@article {2022, title = {Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces.}, journal = {Langmuir}, volume = {38}, year = {2022}, month = {2022 Feb 01}, pages = {1313-1323}, abstract = {

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 multiscale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and self-assembled monolayer (SAM)-functionalized gold surfaces. We monitored the enzyme position and orientation during the molecular dynamics (MD) trajectories and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but less specific, and more likely to disrupt the enzyme\&$\#$39;s function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a key point when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.

}, issn = {1520-5827}, doi = {10.1021/acs.langmuir.1c01774}, author = {Bourassin, Nicolas and Barbault, Florent and Marc Baaden and S Sacquin-Mora} } @article {2022|2156, title = {Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies}, journal = {Frontiers in Molecular Biosciences}, volume = {9}, year = {2022}, pages = {826136}, abstract = {

Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2022.826136}, url = {https://www.frontiersin.org/article/10.3389/fmolb.2022.826136}, author = {Molza, Anne-Elisabeth and Westermaier, Yvonne and Moutte, Magali and Ducrot, Pierre and Danilowicz, Claudia and Godoy-Carter, Veronica and Prentiss, Mara and Robert, Charles H. and Marc Baaden and Pr{\'e}vost, Chantal} } @article {2022|2159, title = {Design {\textendash} a new way to look at old molecules}, journal = {Journal of Integrative Bioinformatics}, volume = {19}, year = {2022}, pages = {20220020}, doi = {doi:10.1515/jib-2022-0020}, url = {https://doi.org/10.1515/jib-2022-0020}, author = {Davide Spalvieri and Anne-Marine Mauviel and Matthieu Lambert and Nicolas F{\'e}rey and S Sacquin-Mora and Matthieu Chavent and Marc Baaden} } @article {2021|2147, title = {Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.}, journal = {Front Chem}, volume = {9}, year = {2021}, month = {2021}, pages = {650651}, abstract = {

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 that could accommodate dioxygen molecules. We investigate the heme-to-heme electron transfer. We find a reaction free energy of a few tenths of eV (ca. -0.3 eV) and a reorganization free energy of around 1.1 eV (0.8 eV after including electrostatic induction corrections). The former indicates thermodynamically favorable ET, while the latter falls in the expected values for transmembrane inter-heme ET. We estimate the electronic coupling to fall in the range of the μeV. We identify electron tunneling pathways showing that not only the W378 residue is playing a central role, but also F348. Finally, we reveal the existence of two connected Obinding pockets near the outer heme with fast exchange between the two sites on the nanosecond timescale. We show that when the terminal heme is reduced, O binds closer to it, affording a more efficient tunneling pathway than when the terminal heme is oxidized, thereby providing an efficient mechanism to catalyze superoxide production in the final step. Overall, our study reveals some key molecular mechanisms permitting reactive oxygen species production by NOX5 and paves the road for further investigation of ET processes in the wide family of NADPH oxidases by computer simulations.

}, issn = {2296-2646}, doi = {10.3389/fchem.2021.650651}, author = {Wu, Xiaojing and J{\'e}r{\^o}me H{\'e}nin and Baciou, Laura and Marc Baaden and Cailliez, Fabien and de la Lande, Aur{\'e}lien} } @article {2020|2075, title = {Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.}, journal = {Phys Chem Chem Phys}, volume = {22}, year = {2020}, month = {2020 Jan 21}, pages = {1611-1623}, abstract = {

Electronic circular dichroism is one of the most used spectroscopic techniques for peptide and protein structural characterization. However, while valuable experimental spectra exist for α-helix, β-sheet and random coil secondary structures, previous studies showed important discrepancies for β-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized β-turns in peptides, namely types I, II, I\&$\#$39; and II\&$\#$39;. In particular, by combining classical molecular dynamics simulations and state-of-the-art quantum time-dependent density functional theory (with the polarizable embedding multiscale model) computations, two common electronic circular dichroism patterns were found for couples of β-turn types (namely, type I/type II\&$\#$39; and type II/type I\&$\#$39;), at first for a minimal di-peptide model (Ace-Ala-Ala-NHMe), but also for all sequences tested with non-aromatic residues in the central positions. On the other hand, as expected, aromatic substitution causes important perturbations to the previously found ECD patterns. Finally, by applying suitable approximations, these patterns were subsequently rationalized based on the exciton chirality rule. All these results provide useful predictions and pave the way for a possible experimental characterization of β-turns based on circular dichroism spectroscopy.

}, keywords = {Circular Dichroism, Computational Chemistry, Computer Simulation, Molecular Dynamics Simulation, Protein Conformation, beta-Strand, Protein Structure, Tertiary}, issn = {1463-9084}, doi = {10.1039/c9cp05776e}, author = {Migliore, Mattia and Bonvicini, Andrea and Tognetti, Vincent and Guilhaudis, Laure and Marc Baaden and Oulyadi, Hassan and Joubert, Laurent and S{\'e}galas-Milazzo, Isabelle} } @conference {2020|2100, title = {Computer Simulations Provide Guidance for Molecular Medicine Through Insights on Dynamics and Mechanisms at the Atomic Scale}, booktitle = {7th International Conference on the Development of Biomedical Engineering in Vietnam (BME7)}, year = {2020}, publisher = {Springer}, organization = {Springer}, address = {Singapore}, abstract = {

Computer simulations provide crucial insights and rationales for the design of molecular approaches in medicine. Several case studies illustrate how molecular model building and molecular dynamics simulations of complex molecular assemblies such as membrane proteins help in that process. Important aspects relate to build relevant molecular models with and without a crystal structure, to model membrane aggregates, then to link (dynamic) models to function, and finally to understand key disease-triggering phenomena such as aggregation. Through selected examples\—including key signaling pathways in neurotransmission\—the links between a molecular-level understanding of biological mechanisms and original approaches to treat disease conditions will be illuminated. Such treatments may be symptomatic, e.g. by better understanding the function and pharmacology of macromolecular key players, or curative, e.g. through molecular inhibition of disease-inducing molecular processes.

}, keywords = {Model building, molecular dynamics, Molecular mechanisms of disease}, isbn = {9789811358593}, doi = {10.1007/978-981-13-5859-3_47}, author = {Marc Baaden}, editor = {Van Toi, Vo and Le, Trung Quoc and Ngo, Hoan Thanh and Nguyen, Thi-Hiep} } @article {2020|2144, title = {Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation}, journal = {J Phys Chem B}, volume = {124}, year = {2020}, month = {Oct}, pages = {8516{\textendash}8523}, author = {Bourassin, N. and Marc Baaden and Lojou, E. and S Sacquin-Mora} } @article {2020|2098, title = {Scruter les mol{\'e}cules en r{\'e}alit{\'e} virtuelle, pour quoi faire ?}, journal = {L{\textquoteright}Actualit{\'e} Chimique}, year = {2020}, pages = {23{\textendash}26}, abstract = {

Les repr{\'e}sentations des mol{\'e}cules ont pris une place importante dans la communication d\’id{\'e}es, la g{\'e}n{\'e}ration d\’hypoth{\`e}ses sur les m{\'e}canismes biologiques et l\’analyse de simulations mol{\'e}culaires. Pourtant, les dispositifs pour les observer et les manipuler restent souvent cantonn{\'e}s aux deux dimensions des {\'e}crans et {\`a} l\’interaction limit{\'e}e d\’une souris et d\’un clavier. D\’autres solutions plus performantes et {\`a} port{\'e}e de tous existent, notamment avec les derni{\`e}res {\'e}volutions de la r{\'e}alit{\'e} virtuelle pour le grand public. Des adaptations sont n{\'e}anmoins n{\'e}cessaires pour b{\'e}n{\'e}ficier pleinement des avantages li{\'e}s {\`a} l\’utilisation de la r{\'e}alit{\'e} virtuelle pour la visualisation scientifique. Cet article pr{\'e}sente quelques exemples r{\'e}alis{\'e}s avec le logiciel UnityMol. En plus des applications directes dans l\’enseignement, le changement de paradigme d\’interaction et la perception accrue de la profondeur et des formes des mol{\'e}cules biologiques facilitent d{\`e}s {\`a} pr{\'e}sent la compr{\'e}hension de ces syst{\`e}mes complexes et am{\`e}neront certainement {\`a} la d{\'e}couverte de nouveaux savoirs scientifiques.

}, issn = {0151-9093}, url = {http://www.lactualitechimique.org/Scruter-les-molecules-en-realite-virtuelle-pour-quoi-faire}, author = {Martinez, Xavier and Marc Baaden} } @article {2020|2077, title = {Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.}, journal = {Protein Sci}, volume = {29}, year = {2020}, month = {2020 Jan}, pages = {237-246}, abstract = {

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson-Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.

}, issn = {1469-896X}, doi = {10.1002/pro.3773}, author = {Laureanti, Joseph and Brandi, Juan and Offor, Elvis and Engel, David and Rallo, Robert and Ginovska, Bojana and Martinez, Xavier and Marc Baaden and Baker, Nathan A} } @article {2020|2074, title = {Visualizing protein structures - tools and trends.}, journal = {Biochem Soc Trans}, year = {2020}, month = {2020 Mar 20}, abstract = {

Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few \&$\#$39;Swiss Army knives\&$\#$39; geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.

}, issn = {1470-8752}, doi = {10.1042/BST20190621}, author = {Martinez, Xavier and Chavent, Matthieu and Marc Baaden} } @article {2019|2076, title = {Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.}, journal = {Proc Natl Acad Sci U S A}, volume = {116}, year = {2019}, month = {2019 12 17}, pages = {26057-26065}, abstract = {

Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an intramolecular disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Physiological reductases, thioredoxins and glutaredoxins, could not dissolve AtGAPC1 aggregates but could efficiently contrast their growth. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.

