WorldCat Identities

Tarek, Mounir

Overview
Works: 19 works in 24 publications in 2 languages and 53 library holdings
Roles: Other, Thesis advisor, Opponent, Author
Classifications: QH345, 553.7
Publication Timeline
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Most widely held works by Mounir Tarek
L'eau à découvert by Luc Abbadie( )

2 editions published in 2017 in French and held by 27 WorldCat member libraries worldwide

Indispensable à la régulation du climat, au développement de la vie sur Terre, au maintien des écosystèmes, aux populations, au développement de l'agriculture, de l'industrie comme à la production d'énergie, l'eau est un élément vital. Il convient donc, dans un contexte de changement global, d'analyser dans toute sa diversité la place et le rôle de l'eau et de se donner ainsi les moyens de mieux la préserver. Autour de cet enjeu qui engage toute l'humanité, Agathe Euzen, Catherine Jeandel et Rémy Mosseri ont réuni près de cent cinquante contributions, visant à apporter un éclairage sur chacun des domaines et des approches que couvre cette thématique. Quelle est l'origine de l'eau? Son rapport avec l'apparition de la vie? Quel rôle a-t-elle joué dans l'histoire de la planète et dans le développement de la vie végétale, animale et humaine? Quel est son cycle? Quelles sont ses propriétés chimiques? Comment les sociétés se sont-elles emparées de cet élément précieux? Allons-nous manquer d'eau? L'eau est-elle source de conflits? Comment l'eau est-elle gérée? Comment recycle-t-on une eau polluée? Quels sont les risques pour la santé mondiale? Quels sont les grands enjeux liés à l'eau au xxie siècle? Comprendre et proposer des solutions à ces défis majeurs est l'intention de cet ouvrage
CONTRIBUTION A L'ETUDE DE L'ADSORPTION D'ALCANES LEGERS DANS LA ZEOLITHE NAX by MOUNIR TAREK( Book )

2 editions published in 1994 in French and held by 3 WorldCat member libraries worldwide

LA MODELISATION DES ISOTHERMES D'ALCANES C#3 A C#7 MONTRE QUE LA PHASE ADSORBEE EST LOCALISEE. LES CHALEURS D'ADSORPTION AUGMENTENT LINEAIREMENT AVEC LE NOMBRE DE CARBONES. LES INTERACTIONS MOLECULE/MOLECULE, INFERIEURS AUX INTERACTIONS EN PHASE LIQUIDE SONT NON NEGLIGEABLES. L'ANALYSE DES DIAGRAMES DE DIFFRACTIONS DE NEUTRONS MONTRE QUE LE PROPANE ET L'HEPTANE SONT ACCROCHES PAR LES GROUPEMENTS CH#3 AUX OXYGENES DU RESEAU, ET QUE L'HEPTANE EST DANS UNE CONFORMATION NON LINEAIRE
Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory by Zoe Cournia( )

1 edition published in 2015 in English and held by 2 WorldCat member libraries worldwide

Applications of theoretical models of lipid membrane electroporation : doctoral dissertation by Lea Rems( Book )

1 edition published in 2016 in English and held by 2 WorldCat member libraries worldwide

Molecular Dynamics Simulations of Lipid Membrane Electroporation by Lucie Delemotte( )

1 edition published in 2012 in English and held by 2 WorldCat member libraries worldwide

Propriétés d'auto-assemblage de phospholipides riches en acides gras polyinsaturés : caractérisation physico-chimique et simulation de bicouches par dynamique moléculaire by Pascale Sautot( Book )

2 editions published in 2011 in French and held by 2 WorldCat member libraries worldwide

