Marc Baaden
Centre national de la recherche scientifique
Human–computer interactionBiophysicsChemical physicsNanotechnologyChemistryData scienceGLICSoftwareMoleculeVisualizationLipid bilayerComputer scienceMembraneProtein structureIon channelMolecular dynamicsStereochemistryCrystallographyLigand-gated ion channelBiology
Publications 160
#2Luigi Del Debbio (Edin.: University of Edinburgh)H-Index: 52
Last. Janne Ignatius (CSC – IT Center for Science)
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PRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations are a pillar of research to assess the risks of different scenarios and investigate mitigation strategies. While the world deals with the subsequent ...
#1Marc Baaden (PSL Research University)H-Index: 38
#1Nicolas Bourassin (CNRS: Centre national de la recherche scientifique)H-Index: 2
#2Florent Barbault (University of Paris)H-Index: 20
Last. Sophie Sacquin-Mora (CNRS: Centre national de la recherche scientifique)H-Index: 19
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The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multi-scale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of {beta}-glucosidase A ({beta}GA) on bare and SAM-functionalized gold surfaces. We monitored the enzyme position and orientation during the MD trajectories, and me...
#1Makamte S (University of Paris)
#2Jabrani A (University of Paris)
Last. Biou (University of Paris)
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Hedgehog (Hh) pathway inhibition by the conserved protein Suppressor of Fused (SuFu) is crucial to vertebrate development. By constrast, SuFu removal has little effect in drosophila. null Previous publications showed that the crystal structures of human and drosophila SuFu consist of two ordered domains that are capable of breathing motions upon ligand binding. However, the crystal structure of human SuFu does not give information about 20 N-terminal residues (IDR1) and an eighty-residue-long di...
#1Xavier Martinez (University of Paris)
#2Marc Baaden (University of Paris)H-Index: 38
Motivated by the current COVID-19 pandemic, which has spurred a substantial flow of structural data, the use of molecular-visualization experiences to make these data sets accessible to a broad audience is described. Using a variety of technology vectors related to the cloud, 3D and virtual reality gear, how to share curated visualizations of structural biology, modeling and/or bioinformatics data sets for interactive and collaborative exploration is examined. FAIR is discussed as an overarching...
#1Arthur Hardiagon (University of Paris)H-Index: 1
#2Samuel Murail (University of Paris)H-Index: 17
Last. Marc Baaden (University of Paris)H-Index: 38
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Understanding water transport mechanisms at the nanoscale level remains a challenge for theoretical chemical physics. Major advances in chemical synthesis have allowed us to discover new artificial water channels, rivaling with or even surpassing water conductance and selectivity of natural protein channels. In order to interpret experimental features and understand microscopic determinants for performance improvements, numerical approaches based on all-atom molecular dynamics simulations and en...
Artificial water channels (AWCs) are known to selectively transport water, with ion exclusion. Similarly to natural porins, AWCs encapsulate water wires or clusters, offering continuous and iterative H-bonding that plays a vital role in their stabilization. Herein, we report octyl-ureido-polyol AWCs capable of self-assembly into hydrophilic hydroxy channels. Variants of ethanol, propanediol, and trimethanol are used as head groups to modulate the water transport permeabilities, with rejection of...
#1Arthur HardiagonH-Index: 1
#2Samuel MurailH-Index: 17
Last. Marc BaadenH-Index: 38
view all 6 authors...
Nanopores that efficiently and selectively transport water have been intensively studied at the nanoscale level. A key challenge relates to linking the nanoscale to the compound's macroscopic properties, which are hardly accessible at the smaller scale. Here we numerically investigate the influence of varying the dimensions of a self-assembled Imidazole I-quartet (I4) aggregate in lipid bilayers on the water permeation properties of these highly packed water channels. Quantitative transport stud...
#1Xiaojing Wu (University of Paris)
#2Jérôme HéninH-Index: 24
Last. Aurélien de la LandeH-Index: 19
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NOX5 is a member of the NADPH oxidase family which is dedicated to the production of reactive oxygen species. The molecular mechanisms governing transmembrane electron transfer (ET) that permits to shuttle electrons over the biological membrane have remained elusive for a long time. Using computer simulations, we report conformational dynamics of NOX5 embedded within a realistic membrane environment. We assess the stability of the protein within the membrane and monitor the existence of cavities...
#1Dmytro StriletsH-Index: 1
#2Shixin Fa (Kyoto University)H-Index: 10
Last. Mihail BarboiuH-Index: 51
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Artificial water channels mimicking natural aquaporins (AQPs) can be used for selective and fast transport of water. Here, we quantify the transport performances of peralkyl-carboxylate-pillar[5]arenes dimers in bilayer membranes. They can transport % 10 7 water molecules/channel/ second, within one order of magnitude of the transport rates of AQPs, rejecting Na + and K + cations. The dimers have a tubular structure, superposing pillar[5]arene pores of 5 diameter with twisted carboxy-phenyl pore...
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