s)
- Pieter Pannus
- SD Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Kristof Y Neven
- SD Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | - Leo Heyndrickx
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Daphnée Georges
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Université libre de Bruxelles (ULB), Gosselies, Belgium
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Liège, Belgium
| | - Johan Michiels
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | | | | | | | | | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Liège, Belgium
| | - Isabelle Thomas
- SD Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | | | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Stanislas Goriely
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Université libre de Bruxelles (ULB), Gosselies, Belgium
| | | | - Kevin K Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Arnaud Marchant
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Université libre de Bruxelles (ULB), Gosselies, Belgium
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Remans K, De Marco A, Berrow N, Lebendiker M, Garcia-Alai M, Knauer S, Lopez-Mendez B, Matagne A, Parret A, Uebel S, Raynal B. Protein quality control for improved data reproducibility and reliability. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322096395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Nyssen P, Maho A, Malempre R, Matagne A, Mouithys-Mickalad A, Hoebeke M. Propofol inhibits the myeloperoxidase activity by acting as substrate through a redox process. Biochim Biophys Acta Gen Subj 2022; 1866:130100. [PMID: 35150774 DOI: 10.1016/j.bbagen.2022.130100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/24/2021] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Propofol (2,6-diisopropylphenol) is frequently used as intravenous anesthetic agent, especially in its injectable form (Diprivan), to initiate and maintain sedative state during surgery or in intensive care units. Numerous studies have reported the antioxidant and anti-inflammatory effect of propofol. The oxidant enzyme myeloperoxidase (MPO), released from activated neutrophils, plays a key role in host defense. An increase of the circulating MPO concentration has been observed in patients admitted in intensive care unit and presenting a systemic inflammatory response related to septic shock or trauma. METHODS This study investigates the immunomodulatory action of propofol and Diprivan as inhibitor of the oxidant activity of MPO. The understanding of the redox action mechanism of propofol and Diprivan on the myeloperoxidase chlorination and peroxidase activities has been refined using the combination of fluorescence and absorption spectroscopies with docking and cyclic voltammetry. RESULTS Propofol acts as a reversible MPO inhibitor. The molecule interacts as a reducing substrate in the peroxidase cycle and promotes the accumulation of compound II. At acidic pH (5.5), propofol and Diprivan do not inhibit the chlorination activity, but their action increases at physiological pH (7.4). The main inhibitory action of Diprivan could be attributed to its HOCl scavenging property. GENERAL SIGNIFICANCE Propofol can act as a reversible MPO inhibitor at clinical concentrations. This property could, in addition to other previously proven anti-inflammatory actions, induce an immunomodulatory action, beneficial during clinical use, particularly in the treatment of systemic inflammation response syndrome.
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Affiliation(s)
- P Nyssen
- Biomedical Spectroscopy Laboratory, Department of Physics, CESAM, University of Liège, Building B5a, Quartier Agora, Allée du 6 Août, 19, Sart-Tilman, 4000 Liège, Belgium.
| | - A Maho
- Greenmat, Department of Chemistry, CESAM, University of Liège, Building B6c, Quartier Agora, Allée du 6 Août, 19, Sart-Tilman, 4000 Liège, Belgium
| | - R Malempre
- Laboratory of Enzymology and Protein folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6a, Quartier Agora, Allée du 6 Août, 19, Sart-Tilman, 4000 Liège, Belgium
| | - A Matagne
- Laboratory of Enzymology and Protein folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6a, Quartier Agora, Allée du 6 Août, 19, Sart-Tilman, 4000 Liège, Belgium
| | - A Mouithys-Mickalad
- CORD, Department of Chemistry, CIRM, University of Liège, Building B6a, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, 4000 Liège, Belgium
| | - M Hoebeke
- Biomedical Spectroscopy Laboratory, Department of Physics, CESAM, University of Liège, Building B5a, Quartier Agora, Allée du 6 Août, 19, Sart-Tilman, 4000 Liège, Belgium
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Mignon J, Mottet D, Verrillo G, Matagne A, Perpète EA, Michaux C. Revealing Intrinsic Disorder and Aggregation Properties of the DPF3a Zinc Finger Protein. ACS Omega 2021; 6:18793-18801. [PMID: 34337219 PMCID: PMC8319922 DOI: 10.1021/acsomega.1c01948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 05/27/2023]
Abstract
Double PHD fingers 3 (DPF3) is a human epigenetic factor found in the multiprotein BRG1-associated factor (BAF) chromatin remodeling complex. It has two isoforms: DPF3b and DPF3a, but very little is known about the latter. Despite the lack of structural data, it has been established that DPF3a is involved in various protein-protein interactions and that it is subject to phosphorylation. These features are typical of intrinsically disordered proteins (IDPs) for which the disorder is essential to their functionality. IDPs are also prone to aggregation and can assemble into cytotoxic amyloid fibrils in specific pathological contexts. In the present work, the DPF3a disordered nature and propensity to aggregation have been investigated using a combination of disorder predictors and biophysical methods. The DPF3a-predicted disordered character has been correlated to a characteristic random coil signal in far-UV circular dichroism (CD) and to a fluorescence emission band typical of Trp residues fully exposed to the solvent. After DPF3a purification and 24 h of incubation at room temperature, dynamic light scattering confirmed the presence of DPF3a aggregates whose amyloid nature have been highlighted by a specific deep-blue autofluorescence signature, as well as by an increase in thioflavin T fluorescence upon binding. These results are supported by an enrichment in twisted β-sheets as observed in far-UV CD and a blue shift in intrinsic Trp fluorescence. Both indicate that DPF3a spontaneously tends to orderly aggregate into amyloid fibrils. The diversity of optical signatures originates from dynamical transitions between the disordered and aggregated states of the protein during the incubation. Transmission electron microscopy micrographs reveal that the DPF3a fibrillation process leads to the formation of short needle-shape filaments.
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Affiliation(s)
- Julien Mignon
- Laboratoire
de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Denis Mottet
- GIGA-Molecular
Biology of Diseases, University of Liège, Quartier Hôpital, Avenue
de l’Hôpital 11, 4000 Liège, Belgium
| | - Giulia Verrillo
- GIGA-Molecular
Biology of Diseases, University of Liège, Quartier Hôpital, Avenue
de l’Hôpital 11, 4000 Liège, Belgium
| | - André Matagne
- Laboratoire
d’Enzymologie et Repliement des Protéine, Centre d’Ingénierie
des Protéines, InBioS, University
of Liège, Building B6C, Quartier Agora, Allée du 6 Août 13, 4000 Liège, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
- Namur
Institute of Structured Matter, University
of Namur, 5000 Namur, Belgium
- Institute
of Life-Earth-Environment, University of
Namur, 5000 Namur, Belgium
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
- Namur
Institute of Structured Matter, University
of Namur, 5000 Namur, Belgium
- Namur
Research
Institute for Life Sciences, University
of Namur, 5000 Namur, Belgium
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de Marco A, Berrow N, Lebendiker M, Garcia-Alai M, Knauer SH, Lopez-Mendez B, Matagne A, Parret A, Remans K, Uebel S, Raynal B. Quality control of protein reagents for the improvement of research data reproducibility. Nat Commun 2021; 12:2795. [PMID: 33990604 PMCID: PMC8121922 DOI: 10.1038/s41467-021-23167-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/19/2021] [Indexed: 11/23/2022] Open
Abstract
Proteins and peptides are amongst the most widely used research reagents but often their quality is inadequate and can result in poor data reproducibility. Here we propose a simple set of guidelines that, when correctly applied to protein reagents should provide more reliable experimental data.
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Affiliation(s)
- Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipava, Vipava, Slovenia
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mario Lebendiker
- Protein Purification Facility, Wolfson Centre for Applied Structural Biology, Edmund J. Safra Campus - The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Stefan H Knauer
- Biochemistry IV - Biopolymers, University of Bayreuth, Bayreuth, Germany
| | - Blanca Lopez-Mendez
- Protein Production and Characterization Platform, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Department of Life Sciences, University of Liège, Building B6C, Allée du 6 Août, 13, Liège, Belgium
| | - Annabel Parret
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Kim Remans
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique moléculaire, Department of Structural Biology and Chemistry, Paris, France.
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10
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Kellner R, Malempré R, Vandenameele J, Brans A, Hennen AF, Rochus N, Di Paolo A, Vandevenne M, Matagne A. Protein formulation through automated screening of pH and buffer conditions, using the Robotein® high throughput facility. Eur Biophys J 2021; 50:473-490. [PMID: 33611612 DOI: 10.1007/s00249-021-01510-y] [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] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/26/2021] [Accepted: 02/08/2021] [Indexed: 12/30/2022]
Abstract
Among various factors, the direct environment (e.g. pH, buffer components, salts, additives, etc.…) is known to have a crucial effect on both the stability and activity of proteins. In particular, proper buffer and pH conditions can improve their stability and function significantly during purification, storage and handling, which is highly relevant for both academic and industrial applications. It can also promote data reproducibility, support the interpretation of experimental results and, finally, contribute to our general understanding of the biophysical properties of proteins. In this study, we have developed a high throughput screen of 158 different buffers/pH conditions in which we evaluated: (i) the protein stability, using differential scanning fluorimetry and (ii) the protein function, using either enzymatic assays or binding activity measurements, both in an automated manner. The modular setup of the screen allows for easy implementation of other characterization methods and parameters, as well as additional test conditions. The buffer/pH screen was validated with five different proteins used as models, i.e. two active-site serine β-lactamases, two metallo-β-lactamases (one of which is only active as a tetramer) and a single-domain dromedary antibody fragment (VHH or nanobody). The formulation screen allowed automated and fast determination of optimum buffer and pH profiles for the tested proteins. Besides the determination of the optimum buffer and pH, the collection of pH profiles of many different proteins may also allow to delineate general concepts to understand and predict the relationship between pH and protein properties.