The literature of recent decades is replete with references regarding the benefits of omega 3 fatty acids such as EPA (C20:5 n-3) and DHA (C22:6 n-3) which play an essential role in preventing many diseases such as neurodegenerative diseases (Alzheimer's type). The major sources of EPA and DHA are those of marine origin. It is within this context that this study chose to deal with phospholipids from salmon heads. The objective was to extract, purify phosphatidylcholine (PC) derived from the mixture of lipids and determine its properties of self-assembly into bilayers. An experimental approach by the physicochemical characterization of this PC was supplemented by a theoretical study of the same compound using the techniques of molecular dynamics simulation that allowed a molecular-scale characterization of lipid bilayers. The characterization resulted in detailed profile of the mixture composition of salmon PC, to draw up the phase diagram of PC-water, to determine the packing and hydration properties of this lipid. The parameters chosen for the study of molecular dynamics have faithfully reproduced the experimental results, thus validating the model and simulation conditions determined in advance. The characterization of structural properties of the PC as a multilayer salmon has deepened the understanding of interaction mechanisms at the molecular level between unsaturated lipids themselves
Experimental and stimulation analyses of fluorescent solvent relaxation process in biomembranes : Inflence of ions and molecular interpretation of the dye dynamics by Justyna Barucha-Kraszewska( Book )

3 editions published between 2012 and 2016 in English and held by 2 WorldCat member libraries worldwide

Many biologically important processes and phcnomena in lipid membranes are still not fully understood. The presence of ions and water molœules has a significant influence on the structural and dynamical properties of lipid bilayers. Fluorescent techniques are versatile tools for studying the lipid membranes, because the fluorescence emission is strongly sensitive to dye environment. We have conducted fluorescent solvent relaxation (SR) experiments to explore the hydration and mobility properties in lipid membranes in the presence of different chaotropic ions. We have also carried out Quantum Mechanical (QM) calculations and Molecular Dynamics (MD) simulations for supporting the SR experiments. SR experiments show that small cation (Na+) is attracted to the membrane and increases rigidity ofbilayer, while larger cations (NH/, Cs+) should not. Large anions (CI04·, SCN') adsorl, at the membrane interface more easily than smaller ones (Cl') and significantly change tl!e mobility and hydration of the headgroup region oflipid bilayer. SR study ofhydrophobic part of the membrane show that SR processes are complex there and reflect botl!: faster, intramolecular (torsional relaxation or fonnation of charge transfer state) and slower, intermolecular (SR) relaxation processes. QM calculatiom were used to create force-field for three fluorescent dyes (Prodan, Laurdan and C-laurdan). MD simulations allow detennining position of the dye in the lipid membrane in the ground state and after excitation and reproduce correctly SR timescale- ps in water and ns in the membrane. MD simulations extend the capabilities of SR method and allow observing the behaviour of individual molecules
Electrical properties of planar lipid bilayers formed from lipid mixtures : doctoral thesis by Andraž Polak( Book )

1 edition published in 2014 in English and held by 2 WorldCat member libraries worldwide

Fonction et modulation des canaux potassiques voltage-dépendants : étude par simulations de dynamique moléculaire by Lucie Delemotte( )

1 edition published in 2011 in English and held by 1 WorldCat member library worldwide

Voltage gated ion channels (VGCs) are ubiquitous transmembrane (TM) proteins involved in electrical signaling in excitable cells. Their gating (opening-closing), triggered by changes in the TM voltage, proceeds through a sensing mechanism involving conserved positively charged residues belonging to the voltage sensor domain (VSD). Details on the function of such channels have been revealed thanks to decades of experimental investigations but questions concerning the molecular level function of these proteins still remain under active debate. Starting from the "open state" crystal structure of the rat potassium VGC Kv1.2, we have carried out large-scale all-atom molecular dynamics simulations of the channel embedded in its lipidic environment submitted to a hyperpolarized potential. This allowed to follow the deactivation of the VSD and to uncover three intermediate states between the open and closed conformations. We report gating charge calculations or else state dependent molecular contacts that comply with experimental results and propose accordingly a model of the entire deactivation that conciliates the diverging views proposed so far. Using this model, we further characterize at the molecular level the modulation mechanisms of VGCs: specific mutations of basic residues of the VSD involved in genetic diseases are shown to induce state-dependent "omega" leak currents, in agreement with electrophysiology and a partial conclusion is proposed to explain the alteration of VGC voltage-dependency when the lipids embedding them are chemically modified. We conclude by extending this study to human VGCs (Kv7 family) of physiological relevance
Exploration de la transmission synaptique et de la régulation des récepteurs ionotropes par simulations de dynamique moléculaire et électrophysiologie numérique by Adrien Cerdan( )