}, issn = {1091-6490}, doi = {10.1073/pnas.1914484116}, author = {Zaffagnini, Mirko and Marchand, Christophe H and Malferrari, Marco and Murail, Samuel and Bonacchi, Sara and Genovese, Damiano and Montalti, Marco and Venturoli, Giovanni and Falini, Giuseppe and Marc Baaden and Lemaire, St{\'e}phane D and Fermani, Simona and Trost, Paolo} } @article {2019|2080, title = {Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK.}, journal = {Chem Commun (Camb)}, volume = {55}, year = {2019}, month = {2019 Apr 07}, pages = {3853-3858}, issn = {1364-548X}, doi = {10.1039/c9cc90112d}, author = {Barboiu, Mihail and Kumar, Manish and Marc Baaden and Gale, Philip A and Hinds, Bruce J} } @article {2019|2122, title = {Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics}, journal = {Scientific Reports}, volume = {9}, year = {2019}, pages = {16450}, abstract = {

In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.

}, isbn = {2045-2322}, doi = {10.1038/s41598-019-52760-y}, url = {https://doi.org/10.1038/s41598-019-52760-y}, author = {F. Brandner, Astrid and Timr, Stepan and Melchionna, Simone and Philippe Derreumaux and Marc Baaden and Sterpone, Fabio} } @article {2019|2079, title = {Molecular Graphics: Bridging Structural Biologists and Computer Scientists.}, journal = {Structure}, volume = {27}, year = {2019}, month = {2019 11 05}, pages = {1617-1623}, abstract = {

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.

}, issn = {1878-4186}, doi = {10.1016/j.str.2019.09.001}, author = {Martinez, Xavier and Krone, Michael and Alharbi, Naif and Rose, Alexander S and Laramee, Robert S and O{\textquoteright}Donoghue, Sean and Marc Baaden and Chavent, Matthieu} } @article {2019|2068, title = {Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching}, journal = {Interface focus}, volume = {9}, year = {2019}, pages = {20180065}, author = {Antoine Taly and Nitti, Francesco and Marc Baaden and Pasquali, S} } @article {2019|2073, title = {A molecular perspective on mitochondrial membrane fusion: from the key players to oligomerization and tethering of mitofusin}, journal = {The Journal of membrane biology}, volume = {252}, year = {2019}, pages = {293{\textendash}306}, author = {De Vecchis, Dario and Brandner, Astrid and Marc Baaden and Cohen, Micka{\"e}l M and Antoine Taly} } @article {2019|2072, title = {Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking}, journal = {Mitochondrion}, volume = {49}, year = {2019}, pages = {234{\textendash}244}, author = {Brandner, Astrid and De Vecchis, Dario and Marc Baaden and Cohen, Micka{\"e}l M and Antoine Taly} } @conference {2019|2099, title = {QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces}, booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data}, year = {2019}, publisher = {The Eurographics Association}, organization = {The Eurographics Association}, isbn = {978-3-03868-085-7}, doi = {10.2312/molva.20191095}, author = {Martinez, Xavier and Krone, Michael and Marc Baaden}, editor = {Byska, Jan and Krone, Michael and Sommer, Bj{\"o}rn} } @article {2019|2078, title = {Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.}, journal = {Data Brief}, volume = {26}, year = {2019}, month = {2019 Oct}, pages = {104460}, abstract = {

In this work we present a novel set of possible auto-oligomerisation states of yeast protein Fzo1 in the context of membrane docking. The dataset reports atomistic models and trajectories derived from a molecular dynamics study of the yeast mitofusin Fzo1, residues 101-855. The initial modelling was followed by coarse-grained molecular dynamics simulation to evaluate the stability and the dynamics of each structural model in a solvated membrane environment. Simulations were run for 1\ μs and collected with GROMACS v5.0.4 using the martini v2.1 force field. For each structural model, the dataset comprises the production phase under semi-isotropic condition at 1\ bar, 310 K and 150 mn NaCl. The integration step is 20 fs and coordinates have been saved every 1 ns. Each trajectory is associated with a ready-available visualization state for the VMD software. These structural detailed informations are a ready-available platform to plan integrative studies on the mitofusin Fzo1 and will aid the community to further elucidate the mitochondrial tethering process during membrane fusion. This dataset is based on the publication \"Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking.\" (Brandner and De Vecchis et\ al., 2019)\".

}, issn = {2352-3409}, doi = {10.1016/j.dib.2019.104460}, author = {Brandner, Astrid and De Vecchis, Dario and Marc Baaden and Cohen, Micka{\"e}l M and Antoine Taly} } @article {2019|2081, title = {Visualizing Biological Membrane Organization and Dynamics.}, journal = {J Mol Biol}, volume = {431}, year = {2019}, month = {2019 05 03}, pages = {1889-1919}, abstract = {

Biological membranes are fascinating. Santiago Ram{\'o}n y Cajal, who received the Nobel prize in 1906 together with Camillo Golgi for their work on the nervous system, wrote \"[\…]in the study of this membrane[\…] I felt more profoundly than in any other subject of study the shuddering sensation of the unfathomable mystery of life\". The visualization and conceptualization of these biological objects have profoundly shaped many aspects of modern biology, drawing inspiration from experiments, computer simulations, and the imagination of scientists and artists. The aim of this review is to provide a fresh look on current ideas of biological membrane organization and dynamics by discussing selected examples across fields.

}, keywords = {Animals, Cell Membrane, Humans, Lipid Bilayers, Microscopy, Atomic Force, Microscopy, Electron, Transmission, Molecular Dynamics Simulation}, issn = {1089-8638}, doi = {10.1016/j.jmb.2019.02.018}, author = {Marc Baaden} } @article {2018|2086, title = {Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 09 10}, pages = {13540}, abstract = {

Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. The Laguerre partition specifies inter-atomic contacts, formalized in graphs. The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. Inside FepA, the solvent splits into isolated clusters and an intricate network connecting both sides of the lipid bilayer. The network is dynamic, connections set on and off, occasionally substantially relocating traversing paths. Subtle differences are detected between two forms of FepA, ligand-free and complexed with its natural iron carrier, the enterobactin. The complexed form has more constricted and more centered openings in the upper part whereas, in the lower part, constriction is released: two main channels between the plug and barrel lead directly to the periplasm. Reliability, precision and the variety of topological features are the main interest of the method.

}, keywords = {Bacterial Outer Membrane Proteins, Carrier Proteins, Enterobactin, Molecular Dynamics Simulation, Protein Stability, Protein Structure, Secondary, Receptors, Cell Surface, Structure-Activity Relationship, Water}, issn = {2045-2322}, doi = {10.1038/s41598-018-31422-5}, author = {Esque, J{\'e}r{\'e}my and Sansom, Mark S P and Marc Baaden and Oguey, Christophe} } @inbook {2018|2085, title = {Applications to water transport systems: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {389-414}, issn = {1364-5498}, doi = {10.1039/c8fd90022a}, author = {Marc Baaden and Barboiu, Mihail and Borthakur, Manash Pratim and Chen, Chun-Long and Coalson, Rob and Davis, Jeffery and Freger, Viatcheslav and Gong, Bing and H{\'e}lix-Nielsen, Claus and Hickey, Robert and Hinds, Bruce and Hirunpinyopas, Wisit and Horner, Andreas and Hou, Jun-Li and Hummer, Gerhard and Iamprasertkun, Pawin and Kazushi, Kinbara and Kumar, Manish and Legrand, Yves-Marie and Lokesh, Mahesh and Mi, Baoxia and Mitra, Sushanta and Murail, Samuel and Noy, Aleksandr and Nunes, Suzana and Pohl, Peter and Song, Qilei and Song, Woochul and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish} } @inbook {2018|2082, title = {Biomimetic water channels: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {205-229}, issn = {1364-5498}, doi = {10.1039/c8fd90020e}, author = {Marc Baaden and Barboiu, Mihail and Bill, Roslyn M and Chen, Chun-Long and Davis, Jeffery and Di Vincenzo, Maria and Freger, Viatcheslav and Fr{\"o}ba, Michael and Gale, Philip A and Gong, Bing and H{\'e}lix-Nielsen, Claus and Hickey, Robert and Hinds, Bruce and Hou, Jun-Li and Hummer, Gerhard and Kumar, Manish and Legrand, Yves-Marie and Lokesh, Mahesh and Mi, Baoxia and Murail, Samuel and Pohl, Peter and Sansom, Mark and Song, Qilei and Song, Woochul and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish and V{\"o}gele, Martin} } @article {2018|2046, title = {Controlling Redox Enzyme Orientation at Planar Electrodes}, journal = {Catalysts}, volume = {8}, year = {2018}, abstract = {

Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.