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Affiliation(s)
- Ruth Kellner
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Romain Malempré
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Alain Brans
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | | | - Noémie Rochus
- Eurogentec S.A., Rue Bois Saint-Jean, 5, 4102, Seraing, Belgium
| | - Alexandre Di Paolo
- Eurogentec S.A., Rue Bois Saint-Jean, 5, 4102, Seraing, Belgium.,Xpress Biologics SA, Accessia Pharma Site, Avenue du Parc Industriel, 89, 4041, Milmort, Belgium
| | - Marylène Vandevenne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
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11
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Turupcu A, Bowen AM, Di Paolo A, Matagne A, Oostenbrink C, Redfield C, Smith LJ. An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose. Proteins 2020; 88:82-93. [PMID: 31294851 PMCID: PMC6916166 DOI: 10.1002/prot.25770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 02/06/2023]
Abstract
The X-ray structure of lysozyme from bacteriophage lambda (λ lysozyme) in complex with the inhibitor hexa-N-acetylchitohexaose (NAG6) (PDB: 3D3D) has been reported previously showing sugar units from two molecules of NAG6 bound in the active site. One NAG6 is bound with four sugar units in the ABCD sites and the other with two sugar units in the E'F' sites potentially representing the cleavage reaction products; each NAG6 cross links two neighboring λ lysozyme molecules. Here we use NMR and MD simulations to study the interaction of λ lysozyme with the inhibitors NAG4 and NAG6 in solution. This allows us to study the interactions within the complex prior to cleavage of the polysaccharide. 1 HN and 15 N chemical shifts of λ lysozyme resonances were followed during NAG4/NAG6 titrations. The chemical shift changes were similar in the two titrations, consistent with sugars binding to the cleft between the upper and lower domains; the NMR data show no evidence for simultaneous binding of a NAG6 to two λ lysozyme molecules. Six 150 ns MD simulations of λ lysozyme in complex with NAG4 or NAG6 were performed starting from different conformations. The simulations with both NAG4 and NAG6 show stable binding of sugars across the D/E active site providing low energy models for the enzyme-inhibitor complexes. The MD simulations identify different binding subsites for the 5th and 6th sugars consistent with the NMR data. The structural information gained from the NMR experiments and MD simulations have been used to model the enzyme-peptidoglycan complex.
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Affiliation(s)
- Aysegul Turupcu
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences ViennaViennaAustria
| | | | - Alexandre Di Paolo
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des ProtéinesInstitut de Chimie, Université de LiègeLiègeBelgium
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des ProtéinesInstitut de Chimie, Université de LiègeLiègeBelgium
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences ViennaViennaAustria
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12
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Lopes-Rodrigues M, Matagne A, Zanuy D, Alemán C, Perpète EA, Michaux C. Structural and functional characterization of Solanum tuberosum VDAC36. Proteins 2019; 88:729-739. [PMID: 31833115 DOI: 10.1002/prot.25861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 11/05/2022]
Abstract
As it forms water-filled channel in the mitochondria outer membrane and diffuses essential metabolites such as NADH and ATP, the voltage-dependent anion channel (VDAC) protein family plays a central role in all eukaryotic cells. In comparison with their mammalian homologues, little is known about the structural and functional properties of plant VDACs. In the present contribution, one of the two VDACs isoforms of Solanum tuberosum, stVDAC36, has been successfully overexpressed and refolded by an in-house method, as demonstrated by the information on its secondary and tertiary structure gathered from circular dichroism and intrinsic fluorescence. Cross-linking and molecular modeling studies have evidenced the presence of dimers and tetramers, and they suggest the formation of an intermolecular disulfide bond between two stVDAC36 monomers. The pore-forming activity was also assessed by liposome swelling assays, indicating a typical pore diameter between 2.0 and 2.7 nm. Finally, insights about the ATP binding inside the pore are given by docking studies and electrostatic calculations.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, Belgium
| | - David Zanuy
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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13
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Hanozin E, Grifnée E, Gattuso H, Matagne A, Morsa D, Pauw ED. Covalent Cross-Linking as an Enabler for Structural Mass Spectrometry. Anal Chem 2019; 91:12808-12818. [PMID: 31490660 DOI: 10.1021/acs.analchem.9b02491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of studies referring to the structural elucidation of intact biomolecular systems using mass spectrometry techniques has gradually increased in the post-2000s literature topics. As part of native mass spectrometry, this domain capitalizes on the kinetic trapping of physiological folds in view of probing solution-like conformational properties of isolated molecules or complexes after their electrospray transfer to the gas phase. Despite its efficiency for a wide array of analytes, this approach is expected to be pushed to its limits when considering highly dynamic systems or when dealing with nonideal operating conditions. To circumvent these limitations, we challenge the adequacy of an original strategy based on cross-linkers to improve the gas-phase stability of isolated proteins and ensure the preservation of folded conformations when measuring with strong transmission voltages, by spraying from denaturing solvents, or trapping for extended periods of time. Tested on cytochrome c, myoglobin, and β-lactoglobulin cross-linked using BS3, we validated the process as structurally nonintrusive in solution using far-ultraviolet circular dichroism and unraveled the preservation of folded conformations showing better resilience to denaturation on cross-linked species using ion mobility. The resulting collision cross sections were found in agreement with the native fold, and a preservation of the proteins' secondary and tertiary structures was evidenced using molecular dynamics simulations. Our results provide new insights concerning the fate of electro-sprayed cross-linked conformers in the gas phase, while constituting promising evidence for the validation of this technique as part of future structural mass spectrometry workflows.
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14
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Neirinckx V, Hau AC, Schuster A, Fritah S, Tiemann K, Klein E, Nazarov PV, Matagne A, Szpakowska M, Meyrath M, Chevigné A, Schmidt MHH, Niclou SP. The soluble form of pan-RTK inhibitor and tumor suppressor LRIG1 mediates downregulation of AXL through direct protein-protein interaction in glioblastoma. Neurooncol Adv 2019; 1:vdz024. [PMID: 32642659 PMCID: PMC7212925 DOI: 10.1093/noajnl/vdz024] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Targeted approaches for inhibiting epidermal growth factor receptor (EGFR) and other receptor tyrosine kinases (RTKs) in glioblastoma (GBM) have led to therapeutic resistance and little clinical benefit, raising the need for the development of alternative strategies. Endogenous LRIG1 (Leucine-rich Repeats and ImmunoGlobulin-like domains protein 1) is an RTK inhibitory protein required for stem cell maintenance, and we previously demonstrated the soluble ectodomain of LRIG1 (sLRIG1) to potently inhibit GBM growth in vitro and in vivo. Methods Here, we generated a recombinant protein of the ectodomain of LRIG1 (sLRIG1) and determined its activity in various cellular GBM models including patient-derived stem-like cells and patient organoids. We used proliferation, adhesion, and invasion assays, and performed gene and protein expression studies. Proximity ligation assay and NanoBiT complementation technology were applied to assess protein-protein interactions. Results We show that recombinant sLRIG1 downregulates EGFRvIII but not EGFR, and reduces proliferation in GBM cells, irrespective of their EGFR expression status. We find that sLRIG1 targets and downregulates a wide range of RTKs, including AXL, and alters GBM cell adhesion. Mechanistically, we demonstrate that LRIG1 interferes with AXL but not with EGFR dimerization. Conclusions These results identify AXL as a novel sLRIG1 target and show that LRIG1-mediated RTK downregulation depends on direct protein interaction. The pan-RTK inhibitory activity of sLRIG1 warrants further investigation for new GBM treatment approaches.
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Affiliation(s)
- Virginie Neirinckx
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Ann-Christin Hau
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Anne Schuster
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Katja Tiemann
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Eliane Klein
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Petr V Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - André Matagne
- Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Martyna Szpakowska
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg, Germany
| | - Max Meyrath
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg, Germany
| | - Andy Chevigné
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg, Germany
| | - Mirko H H Schmidt
- Molecular Signal Transduction Laboratories, Institute for Microscopic Anatomy and Neurobiology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
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15
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De Franco S, Vandenameele J, Brans A, Verlaine O, Bendak K, Damblon C, Matagne A, Segal DJ, Galleni M, Mackay JP, Vandevenne M. Exploring the suitability of RanBP2-type Zinc Fingers for RNA-binding protein design. Sci Rep 2019; 9:2484. [PMID: 30792407 PMCID: PMC6384913 DOI: 10.1038/s41598-019-38655-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022] Open
Abstract
Transcriptomes consist of several classes of RNA that have wide-ranging but often poorly described functions and the deregulation of which leads to numerous diseases. Engineering of functionalized RNA-binding proteins (RBPs) could therefore have many applications. Our previous studies suggested that the RanBP2-type Zinc Finger (ZF) domain is a suitable scaffold to investigate the design of single-stranded RBPs. In the present work, we have analyzed the natural sequence specificity of various members of the RanBP2-type ZF family and characterized the interaction with their target RNA. Surprisingly, our data showed that natural RanBP2-type ZFs with different RNA-binding residues exhibit a similar sequence specificity and therefore no simple recognition code can be established. Despite this finding, different discriminative abilities were observed within the family. In addition, in order to target a long RNA sequence and therefore gain in specificity, we generated a 6-ZF array by combining ZFs from the RanBP2-type family but also from different families, in an effort to achieve a wider target sequence repertoire. We showed that this chimeric protein recognizes its target sequence (20 nucleotides), both in vitro and in living cells. Altogether, our results indicate that the use of ZFs in RBP design remains attractive even though engineering of specificity changes is challenging.