1 edition published in 2019 in English and held by 1 WorldCat member library worldwide

Signals within neurons are mostly transmitted through chemical synapses. Signal transduction arises from the binding of neurotransmitters to membrane receptors in order to open ion channels. The Glycine Receptor (GlyR) is an ionotropic receptor which is involved in several neurological disorders such as addiction, chronic pain, or hyperekplexia. Because of its implication in human diseases, it is interesting to design novel drugs targeting this receptor. We used Molecular Dynamics (MD) simulations and computational electrophysiology to probe the function of available GlyR structures. We showed that none of the experimental structures display the physiological behavior of the conductive state. Using MD simulations, we captured a novel conformation of the GlyR compatible with a conductive state and demonstrated the importance of lateral portals for ionic permeation. Lastly, we proposed an original protocol, named state-based pharmacology, to discover modulators of allosteric proteins
Nouvelle approche basée sur la dynamique moléculaire et la RMN pour l'étude et l'optimisation de nouveaux inhibiteurs de peroxyrédoxines humaines, impliquées dans les chocs ischémiques by Laura Troussicot( )

1 edition published in 2017 in French and held by 1 WorldCat member library worldwide

La description des interactions protéine-ligand est d'une importance capitale pour la compréhension de phénomènes biologiques de toutes sortes, et dans le procédé de conception de nouvelles molécules bioactives. Avec l'avènement de nouveaux moyens de calculs numériques, la modélisation des équilibres d'interaction utilisant la dynamique moléculaire est de plus en plus utilisée pour l'étude au niveau microscopique permettant ainsi de guider la conception et l'optimisation de nouveaux inhibiteurs biologiques. Cette thèse est centrée sur l'utilisation de la funnel-métadynamique pour la prédiction d'affinités protéine-ligand et la description des interactions, en corrélation avec des données expérimentales de RMN et de cinétique enzymatique. Sur le modèle biologique des peroxyrédoxines humaines impliquées dans la cascade inflammatoire survenant après un choc ischémique, l'interaction et l'inhibition de composés catéchols ont été étudiées. Les données obtenues par dynamique sur l'interaction de dérivés catéchols ont été utilisées pour guider l'optimisation de cette molécule fragment pour une meilleure affinité et inhibition des peroxyrédoxines humaines. Nos résultats ont montré que la funnel-métadynamique, en plus de permettre la prédiction des affinités protéine-ligand, donnait une description réaliste de l'interaction pouvant mener à l'identification et l'optimisation de nouvelles molécules bioactives dont le potentiel inhibiteur a pu être examiné par cinétique enzymatique. Cette recherche fournit un aperçu des possibilités offertes par les nouvelles méthodes numériques, et leur application en chimie médicinale par exemple
Interaction of pulsed electric fields with membrane models for controlled release of drugs by Maura Casciola( )

1 edition published in 2016 in English and held by 1 WorldCat member library worldwide

