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5 results on '"Mathilde Bouakil"'

1. Extended disorder at the cell surface: The conformational landscape of the ectodomains of syndecans

Author

Frank Gondelaud, Mathilde Bouakil, Aurélien Le Fèvre, Adriana Erica Miele, Fabien Chirot, Bertrand Duclos, Adam Liwo, and Sylvie Ricard-Blum

Subjects
Syndecans, Intrinsically disordered proteins, Conformations, Cell-matrix interactions, Biology (General), QH301-705.5
Abstract

Syndecans are membrane proteoglycans regulating extracellular matrix assembly, cell adhesion and signaling. Their ectodomains can be shed from the cell surface, and act as paracrine and autocrine effectors or as competitors of full-length syndecans. We report the first biophysical characterization of the recombinant ectodomains of the four human syndecans using biophysical techniques, and show that they behave like flexible random-coil intrinsically disordered proteins, and adopt several conformation ensembles in solution. We have characterized their conformational landscapes using native mass spectrometry (MS) and ion-mobility MS, and demonstrated that the syndecan ectodomains explore the majority of their conformational landscape, from minor compact, globular-like, conformations to extended ones. We also report that the ectodomain of syndecan-4, corresponding to a natural isoform, is able to dimerize via a disulfide bond. We have generated a three-dimensional model of the C-terminus of this dimer, which supports the dimerization via a disulfide bond. Furthermore, we have mapped the NXIP adhesion motif of syndecans and their sequences involved in the formation of ternary complexes with integrins and growth factor receptors on the major conformations of their ectodomains, and shown that these sequences are not accessible in all the conformations, suggesting that only some of them are biologically active. Lastly, although the syndecan ectodomains have a far lower number of amino acid residues than their membrane partners, their intrinsic disorder and flexibility allow them to adopt extended conformations, which have roughly the same size as the cell surface receptors (e.g., integrins and growth factor receptors) they bind to.

Published
2021
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2. Photo-control of bimolecular reactions: reactivity of the long-lived Rhodamine 6G triplet excited state with ˙NO

Author

Luke MacAleese, Richard A. J. O'Hair, Bun Chan, Philippe Dugourd, Mathilde Bouakil, Spectrométrie des biomolécules et agrégats (SPECTROBIO), Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Nagasaki University, School of Chemistry [Melbourne], Faculty of Science [Melbourne], and University of Melbourne-University of Melbourne

Subjects
Reactive intermediate, education, General Physics and Astronomy, Nitric Oxide, 010402 general chemistry, Photochemistry, 01 natural sciences, Chemical reaction, Mass Spectrometry, Rhodamine 6G, Rhodamine, chemistry.chemical_compound, [SPI]Engineering Sciences [physics], Stepwise reaction, [CHIM]Chemical Sciences, Reactivity (chemistry), Singlet state, Physical and Theoretical Chemistry, Density Functional Theory, [PHYS]Physics [physics], Molecular Structure, Rhodamines, 010405 organic chemistry, Photochemical Processes, 0104 chemical sciences, chemistry, Excited state
Abstract

Photo-chemistry provides a non-intuitive but very powerful way to probe kinetically limited, sometimes thermodynamically non-favored reactions and, thus, access highly specific products. However, reactivity in the excited state is difficult to characterize directly, due to short lifetimes and challenges in controlling the reaction medium. Among photo-activatable reagents, rhodamine dyes find widespread uses due to a number of favorable properties including their high absorption coefficient. Their readily adaptable synthesis allows development of tailor-made dyes for specific applications. Remarkably, few studies have directly probed the chemical reactivity of their triplet excited state. Here we present a new conceptual approach to examine the specific chemistry of the triplet excited state. We have developed a pump (488 nm) – probe (600 nm) strategy to examine the gas-phase lifetime and reactivity of the triplet cation of Rhodamine 6G (3Rh6G+) in an ion trap mass spectrometer. The confounding effects of solvent, aggregation and formation of other reactive intermediates is thus avoided allowing fundamental reactivity to be explored. In the presence, in the ion trap, of helium seeded with 1% of nitric oxide (˙NO) (∼ 60 ion/˙NO collisions per second), the triplet lifetime is shortened from 1.9 s to 0.7 s. Simultaneously, the reaction products [Rh6G-H]˙+ and [Rh6G-H + NO]+ are observed. Reaction of 3Rh6G+ with ˙NO2 yields [Rh6G-H]˙+, [Rh6G-H + NO2]+ and [Rh6G-2H]+. None of these products are observed for the singlet, 1Rh6G+. DFT calculations suggest a stepwise mechanism only allowed from 3Rh6G+, in which H atom abstraction by ˙NOx (x = 1 or 2) yields [Rh6G-H]˙+ which, then, reacts with another ˙NOx molecule. This illustrates the power of light to initiate specific chemical reactions, and the relevance of gas-phase ion–molecule reaction approaches to understand stepwise reaction mechanism from specific excited states.