}, issn = {2073-4344}, doi = {10.3390/catal8050192}, url = {http://www.mdpi.com/2073-4344/8/5/192}, author = {Hitaishi, Vivek Pratap and Clement, Romain and Bourassin, Nicolas and Marc Baaden and de Poulpiquet, Anne and S Sacquin-Mora and Ciaccafava, Alexandre and Lojou, Elisabeth} } @article {2018|2093, title = {Dystrophin{\textquoteright}s central domain forms a complex filament that becomes disorganized by in-frame deletions.}, journal = {J Biol Chem}, volume = {293}, year = {2018}, month = {2018 05 04}, pages = {6637-6646}, abstract = {

Dystrophin, encoded by the gene, is critical for maintaining plasma membrane integrity during muscle contraction events. Mutations in the gene disrupting the reading frame prevent dystrophin production and result in severe Duchenne muscular dystrophy (DMD); in-frame internal deletions allow production of partly functional internally deleted dystrophin and result in less severe Becker muscular dystrophy (BMD). Many known BMD deletions occur in dystrophin\&$\#$39;s central domain, generally considered to be a monotonous rod-shaped domain based on the knowledge of spectrin family proteins. However, the effects caused by these deletions, ranging from asymptomatic to severe BMD, argue against the central domain serving only as a featureless scaffold. We undertook structural studies combining small-angle X-ray scattering and molecular modeling in an effort to uncover the structure of the central domain, as dystrophin has been refractory to characterization. We show that this domain appears to be a tortuous and complex filament that is profoundly disorganized by the most severe BMD deletion (loss of exons 45-47). Despite the preservation of large parts of the binding site for neuronal nitric oxide synthase (nNOS) in this deletion, computational approaches failed to recreate the association of dystrophin with nNOS. This observation is in agreement with a strong decrease of nNOS immunolocalization in muscle biopsies, a parameter related to the severity of BMD phenotypes. The structural description of the whole dystrophin central domain we present here is a first necessary step to improve the design of microdystrophin constructs toward the goal of a successful gene therapy for DMD.

}, keywords = {Binding Sites, Dystrophin, Exons, Gene Deletion, Humans, Molecular Docking Simulation, Muscular Dystrophy, Duchenne, Nitric Oxide Synthase Type I, Protein Domains, Reading Frames, Scattering, Small Angle, Solutions, X-Ray Diffraction}, issn = {1083-351X}, doi = {10.1074/jbc.M117.809798}, author = {Delalande, Olivier and Molza, Anne-Elisabeth and Dos Santos Morais, Raphael and Ch{\'e}ron, Ang{\'e}lique and Pollet, {\'E}meline and Raguenes-Nicol, C{\'e}line and Tascon, Christophe and Giudice, Emmanuel and Guilbaud, Marine and Nicolas, Aur{\'e}lie and Bondon, Arnaud and Leturcq, France and Nicolas F{\'e}rey and Marc Baaden and Perez, Javier and Roblin, Pierre and Pi{\'e}tri-Rouxel, France and Hubert, Jean-Fran{\c c}ois and Czjzek, Mirjam and Le Rumeur, Elisabeth} } @article {2018|2088, title = {From Virtual Reality to Immersive Analytics in Bioinformatics.}, journal = {J Integr Bioinform}, volume = {15}, year = {2018}, month = {2018 Jul 09}, abstract = {

Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information includes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural - usually molecular - data plays an important role in the aforementioned contexts. For decades, virtual reality (VR)-related technologies were developed and applied to Bioinformatics problems. Often, these approaches provide \"just\" visual support of the analysis, e.g. in the case of exploring and interacting with a protein on a 3D monitor and compatible interaction hardware. Moreover, in the past these approaches were limited to cost-intensive professional visualization facilities. The advent of new affordable, and often mobile technologies, provides high potential for using similar approaches on a regular basis for daily research. Visual Analytics is successfully being used for several years to analyze complex and heterogeneous datasets. Immersive Analytics combines these approaches now with new immersive and interactive technologies. This publication provides a short overview of related technologies, their history and Bioinformatics-related approaches. Six new applications on the path from VR to Immersive Analytics are being introduced and discussed.

}, keywords = {Computer Graphics, Imaging, Three-Dimensional, Molecular Conformation, Proteins, Software, User-Computer Interface, Virtual Reality}, issn = {1613-4516}, doi = {10.1515/jib-2018-0043}, author = {Sommer, Bj{\"o}rn and Marc Baaden and Krone, Michael and Woods, Andrew} } @article {2018|2094, title = {Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution.}, journal = {J Chem Theory Comput}, volume = {14}, year = {2018}, month = {2018 Feb 13}, pages = {1045-1058}, abstract = {

The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this complex, the DNA wraps around eight histone proteins to form a superhelical double helix. The resulting bending, stronger than anything observed in free DNA, raises the question of how such a distortion is stabilized by the proteic and solvent environments. In this work, the DNA-histone interface in solution was exhaustively analyzed from nucleosome structures generated by molecular dynamics. An original Voronoi tessellation technique, measuring the topology of interacting elements without any empirical or subjective adjustment, was used to characterize the interface in terms of contact area and occurrence. Our results revealed an interface more robust than previously known, combining extensive, long-lived nonelectrostatic and electrostatic interactions between DNA and both structured and unstructured histone regions. Cation accumulation makes the proximity of juxtaposed DNA gyres in the superhelix possible by shielding the strong electrostatic repulsion of the charged phosphate groups. Overall, this study provides new insights on the nucleosome cohesion, explaining how DNA distortions can be maintained in a nucleoprotein complex.

}, keywords = {DNA, Histones, Molecular Dynamics Simulation, Nucleosomes, Solutions, Static Electricity}, issn = {1549-9626}, doi = {10.1021/acs.jctc.7b00936}, author = {Elbahnsi, Ahmad and Retureau, Romain and Marc Baaden and Hartmann, Brigitte and Oguey, Christophe} } @article {2018|2087, title = {The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation .}, journal = {Elife}, volume = {7}, year = {2018}, month = {2018 07 19}, abstract = {

, the primary molecular mechanotransductive events mechanically initiating cell differentiation remain unknown. Here we find the molecular stretching of the highly conserved Y654-β-catenin-D665-E-cadherin binding site as mechanically induced by tissue strain. It triggers the increase of accessibility of the Y654 site, target of the Src42A kinase phosphorylation leading to irreversible unbinding. Molecular dynamics simulations of the β-catenin/E-cadherin complex under a force mimicking a 6 pN physiological mechanical strain predict a local 45\% stretching between the two α-helices linked by the site and a 15\% increase in accessibility of the phosphorylation site. Both are quantitatively observed using FRET lifetime imaging and non-phospho Y654 specific antibody labelling, in response to the mechanical strains developed by endogenous and magnetically mimicked early mesoderm invagination of gastrulating embryos. This is followed by the predicted release of 16\% of β-catenin from junctions, observed in FRAP, which initiates the mechanical activation of the β-catenin pathway process.

}, keywords = {Amino Acid Sequence, Animals, Armadillo Domain Proteins, Binding Sites, Cadherins, Cell Differentiation, Drosophila melanogaster, Drosophila Proteins, Fluorescence Resonance Energy Transfer, Mechanotransduction, Cellular, Molecular Dynamics Simulation, Phosphorylation, Protein Binding, Protein Conformation, Proto-Oncogene Proteins pp60(c-src), Sequence Homology, Transcription Factors}, issn = {2050-084X}, doi = {10.7554/eLife.33381}, author = {R{\"o}per, Jens-Christian and Mitrossilis, D{\'e}mosth{\`e}ne and Guillaume Stirnemann and Waharte, Fran{\c c}ois and Brito, Isabel and Fernandez-Sanchez, Maria-Elena and Marc Baaden and Salamero, Jean and Farge, Emmanuel} } @article {2018|2091, title = {MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.}, journal = {J Integr Bioinform}, volume = {15}, year = {2018}, month = {2018 Jun 21}, abstract = {

Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.

}, keywords = {Algal Proteins, Chlamydomonas reinhardtii, Computer Graphics, Imaging, Three-Dimensional, Models, Structural, Oxidation-Reduction, Protein Conformation, Protein Interaction Maps, Protein Processing, Post-Translational, Proteome, Proteomics, Software, Virtual Reality}, issn = {1613-4516}, doi = {10.1515/jib-2018-0006}, author = {Maes, Alexandre and Martinez, Xavier and Druart, Karen and Laurent, Benoist and Gu{\'e}gan, Sean and Marchand, Christophe H and Lemaire, St{\'e}phane D and Marc Baaden} } @inbook {2018|2084, title = {The modelling and enhancement of water hydrodynamics: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {273-285}, issn = {1364-5498}, doi = {10.1039/c8fd90021c}, author = {Marc Baaden and Borthakur, Manash Pratim and Casanova, Serena and Coalson, Rob and Freger, Viatcheslav and Gonzalez, Miguel and G{\'o}ra, Artur and Hinds, Bruce and Hirunpinyopas, Wisit and Hummer, Gerhard and Kumar, Manish and Lynch, Charlotte and Murail, Samuel and Noy, Aleksandr and Sansom, Mark and Song, Qilei and Vashisth, Harish and V{\"o}gele, Martin} } @article {2018|2092, title = {Oriented chiral water wires in artificial transmembrane channels.}, journal = {Sci Adv}, volume = {4}, year = {2018}, month = {2018 03}, pages = {eaao5603}, abstract = {

Aquaporins (AQPs) feature highly selective water transport through cell membranes, where the dipolar orientation of structured water wires spanning the AQP pore is of considerable importance for the selective translocation of water over ions. We recently discovered that water permeability through artificial water channels formed by stacked imidazole I-quartet superstructures increases when the channel water molecules are highly organized. Correlating water structure with molecular transport is essential for understanding the underlying mechanisms of (fast) water translocation and channel selectivity. Chirality adds another factor enabling unique dipolar oriented water structures. We show that water molecules exhibit a dipolar oriented wire structure within chiral I-quartet water channels both in the solid state and embedded in supported lipid bilayer membranes (SLBs). X-ray single-crystal structures show that crystallographic water wires exhibit dipolar orientation, which is unique for chiral I-quartets. The integration of I-quartets into SLBs was monitored with a quartz crystal microbalance with dissipation, quantizing the amount of channel water molecules. Nonlinear sum-frequency generation vibrational spectroscopy demonstrates the first experimental observation of dipolar oriented water structures within artificial water channels inserted in bilayer membranes. Confirmation of the ordered confined water is obtained via molecular simulations, which provide quantitative measures of hydrogen bond strength, connectivity, and the stability of their dipolar alignment in a membrane environment. Together, uncovering the interplay between the dipolar aligned water structure and water transport through the self-assembled I-quartets is critical to understanding the behavior of natural membrane channels and will accelerate the systematic discovery for developing artificial water channels for water desalting.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aao5603}, author = {Kocsis, Istvan and Sorci, Mirco and Vanselous, Heather and Murail, Samuel and Sanders, Stephanie E and Licsandru, Erol and Legrand, Yves-Marie and van der Lee, Arie and Marc Baaden and Petersen, Poul B and Belfort, Georges and Barboiu, Mihail} } @article {2018|2089, title = {Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.}, journal = {J Integr Bioinform}, volume = {15}, year = {2018}, month = {2018 Jul 09}, abstract = {

The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.