Électroporation (EP) est une technique utilisée pour affecter l'intégrité des membranes cellulaires de plasma et/ou organites internes, conséquence de l'application d'un champ électrique d'énergie suffisante, dépendant de son intensité et sa durée. Il a été montré in- directement par de nombreuses études expérimentales et in-silico que ce phénomène résulte de la perméabilisation de la membrane par la formation pores aqueux. L'EP permet ainsi la vectorisation de molécules normalement non perméantes. Les applications de l'EP vont de l'électrochimiothérapie, à la vaccination à ADN. Les impulsions électriques utilisées dans l'EP sont classées en deux familles: Les msPEF dont la longueur des impulsions est de l'ordre de la microseconde et l'amplitude de l'ordre de quelques kV/cm. Ils affectent principalement la membrane cellulaire plasmique. Les nsPEFs d'intensité de MV/m de durée de l'ordre de la nanoseconde, ceux eux sont capables de perméabiliser organites internes ainsi que la membrane plasmique et présentent l'avantage d'éviter les effets thermiques indésirables. Les simulations de dynamique moléculaire (DM) qui permettent la description atomique, de la structure de la membrane et de son interaction avec la solution environnante, constituent un appui précieux aux résultats expérimentaux. Plusieurs études utilisant la DM été consacrées à décrire certains des aspects de l'EP (par exemple la formation de pores, leur évolution, le rôle de l'eau et des groupes de tête lipidiques, ...) néanmoins des questions en suspens restent inexplorées : • Comment la composition de la membrane affecte le seuil d'EP ? • Quelles sont la morphologie, la taille et la conductance des pores formés ? • Quels sont le mécanisme et l'échelle de temps de translocation de petites molécules à travers ces électropores ? • Y-a-t-il une différence notoire entre les effets des msPEFs et des nsPEFs ? Dans le cadre de ce travail, en utilisant des simulations de DM nous avons abordé ces questions pertinentes. Nous avons quantifié le seuil d'EP de bicouches lipidiques contenant des concentrations croissantes de cholestérol utilisant des protocoles qui miment les deux modes types de pulses nsPEFs et msPEFs. Les résultats obtenus indiquent que dans les deux cas les modèles de membranes à concentration en cholestérol croissante, nécessitent un voltage transmembranaire plus élevé pour perméabiliser la bicouche lipidique. Nous avons développé une procédure, mimant l'effet des msPEFs en adéquation avec les expériences, qui permet de stabiliser les voltages appliqués à la membrane suffisamment longtemps pour déterminer la dimension des pores, leur conductance et sélectivité ionique. Nous avons utilisé le même protocole pour étudier le transport de petites molécules chargées, utilisés dans l'administration de médicaments, et comparé nos résultats avec des études similaires menées dans des conditions nsPEFs. Nous avons montré que le transport assisté par EP a lieu dans la même échelle de temps (ns) que sous nsPEFs. Bien que les nsPEF ont l'avantage d'affecter les membranes cellulaires et celles des organites internes, la possibilité d'exploiter de telles impulsions pour la vectorisation de médicaments est encore en cours d'étude, car la capacité à fournir de manière fiable à des échantillons «biologiques» ces impulsions intenses ultra-courtes n'est pas trivial. Une attention particulière doit être accordée à la conception de micro-chambres afin de réaliser un dispositif à large bande passante afin de transmettre sans atténuation et distorsion les pulses ns, qui sont caractérisés par une grandes composante spectrale, jusqu'à GHz. Une partie importante de cette thèse mené en cotutelle, a été consacrée à la conception théorique (utilisant la Méthode des éléments Finis) d'un dispositif d'exposition, basé sur des systèmes de propagations de micro-ondes, capable de délivrer des impulsions aussi courtes que la ns avec des temps de monté et de chute de 0,5 ns
Investigation des mécanismes d'activation et de couplage du canal potassique voltage-dépendant KV7.1 dans les cardiomyocytes à l'aide de méthodes computationnelles by Audrey Deyawe Kongmeneck( )

1 edition published in 2020 in English and held by 1 WorldCat member library worldwide

Modulation de canaux potassiques sensibles au voltage par le phosphatidylinositol-4,5-bisphosphate by Marina Kasimova( )

1 edition published in 2014 in English and held by 1 WorldCat member library worldwide

