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17 results on '"Vaitinadapoule"'

8. Ex vivo models of corneal epithelial regeneration in bioreactor: Respective roles of limbal, conjunctival and corneal epithelia

Author

Zhiguo He, Chantal Perrache, Sylvain Poinard, Fabien Forest, Inès Aouimeur, Louise Coulomb, Olfa Ben Moussa, Hanielle Vaitinadapoule, Benjamin Peyret, Oliver Dorado Cortez, Tomy Sagnial, Marielle Mentek, Emmanuel Crouzet, Sébastien Urbaniak, Jean‐Marie Papillon, Corantin Maurin, Sandrine Ninotta, Frederic Mascarelli, Philippe Gain, and Gilles Thuret

Subjects
Ophthalmology, General Medicine
Published
2022
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9. Ex vivo models of corneal epithelial regeneration in bioreactor: Respective roles of limbal, conjunctival and corneal epithelia

Author

He, Zhiguo, primary, Perrache, Chantal, additional, Poinard, Sylvain, additional, Forest, Fabien, additional, Aouimeur, Inès, additional, Coulomb, Louise, additional, Moussa, Olfa Ben, additional, Vaitinadapoule, Hanielle, additional, Peyret, Benjamin, additional, Cortez, Oliver Dorado, additional, Sagnial, Tomy, additional, Mentek, Marielle, additional, Crouzet, Emmanuel, additional, Urbaniak, Sébastien, additional, Papillon, Jean‐Marie, additional, Maurin, Corantin, additional, Ninotta, Sandrine, additional, Mascarelli, Frederic, additional, Gain, Philippe, additional, and Thuret, Gilles, additional

Published
2022
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12. Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO

Author

Aurore, Vaitinadapoule and Catherine, Etchebest

Subjects
Models, Molecular, Receptors, GABA, Protein Conformation, Cryoelectron Microscopy, Computational Biology, Humans, Membrane Transport Proteins, Amino Acid Sequence, Molecular Dynamics Simulation, Software
Abstract

This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.

Published
2017

13. Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO

Author

Aurore Vaitinadapoule and Catherine Etchebest

Subjects
0301 basic medicine, Quantitative Biology::Biomolecules, Protein function, Molecular model, Cryo-electron microscopy, Computer science, business.industry, Low resolution, A protein, Force field (chemistry), 03 medical and health sciences, Molecular dynamics, 030104 developmental biology, Software, Biophysics, business, Biological system
Abstract

This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.

Published
2017
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14. Comparative Genomics of Odorant Binding Proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus

Author

Matthieu Ng Fuk Chong, Aurore Vaitinadapoule, Etienne Frumence, Malini Manoharan, Bernard Offmann, and Ramanathan Sowdhamini

Subjects
Odorant binding, Culex, Anopheles gambiae, Genome, Insect, mosquito, Aedes aegypti, phylogeny, Receptors, Odorant, OBP, Aedes, Anopheles, parasitic diseases, Genetics, Animals, Ecology, Evolution, Behavior and Systematics, Comparative genomics, biology, Ecology, fungi, Culex quinquefasciatus, Genomics, biology.organism_classification, Adaptation, Physiological, Protein Structure, Tertiary, Evolutionary biology, odorant binding proteins, Research Article, olfaction
Abstract

About 1 million people in the world die each year from diseases spread by mosquitoes, and understanding the mechanism of host identification by the mosquitoes through olfaction is at stake. The role of odorant binding proteins (OBPs) in the primary molecular events of olfaction in mosquitoes is becoming an important focus of biological research in this area. Here, we present a comprehensive comparative genomics study of OBPs in the three disease-transmitting mosquito species Anopheles gambiae, Aedes aegypti ,a nd Culex quinquefasciatus starting with the identification of 110 new OBPs in these three genomes. We have characterized their genomic distribution and orthologous and phylogenetic relationships. The diversity and expansion observed with respect to the Aedes and Culex genomes suggests that the OBP gene family acquired functional diversity concurrently with functional constraints posed on these two species. Sequences with unique features have been characterized such as the “two-domain OBPs” (previously known as Atypical OBPs) and “MinusC OBPs” in mosquito genomes. The extensive comparative genomics featured in this work hence provides useful primary insights into the role of OBPs in the molecular adaptations of mosquito olfactory system and could provide more clues for the identification of potential targets for insect repellants and attractants.

Published
2013
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15. Construction and validation of an atomic model for bacterial TSPO from electron microscopy density, evolutionary constraints, and biochemical and biophysical data

Author

Catherine Etchebest, Mariano A. Ostuni, Konrad Hinsen, Aurore Vaitinadapoule, Jean-Jacques Lacapère, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 (UPMC), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), and Frapart, Isabelle

Subjects
Models, Molecular, Molecular Sequence Data, Biophysics, Protoporphyrins, Rhodobacter sphaeroides, Biology, Transporter, Ligands, Biochemistry, Protein Structure, Secondary, chemistry.chemical_compound, Bacterial Proteins, Atomic model, Amino Acid Sequence, Conserved Sequence, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], chemistry.chemical_classification, Binding Sites, Cryoelectron Microscopy, Cell Biology, Ligand (biochemistry), biology.organism_classification, Isoquinolines, Transmembrane protein, Amino acid, Translocase 18kDa, Transmembrane domain, Monomer, Cholesterol, chemistry, Membrane protein, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Protein Multimerization, Carrier Proteins, Crystallization, Sequence Alignment, Protein Binding
Abstract

International audience; The 18kDa protein TSPO is a highly conserved transmembrane protein found in bacteria, yeast, animals and plants. TSPO is involved in a wide range of physiological functions, among which the transport of several molecules. The atomic structure of monomeric ligand-bound mouse TSPO in detergent has been published recently. A previously published low-resolution structure of Rhodobacter sphaeroides TSPO, obtained from tubular crystals with lipids and observed in cryo-electron microscopy, revealed an oligomeric structure without any ligand. We analyze this electron microscopy density in view of available biochemical and biophysical data, building a matching atomic model for the monomer and then the entire crystal. We compare its intra- and inter-molecular contacts with those predicted by amino acid covariation in TSPO proteins from evolutionary sequence analysis. The arrangement of the five transmembrane helices in a monomer of our model is different from that observed for the mouse TSPO. We analyze possible ligand binding sites for protoporphyrin, for the high-affinity ligand PK 11195, and for cholesterol in TSPO monomers and/or oligomers, and we discuss possible functional implications.

Published
2014
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16. PB-PENTAdb : a web resource for the analysis and prediction of local backbone structure and flexibility using pentapeptide protein blocks

Author

Offmann, Bernard, Tyagi, M., Joseph, A., Drula, M., Grondin, M., Frumence, E., Vaitinadapoule, Aurore, Cadet, Frédéric, Srinivasan, Narayanaswamy, De Brevern, Alexandre, Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Transfusion Sanguine [Paris] (INTS), Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Molecular Biophysics Unit, Indian Institute of Science, Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Alarcon, Nicolas

Subjects
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2010

17. Identification and characterisation of novel atypical odorant binding proteins in the mosquito genomes

Author

Manoharan, Malini, Ng Fuk Chong, Matthieu, Vaitinadapoule, Aurore, Frumence, E., Sowdhamini, Ramanathan, Offmann, Bernard, Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Transfusion Sanguine [Paris] (INTS), and Alarcon, Nicolas

Subjects
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2010

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