}, keywords = {Computer Graphics, Humans, Imaging, Three-Dimensional, Models, Structural, Semantics, Software, Statistics as Topic, User-Computer Interface}, issn = {1613-4516}, doi = {10.1515/jib-2018-0004}, author = {Trellet, Mikael and Nicolas F{\'e}rey and Floty{\'n}ski, Jakub and Marc Baaden and Bourdot, Patrick} } @inbook {2018|2083, title = {Structure and function of natural proteins for water transport: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {83-95}, keywords = {Molecular Structure, Proteins, Water}, issn = {1364-5498}, doi = {10.1039/c8fd90019a}, author = {Marc Baaden and Barboiu, Mihail and Bill, Roslyn M and Casanova, Serena and Chen, Chun-Long and Conner, Matthew and Freger, Viatcheslav and Gong, Bing and G{\'o}ra, Artur and Hinds, Bruce and Horner, Andreas and Hummer, Gerhard and Kumar, Manish and Lokesh, Mahesh and Mitra, Sushanta and Noy, Aleksandr and Pohl, Peter and Sadet, Aude and Sansom, Mark and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish} } @booklet {2018|2066, title = {Ten simple rules to create a serious game, illustrated with examples from structural biology}, year = {2018}, author = {Marc Baaden and Delalande, Olivier and Nicolas F{\'e}rey and Pasquali, Samuela and Waldisp{\"u}hl, J{\'e}r{\^o}me and Antoine Taly} } @article {2018|2090, title = {Water permeation across artificial I-quartet membrane channels: from structure to disorder.}, journal = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {125-148}, abstract = {

Artificial water channels (AWCs) have been designed for water transport across membranes with the aim to mimic the high water permeability observed for biological systems such as aquaporins (\∼108-109 water molecules per s per channel), as well as their selectivity to reject ion permeation at the same time. Recent works on designed self-assembling alkylureido-ethylimidazole compounds forming imidazole-quartet channels (I-quartets), have shown both high water permeability and total ionic-rejection. I-quartets are thus promising candidates for further development of AWCs. However, the molecular mechanism of water permeation as well as I-quartet organization and stability in a membrane environment need to be fully understood to guide their optimal design. Here, we use a wide range of all-atom molecular dynamics (MD) simulations and their analysis to understand the structure/activity relationships of the I-quartet channels. Four different types with varying alkyl chain length or chirality have been studied in a complex fully hydrated lipid bilayer environment at both microsecond and nanosecond scale. Microsecond simulations show two distinct behaviors; (i) two out of four systems maintain chiral dipolar oriented water wires, but also undergo a strong reorganization of the crystal shape, (ii) the two other I-quartet channels completely lose the initial organization, nonetheless keeping a water transport activity. Short MD simulations with higher time resolution were conducted to characterize the dynamic properties of water molecules in these model channels and provided a detailed hypothesis on the molecular mechanism of water permeation. The ordered confined water was characterized with quantitative measures of hydrogen-bond life-time and single particle dynamics, showing variability among I-quartet channels. We will further discuss the underlying assumptions, currently based on self-aggregation simulations and crystal patches embedded in lipid bilayer simulations and attempt to describe possible alternative approaches to computationally capture the water permeation mechanism and the self-assembly process of these AWCs.

}, issn = {1364-5498}, doi = {10.1039/c8fd00046h}, author = {Murail, Samuel and Vasiliu, Tudor and Neamtu, Andrei and Barboiu, Mihail and Sterpone, Fabio and Marc Baaden} } @article {2017|2021, title = {A membrane-inserted structural model of the yeast mitofusin Fzo1}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 Aug 31}, pages = {10217}, type = {Research Article}, abstract = {

Mitofusins are large transmembrane GTPases of the dynamin-related protein family, and are required for the tethering and fusion of mitochondrial outer membranes. Their full-length structures remain unknown, which is a limiting factor in the study of outer membrane fusion. We investigated the structure and dynamics of the yeast mitofusin Fzo1 through a hybrid computational and experimental approach, combining molecular modelling and all-atom molecular dynamics simulations in a lipid bilayer with site-directed mutagenesis and in vivo functional assays. The predicted architecture of Fzo1 improves upon the current domain annotation, with a precise description of the helical spans linked by flexible hinges, which are likely of functional significance. In vivo site-directed mutagenesis validates salient aspects of this model, notably, the long-distance contacts and residues participating in hinges. GDP is predicted to interact with Fzo1 through the G1 and G4 motifs of the GTPase domain. The model reveals structural determinants critical for protein function, including regions that may be involved in GTPase domain-dependent rearrangements.

}, issn = {2045-2322}, doi = {10.1038/s41598-017-10687-2}, author = {De Vecchis, Dario and Cavellini, Laetitia and Marc Baaden and J{\'e}r{\^o}me H{\'e}nin and Cohen, Micka{\"e}l M and Antoine Taly} } @conference {2017|2101, title = {Molecular Visualization of Computational Biology Data: A Survey of Surveys}, booktitle = {EuroVis 2017 - Short Papers}, year = {2017}, publisher = {The Eurographics Association}, organization = {The Eurographics Association}, isbn = {978-3-03868-043-7}, doi = {10.2312/eurovisshort.20171146}, author = {Alharbi, Naif and Alharbi, Mohammad and Martinez, Xavier and Krone, Michael and Rose, Alexander S. and Marc Baaden and Laramee, Robert S. and Chavent, Matthieu}, editor = {Barbora Kozlikova and Tobias Schreck and Thomas Wischgoll} } @article {2017|2029, title = {Multi-scale simulations of biological systems using the OPEP coarse-grained model.}, journal = {Biochem Biophys Res Commun}, year = {2017}, month = {2017 Sep 14}, abstract = {

Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.

}, issn = {1090-2104}, doi = {10.1016/j.bbrc.2017.08.165}, author = {Sterpone, Fabio and Doutreligne, S{\'e}bastien and Tran, Thanh Thuy and Melchionna, Simone and Marc Baaden and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2017|2095, title = {Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.}, journal = {J Phys Chem B}, volume = {121}, year = {2017}, month = {2017 06 08}, pages = {5483-5498}, abstract = {

Transforming growth factors (TGF-βs) are proteins that regulate cell growth by binding to their receptors. In contrast to transforming growth factor (TGF) β1, TGF-β3 homodimer is believed to exist also in an open conformation, in which both of its monomers are loosely packed against each other. At the origin of this difference is the H3-helix. Its sequence and degree of structuration seem to govern the outcome of TGF dimerization. We docked two monomers of TGF-β3 with intact and altered H3 α-helix against each other using HADDOCK. TGF-β3 monomer with an intact H3-helix exclusively forms closed conformations of homodimer, whereas the open conformation may coexist with the closed one when a part of the H3 α-helix is destabilized. We quantify the difference in its conformational preference for the open versus the closed structure by calculating the binding energy between monomers using the MMPBSA approach. We compare the wild type (wt) TGFβ3/TGFβ1 homodimers in the Protein Data Bank to a swapped mutant where all residues of the H3-helix were mutated to the respective TGFβ1/TGFβ3 sequence. Swapping stabilizes the closed conformation and destabilizes the open conformation of TGFβ3. Further detailed insight is derived from molecular dynamics simulation studies suggesting that Val 61 of the H3-helix may act as an anchor residue for the closed conformation of TGFβ3. Computational alanine scanning mutagenesis confirms that several residues of the H3-helix are the hot residues for the closed conformation of TGFβ3. These observations may bear relevance to general conformational transitions in proteins and specifically in the TGFβ superfamily.

}, keywords = {Molecular Dynamics Simulation, Protein Conformation, alpha-Helical, Transforming Growth Factor beta3}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.7b01867}, author = {Nayeem, Shahid M and Oteri, Francesco and Marc Baaden and Deep, Shashank} } @article {2017|2096, title = {String method solution of the gating pathways for a pentameric ligand-gated ion channel.}, journal = {Proc Natl Acad Sci U S A}, volume = {114}, year = {2017}, month = {2017 05 23}, pages = {E4158-E4167}, abstract = {

Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.