Voltage-gated potassium (Kv) channels are transmembrane proteins that enable the passive flow of potassium ions across a plasma membrane when the latter is depolarized. They consist of four peripheral voltage sensor domains, responding to the applied voltage, and a central pore domain that encompasses a hydrophilic path for passing ions. The voltage sensors and the pore are coupled, meaning that the activation of the voltage sensors triggers the pore opening, and the open pore promotes the activation of the voltage sensors. Phosphatidylinositol-4,5-bisphosphate (PIP2) is a minor lipid of the inner plasma membrane leaflet. This highly negatively charged lipid was shown to modulate the functioning of several ion channels including members of the Kv family. In particular, application of this lipid to Kv1.2 and Kv7.1, two homologous channels, enhances their ionic current. However, while Kv1.2 is able to open without PIP2, in the case of Kv7.1, this lipid is absolutely required for opening. Additionally, in Kv1.2, PIP2 induces a loss of functioning, which is manifested by delayed motions of the voltage sensors. So far, the mechanism underlying the Kv channels modulation by PIP2 remains unknown. In the present manuscript, we attempt to shed light on this mechanism using molecular dynamics (MD) simulations combined with experiments, which was undertaken by our collaborators. Using unconstrained MD simulations, we have identified potential PIP2 binding sites in Kv1.2. In one of these sites, PIP2 interacts with the channel in a state-dependent manner forming salt bridges either with the voltage sensor or with the pore. Based on these findings, we propose a model rationalizing the known experimental data. Further, we aimed to estimate the loss of functioning effect induced by PIP2 on the Kv1.2 voltage sensors. In particular, we have calculated the free energy of the first two transitions along the activation path in the presence and absence of this lipid. We found that PIP2 affects both the relative stability of the voltage sensor states and the free energy barriers separating them. Finally, we studied the interactions between PIP2 and another member of the Kv family, the cardiac channel Kv7.1. In the PIP2 binding site that we have identified for this channel, the interaction between positive residues of Kv7.1 and the lipid was state-dependent, as in the case of Kv1.2. This state-dependent interaction, however, is prominent for coupling between the voltage sensors and the pore, which is otherwise weakened due to electrostatic repulsion of some positive residues. These findings are in a good agreement with the experimental data obtained by our collaborators
Allosteric modulation of pentameric ligand gated ion channels : from the jiggling of atoms to neuropharmacological strategies by Nicolas Martin( )

1 edition published in 2017 in French and held by 1 WorldCat member library worldwide

Pentameric ligand gated ion channels (pLGICs) are brain receptors involved in fast neurotransmission and include nAchR, GABAR, GlyR or 5HT3R. When dysfunctioning, they are involved in diseases such as Alzheimer's and Parkinson's. In this study we have performed molecular dynamic simulations of an eukaryotic homologue of the pLGICs (GluCl) to understand the gating mechanism of pLGICs. Thanks to the analysis of two 2.5 us long simulations in which we could capture the full closing of the receptor we described in great details a gating mechanism in two steps, first twisting then blooming, that we believe applicable to the whole pLGICs family. In a second time we used our description of the gating mechanism to perform free energy calculations along the twisting reaction coordinate, for various ligands in complex with GluCl. Doing so we could show a significant difference between IVM-bound and non-bound states and provide hints for the design of new treatments
Vectorisation de peptides et de fonctionnelles à visées thérapeutiques à travers des membranes biologiques by Daniel Bonhenry( )

1 edition published in 2013 in French and held by 1 WorldCat member library worldwide

The transfer of a lysine amino acid analog across phospholipid membrane models was investigated using molecular dynamics simulations. The evolution of the protonation state of this small peptide as a function of its position inside the membrane was studied by determining the local pKa by means of free energy calculations. Permeability and mean first time passage were evaluated and showed that the transferoccurs on the sub-ms time scale. Comparative studies were conducted to evaluate the changes in the local pKa arising from the differences in the phospholipid chemical structure. We compared hence the effect of the ether vs ester linkage of the lipid head group as well as the linear vs branched lipid tails. The study reveals that protonated lysine residues can be buried further inside ether lipid membrane than ester lipid membrane while branched lipids are found to stabilize less the charged form compared to their un-branched lipid chain counterparts. As a result, the permeability and the transfer rate across a membrane constituted by ether lipid was found to slower than in membranes constituted by esterified lipids. Finally, multidimensionnal free-energy surfaces for the transfer of the peptide in its both states, charged and neutral, were estimated. The coordination of the amine with the water molecules in its first hydration shell with the projection of the distance from the center of the membrane were used as reaction coordinates. New possibilities for the deprotonation reaction were found, the latter appearing closer to the headgroup region. This finding suggests that if the lysine analog were less coordinated by water molecule a deprotonation is possible in the headgroup region
Structural properties of archaeal lipid bilayers : small-angle x-ray scattering and molecular dynamics simulation study( )