Published
2021
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3. Isolated Collagen Mimetic Peptide Assemblies Have Stable Triple-Helix Structures

Author

Clothilde Comby-Zerbino, Mathilde Bouakil, Fabien Chirot, Jean-Christophe Poully, Mathieu Lalande, Philippe Dugourd, Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Institut Lumière Matière [Villeurbanne] (ILM), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, ANABIO-MS - Analyse biomoléculaire par spectrométrie de masse - Biological Analysis by Mass Spectrometry, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), CNRS is acknowledged for funding through the French GDR EMIE. M.L. and J.C.P. thank the 'Region Normandie' for a Ph.D. grant and for funding through the IRHEMME project (agreement #15P02908-15P02909). The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Program (FP7/2007-2013 Grant agreement No. 320659)., European Project: 0320659(2003), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
collagen, Proline, Hydroxylation, 010402 general chemistry, 01 natural sciences, Protein Structure, Secondary, Catalysis, Hydroxyproline, chemistry.chemical_compound, Biomimetic Materials, Tandem Mass Spectrometry, triple helix, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Phase (matter), [CHIM]Chemical Sciences, Molecule, structure, Protein Stability, 010405 organic chemistry, Organic Chemistry, Hydrogen Bonding, Stereoisomerism, General Chemistry, stability, 0104 chemical sciences, Solvent, chemistry, peptides, Biophysics, Stoichiometry, Triple helix
Abstract

International audience; The origin of the triple-helix structure and high stability of collagen has been debated for many years. As models of the triple helix and building blocks for new biomaterials, collagen mimetic peptide (CMP) assemblies have been deeply studied in the condensed phase. In particular, it was found that hydroxylation of proline, an abundant post-translational modification in collagen, increases its stability. Two main hypotheses emerged to account for this behavior: 1) intra-helix stereoelectronic effects, and 2) the role of water molecules H-bound to hydroxyproline side-chains. However, in condensed-phase investigations, the influence of water cannot be fully removed. Therefore, we employed a combination of tandem ion mobility and mass spectrometries to assess the structure and stability of CMP assemblies in the gas phase. These results show a conservation of the structure and stability properties of triple helix models in the absence of solvent, supporting an important role of stereoelectronic effects. Moreover, evidence that small triple helix assemblies with controlled stoichiometry can be studied in the gas phase is given, which opens new perspectives in the understanding of the first steps of collagen fiber growth.

Published
2018
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4. Secondary structure effects on internal proton transfer in poly-peptides

Author

Luke MacAleese, Philippe Dugourd, Fabien Chirot, Mathilde Bouakil, Marion Girod, Spectrométrie des biomolécules et agrégats (SPECTROBIO), Institut Lumière Matière [Villeurbanne] (ILM), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, ANABIO-MS - Analyse biomoléculaire par spectrométrie de masse - Biological Analysis by Mass Spectrometry, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), This research received funding from the European Research Council under the European Union's Seventh Framework Program (FP7/2007-2013 Grant Agreement No. 320659). L.M.A. thanks Professor F. Kulzer for discussions and advice on the bootstrap approach., European Project: 320659,EC:FP7:ERC,ERC-2012-ADG_20120216,LASER-IMS(2013), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Photodissociation, Proton, Gas phase, Peptide, 02 engineering and technology, Experimental Methodologies, 01 natural sciences, Conformational dynamics, ARTICLES, Charge transfer, Fragmentation (mass spectrometry), 0103 physical sciences, lcsh:QD901-999, Ion-trap, 010306 general physics, Instrumentation, Protein secondary structure, Spectroscopy, Histidine, chemistry.chemical_classification, Radiation, Mass spectrometry, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Tryptophan, Pump probe experiments, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Amino acid, Crystallography, Helix, Ion mobility spectroscopy, lcsh:Crystallography, Peptides, 0210 nano-technology
Abstract

International audience; A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a series of poly-peptide radical cations containing both histidine and tryptophan. The proton transfer is driven by the gas-phase basicity difference between residues. The fragmentation scheme indicates that the gas-phase basicity of histidine is lower than that of radical tryptophan so that histidine is always pulling the proton away from tryptophan. However, the proton transfer requires the two basic sites to be in close proximity, which is rate limited by the peptide conformational dynamics. PT rate measurements were used to probe and explore the peptide conformational dynamics in several poly-glycines/prolines/alanines. For small and unstructured peptides, the PT rate decreases with the size, as expected from a statistical point of view in a flat conformational space. Conversely, if structured conformations are accessible, the structural flexibility of the peptide is decreased. This slows down the occurrence of conformations favorable to proton transfer. A dramatic decrease in the PT rates was observed for peptides HAnW, when n changes from 5 to 6. This is attributed to the onset of a stable helix for n = 6. No such discontinuity is observed for poly-glycines or poly-prolines. In HAnW, the gas-phase basicity and helix propensity compete for the position of the charge. Interestingly, in this competition between PT and helix formation in HA6W, the energy gain associated with helix formation is large enough to slow down the PT beyond experimental time but does not ultimately prevail over the proton preference for histidine

Published
2020
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