}, keywords = {Computer Simulation, Ligand-Gated Ion Channels, Models, Biological, Models, Chemical}, issn = {1091-6490}, doi = {10.1073/pnas.1617567114}, author = {Lev, Bogdan and Murail, Samuel and Poitevin, Fr{\'e}d{\'e}ric and Cromer, Brett A and Marc Baaden and Delarue, Marc and Allen, Toby W} } @article {2017|2102, title = {Visualization of Biomolecular Structures: State of the Art Revisited: Visualization of Biomolecular Structures}, journal = {Computer Graphics Forum}, volume = {36}, year = {2017}, pages = {178{\textendash}204}, issn = {01677055}, doi = {10.1111/cgf.13072}, url = {http://doi.wiley.com/10.1111/cgf.13072}, author = {Kozlikova, B. and Krone, M. and Falk, M. and Lindow, N. and Marc Baaden and Baum, D. and Viola, I. and Parulek, J. and Hege, H.-C.} } @article {2017|2042, title = {What Can Human-Guided Simulations Bring to RNA Folding?}, journal = {Biophys J}, volume = {113}, year = {2017}, month = {2017 Jul 25}, pages = {302-312}, abstract = {

Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.

}, keywords = {Access to Information, Computer Simulation, Feedback, Psychological, Humans, Internet, Models, Genetic, Models, Molecular, RNA, RNA Folding, Software, Solvents}, issn = {1542-0086}, doi = {10.1016/j.bpj.2017.05.047}, author = {Mazzanti, Liuba and Doutreligne, S{\'e}bastien and Gageat, Cedric and Philippe Derreumaux and Antoine Taly and Marc Baaden and Pasquali, Samuela} } @conference {2016|1415, title = {Interactive visual analytics of molecular data in immersive environments via a semantic definition of the content and the context}, booktitle = {2016 Workshop on Immersive Analytics (IA)}, year = {2016}, month = {March}, abstract = {

Bringing together, in a unique immersive environment, visualization and analysis of scientific and complex data requires a thorough approach in order to fulfill scientists\&$\#$39; specific expectations. Such an approach needs to consider the highly heterogeneous nature of data, the dynamic interactions between experts and data, and the large amount of data involved in scientific studies. Whereas small and static scientific datasets can quickly be deciphered thanks to standard immersive tools such as 3D visualization software packages, bigger and dynamic datasets exceed the analytical capacity of these tools, requiring an efficient platform for their manipulation. Through the example of the structural biology field we discuss the need for an approach based on a high-level definition of the content (scientific data) and the context (immersive environments and interfaces). Our design is illustrated by a platform for dynamic and intelligent representation of data to the user. The data hierarchical classification will provide new ways to interact with the data via intelligent and direct relationships between them. This approach is based on the semantic definition of all the concepts manipulated in the virtual environment, either abstract or concrete, which allows for an adaptive and interactive experience of both visualization and analysis.