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Affiliation(s)
- Simona De Franco
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium
| | - Julie Vandenameele
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium
| | - Alain Brans
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium
| | - Olivier Verlaine
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium
| | - Katerina Bendak
- Children's Cancer Institute Lowy Cancer Research, Kensington, 2033, Australia
| | - Christian Damblon
- Laboratoire de Chimie Biologique Structurale (CBS), Département de Chimie, Université de Liège, Liège, 4000, Belgium
| | - André Matagne
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, 95616, USA
| | - Moreno Galleni
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, N.S.W, 2006, Australia
| | - Marylène Vandevenne
- InBioS-Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium.
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16
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Azarkan M, Feller G, Vandenameele J, Herman R, El Mahyaoui R, Sauvage E, Vanden Broeck A, Matagne A, Charlier P, Kerff F. Biochemical and structural characterization of a mannose binding jacalin-related lectin with two-sugar binding sites from pineapple (Ananas comosus) stem. Sci Rep 2018; 8:11508. [PMID: 30065388 PMCID: PMC6068142 DOI: 10.1038/s41598-018-29439-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 02/12/2018] [Accepted: 07/06/2018] [Indexed: 02/07/2023] Open
Abstract
A mannose binding jacalin-related lectin from Ananas comosus stem (AcmJRL) was purified and biochemically characterized. This lectin is homogeneous according to native, SDS-PAGE and N-terminal sequencing and the theoretical molecular mass was confirmed by ESI-Q-TOF-MS. AcmJRL was found homodimeric in solution by size-exclusion chromatography. Rat erythrocytes are agglutinated by AcmJRL while no agglutination activity is detected against rabbit and sheep erythrocytes. Hemagglutination activity was found more strongly inhibited by mannooligomannosides than by D-mannose. The carbohydrate-binding specificity of AcmJRL was determined in some detail by isothermal titration calorimetry. All sugars tested were found to bind with low affinity to AcmJRL, with Ka values in the mM range. In agreement with hemagglutination assays, the affinity increased from D-mannose to di-, tri- and penta-mannooligosaccharides. Moreover, the X-ray crystal structure of AcmJRL was obtained in an apo form as well as in complex with D-mannose and methyl-α-D-mannopyranoside, revealing two carbohydrate-binding sites per monomer similar to the banana lectin BanLec. The absence of a wall separating the two binding sites, the conformation of β7β8 loop and the hemagglutinating activity are reminiscent of the BanLec His84Thr mutant, which presents a strong anti-HIV activity in absence of mitogenic activity.
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Affiliation(s)
- Mohamed Azarkan
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070, Brussels, Belgium
| | - Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, Institute of Chemistry B6a, University of Liège, 4000, Liège, Belgium
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering-InBioS, Institut de Chimie B6, University of Liège, 4000, Liège, Belgium
| | - Raphaël Herman
- Laboratory of crystallography, Center for Protein Engineering-InBioS, B5a, University of Liège, 4000, Liège, Belgium
| | - Rachida El Mahyaoui
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070, Brussels, Belgium
| | - Eric Sauvage
- Laboratory of crystallography, Center for Protein Engineering-InBioS, B5a, University of Liège, 4000, Liège, Belgium
| | - Arnaud Vanden Broeck
- Laboratory of crystallography, Center for Protein Engineering-InBioS, B5a, University of Liège, 4000, Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering-InBioS, Institut de Chimie B6, University of Liège, 4000, Liège, Belgium
| | - Paulette Charlier
- Laboratory of crystallography, Center for Protein Engineering-InBioS, B5a, University of Liège, 4000, Liège, Belgium
| | - Frédéric Kerff
- Laboratory of crystallography, Center for Protein Engineering-InBioS, B5a, University of Liège, 4000, Liège, Belgium.
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Dahmane I, Montagner C, Matagne A, Dumbre S, Herdewijn P, Terrak M. Peptidoglycan glycosyltransferase-ligand binding assay based on tryptophan fluorescence quenching. Biochimie 2018; 152:1-5. [PMID: 29909047 DOI: 10.1016/j.biochi.2018.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/13/2018] [Indexed: 11/28/2022]
Abstract
Peptidoglycan glycosyltransferases (GTase) of family 51 are essential enzymes for the synthesis of the glycan chains of the bacterial cell wall. They are considered potential antibacterial target, but discovery of inhibitors was hampered so far by the lack of efficient and affordable screening assay. Here we used Staphylococcus aureus MtgA to introduce a single tryptophan reporter residue in selected positions flanking the substrates binding cavity of the protein. We selected a mutant (Y181W) that shows strong fluorescence quenching in the presence of moenomycin A and two lipid II analogs inhibitors. The assay provides a simple method to study GTase-ligand interactions and can be used as primary high throughput screening of GTase inhibitors without the need for lipid II substrate or reporter ligands.
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Affiliation(s)
- Ismahene Dahmane
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium
| | - Caroline Montagner
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium
| | - André Matagne
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium
| | - Shrinivas Dumbre
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines-InBioS, University of Liège, B6a, Quartier Agora, Allée du six Août 11, 4000, Liège 1, Belgium.
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18
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Dalla Serra M, Gilbert RJC, Matagne A, England P. Biophysical Approaches to Protein Folding and Disease, a satellite meeting to the IUPAB-EBSA congress. Eur Biophys J 2018; 47:95-96. [PMID: 29480327 DOI: 10.1007/s00249-018-1288-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Mauro Dalla Serra
- CNR-Institute of Biophysics, Via alla Cascata, 56, 38123, Trento, Italy
| | - Robert J C Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| | - André Matagne
- Centre for Protein Engineering, Department of Life Sciences, Institut de Chimie B6, Allée de la Chimie, 3, University of Liège, 4000, Liège (Sart-Tilman), Belgium
| | - Patrick England
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75015, Paris, France
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19
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Roussel G, Caudano Y, Matagne A, Sansom MS, Perpète EA, Michaux C. Peptide-surfactant interactions: A combined spectroscopic and molecular dynamics simulation approach. Spectrochim Acta A Mol Biomol Spectrosc 2018; 190:464-470. [PMID: 28961531 DOI: 10.1016/j.saa.2017.09.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 05/08/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
In the present contribution, we report a combined spectroscopic and computational approach aiming to unravel at atomic resolution the effect of the anionic SDS detergent on the structure of two model peptides, the α-helix TrpCage and the β-stranded TrpZip. A detailed characterization of the specific amino acids involved is performed. Monomeric (single molecules) and micellar SDS species differently interact with the α-helix and β-stranded peptides, emphasizing the different mechanisms occurring below and above the critical aggregation concentration (CAC). Below the CAC, the α-helix peptide is fully unfolded, losing its hydrophobic core and its Asp-Arg salt bridge, while the β-stranded peptide keeps its native structure with its four Trp well oriented. Above the CAC, the SDS micelles have the same effect on both peptides, that is, destabilizing the tertiary structure while keeping their secondary structure. Our studies will be helpful to deepen our understanding of the action of the denaturant SDS on peptides and proteins.
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Affiliation(s)
- Guillaume Roussel
- Department of Physiology and Biophysics, University of California, D340 Medical Sciences I, Irvine, CA 92697-4560, USA
| | - Yves Caudano
- Research Centre in Physics of Matter and Radiation (PMR), University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institut de Chimie B6, University of Liège, Belgium
| | - Mark S Sansom
- Department of Biochemistry, University of Oxford, South Park Road, OX13QU Oxford, United Kingdom
| | - Eric A Perpète
- Laboratory of Physical Chemistry of Biomolecules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, 61, Rue de Bruxelles, 5000 Namur, Belgium
| | - Catherine Michaux
- Laboratory of Physical Chemistry of Biomolecules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, 61, Rue de Bruxelles, 5000 Namur, Belgium.