1 edition published in 2014 in English and held by 1 WorldCat member library worldwide

Modélisation moléculaire des modifications post-translationnelles dans Bcl-xL et des sels de céténiminium by Gamze Tanrıver( )

1 edition published in 2021 in English and held by 1 WorldCat member library worldwide

In recent years, computation chemistry plays important role in order to understand and give insight on structural properties of systems (protein, small molecules etc.) by mimicking their environment. This dissertation consists of two main topics, namely understanding impact of Bcl-xL deamidation by means of molecular dynamics (MD) simulations and investigation of keteniminium salt (KI) by quantum mechanical (QM) methods. Investigation of post-translational modifications (PTMs) gains importance to understand their roles on structure and functions of proteins. Deamidation, one of the post-translational modifications is a crucial switch used for regulating the biological function of anti-apoptotic Bcl-xL. In the first part of the thesis, deamidation-induced conformational changes in Bcl-xL were explored to gain insight into its loss of function by performing molecular dynamics (MD) simulations. The outcomes of this study will provide a unique perspective on the underlying mechanism of Bcl-xL deamidation-induced cell death.Keteniminium salt, nitrogen analog of ketene is widely used intermediate for the synthesis of various scaffolds/substances due to its higher electrophilicity, reactivity and regioselectivity. In the second part of the thesis, keteniminium salt was scrutinized from formation to its involved reactions by means of DFT study. Experimentally observed reactivity differences in the [2 + 2] cycloaddition and electrocyclization reactions were rationalized via a range of different analysis techniques. The outcomes of this study are expected to contribute to the understanding of formation and reactivity differences of keteniminium salt and aid synthetic applications
Etude des cycles peptidiques en interaction avec les membranes lipidiques par simulations de dynamique moléculaire utilisant l'approche gros grains by Adil Khalfa( )

1 edition published in 2009 in French and held by 1 WorldCat member library worldwide

Les cycles peptidiques (CPs) composés d'un nombre paire d'acides aminés avec l'alternance de chiralité L/D, sont capables de s'auto assembler pour former des nanotubes peptidiques tubulaires creux grâce à un réseau de liaisons d'hydrogène. La partition des CPs hydrophobes dans une membrane lipidique forme un nanotube transmembranaire, alors que les CPs chargés caractérisé par l'amphipacité montrent une forte activité antibactérienne contre les bactéries gram+/-. Le but de ce travail consiste principalement à étudier les interactions des CPs avec des membranes lipidiques par simulations de dynamique moléculaire utilisant l'approche gros grains, pour mieux caractériser le processus d'auto assemblage, la formation de nanotubes transmembranaires et l'action antibactérienne des CPs. Les résultats obtenus montrent que l'activité de CPs est gouvernée par les propriétés physico-chimiques de la l'interaction des CPs avec les têtes polaires de la membrane. Dans le cas des CPs hydrophobes, les peptides s'auto-assemblent en amas à la surface des membranes avant de s'auto organiser à l'intérieur des bicouches lipidiques pour former des nanotubes transmembranaires. Dans le cas des CPs chargés, leur action antibactérienne semble résulter de l'extraction et la libération de micelles de phospholipides de la membrane qui est précédée par l'adsorption des peptides à la surface des membranes en mode dit carpet-like. L'ensemble de cette étude a nécessité un grand effort d'optimisation des champs de forces gros grains existants. Nous avons en effet montré leurs limites et optimisés les paramètres d'interaction impliquant plusieurs acides amines comme les résidus Leu, Trp, Arg et Lys. Nous avons étendu l'étude au repliement de peptides hélicoïdaux transmembranaires et antimicrobiens montrant ainsi la transférabilité du champ de force GG optimisé
 
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Alternative Names
Mounir Tarek wetenschapper

Languages
English (14)

French (10)