}, keywords = {Computer Graphics [I.3.7]: Three-Dimensional Graphics and Realism-Virtual Reality, content high-level definition, content management, content semantic definition, Context, context high-level definition, context semantic definition, data analysis, data dynamic representation, data intelligent representation, data visualisation, Data visualization, molecular data interactive visual analysis, Ontologies, Resource description framework, Semantics, static scientific datasets, structural biology field, Three-dimensional displays, Tools, virtual environment, Virtual Reality}, doi = {10.1109/IMMERSIVE.2016.7932383}, author = {M. Trellet and Nicolas F{\'e}rey and Marc Baaden and P. Bourdot} } @article {2016|1447, title = {{S}alt-{E}xcluding {A}rtificial {W}ater {C}hannels {E}xhibiting {E}nhanced {D}ipolar {W}ater and {P}roton {T}ranslocation}, journal = {J. Am. Chem. Soc.}, volume = {138}, number = {16}, year = {2016}, month = {apr}, pages = {5403{\textendash}5409}, author = {Licsandru, E. and Kocsis, I. and Shen, Y. X. and Murail, S. and Legrand, Y. M. and van der Lee, A. and Tsai, D. and Marc Baaden and Kumar, M. and Barboiu, M.} } @article {2016|1550, title = {{S}ites of {A}nesthetic {I}nhibitory {A}ction on a {C}ationic {L}igand-{G}ated {I}on {C}hannel}, journal = {Structure}, volume = {24a}, number = {4}, year = {2016}, month = {apr}, pages = {595{\textendash}605}, author = {Laurent, B. and Murail, S. and Shahsavar, A. and Sauguet, L. and Delarue, M. and Marc Baaden} } @article {2016, title = {Visual Analysis of Biomolecular Cavities: State of the Art}, journal = {Comput. Graphics Forum}, volume = {35}, number = {3}, year = {2016}, month = {jun}, pages = {527{\textendash}551}, keywords = {AMBIENT OCCLUSION, ANALYTICAL SHAPE, BINDING-SITE IDENTIFICATION, LIGAND-BINDING, PORE DIMENSIONS, PROTEIN CAVITIES, SURFACE, TIME MOLECULAR VISUALIZATION, TRAVEL DEPTH, WEB SERVER}, url = {https://hal.archives-ouvertes.fr/hal-01400464}, author = {Krone, M. and Kozlikova, B. and Lindow, N. and Marc Baaden and Baum, D. and Parulek, J. and Hege, H.-C. and Viola, I.} } @article {2016|1401, title = {Visualization of Biomolecular Structures: State of the Art Revisited}, journal = {Comput. Graphics Forum}, year = {2016}, month = {nov}, url = {https://hal.archives-ouvertes.fr/hal-01400465}, author = {Kozlikova, B. and Krone, M. and Falk, M. and Lindow, N. and Marc Baaden and Baum, D. and Viola, I. and Parulek, J. and Hege, H.-C.} } @conference {2015|1556, title = {Content and task based navigation for structural biology in 3D environments}, booktitle = {Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on}, year = {2015}, month = {mar}, pages = {31{\textendash}36}, keywords = {3D environment, biology computing, Cameras, content navigation, data visualisation, feature extraction, molecular biology, molecule visualisation, Navigation, Pro, rendering (computer graphics), stereoscopic rendering feature, structural biology, task based navigation}, author = {M. Trellet and Nicolas F{\'e}rey and Marc Baaden and P. Bourdot} } @article {2015|1780, title = {{E}pock: rapid analysis of protein pocket dynamics}, journal = {Bioinformatics}, volume = {31}, number = {9}, year = {2015}, month = {may}, pages = {1478{\textendash}1480}, doi = {10.1093/bioinformatics/btu822}, author = {Laurent, Benoist and Matthieu Chavent and Cragnolini, Tristan and Dahl, Anna Caroline E. and Pasquali, Samuela and Philippe Derreumaux and Sansom, Mark S. P. and Marc Baaden} } @article {2015|1975, title = {{A}llosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {112}, number = {9}, year = {2015}, month = {mar}, pages = {2865{\textendash}2870}, author = {Moraga-Cid, G. and Sauguet, L. and Huon, C. and Malherbe, L. and Girard-Blanc, C. and Petres, S. and Murail, S. and Antoine Taly and Marc Baaden and Delarue, M. and Corringer, P. J.} } @article {2015|1549, title = {{N}othing to sneeze at: a dynamic and integrative computational model of an influenza {A} virion}, journal = {Structure}, volume = {23}, number = {3}, year = {2015}, month = {mar}, pages = {584{\textendash}597}, author = {Reddy, T. and Shorthouse, D. and Parton, D. L. and Jefferys, E. and Fowler, P. W. and Matthieu Chavent and Marc Baaden and Sansom, M. S.} } @article {2015|1449, title = {{P}redicting and exploring complex nucleic acids architectures through a coarse-grained model}, journal = {J. Biomol. Struct. Dyn.}, volume = {33 Suppl 1}, year = {2015}, pages = {30{\textendash}31}, author = {Cragnolini, T. and Doutreligne, S. and Marc Baaden and Philippe Derreumaux and Pasquali, S.} } @article {2015|1701, title = {Predicting and exploring complex nucleic acids architectures through a coarse-grained model}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {33}, year = {2015}, pages = {30{\textendash}31}, doi = {10.1080/07391102.2015.1032593}, author = {Cragnolini, T. and Doutreligne, S. and Marc Baaden and Philippe Derreumaux and Pasquali, S.} } @article {2015, title = {{T}aming molecular flexibility to tackle rare diseases}, journal = {Biochimie}, volume = {113}, year = {2015}, pages = {54{\textendash}58}, author = {Cubellis, M. V. and Marc Baaden and Andreotti, G.} } @article {2015|1414, title = {{T}hree-dimensional representations of complex carbohydrates and polysaccharides{\textendash}{S}weet{U}nity{M}ol: a video game-based computer graphic software}, journal = {Glycobiology}, volume = {25}, number = {5}, year = {2015}, month = {may}, pages = {483{\textendash}491}, author = {Perez, S. and Tubiana, T. and Imberty, A. and Marc Baaden} } @conference {2015|1555, title = {UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules}, booktitle = {Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on}, year = {2015}, month = {mar}, pages = {1{\textendash}6}, keywords = {biomolecular systems, coarse-grained RNA, collaborative research applications, data visualisation, feature extracti, HireRNA physics engine, interactive systems, Ludic visual manipulation, molecular biophysics, RNA, software architecture, teaching, UnityMol framework}, author = {S. Doutreligne and C. Gageat and T. Cragnolini and Antoine Taly and S. Pasquali and Philippe Derreumaux and Marc Baaden} } @conference {2015|1408, title = {Visualization of Biomolecular Structures: State of the Art}, booktitle = {Eurographics Conference on Visualization (EuroVis) - STARs}, year = {2015}, publisher = {The Eurographics Association}, organization = {The Eurographics Association}, author = {Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Marc Baaden and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, editor = {R. Borgo and F. Ganovelli and I. Viola} } @conference {2014|1385, title = {Content-guided Navigation in Multimeric Molecular Complexes}, booktitle = {{BIOIMAGING} 2014 - Proceedings of the International Conference on Bioimaging, ESEO, Angers, Loire Valley, France, 3-6 March, 2014}, year = {2014}, pages = {76{\textendash}81}, doi = {10.5220/0004914300760081}, author = {M. Trellet and Nicolas F{\'e}rey and Marc Baaden and P. Bourdot} } @article {2014|1433, title = {{A} cooperative mechanism of clotrimazoles in {P}450 revealed by the dissociation picture of clotrimazole from {P}450}, journal = {J. Chem. Inf. Model.}, volume = {54}, number = {4}, year = {2014}, note = {[DOI:\href{http://dx.doi.org/10.1021/ci400660e}{10.1021/ci400660e}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/24611729}{24611729}]}, month = {apr}, pages = {1218{\textendash}1225}, author = {Wang, M. and Marc Baaden and Wang, J. and Liang, Z.} } @article {2014|1412, title = {{E}xa{V}iz: a flexible framework to analyse, steer and interact with molecular dynamics simulations}, journal = {Faraday Discuss.}, volume = {169}, year = {2014}, note = {[DOI:\href{http://dx.doi.org/10.1039/c3fd00142c}{10.1039/c3fd00142c}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/25340956}{25340956}]}, pages = {119{\textendash}142}, author = {Dreher, M and Prevoteau-Jonquet, J and Trellet, M and Piuzzi, M and Marc Baaden and Raffin, B and Nicolas F{\'e}rey and Robert, S and Limet, S.} } @inbook {2014|1720, title = {Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins}, booktitle = {Membrane Proteins Production for Structural Analysis}, year = {2014}, pages = {347{\textendash}392}, publisher = {Springer New York}, organization = {Springer New York}, author = {J{\'e}r{\^o}me H{\'e}nin and Marc Baaden and Antoine Taly} } @article {2014|1411, title = {{I}nnovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly}, journal = {Faraday Discuss.}, volume = {169}, year = {2014}, note = {[DOI:\href{http://dx.doi.org/10.1039/c3fd00134b}{10.1039/c3fd00134b}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/25340652}{25340652}]}, pages = {45{\textendash}62}, author = {Molza, A. E and Nicolas F{\'e}rey and Czjzek, M and Le Rumeur, E and Hubert, J. F and Tek, A and Laurent, B and Marc Baaden and Delalande, O.} } @article {2014|1413, title = {{M}olecular simulations and visualization: introduction and overview}, journal = {Faraday Discuss.}, volume = {169}, year = {2014}, note = {[DOI:\href{http://dx.doi.org/10.1039/c4fd90024c}{10.1039/c4fd90024c}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/25285906}{25285906}]}, pages = {9{\textendash}22}, author = {Hirst, J. D. and Glowacki, D. R. and Marc Baaden} } @article {2014|2015, title = {Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans}, journal = {J. Phys. Chem. B}, volume = {118}, number = {48}, year = {2014}, month = {dec}, pages = {13800{\textendash}13811}, doi = {10.1021/jp5089965}, author = {Oteri, F and Marc Baaden and Lojou, E and S Sacquin-Mora} } @article {2014|1798, title = {The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems}, journal = {Chem. Soc. Rev.}, volume = {43}, number = {13}, year = {2014}, pages = {4871{\textendash}4893}, doi = {10.1039/c4cs00048j}, author = {F. Sterpone and S. Melchionna and Pierre Tuffery and S. Pasquali and N. Mousseau and T. Cragnolini and Y Chebaro and J.-F. St-Pierre and M. Kalimeri and A. Barducci and Y. Laurin and A. Tek and Marc Baaden and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2014|1518, title = {{T}he weak, fluctuating, dipole moment of membrane-bound hydrogenase from {A}quifex aeolicus accounts for its adaptability to charged electrodes}, journal = {Phys. Chem. Chem. Phys.}, volume = {16}, number = {23}, year = {2014}, month = {may}, pages = {11318{\textendash}11322}, author = {Oteri, F and Ciaccafava, A and Poulpiquet, A and Marc Baaden and Lojou, E and S Sacquin-Mora} } @conference {2014|1496, title = {UnityMol: Interactive scientific visualization for integrative biology}, booktitle = {Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on}, year = {2014}, month = {nov}, pages = {109{\textendash}110}, keywords = {biology computing, biomolecular system visualization, data analysis, data exploration, data representation, data visualisation, information extraction, integrative biology, interactive scientific visualization, interactive virtual lab, molecular biophysics, UnityMol}, author = {S. Doutreligne and T. Cragnolini and S. Pasquali and Philippe Derreumaux and Marc Baaden} } @article {2013|1403, title = {{C}oarse-grain modelling of protein-protein interactions}, journal = {Curr. Opin. Struct. Biol.