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20
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Matagne A, Bolle L, El Mahyaoui R, Baeyens-Volant D, Azarkan M. The proteolytic system of pineapple stems revisited: Purification and characterization of multiple catalytically active forms. Phytochemistry 2017; 138:29-51. [PMID: 28238440 DOI: 10.1016/j.phytochem.2017.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 10/12/2016] [Revised: 01/31/2017] [Accepted: 02/15/2017] [Indexed: 06/06/2023]
Abstract
Crude pineapple proteases extract (aka stem bromelain; EC 3.4.22.4) is an important proteolytic mixture that contains enzymes belonging to the cysteine proteases of the papain family. Numerous studies have been reported aiming at the fractionation and characterization of the many molecular species present in the extract, but more efforts are still required to obtain sufficient quantities of the various purified protease forms for detailed physicochemical, enzymatic and structural characterization. In this work, we describe an efficient strategy towards the purification of at least eight enzymatic forms. Thus, following rapid fractionation on a SP-Sepharose FF column, two sub-populations with proteolytic activity were obtained: the unbound (termed acidic) and bound (termed basic) bromelain fractions. Following reversible modification with monomethoxypolyethylene glycol (mPEG), both fractions were further separated on Q-Sepharose FF and SP-Sepharose FF, respectively. This procedure yielded highly purified molecular species, all titrating ca. 1 mol of thiol group per mole of enzyme, with distinct biochemical properties. N-terminal sequencing allowed identifying at least eight forms with proteolytic activity. The basic fraction contained previously identified species, i.e. basic bromelain forms 1 and 2, ananain forms 1 and 2, and comosain (MEROPS identifier: C01.027). Furthermore, a new proteolytic species, showing similarities with basic bomelain forms 1 and 2, was discovered and termed bromelain form 3. The two remaining species were found in the acidic bromelain fraction and were arbitrarily named acidic bromelain forms 1 and 2. Both, acidic bromelain forms 1, 2 and basic bromelain forms 1, 2 and 3 are glycosylated, while ananain forms 1 and 2, and comosain are not. The eight protease forms display different amidase activities against the various substrates tested, namely small synthetic chromogenic compounds (DL-BAPNA and Boc-Ala-Ala-Gly-pNA), fluorogenic compounds (like Boc-Gln-Ala-Arg-AMC, Z-Arg-Arg-AMC and Z-Phe-Arg-AMC), and proteins (azocasein and azoalbumin), suggesting a specific organization of their catalytic residues. All forms are completely inhibited by specific cysteine and cysteine/serine protease inhibitors, but not by specific serine and aspartic protease inhibitors, with the sole exception of pepstatin A that significantly affects acidic bromelain forms 1 and 2. For all eight protease forms, inhibition is also observed with 1,10-phenanthrolin, a metalloprotease inhibitor. Metal ions (i.e. Mn2+, Mg2+ and Ca2+) showed various effects depending on the protease under consideration, but all of them are totally inhibited in the presence of Zn2+. Mass spectrometry analyses revealed that all forms have a molecular mass of ca. 24 kDa, which is characteristic of enzymes belonging to the papain-like proteases family. Far-UV CD spectra analysis further supported this analysis. Interestingly, secondary structure calculation proves to be highly reproducible for all cysteine proteases of the papain family tested so far (this work; see also Azarkan et al., 2011; Baeyens-Volant et al., 2015) and thus can be used as a test for rapid identification of the classical papain fold.
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Affiliation(s)
- André Matagne
- Université de Liège, Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Liège, Belgium
| | - Laetitia Bolle
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium
| | - Rachida El Mahyaoui
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium
| | - Danielle Baeyens-Volant
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium
| | - Mohamed Azarkan
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium
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21
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Chevigné A, Campizi V, Szpakowska M, Bourry D, Dumez ME, Martins JC, Matagne A, Galleni M, Jacquet A. The Lys-Asp-Tyr Triad within the Mite Allergen Der p 1 Propeptide Is a Critical Structural Element for the pH-Dependent Initiation of the Protease Maturation. Int J Mol Sci 2017; 18:ijms18051087. [PMID: 28531096 PMCID: PMC5454996 DOI: 10.3390/ijms18051087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022] Open
Abstract
The major house dust mite allergen, Der p 1, is a papain-like cysteine protease expressed as an inactive precursor, proDer p 1, carrying an N-terminal propeptide with a unique structure. The maturation of the zymogen into an enzymatically-active form of Der p 1 is a multistep autocatalytic process initiated under acidic conditions through conformational changes of the propeptide, leading to the loss of its inhibitory ability and its subsequent gradual cleavage. The aims of this study were to characterize the residues present in the Der p 1 propeptide involved in the initiation of the zymogen maturation process, but also to assess the impact of acidic pH on the propeptide structure, the activity of Der p 1 and the fate of the propeptide. Using various complementary enzymatic and structural approaches, we demonstrated that a structural triad K17p-D51p-Y19p within the N-terminal domain of the propeptide is essential for its stabilization and the sensing of pH changes. Particularly, the protonation of D51p under acidic conditions unfolds the propeptide through disruption of the K17p-D51p salt bridge, reduces its inhibition capacity and unmasks the buried residues K17p and Y19p constituting the first maturation cleavage site of the zymogen. Our results also evidenced that this triad acts in a cooperative manner with other propeptide pH-responsive elements, including residues E56p and E80p, to promote the propeptide unfolding and/or to facilitate its proteolysis. Furthermore, we showed that acidic conditions modify Der p 1 proteolytic specificity and confirmed that the formation of the first intermediate represents the limiting step of the in vitro Der p 1 maturation process. Altogether, our results provide new insights into the early events of the mechanism of proDer p 1 maturation and identify a unique structural triad acting as a stabilizing and a pH-sensing regulatory element.
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Affiliation(s)
- Andy Chevigné
- Macromolécules Biologiques, Centre for Protein Engineering, University of Liège, B-4000 Liège, Belgium.
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg.
| | - Vincenzo Campizi
- Macromolécules Biologiques, Centre for Protein Engineering, University of Liège, B-4000 Liège, Belgium.
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg.
| | - Martyna Szpakowska
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg.
| | - David Bourry
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium.
| | - Marie-Eve Dumez
- Macromolécules Biologiques, Centre for Protein Engineering, University of Liège, B-4000 Liège, Belgium.
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg.
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium.
| | - André Matagne
- Laboratoire d'Enzymologie, Centre for Protein Engineering, University of Liège, B-4000 Liège, Belgium.
| | - Moreno Galleni
- Macromolécules Biologiques, Centre for Protein Engineering, University of Liège, B-4000 Liège, Belgium.
| | - Alain Jacquet
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
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22
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Abstract
We propose in this paper that protein microarrays could be analysed by infrared imaging in place of enzymatic or fluorescence labelling.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics
- Laboratory for the Structure and Function of Biological Membranes
- Campus Plaine CP206/02
- Université Libre de Bruxelles CP206/2
- B1050 Brussels
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding
- Centre for Protein Engineering
- University of Liège
- 4000 Liège
- Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding
- Centre for Protein Engineering
- University of Liège
- 4000 Liège
- Belgium
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics
- Laboratory for the Structure and Function of Biological Membranes
- Campus Plaine CP206/02
- Université Libre de Bruxelles CP206/2
- B1050 Brussels
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23
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Figueroa M, Vandenameele J, Goormaghtigh E, Valerio-Lepiniec M, Minard P, Matagne A, Van de Weerdt C. Biophysical characterization data of the artificial protein Octarellin V.1 and binding test with its X-ray helpers. Data Brief 2016; 8:1221-6. [PMID: 27547801 PMCID: PMC4982917 DOI: 10.1016/j.dib.2016.07.036] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/01/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
The artificial protein Octarellin V.1 (http://dx.doi.org/10.1016/j.jsb.2016.05.004[1]) was obtained through a direct evolution process over the de novo designed Octarellin V (http://dx.doi.org/10.1016/S0022-2836(02)01206-8[2]). The protein has been characterized by circular dichroism and fluorescence techniques, in order to obtain data related to its thermo and chemical stability. Moreover, the data for the secondary structure content studied by circular dichroism and infra red techniques is reported for the Octarellin V and V.1. Two crystallization helpers, nanobodies (http://dx.doi.org/10.1038/nprot.2014.039[3]) and αRep (http://dx.doi.org/10.1016/j.jmb.2010.09.048[4]), have been used to create stable complexes. Here we present the data obtained of the binding characterization of the Octarellin V.1 with the crystallization helpers by isothermal titration calorimetry.
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Affiliation(s)
- Maximiliano Figueroa
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium; Biochemistry and Molecular Biology Department, University of Concepcion, Concepción, Chile
| | - Julie Vandenameele
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Cécile Van de Weerdt
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
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24
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Jourdan S, Francis IM, Kim MJ, Salazar JJC, Planckaert S, Frère JM, Matagne A, Kerff F, Devreese B, Loria R, Rigali S. The CebE/MsiK Transporter is a Doorway to the Cello-oligosaccharide-mediated Induction of Streptomyces scabies Pathogenicity. Sci Rep 2016; 6:27144. [PMID: 27250236 PMCID: PMC4890002 DOI: 10.1038/srep27144] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/16/2016] [Indexed: 11/15/2022] Open
Abstract
Streptomyces scabies is an economically important plant pathogen well-known for damaging root and tuber crops by causing scab lesions. Thaxtomin A is the main causative agent responsible for the pathogenicity of S. scabies and cello-oligosaccharides are environmental triggers that induce the production of this phytotoxin. How cello-oligosaccharides are sensed or transported in order to induce the virulent behavior of S. scabies? Here we report that the cellobiose and cellotriose binding protein CebE, and MsiK, the ATPase providing energy for carbohydrates transport, are the protagonists of the cello-oligosaccharide mediated induction of thaxtomin production in S. scabies. Our work provides the first example where the transport and not the sensing of major constituents of the plant host is the central mechanism associated with virulence of the pathogen. Our results allow to draw a complete pathway from signal transport to phytotoxin production where each step of the cascade is controlled by CebR, the cellulose utilization regulator. We propose the high affinity of CebE to cellotriose as possible adaptation of S. scabies to colonize expanding plant tissue. Our work further highlights how genes associated with primary metabolism in nonpathogenic Streptomyces species have been recruited as basic elements of virulence in plant pathogenic species.
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Affiliation(s)
- Samuel Jourdan
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - Isolde Maria Francis
- Department of Biology, California State University Bakersfield, Bakersfield, CA 93311-1022, USA
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0180, USA
| | - Min Jung Kim
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0180, USA
| | - Joren Jeico C. Salazar
- Department of Biology, California State University Bakersfield, Bakersfield, CA 93311-1022, USA
| | - Sören Planckaert
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Jean-Marie Frère
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - André Matagne
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - Frédéric Kerff
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Rosemary Loria
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0180, USA
| | - Sébastien Rigali
- Centre for Protein Engineering, Integrative Biological Sciences (InBioS) Research Unit, University of Liège, Institut de Chimie B6a, B-4000, Liège, Belgium
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25
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Montagner C, Nigen M, Jacquin O, Willet N, Dumoulin M, Karsisiotis AI, Roberts GCK, Damblon C, Redfield C, Matagne A. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase. J Biol Chem 2016; 291:16124-37. [PMID: 27235401 DOI: 10.1074/jbc.m116.719005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 03/03/2016] [Indexed: 11/06/2022] Open
Abstract
Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate-binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (ΔG(0)) of 32 ± 2 kJ·mol(-1) For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site, and the protein displays a well organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. Two-dimensional NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ΔG(0) value of 65 ± 1.4 kJ·mol(-1) These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well defined conformation for both active site loops to maintain enzymatic activity.
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Affiliation(s)
- Caroline Montagner
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Michaël Nigen
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Olivier Jacquin
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Nicolas Willet
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Mireille Dumoulin
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Andreas Ioannis Karsisiotis
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Gordon C K Roberts
- the Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom, and
| | - Christian Damblon
- Département de Chimie, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Christina Redfield
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - André Matagne
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
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26
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Michaux C, Roussel G, Lopes-Rodrigues M, Matagne A, Perpète E. Unravelling the mechanisms of a protein refolding process based on the association of detergents and co-solvents. J Pept Sci 2016; 22:485-91. [DOI: 10.1002/psc.2893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 02/03/2023]
Affiliation(s)
- C. Michaux
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| | - G. Roussel
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| | - M. Lopes-Rodrigues
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
| | - A. Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institut de Chimie B6; University of Liège; 7 Place du 20 août 4000 Liège Belgium
| | - E.A. Perpète
- Laboratory of Physical Chemistry of Biomolecules, Chemistry Department; University of Namur; 61 rue de Bruxelles 5000 Namur Belgium
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27
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Figueroa M, Sleutel M, Vandevenne M, Parvizi G, Attout S, Jacquin O, Vandenameele J, Fischer AW, Damblon C, Goormaghtigh E, Valerio-Lepiniec M, Urvoas A, Durand D, Pardon E, Steyaert J, Minard P, Maes D, Meiler J, Matagne A, Martial JA, Van de Weerdt C. The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools. J Struct Biol 2016; 195:19-30. [PMID: 27181418 DOI: 10.1016/j.jsb.2016.05.004] [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: 02/15/2016] [Revised: 04/19/2016] [Accepted: 05/12/2016] [Indexed: 12/26/2022]
Abstract
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.
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Affiliation(s)
- Maximiliano Figueroa
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
| | - Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marylene Vandevenne
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Gregory Parvizi
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Sophie Attout
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Olivier Jacquin
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Julie Vandenameele
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Axel W Fischer
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Joseph A Martial
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Cécile Van de Weerdt
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
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28
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Baeyens-Volant D, Matagne A, El Mahyaoui R, Wattiez R, Azarkan M. A novel form of ficin from Ficus carica latex: Purification and characterization. Phytochemistry 2015; 117:154-167. [PMID: 26083455 DOI: 10.1016/j.phytochem.2015.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 10/09/2014] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 05/28/2023]
Abstract
A novel ficin form, named ficin E, was purified from fig tree latex by a combination of cation-exchange chromatography on SP-Sepharose Fast Flow, Thiopropyl Sepharose 4B and fplc-gel filtration chromatography. The new ficin appeared not to be sensitive to thiol derivatization by a polyethylene glycol derivative, allowing its purification. The protease is homogeneous according to PAGE, SDS-PAGE, mass spectrometry, N-terminal micro-sequencing analyses and E-64 active site titration. N-terminal sequencing of the first ten residues has shown high identity with the other known ficin (iso)forms. The molecular weight was found to be (24,294±10)Da by mass spectrometry, a lower value than the apparent molecular weight observed on SDS-PAGE, around 27 kDa. Far-UV CD data revealed a secondary structure content of 22% α-helix and 26% β-sheet. The protein is not glycosylated as shown by carbohydrate analysis. pH and temperature measurements indicated maxima activity at pH 6.0 and 50 °C, respectively. Preliminary pH stability analyses have shown that the protease conserved its compact structure in slightly acidic, neutral and alkaline media but at acidic pH (<3), the formation of some relaxed or molten state was evidenced by 8-anilino-1-naphtalenesulfonic acid binding characteristics. Comparison with the known ficins A, B, C, D1 and D2 (iso)forms revealed that ficin E showed activity profile that looked like ficin A against two chromogenic substrates while it resembled ficins D1 and D2 against three fluorogenic substrates. Enzymatic activity of ficin E was not affected by Mg(2+), Ca(2+) and Mn(2+) at a concentration up to 10mM. However, the activity was completely suppressed by Zn(2+) at a concentration of 1mM. Inhibitory activity measurements clearly identified the enzyme as a cysteine protease, being unaffected by synthetic (Pefabloc SC, benzamidine) and by natural proteinaceous (aprotinin) serine proteases inhibitors, by aspartic proteases inhibitors (pepstatin A) and by metallo-proteases inhibitors (EDTA, EGTA). Surprisingly, it was well affected by the metallo-protease inhibitor o-phenanthroline. The enzymatic activity was however completely blocked by cysteine proteases inhibitors (E-64, iodoacetamide), by thiol-blocking compounds (HgCl2) and by cysteine/serine proteases inhibitors (TLCK and TPCK). This is a novel ficin form according to peptide mass fingerprint analysis, specific amidase activity, SDS-PAGE and PAGE electrophoretic mobility, N-terminal sequencing and unproneness to thiol pegylation.
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Affiliation(s)
- Danielle Baeyens-Volant
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium
| | - André Matagne
- University of Liège, Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Liège, Belgium
| | - Rachida El Mahyaoui
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium
| | - Ruddy Wattiez
- University of Mons-Hainaut, Faculty of Sciences, Department of Proteomics and Microbiology, Interdisciplinary Center of Mass Spectrometry (CISMa), Mons, Belgium
| | - Mohamed Azarkan
- Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 route de Lennik, 1070 Brussels, Belgium.
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Bury D, Dahmane I, Derouaux A, Dumbre S, Herdewijn P, Matagne A, Breukink E, Mueller-Seitz E, Petz M, Terrak M. Positive cooperativity between acceptor and donor sites of the peptidoglycan glycosyltransferase. Biochem Pharmacol 2014; 93:141-50. [PMID: 25462814 DOI: 10.1016/j.bcp.2014.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 12/01/2022]
Abstract
The glycosyltransferases of family 51 (GT51) catalyze the polymerization of lipid II to form linear glycan chains, which, after cross linking by the transpeptidases, form the net-like peptidoglycan macromolecule. The essential function of the GT makes it an attractive antimicrobial target; therefore a better understanding of its function and its mechanism of interaction with substrates could help in the design and the development of new antibiotics. In this work, we have used a surface plasmon resonance Biacore(®) biosensor, based on an amine derivative of moenomycin A immobilized on a sensor chip surface, to investigate the mechanism of binding of substrate analogous inhibitors to the GT. Addition of increasing concentrations of moenomycin A to the Staphylococcus aureus MtgA led to reduced binding of the protein to the sensor chip as expected. Remarkably, in the presence of low concentrations of the most active disaccharide inhibitors, binding of MtgA to immobilized moenomycin A was found to increase; in contrast competition with moenomycin A occurred only at high concentrations. This finding suggests that at low concentrations, the lipid II analogs bind to the acceptor site and induce a cooperative binding of moenomycin A to the donor site. Our results constitute the first indication of the existence of a positive cooperativity between the acceptor and the donor sites of peptidoglycan GTs. In addition, our study indicates that a modification of two residues (L119N and F120S) within the hydrophobic region of MtgA can yield monodisperse forms of the protein with apparently no change in its secondary structure content, but this is at the expense of the enzyme function.
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Affiliation(s)
- Daniel Bury
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany.
| | - Ismahene Dahmane
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Shrinivas Dumbre
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - André Matagne
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Erika Mueller-Seitz
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany
| | - Michael Petz
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium.
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Leclercq K, Matagne A, Kaminski RM. Low potency and limited efficacy of antiepileptic drugs in the mouse 6 Hz corneal kindling model. Epilepsy Res 2014; 108:675-83. [PMID: 24661426 DOI: 10.1016/j.eplepsyres.2014.02.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [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: 06/06/2013] [Revised: 02/10/2014] [Accepted: 02/23/2014] [Indexed: 01/03/2023]
Abstract
Corneal kindling is a useful alternative to electrically induced amygdala or hippocampal kindling, which requires advanced surgical and EEG techniques that may not be easily available in many laboratories. Therefore the first aim of this study was to evaluate whether repeated 6 Hz corneal stimulation in mice would lead to an increased and persistent seizure response as described for higher frequency (50/60 Hz) corneal kindling. Male NMRI mice stimulated twice daily (except weekends) for 3 s with 6 Hz electrical current at 44 mA displayed robust kindling development, i.e., a progressive increase in seizure severity. The majority of the animals (about 90%) developed a fully kindled state, defined as at least 10 consecutive stage 3-5 seizures within 5 weeks of corneal stimulation. Afterwards, the fully kindled state was maintained for at least 8 weeks with only two days of stimulations per week. Next, the protective efficacy of four mechanistically different antiepileptic drugs (AEDs; clonazepam, valproate, carbamazepine and levetiracetam) was assessed and compared between 6 Hz and 50 Hz fully kindled mice. All tested AEDs showed a relatively lower potency in the 6 Hz kindling model and a limited efficacy against partial seizures was observed with carbamazepine and levetiracetam. We can conclude that 6 Hz kindling may be more advantageous than the previously described 50/60 Hz corneal kindling models due to its robustness and persistence of the fully kindled state. Furthermore, the observed low potency and limited efficacy of AEDs in 6 Hz fully kindled mice suggest that this model could be a useful tool in the discovery of novel AEDs targeting treatment resistant epilepsy.