}, volume = {23}, number = {6}, year = {2013}, pages = {878{\textendash}886}, author = {Marc Baaden and Marrink, S. J.} } @article {2013|1525, title = {{F}ormation of raft-like assemblies within clusters of influenza hemagglutinin observed by {M}{D} simulations}, journal = {Plos Comput. Biol.}, volume = {9}, number = {4}, year = {2013}, month = {apr}, pages = {e1003034}, author = {Parton, D. L. and Tek, A. and Marc Baaden and Sansom, M. S.} } @article {2013|1528, title = {{G}ame on, science - how video game technology may help biologists tackle visualization challenges}, journal = {Plos One}, volume = {8}, number = {3}, year = {2013}, pages = {e57990}, author = {Lv, Z. and Tek, A. and Da Silva, F. and Empereur-mot, C. and Matthieu Chavent and Marc Baaden} } @article {2013|1531, title = {Interactive Molecular Dynamics: Scaling up to Large Systems.}, journal = {Procedia Comput. Sci.}, volume = {18}, year = {2013}, pages = {20{\textendash}29}, doi = {10.1016/j.procs.2013.05.165}, author = {M. Dreher and M. Piuzzi and A. Turki and Matthieu Chavent and Marc Baaden and Nicolas F{\'e}rey and S. Limet and B. Raffin and S. Robert} } @article {2013|1426, title = {MANHaptic: A Haptic Adaptive Method for Precise Manipulation, Assembly \and Navigation}, journal = {International Journal on Human Machine Interaction}, volume = {1}, year = {2013}, pages = {60{\textendash}67}, author = {A. Tek and Marc Baaden and Nicolas F{\'e}rey and P. Bourdot} } @conference {2013|1381, title = {Navigation guid{\'e}e par le contenu pour l{\textquoteright}exploration mol{\'e}culaire.}, booktitle = {Actes de l{\textquoteright}AFRV}, year = {2013}, author = {M. Trellet and Nicolas F{\'e}rey and Marc Baaden and P. Bourdot} } @article {2013|1406, title = {{S}tructural basis for ion permeation mechanism in pentameric ligand-gated ion channels}, journal = {Embo J.}, volume = {32}, number = {5}, year = {2013}, month = {mar}, pages = {728{\textendash}741}, author = {Sauguet, L. and Poitevin, F. and Murail, S. and Van Renterghem, C. and Moraga-Cid, G. and Malherbe, L. and Thompson, A. W. and Koehl, P. and Corringer, P. J. and Marc Baaden and Delarue, M.} } @booklet {2013|1576, title = {Structural basis for ion permeation in a pentameric ligand-gated ion channel revealed by x-ray crystallograph}, year = {2013}, note = {44-45}, author = {Marc Baaden and M. Delarue} } @article {2013|1430, title = {{U}nderstanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces}, journal = {J. Biomed. Mater. Res. A}, volume = {101}, number = {4}, year = {2013}, month = {apr}, pages = {1210{\textendash}1222}, author = {Costa, D. and Garrain, P. A. and Marc Baaden} } @inbook {2012|1575, title = {Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations}, year = {2012}, publisher = {Intech, Croatia}, organization = {Intech, Croatia}, chapter = {Protein Interaction / Book 2}, author = {A. Tek and B. Laurent and M. Piuzzi and Z. Lu and Marc Baaden and O. Delalande and Matthieu Chavent and Nicolas F{\'e}rey and C. Martin and L. Piccinali and B. Katz and P. Bourdot and Ludovic Autin}, editor = {W. Cai and H. Hong} } @article {2012|1382, title = {Bient{\^o}t dans votre amphith{\'e}{\^a}tre, la chimie fera son cin{\'e}ma. De la bonne utilisation des ressources informatiques pour l{\textquoteright}enseignement : visualisation mol{\'e}culaire, illustration de processus chimiques et de mod{\`e}les physiques}, journal = {Actualit{\'e} Chimique}, volume = {363}, year = {2012}, author = {Matthieu Chavent and Marc Baaden and E. H{\'e}non and S. Antonczak} } @article {2012|1458, title = {Mixing atomistic and coarse grain solvation models for MD simulations: let WT4 handle the bulk}, journal = {Jctc}, year = {2012}, month = {jun}, doi = {10.1021/ct3001816}, author = {L. Darre and A. Tek and Marc Baaden and S. Pantano} } @article {2012|1546, title = {Modeling complex biological systems: From solution chemistry to membranes and channels}, journal = {Pure Appl. Chem.}, volume = {ASAP}, year = {2012}, month = {nov}, doi = {10.1351/PAC-CON-12-04-10}, author = {B. Laurent and S. Murail and F. Da Silva and P.-J. Corringer and Marc Baaden} } @article {2012|1506, title = {A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel}, journal = {Nature Structural \& Molecular Biology}, year = {2012}, month = {apr}, author = {M. Prevost and L. Sauguet and H. Nury and C. Van Renterghem and C. Huon and F. Poitevin and Marc Baaden and M. Delarue and P.-J. Corringer} } @article {2011|1432, title = {Electrostatically{\textendash}driven fast association and perdeuteration allow transferred cross{\textendash}relaxation detection for G protein{\textendash}coupled receptor ligands with equilibrium dissociation constants in the high{\textendash}to{\textendash}low nanomolar range}, journal = {J Biomolecular Nmr}, volume = {50}, number = {3}, year = {2011}, month = {jul}, pages = {191{\textendash}5}, url = {http://www.ibpc.fr/UMR7099/Publis/pdf/Catoire11.pdf}, author = {L. J. Catoire and M. Damian and Marc Baaden and E. Guittet and J.-L. Ban{\`e}res} } @article {2011|1612, title = {Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase}, journal = {Biophys. J.}, volume = {101}, number = {6}, year = {2011}, pages = {1440{\textendash}1449}, doi = {10.1016/j.bpj.2011.07.048}, author = {Delalande, O. and S Sacquin-Mora and Marc Baaden} } @conference {2011, title = {FvNano: A Virtual Laboratory to Manipulate Molecular Systems}, booktitle = {1st IEEE symposium on biological data visualization, Providence, RI @ ieee visweek, 2011, N$\#$ 136}, year = {2011}, url = {http://www.biovis.net/materials/abstracts/BioVispaper136.pdf}, author = {Matthieu Chavent and Marc Piuzzi and Alex Tek and Marc Baaden} } @article {2011|1437, title = {GPU-accelerated atom and dynamic bond visualization using HyperBalls: a unified algorithm for balls, sticks and hyperboloids}, journal = {J. Comput. Chem.}, volume = {32}, number = {13}, year = {2011}, month = {oct}, pages = {2924{\textendash}2935}, doi = {10.1002/jcc.21861/abstract}, author = {Matthieu Chavent and A. Vanel and A. Tek and B. L{\'e}vy and S. Robert and B. Raffin and Marc Baaden} } @article {2011|1393, title = {GPU-powered tools boost molecular visualization}, journal = {Briefings Bioinf.}, volume = {12}, year = {2011}, month = {feb}, pages = {689{\textendash}701}, author = {Matthieu Chavent and B. L{\'e}vy and M. Krone and K. Bidmon and J. P. Nomin{\'e} and T. Ertl and Marc Baaden} } @article {2011|1505, title = {X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel}, journal = {Nature}, volume = {469}, year = {2011}, month = {jan}, pages = {428{\textendash}431}, keywords = {anaesthetics, desflurane, GLIC, propofol}, url = {http://www.nature.com/nature/journal/v469/n7330/full/nature09647.html}, author = {H. Nury and C. Van Renterghem and Y. Weng and A. Tran and Marc Baaden and V. Dufresne and J.-P. Changeux and J. M. Sonner and M. Delarue and P.-J. Corringer} } @article {2010|1613, title = {Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress}, journal = {Biophys. J.}, volume = {99}, number = {10}, year = {2010}, pages = {3412{\textendash}3419}, doi = {10.1016/j.bpj.2010.09.026}, author = {S Sacquin-Mora and Delalande, O. and Marc Baaden} } @article {2010|1524, title = {{H}ow cations can assist {D}{N}ase {I} in {D}{N}{A} binding and hydrolysis}, journal = {Plos Comput. Biol.}, volume = {6}, year = {2010}, month = {nov}, pages = {e1001000}, author = {M. Gueroult and D. Picot and J. Abi-Ghanem and B. Hartmann and Marc Baaden} } @conference {2010|1410, title = {Interacting with Molecular Simulations using a Multimodal VR Framework}, booktitle = {EuroVR-EVE}, year = {2010}, pages = {1{\textendash}4}, address = {Orsay, France}, author = {A Tek and B Laurent and Nicolas F{\'e}rey and Marc Baaden} } @article {2010|1512, title = {{M}odeling the early stage of {D}{N}{A} sequence recognition within {R}ec{A} nucleoprotein filaments}, journal = {Nucleic Acids Res.}, volume = {38}, year = {2010}, month = {oct}, pages = {6313{\textendash}6323}, author = {A Saladin and Amourda, C. and Poulain, P. and Nicolas F{\'e}rey and Marc Baaden and Martin Zacharias and Delalande, O. and Chantal Pr{\'e}vost} } @article {2010|1516, title = {{M}ulti-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device}, journal = {Pac. Symp. Biocomput.}, year = {2010}, pages = {205{\textendash}215}, author = {Delalande, O. and Nicolas F{\'e}rey and Laurent, B. and Gueroult, M. and Hartmann, B. and Marc Baaden} } @inbook {2010|1569, title = {Molecular dynamics studies of outer membrane proteins : a story of barrels}, year = {2010}, pages = {225{\textendash}247}, publisher = {Royal Society of Chemistry}, organization = {Royal Society of Chemistry}, chapter = {Molecular Simulations and Biomembranes: From Biophysics to Function}, address = {United Kingdom}, author = {S. Khalid and Marc Baaden}, editor = {P.C. Biggin and M.S.P. Sansom} } @article {2010|1529, title = {{O}ne-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {107}, year = {2010}, month = {apr}, pages = {6275{\textendash}6280}, author = {Nury, H. and Poitevin, F. and Van Renterghem, C. and Changeux, J. P. and Corringer, P. J. and Delarue, M. and Marc Baaden} } @article {2010|1395, title = {{P}hotocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination}, journal = {Chembiochem}, volume = {11}, year = {2010}, month = {mar}, pages = {653{\textendash}663}, author = {Sinha, D. K. and Neveu, P. and Gagey, N. and Aujard, I. and Benbrahim-Bouzidi, C. and Le Saux, T. and Rampon, C. and Gauron, C. and Goetz, B. and Dubruille, S. and Marc Baaden and Volovitch, M. and Bensimon, D. and Vriz, S. and Jullien, L.} } @conference {2010|1459, title = {A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors}, booktitle = {JOBIM}, year = {2010}, author = {Matthieu Chavent and A. Vanel and B. L{\'e}vy and B. Raffin and A. Tek and Marc Baaden} } @mastersthesis {2010|1570, title = {Simulations num{\'e}riques de syst{\`e}mes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes}, year = {2010}, school = {Universit{\'e} Paris-Diderot - Paris VII (15/06/2010), Fr{\'e}d{\'e}ric Dardel (Pr.)}, type = {phd}, author = {Marc Baaden} } @article {2010|1444, title = {{T}he molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor {T}om20 from {O}ryza sativa involves an {L}{R}{T}{L}{A} motif}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, month = {nov}, pages = {13839{\textendash}13846}, author = {Y. Zhang and Marc Baaden and J. Yan and J. Shao and S. Qiu and Y. Wu and Y. Ding} } @article {2010|1457, title = {{A}tomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues}, journal = {J. Physiol. (lond.)}, volume = {588}, year = {2010}, month = {feb}, pages = {565{\textendash}572}, author = {Corringer, P. J. and Marc Baaden and Bocquet, N. and Delarue, M. and Dufresne, V. and Nury, H. and Prevost, M. and Van Renterghem, C.