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Affiliation(s)
- K Leclercq
- Neuroscience TA, UCB Pharma, Braine-l'Alleud, Belgium
| | - A Matagne
- Neuroscience TA, UCB Pharma, Braine-l'Alleud, Belgium
| | - R M Kaminski
- Neuroscience TA, UCB Pharma, Braine-l'Alleud, Belgium.
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31
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De Genst E, Chan PH, Pardon E, Hsu STD, Kumita JR, Christodoulou J, Menzer L, Chirgadze DY, Robinson CV, Muyldermans S, Matagne A, Wyns L, Dobson CM, Dumoulin M. A nanobody binding to non-amyloidogenic regions of the protein human lysozyme enhances partial unfolding but inhibits amyloid fibril formation. J Phys Chem B 2013; 117:13245-13258. [PMID: 23919586 DOI: 10.1021/jp403425z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the effects of the interaction of two camelid antibody fragments, generally called nanobodies, namely cAb-HuL5 and a stabilized and more aggregation-resistant variant cAb-HuL5G obtained by protein engineering, on the properties of two amyloidogenic variants of human lysozyme, I56T and D67H, whose deposition in vital organs including the liver, kidney, and spleen is associated with a familial non-neuropathic systemic amyloidosis. Both NMR spectroscopy and X-ray crystallographic studies reveal that cAb-HuL5 binds to the α-domain, one of the two lobes of the native lysozyme structure. The binding of cAb-HuL5/cAb-HuL5G strongly inhibits fibril formation by the amyloidogenic variants; it does not, however, suppress the locally transient cooperative unfolding transitions, characteristic of these variants, in which the β-domain and the C-helix unfold and which represents key early intermediate species in the formation of amyloid fibrils. Therefore, unlike two other nanobodies previously described, cAb-HuL5/cAb-HuL5G does not inhibit fibril formation via the restoration of the global cooperativity of the native structure of the lysozyme variants to that characteristic of the wild-type protein. Instead, it inhibits a subsequent step in the assembly of the fibrils, involving the unfolding and structural reorganization of the α-domain. These results show that nanobodies can protect against the formation of pathogenic aggregates at different stages in the structural transition of a protein from the soluble native state into amyloid fibrils, illustrating their value as structural probes to study the molecular mechanisms of amyloid fibril formation. Combined with their amenability to protein engineering techniques to improve their stability and solubility, these findings support the suggestion that nanobodies can potentially be developed as therapeutics to combat protein misfolding diseases.
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Affiliation(s)
- Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pak-Ho Chan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P.R. China
| | - Els Pardon
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.,Laboratory of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Shang-Te D Hsu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.,Institute of Biological Chemistry, Academia Sinica, No 128, Section 2, Academia Road, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, No 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Janet R Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Gower Street, London WC1E 6BT, U.K
| | - Linda Menzer
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
| | - Dimitri Y Chirgadze
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
| | - Serge Muyldermans
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.,Research Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
| | - Lode Wyns
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.,Laboratory of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
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Dumez ME, Herman J, Campisi V, Bouaziz A, Rosu F, Luxen A, Vandenberghe I, de Pauw E, Frère JM, Matagne A, Chevigné A, Galleni M. The proline-rich motif of the proDer p 3 allergen propeptide is crucial for protease-protease interaction. PLoS One 2013; 8:e68014. [PMID: 24073192 PMCID: PMC3779199 DOI: 10.1371/journal.pone.0068014] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/24/2013] [Indexed: 11/19/2022] Open
Abstract
The majority of proteases are synthesized in an inactive form, termed zymogen, which consists of a propeptide and a protease domain. The propeptide is commonly involved in the correct folding and specific inhibition of the enzyme. The propeptide of the house dust mite allergen Der p 3, NPILPASPNAT, contains a proline-rich motif (PRM), which is unusual for a trypsin-like protease. By truncating the propeptide or replacing one or all of the prolines in the non-glycosylated zymogen with alanine(s), we demonstrated that the full-length propeptide is not required for correct folding and thermal stability and that the PRM is important for the resistance of proDer p 3 to undesired proteolysis when the protein is expressed in Pichia pastoris. Additionally, we followed the maturation time course of proDer p 3 by coupling a quenched-flow assay to mass spectrometry analysis. This approach allowed to monitor the evolution of the different species and to determine the steady-state kinetic parameters for activation of the zymogen by the major allergen Der p 1. This experiment demonstrated that prolines 5 and 8 are crucial for proDer p 3-Der p 1 interaction and for activation of the zymogen.
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Affiliation(s)
- Marie-Eve Dumez
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
| | - Julie Herman
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
| | - Vincenzo Campisi
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
- Laboratoire de Rétrovirologie, Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Ahlem Bouaziz
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
| | - Frédéric Rosu
- Laboratoire de spectrométrie de masse (L.S.M.), GIGA-R, Université de Liège, Liège, Belgium
| | - André Luxen
- Centre de Recherches du cyclotron, Université de Liège, Liège, Belgium
| | - Isabel Vandenberghe
- Laboratory for Protein Biochemistry and Protein Engineering, K.L. Ledeganckstraat 35B, Gent, Belgium
| | - Edwin de Pauw
- Laboratoire de spectrométrie de masse (L.S.M.), GIGA-R, Université de Liège, Liège, Belgium
| | - Jean-Marie Frère
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
- Laboratoire d'enzymologie et repliement des protéines, Centre for Protein Engineering, Université de Liège, Liège, Belgium
| | - André Matagne
- Laboratoire d'enzymologie et repliement des protéines, Centre for Protein Engineering, Université de Liège, Liège, Belgium
| | - Andy Chevigné
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
- Laboratoire de Rétrovirologie, Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Moreno Galleni
- Macromolécules Biologiques, Centre for Protein Engineering, Université de Liège, Liège, Belgium
- * E-mail:
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Figueroa M, Oliveira N, Lejeune A, Kaufmann KW, Dorr BM, Matagne A, Martial JA, Meiler J, Van de Weerdt C. Octarellin VI: using rosetta to design a putative artificial (β/α)8 protein. PLoS One 2013; 8:e71858. [PMID: 23977165 PMCID: PMC3747059 DOI: 10.1371/journal.pone.0071858] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 07/10/2013] [Indexed: 11/22/2022] Open
Abstract
The computational protein design protocol Rosetta has been applied successfully to a wide variety of protein engineering problems. Here the aim was to test its ability to design de novo a protein adopting the TIM-barrel fold, whose formation requires about twice as many residues as in the largest proteins successfully designed de novo to date. The designed protein, Octarellin VI, contains 216 residues. Its amino acid composition is similar to that of natural TIM-barrel proteins. When produced and purified, it showed a far-UV circular dichroism spectrum characteristic of folded proteins, with α-helical and β-sheet secondary structure. Its stable tertiary structure was confirmed by both tryptophan fluorescence and circular dichroism in the near UV. It proved heat stable up to 70°C. Dynamic light scattering experiments revealed a unique population of particles averaging 4 nm in diameter, in good agreement with our model. Although these data suggest the successful creation of an artificial α/β protein of more than 200 amino acids, Octarellin VI shows an apparent noncooperative chemical unfolding and low solubility.
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Affiliation(s)
- Maximiliano Figueroa
- GIGA-Research, Molecular Biology and Genetic Engineering Unit, University of Liège, Liège, Belgium
| | - Nicolas Oliveira
- GIGA-Research, Molecular Biology and Genetic Engineering Unit, University of Liège, Liège, Belgium
| | - Annabelle Lejeune
- GIGA-Research, Molecular Biology and Genetic Engineering Unit, University of Liège, Liège, Belgium
| | - Kristian W. Kaufmann
- Departments of Chemistry and Pharmacology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brent M. Dorr
- Departments of Chemistry and Pharmacology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - André Matagne
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Joseph A. Martial
- GIGA-Research, Molecular Biology and Genetic Engineering Unit, University of Liège, Liège, Belgium
| | - Jens Meiler
- Departments of Chemistry and Pharmacology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Cécile Van de Weerdt
- GIGA-Research, Molecular Biology and Genetic Engineering Unit, University of Liège, Liège, Belgium
- * E-mail:
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Smith LJ, Bowen AM, Di Paolo A, Matagne A, Redfield C. The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations. Chembiochem 2013; 14:1780-8. [DOI: 10.1002/cbic.201300193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 11/09/2022]
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Tenconi E, Guichard P, Motte P, Matagne A, Rigali S. Use of red autofluorescence for monitoring prodiginine biosynthesis. J Microbiol Methods 2013; 93:138-43. [DOI: 10.1016/j.mimet.2013.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
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Struvay C, Negro S, Matagne A, Feller G. Energetics of Protein Stability at Extreme Environmental Temperatures in Bacterial Trigger Factors. Biochemistry 2013; 52:2982-90. [DOI: 10.1021/bi4002387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Caroline Struvay
- Laboratory of Biochemistry and ‡Laboratory of
Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart
Tilman, Belgium
| | - Sonia Negro
- Laboratory of Biochemistry and ‡Laboratory of
Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart
Tilman, Belgium
| | - André Matagne
- Laboratory of Biochemistry and ‡Laboratory of
Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart
Tilman, Belgium
| | - Georges Feller
- Laboratory of Biochemistry and ‡Laboratory of
Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart
Tilman, Belgium
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Roussel G, Perpète EA, Matagne A, Tinti E, Michaux C. Towards a universal method for protein refolding: The trimeric beta barrel membrane Omp2a as a test case. Biotechnol Bioeng 2012; 110:417-23. [DOI: 10.1002/bit.24722] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/09/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
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Roussel G, Matagne A, De Bolle X, Perpète E, Michaux C. Purification, refolding and characterization of the trimeric Omp2a outer membrane porin from Brucella melitensis. Protein Expr Purif 2012; 83:198-204. [DOI: 10.1016/j.pep.2012.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 03/29/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
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Scarafone N, Pain C, Fratamico A, Gaspard G, Yilmaz N, Filée P, Galleni M, Matagne A, Dumoulin M. Amyloid-like fibril formation by polyQ proteins: a critical balance between the polyQ length and the constraints imposed by the host protein. PLoS One 2012; 7:e31253. [PMID: 22438863 PMCID: PMC3305072 DOI: 10.1371/journal.pone.0031253] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 01/05/2012] [Indexed: 11/18/2022] Open
Abstract
Nine neurodegenerative disorders, called polyglutamine (polyQ) diseases, are characterized by the formation of intranuclear amyloid-like aggregates by nine proteins containing a polyQ tract above a threshold length. These insoluble aggregates and/or some of their soluble precursors are thought to play a role in the pathogenesis. The mechanism by which polyQ expansions trigger the aggregation of the relevant proteins remains, however, unclear. In this work, polyQ tracts of different lengths were inserted into a solvent-exposed loop of the β-lactamase BlaP and the effects of these insertions on the properties of BlaP were investigated by a range of biophysical techniques. The insertion of up to 79 glutamines does not modify the structure of BlaP; it does, however, significantly destabilize the enzyme. The extent of destabilization is largely independent of the polyQ length, allowing us to study independently the effects intrinsic to the polyQ length and those related to the structural integrity of BlaP on the aggregating properties of the chimeras. Only chimeras with 55Q and 79Q readily form amyloid-like fibrils; therefore, similarly to the proteins associated with diseases, there is a threshold number of glutamines above which the chimeras aggregate into amyloid-like fibrils. Most importantly, the chimera containing 79Q forms amyloid-like fibrils at the same rate whether BlaP is folded or not, whereas the 55Q chimera aggregates into amyloid-like fibrils only if BlaP is unfolded. The threshold value for amyloid-like fibril formation depends, therefore, on the structural integrity of the β-lactamase moiety and thus on the steric and/or conformational constraints applied to the polyQ tract. These constraints have, however, no significant effect on the propensity of the 79Q tract to trigger fibril formation. These results suggest that the influence of the protein context on the aggregating properties of polyQ disease-associated proteins could be negligible when the latter contain particularly long polyQ tracts.
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Affiliation(s)
- Natacha Scarafone
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Coralie Pain
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Anthony Fratamico
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Gilles Gaspard
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Nursel Yilmaz
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Patrice Filée
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Moreno Galleni
- Biological Macromolecules, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liège, Liège, Belgium
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Azarkan M, Matagne A, Wattiez R, Bolle L, Vandenameele J, Baeyens-Volant D. Selective and reversible thiol-pegylation, an effective approach for purification and characterization of five fully active ficin (iso)forms from Ficus carica latex. Phytochemistry 2011; 72:1718-1731. [PMID: 21665232 DOI: 10.1016/j.phytochem.2011.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 05/28/2023]
Abstract
The latex of Ficus carica constitutes an important source of many proteolytic components known under the general term of ficin (EC 3.4.22.3) which belongs to the cysteine proteases of the papain family. So far, no data on the purification and characterization of individual forms of these proteases are available. An effective strategy was used to fractionate and purify to homogeneity five ficin forms, designated A, B, C, D1 and D2 according to their sequence of elution from a cation-exchange chromatographic support. Following rapid fractionation on a SP-Sepharose Fast Flow column, the different ficin forms were chemically modified by a specific and reversible monomethoxypolyethylene glycol (mPEG) reagent. In comparison with their un-derivatized counterparts, the mPEG-protein derivatives behaved differently on the ion-exchanger, allowing us for the first time to obtain five highly purified ficin molecular species titrating 1mol of thiol group per mole of enzyme. The purified ficins were characterized by de novo peptide sequencing and peptide mass fingerprinting analyzes, using mass spectrometry. Circular dichroism measurements indicated that all five ficins were highly structured, both in term of secondary and tertiary structure. Furthermore, analysis of far-UV CD spectra allowed calculation of their secondary structural content. Both these data and the molecular masses determined by MS reinforce the view that the enzymes belong to the family of papain-like proteases. The five ficin forms also displayed different specific amidase activities against small synthetic substrates like dl-BAPNA and Boc-Ala-Ala-Gly-pNA, suggesting some differences in their active site organization. Enzymatic activity of the five ficin forms was completely inhibited by specific cysteine and cysteine/serine proteases inhibitors but was unaffected by specific serine, aspartic and metallo proteases inhibitors.
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Affiliation(s)
- Mohamed Azarkan
- Free University of Brussels, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, 1070 Brussels, Belgium.
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41
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Cipolla A, D'Amico S, Barumandzadeh R, Matagne A, Feller G. Stepwise adaptations to low temperature as revealed by multiple mutants of psychrophilic α-amylase from Antarctic Bacterium. J Biol Chem 2011; 286:38348-38355. [PMID: 21900238 DOI: 10.1074/jbc.m111.274423] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mutants Mut5 and Mut5CC from a psychrophilic α-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic α-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: compactness; kinetically driven stability; thermodynamic stability; resistance toward chemical denaturation, and the kinetics of unfolding/refolding. Concomitantly to this improved stability, both mutants have lost the kinetic optimization to low temperature activity displayed by the parent psychrophilic enzyme. These results provide strong experimental support to the hypothesis assuming that the disappearance of stabilizing interactions in psychrophilic enzymes increases the amplitude of concerted motions required by catalysis and the dynamics of active site residues at low temperature, leading to a higher activity.
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Affiliation(s)
- Alexandre Cipolla
- Laboratories of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Salvino D'Amico
- Laboratories of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Roya Barumandzadeh
- Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - André Matagne
- Enzymology and Protein Folding, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Georges Feller
- Laboratories of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium.
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42
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Vandevenne M, Gaspard G, Belgsir EM, Ramnath M, Cenatiempo Y, Marechal D, Dumoulin M, Frere JM, Matagne A, Galleni M, Filee P. Effects of monopropanediamino-β-cyclodextrin on the denaturation process of the hybrid protein BlaPChBD. Biochim Biophys Acta 2011; 1814:1146-53. [PMID: 21621654 DOI: 10.1016/j.bbapap.2011.05.007] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 05/08/2011] [Accepted: 05/09/2011] [Indexed: 11/27/2022]
Abstract
Irreversible accumulation of protein aggregates represents an important problem both in vivo and in vitro. The aggregation of proteins is of critical importance in a wide variety of biomedical situations, ranging from diseases (such as Alzheimer's and Parkinson's diseases) to the production (e.g. inclusion bodies), stability, storage and delivery of protein drugs. β-Cyclodextrin (β-CD) is a circular heptasaccharide characterized by a hydrophilic exterior and a hydrophobic interior ring structure. In this research, we studied the effects of a chemically modified β-CD (BCD07056), on the aggregating and refolding properties of BlaPChBD, a hybrid protein obtained by inserting the chitin binding domain of the human macrophage chitotriosidase into the class A β-lactamase BlaP from Bacillus licheniformis 749/I during its thermal denaturation. The results show that BCD07056 strongly increases the refolding yield of BlaPChBD after thermal denaturation and constitutes an excellent additive to stabilize the protein over time at room temperature. Our data suggest that BCD07056 acts early in the denaturation process by preventing the formation of an intermediate which leads to an aggregated state. Finally, the role of β-CD derivatives on the stability of proteins is discussed.
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Affiliation(s)
- Marylène Vandevenne
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, Sart-Tilman, Liège, Belgium.
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43
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Meersman F, Atilgan C, Miles AJ, Bader R, Shang W, Matagne A, Wallace BA, Koch MHJ. Consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics. Biophys J 2011; 99:2255-63. [PMID: 20923660 DOI: 10.1016/j.bpj.2010.07.060] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 07/15/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022] Open
Abstract
Synchrotron radiation circular dichroism, Fourier transform infrared, and nuclear magnetic resonance spectroscopies, and small-angle x-ray scattering were used to monitor the reversible thermal unfolding of hen egg white lysozyme. The results were compared with crystal structures and high- and low-temperature structures derived from molecular-dynamics calculations. The results of both experimental and computational methods indicate that the unfolding process starts with the loss of β-structures followed by the reversible loss of helix content from ∼40% at 20°C to 27% at 70°C and ∼20% at 77°C, beyond which unfolding becomes irreversible. Concomitantly there is a reversible increase in the radius of gyration of the protein from 15 Å to 18 Å. The reversible decrease in forward x-ray scattering demonstrates a lack of aggregation upon unfolding, suggesting the change is due to a larger dilation of hydration water than of bulk water. Molecular-dynamics simulations suggest a similar sequence of events and are in good agreement with the (1)H(N) chemical shift differences in nuclear magnetic resonance. This study demonstrates the power of complementary methods for elucidating unfolding/refolding processes and the nature of both the unfolded structure, for which there is no crystallographic data, and the partially unfolded forms of the protein that can lead to fibril formation and disease.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium.