} } @article {2009|1399, title = {{C}oarse-grain simulations of the {R}-{S}{N}{A}{R}{E} fusion protein in its membrane environment detect long-lived conformational sub-states}, journal = {Chemphyschem}, volume = {10}, year = {2009}, month = {jul}, pages = {1548{\textendash}1552}, author = {Durrieu, M. P. and Bond, P. J. and Sansom, M. S. and Lavery, R. and Marc Baaden} } @article {2009|1435, title = {{C}omplex molecular assemblies at hand via interactive simulations}, journal = {J. Comput. Chem.}, volume = {30}, year = {2009}, month = {nov}, pages = {2375{\textendash}2387}, author = {Delalande, O. and Nicolas F{\'e}rey and Grasseau, G. and Marc Baaden} } @article {2009|1504, title = {{X}-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation}, journal = {Nature}, volume = {457}, year = {2009}, month = {jan}, pages = {111{\textendash}114}, author = {Bocquet, N. and Nury, H. and Marc Baaden and Le Poupon, C. and Changeux, J. P. and Delarue, M. and Corringer, P. J.} } @conference {2008|1557, title = {From Interactive to Immersive Molecular Dynamics}, booktitle = {Workshop on Virtual Reality Interaction and Physical Simulation (VRIPHYS 08 - Eurographics)}, year = {2008}, month = {nov}, pages = {89{\textendash}96}, address = {Grenoble - France}, author = {Nicolas F{\'e}rey and O. Delalande and G. Grasseau and Marc Baaden}, editor = {F. Faure and M. Teschner} } @article {2008, title = {Interactions between neuronal fusion proteins explored by molecular dynamics}, journal = {Biophys. J.}, volume = {94}, number = {9}, year = {2008}, month = {may}, pages = {3436{\textendash}3446}, author = {Durrieu, Marie-Pierre and Lavery, Richard and Marc Baaden} } @article {2008|1390, title = {Microseconds dynamics simulations of the outer-membrane protease T}, journal = {Biophys. J.}, volume = {94}, number = {1}, year = {2008}, month = {jan}, pages = {71{\textendash}78}, author = {Neri, Marilisa and Marc Baaden and Carnevale, Vincenzo and Anselmi, Claudio and Maritan, Amos and Carloni, Paolo} } @article {2008|1409, title = {Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers}, journal = {European Biophysics Journal with Biophysics Letters}, volume = {37}, number = {2}, year = {2008}, month = {feb}, pages = {131{\textendash}141}, author = {Cox, Katherine and Bond, Peter J. and Grottesi, Alessandro and Marc Baaden and Sansom, Mark S. P.} } @conference {2008|1553, title = {A VR Framework for Interacting with Molecular Simulations}, booktitle = {Symposium on Virtual Reality Software and Technology (ACM-VRST 2008)}, year = {2008}, month = {oct}, pages = {91{\textendash}94}, address = {Bordeaux - France}, author = {Nicolas F{\'e}rey and O. Delalande and G. Grasseau and Marc Baaden} } @conference {2007|1517, title = {Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure}, booktitle = {ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications}, volume = {38}, year = {2007}, pages = {729{\textendash}736}, publisher = {John von Neumann Institute for Computing, Juelich, Germany.}, organization = {John von Neumann Institute for Computing, Juelich, Germany.}, url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=8468}, author = {E. Krieger and L. Leger and M.P. Durrieu and N. Taib and P. Bond and M. Laguerre and R. Lavery and M.S.P. Sansom and Marc Baaden}, editor = {C.B.G.R. Joubert and F. Peters and T. Lippert and M. Buecker and B. Gibbon and and B. Mohr} } @inbook {2007|1564, title = {There{\textquoteright}s plenty of room in the middle: multi-scale modelling of biological systems}, year = {2007}, pages = {173{\textendash}195}, publisher = {Research signpost, India}, organization = {Research signpost, India}, chapter = {Recent Advances in Protein engineering}, address = {Trivandrum, Kerala, India}, author = {Marc Baaden and R. Lavery}, editor = {A.G. de Brevern} } @article {2007|1477, title = {Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database}, journal = {Journal of Molecular Graphics \& Modelling}, volume = {25}, number = {6}, year = {2007}, month = {mar}, pages = {896{\textendash}902}, author = {Tai, Kaihsu and Marc Baaden and Murdock, Stuart and Wu, Bing and Ng, Muan Hong and Johnston, Steven and Boardman, Richard and Fangohr, Hans and Cox, Katherine and Essex, Jonathan W. and Sansom, Mark S. P.} } @article {2005|1476, title = {Membrane protein structure quality in molecular dynamics simulation}, journal = {Journal of Molecular Graphics \& Modelling}, volume = {24}, number = {2}, year = {2005}, note = {International Meeting of the Molecular-Graphics-and-Modelling-Society, Manchester, ENGLAND, 2004}, month = {oct}, pages = {157{\textendash}165}, author = {Law, RJ and Capener, C and Marc Baaden and Bond, PJ and Campbell, J and Patargias, G and Arinaminpathy, Y and Sansom, MSP} } @article {2004|1537, title = {Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {57}, number = {4}, year = {2004}, month = {dec}, pages = {783{\textendash}791}, author = {Faraldo-Gomez, JD and Forrest, LR and Marc Baaden and Bond, PJ and Domene, C and Patargias, G and Cuthbertson, J and Sansom, MSP} } @article {2004, title = {OmpT: Molecular dynamics simulations of an outer membrane enzyme}, journal = {Biophys. J.}, volume = {87}, number = {5}, year = {2004}, month = {nov}, pages = {2942{\textendash}2953}, author = {Marc Baaden and Sansom, MSP} } @article {2003, title = {Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA}, journal = {Biochemistry}, volume = {42}, number = {13}, year = {2003}, month = {apr}, pages = {3666{\textendash}3673}, author = {Campbell, JD and Biggin, PC and Marc Baaden and Sansom, MSP} } @article {2003|1475, title = {A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA}, journal = {J. Mol. Biol.}, volume = {331}, number = {1}, year = {2003}, month = {aug}, pages = {177{\textendash}189}, author = {Marc Baaden and Meier, C and Sansom, MSP} } @article {2003|1548, title = {Theoretical studies on lanthanide cation extraction by picolinamides: Ligand-cation interactions and interfacial behavior}, journal = {Solvent Extr. Ion Exch.}, volume = {21}, number = {2}, year = {2003}, pages = {199{\textendash}220}, author = {Marc Baaden and Berny, F and Madic, C and Schurhammer, R and Wipff, G} } @article {2002|1483, title = {Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/{{\textquoteright}{\textquoteright}}oil{{\textquoteright}{\textquoteright}}/TBP solutions with a comparison of supercritical CO2 and chloroform}, journal = {J. Phys. Chem. B}, volume = {106}, number = {2}, year = {2002}, month = {jan}, pages = {434{\textendash}441}, author = {Marc Baaden and Schurhammer, R and Wipff, G} } @article {2001|1479, title = {The chloroform TBP aqueous nitric acid interfacial system: a molecular dynamics investigation}, journal = {J. Mol. Liq.}, volume = {90}, number = {1-3, Sp. Iss. SI}, year = {2001}, note = {26th International Conference on Solution Chemistry (26 ICSC), FUKUOKA, JAPAN, JUL 26-31, 1999}, month = {feb}, pages = {1{\textendash}9}, author = {Marc Baaden and Berny, F and Wipff, G} } @article {2001|1520, title = {Lanthanide cation binding to a phosphoryl-calix{[}4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations}, journal = {Phys. Chem. Chem. Phys.}, volume = {3}, number = {7}, year = {2001}, pages = {1317{\textendash}1325}, author = {Marc Baaden and Burgard, M and Boehme, C and Wipff, G} } @article {2001|1482, title = {TBP at the water-oil interface: The effect of TBP concentration and water acidity investigated by molecular dynamics simulations}, journal = {J. Phys. Chem. B}, volume = {105}, number = {45}, year = {2001}, month = {nov}, pages = {11131{\textendash}11141}, author = {Marc Baaden and Burgard, M and Wipff, G} } @article {2000, title = {Calix{[}4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes}, journal = {Inorg. Chem.}, volume = {39}, number = {10}, year = {2000}, month = {may}, pages = {2033{\textendash}2041}, author = {Lambert, B and Jacques, V and Shivanyuk, A and Matthews, SE and Tunayar, A and Marc Baaden and Wipff, G and Bohmer, V and Desreux, JF} } @article {2000|1490, title = {Cation coordination by calix{[}4]arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs. Na+? A combined NMR and molecular dynamics study}, journal = {Journal of the Chemical Society-perkin Transactions 2}, number = {7}, year = {2000}, pages = {1315{\textendash}1321}, author = {Marc Baaden and Wipff, G and Yaftian, MR and Burgard, M and Matt, D} } @article {2000|1551, title = {Complexation of M3+ lanthanide cations by calix{[}4]arene-CMPO ligands: A molecular dynamics study in methanol solution and at a water/chloroform interface}, journal = {Supramol. Chem.}, volume = {12}, number = {1, Sp. Iss. SI}, year = {2000}, note = {International Symposium on Supramolecular Chemistry, FUKUOKA, JAPAN, 1997}, pages = {27+}, author = {Troxler, L and Marc Baaden and Bohmer, V and Wipff, G} } @article {2000|1501, title = {Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X}, journal = {Mol. Phys.}, volume = {98}, number = {6}, year = {2000}, month = {mar}, pages = {329{\textendash}342}, author = {Marc Baaden and Granger, P and Strich, A} } @mastersthesis {2000|1560, title = {Etudes de mol{\'e}cules extractantes en solution et aux interfaces liquide-liquide: aspects structuraux et m{\'e}canistiques des effets de synergie}, year = {2000}, note = {(N�: 3630), 2 vol., 218/42 pages.}, school = {Universit{\'e} Louis Pasteur, Strasbourg}, type = {phd}, author = {Marc Baaden} } @article {2000|1460, title = {Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study}, journal = {J. Alloys Compd.}, volume = {303}, year = {2000}, note = {22nd Rare Earth Research Conference, ARGONNE, ILLINOIS, JUL 11-15, 1999}, month = {may}, pages = {104{\textendash}111}, author = {Marc Baaden and Berny, F and Boehme, C and Muzet, N and Schurhammer, R and Wipff, G} } @inbook {2000|1559, title = {Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: a molecular dynamics investigation}, booktitle = {ACS Symposium Series 757}, year = {2000}, pages = {71{\textendash}85}, publisher = {Oxford University Press, New York}, organization = {Oxford University Press, New York}, chapter = {Calixarenes for separations}, author = {Marc Baaden and F. Berny and N. Muzet and L. Troxler and G. Wipff}, editor = {G. Lumetta, R.D. Rogers, and A.S. Gopalan} } @article {2000|1481, title = {M3+ lanthanide cation solvation by acetonitrile: The role of cation size, counterions, and polarization effects investigated by molecular dynamics and quantum mechanical simulations}, journal = {J. Phys. Chem. A}, volume = {104}, number = {32}, year = {2000}, month = {aug}, pages = {7659{\textendash}7671}, author = {Marc Baaden and Berny, F and Madic, C and Wipff, G} } @conference {2000|1532, title = {Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores}, booktitle = {Proceedings of the Euradwaste 1999 conference}, year = {2000}, pages = {390{\textendash}393}, address = {EC, Luxembourg}, author = {Marc Baaden and F. Berny and N. Muzet and R. Schurhammer and G. Wipff}, editor = {C. Davies} } @booklet {1999|1558, title = {Molecular Modeling with the ChemOffice Ultra 4.5 program suite.}, year = {1999}, author = {Marc Baaden} }