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Vandenameele J, Matagne A, Damblon C. 1H, 13C and 15N backbone resonance assignments for the BS3 class A β-lactamase from Bacillus licheniformis. Biomol NMR Assign 2010; 4:195-197. [PMID: 20556551 DOI: 10.1007/s12104-010-9241-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 06/07/2010] [Indexed: 05/29/2023]
Abstract
Class A β-lactamases (260-280 amino acids; M ( r ) ~ 29,000) are among the largest proteins studied in term of their folding properties. They are composed of two structural domains: an all-α domain formed by five to eight helices and an α/β domain consisting of a five-stranded antiparallel β-sheet covered by three to four α-helices. The α domain (~150 residues) is made up of the central part of the polypeptide chain whereas the α/β domain (111-135 residues) is constituted by the N- and C-termini of the protein. Our goal is to determine in which order the different secondary structure elements are formed during the folding of BS3. With this aim, we will use pulse-labelling hydrogen/deuterium exchange experiments, in combination with 2D-NMR measurements, to monitor the time-course of formation and stabilization of secondary structure elements. Here we report the backbone resonance assignments as the requirement for further hydrogen/deuterium exchange studies.
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Affiliation(s)
- Julie Vandenameele
- Laboratoire d'Enzymologie et Repliement des protéines, Centre d'Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, 4000, Liège (Sart-Tilman), Belgium.
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Di Paolo A, Balbeur D, De Pauw E, Redfield C, Matagne A. Rapid collapse into a molten globule is followed by simple two-state kinetics in the folding of lysozyme from bacteriophage λ. Biochemistry 2010; 49:8646-57. [PMID: 20806781 DOI: 10.1021/bi101126f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stopped-flow fluorescence and circular dichroism spectroscopy have been used in combination with quenched-flow hydrogen exchange labeling, monitored by two-dimensional NMR and electrospray ionization mass spectrometry, to investigate the folding kinetics of lysozyme from bacteriophage λ (λ lysozyme) at pH 5.6, 20 °C. The first step in the folding of λ lysozyme occurs very rapidly (τ < 1 ms) after refolding is initiated and involves both hydrophobic collapse and formation of a high content of secondary structure but only weak protection from (1)H/(2)H exchange and no fixed tertiary structure organization. This early folding step is reflected in the dead-time events observed in the far-UV CD and ANS fluorescence experiments. Following accumulation of this kinetic molten globule species, the secondary structural elements are stabilized and the majority (ca. 88%) of refolding molecules acquire native-like properties in a highly cooperative two-state process, with τ = 0.15 ± 0.03 s. This is accompanied by the acquisition of substantial native-like protection from hydrogen exchange. A double-mixing experiment and the absence of a denaturant effect reveal that slow (τ = 5 ± 1 s) folding of the remaining (ca. 12%) molecules is rate limited by the cis/trans isomerization of prolines that are trans in the folded enzyme. In addition, native state hydrogen exchange and classical denaturant unfolding experiments have been used to characterize the thermodynamic properties of the enzyme. In good agreement with previous crystallographic evidence, our results show that λ lysozyme is a highly dynamic protein, with relatively low conformational stability (ΔG°(N-U) = 25 ± 2 kJ·mol(-1)).
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Affiliation(s)
- Alexandre Di Paolo
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
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46
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Detrait E, Leclercq K, Löscher W, Potschka H, Niespodziany I, Hanon E, Kaminski R, Matagne A, Lamberty Y. Brivaracetam does not alter spatial learning and memory in both normal and amygdala-kindled rats. Epilepsy Res 2010; 91:74-83. [DOI: 10.1016/j.eplepsyres.2010.06.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 06/25/2010] [Accepted: 06/29/2010] [Indexed: 11/29/2022]
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Chevigné A, Dumez ME, Dumoulin M, Matagne A, Jacquet A, Galleni M. Comparative study of mature and zymogen mite cysteine protease stability and pH unfolding. Biochim Biophys Acta Gen Subj 2010; 1800:937-45. [PMID: 20682463 DOI: 10.1016/j.bbagen.2010.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 05/14/2010] [Accepted: 05/24/2010] [Indexed: 11/26/2022]
Abstract
BACKGROUND Papain-like proteases (CA1) are synthesized as inactive precursors carrying an N-terminal propeptide, which is further removed under acidic conditions to generate active enzymes. METHODS To have a better insight into the mechanism of activation of this protease family, we compared the pH unfolding of the zymogen and the mature form of the mite cysteine protease Der p 1. RESULTS We showed that the presence of the propeptide does not significantly influence the pH-induced unfolding of the catalytic domain but does affect its fluorescence properties by modifying the exposure of the tryptophan 192 to the solvent. In addition, we demonstrated that the propeptide displays weaker pH stability than the protease domain confirming that the unfolding of the propeptide is the key event in the activation process of the zymogen. GENERAL SIGNIFICANCE Finally, we show, using thermal denaturation and enzymatic activity measurements, that whatever the pH value, the propeptide does not stabilize the structure of the catalytic domain but very interestingly, prevents its autolysis.
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Affiliation(s)
- Andy Chevigné
- Macromolécules Biologiques, Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, Sart Tilman Liège B-4000, Belgique
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48
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Vandenameele J, Lejeune A, Di Paolo A, Brans A, Frère JM, Schmid FX, Matagne A. Folding of Class A β-Lactamases Is Rate-Limited by Peptide Bond Isomerization and Occurs via Parallel Pathways. Biochemistry 2010; 49:4264-75. [DOI: 10.1021/bi100369d] [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: 11/29/2022]
Affiliation(s)
- Julie Vandenameele
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Annabelle Lejeune
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Alexandre Di Paolo
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Alain Brans
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Jean-Marie Frère
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - André Matagne
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
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49
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Di Paolo A, Duval V, Matagne A, Redfield C. Backbone 1H, 13C, and 15N resonance assignments for lysozyme from bacteriophage lambda. Biomol NMR Assign 2010; 4:111-114. [PMID: 20300891 PMCID: PMC2862172 DOI: 10.1007/s12104-010-9219-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/02/2010] [Indexed: 05/29/2023]
Abstract
Lysozyme from lambda bacteriophage (lambda lysozyme) is an 18 kDa globular protein displaying some of the structural features common to all lysozymes; in particular, lambda lysozyme consists of two structural domains connected by a helix, and has its catalytic residues located at the interface between these two domains. An interesting feature of lambda lysozyme, when compared to the well-characterised hen egg-white lysozyme, is its lack of disulfide bridges; this makes lambda lysozyme an interesting system for studies of protein folding. A comparison of the folding properties of lambda lysozyme and hen lysozyme will provide important insights into the role that disulfide bonds play in the refolding pathway of the latter protein. Here we report the (1)H, (13)C and (15)N backbone resonance assignments for lambda lysozyme by heteronuclear multidimensional NMR spectroscopy. These assignments provide the starting point for detailed investigation of the refolding pathway using pulse-labelling hydrogen/deuterium exchange experiments monitored by NMR.
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Affiliation(s)
- Alexandre Di Paolo
- Laboratoire d’Enzymologie et Repliement des protéines, Centre d’Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B4000 Liège (Sart-Tilman), Belgium
| | - Valérie Duval
- Laboratoire d’Enzymologie et Repliement des protéines, Centre d’Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B4000 Liège (Sart-Tilman), Belgium
| | - André Matagne
- Laboratoire d’Enzymologie et Repliement des protéines, Centre d’Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B4000 Liège (Sart-Tilman), Belgium
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU United Kingdom
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El Hajjaji H, Dumoulin M, Matagne A, Colau D, Roos G, Messens J, Collet JF. The zinc center influences the redox and thermodynamic properties of Escherichia coli thioredoxin 2. J Mol Biol 2008; 386:60-71. [PMID: 19073194 DOI: 10.1016/j.jmb.2008.11.046] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 11/19/2008] [Indexed: 11/27/2022]
Abstract
Thioredoxins are small, ubiquitous redox enzymes that reduce protein disulfide bonds by using a pair of cysteine residues present in a strictly conserved WCGPC catalytic motif. The Escherichia coli cytoplasm contains two thioredoxins, Trx1 and Trx2. Trx2 is special because it is induced under oxidative stress conditions and it has an additional N-terminal zinc-binding domain. We have determined the redox potential of Trx2, the pK(a) of the active site nucleophilic cysteine, as well as the stability of the oxidized and reduced form of the protein. Trx2 is more oxidizing than Trx1 (-221 mV versus -284 mV, respectively), which is in good agreement with the decreased value of the pK(a) of the nucleophilic cysteine (5.1 versus 7.1, respectively). The difference in stability between the oxidized and reduced forms of an oxidoreductase is the driving force to reduce substrate proteins. This difference is smaller for Trx2 (DeltaDeltaG degrees(H2O)=9 kJ/mol and DeltaT(m)=7. 4 degrees C) than for Trx1 (DeltaDeltaG degrees(H2O)=15 kJ/mol and DeltaT(m)=13 degrees C). Altogether, our data indicate that Trx2 is a significantly less reducing enzyme than Trx1, which suggests that Trx2 has a distinctive function. We disrupted the zinc center by mutating the four Zn(2+)-binding cysteines to serine. This mutant has a more reducing redox potential (-254 mV) and the pK(a) of its nucleophilic cysteine shifts from 5.1 to 7.1. The removal of Zn(2+) also decreases the overall stability of the reduced and oxidized forms by 3.2 kJ/mol and 5.8 kJ/mol, respectively. In conclusion, our data show that the Zn(2+)-center of Trx2 fine-tunes the properties of this unique thioredoxin.
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Affiliation(s)
- Hayat El Hajjaji
- de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
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