@article {2024, title = {A Perspective on the Prospective Use of AI in Protein Structure Prediction}, journal = {J Chem Inf Model}, volume = {64}, year = {2024}, month = {Jan}, pages = {26{\textendash}41}, author = {Versini, R. and Sritharan, S. and Aykac Fas, B. and Tubiana, T. and Aimeur, S. Z. and Henri, J. and Erard, M. and N{\"u}sse, O. and Andreani, J. and Baaden, M. and Fuchs, P. and Galochkina, T. and Chatzigoulas, A. and Cournia, Z. and Santuz, H. and S Sacquin-Mora and Taly, A.} } @article {2024|2169, title = {Structural profiles of the full phagocyte NADPH oxidase unveiled by combining computational biology and experimental knowledge}, journal = {J. Biol. Chem.}, volume = {300}, year = {2024}, pages = {107943}, abstract = {

The phagocyte NADPH oxidase (NOX2) is an enzyme, crucial for innate immune defense, producing reactive oxygen species necessary for pathogen destruction. Its activation requires the assembly of soluble proteins (p47phox, p40phox, p67phox, and Rac) with the membrane-bound flavocytochrome b558 (cytb558). We combined circular-dichroism analyses, with decades of experimental data, to filter structural models of the NADPH oxidase complex generated by the artificial intelligence program AlphaFold2 (AF2). The predicted patterns tend to closely resemble the active states of the proteins, as shown by the compact structure of the cytb558, whose dehydrogenase domain is stabilized closer to the membrane. The modeling of the interaction of p47phox with cytb558, which is the initial assembly and activation steps of the NADPH oxidase, enables us to describe how the C terminus of p47phox interacts with the cytb558. Combining the AF2 cytb558-p47phox model and its classical molecular dynamics simulations, we highlighted new hydrophobic lipid insertions of p47phox, particularly at residues Trp80-Phe81 of its PX domain. The AF2 models also revealed the implications of intrinsically disordered regions, such as the fragment between the PX domain and the SH3 regions of p47phox, in ensuring distant protein-protein and membrane-protein interactions. Finally, the AF2 prediction of the cytb558-Trimera model highlighted the importance of leaving Rac1 as a separate protein to reach an active state of the NADPH oxidase complex. Altogether, our step-by-step approach provides a structural model of the active complex showing how disordered regions and specific lipid and protein interactions can enable and stabilize the multisubunit assembly.

}, keywords = {alphafold, Circular Dichroism, Computational biology, lipid-protein interaction, membrane protein, molecular modeling, NADPH oxidase, NOX2, p47(phox), p67(phox), protein assembly, trimera}, author = {Aimeur, Sana and Fas, Burcu Aykac and Serfaty, Xavier and Santuz, Hubert and S Sacquin-Mora and Bizouarn, Tania and Taly, Antoine and Baciou, Laura} } @article {2023|2163, title = {Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology}, journal = {J Chem Inf Model}, year = {2023}, month = {Jun}, author = {Graille, M and S Sacquin-Mora and Antoine Taly} } @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} } @article {2020|2125, title = {Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ Peptide.}, journal = {J Chem Inf Model}, volume = {60}, year = {2020}, month = {2020 Mar 23}, pages = {1399-1408}, abstract = {

There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ trimer from the U-shape conformation and MD simulations starting from Aβ dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ peptide.

}, issn = {1549-960X}, doi = {10.1021/acs.jcim.9b01074}, author = {Minh Hung, Huynh and Nguyen, Minh Tho and Tran, Phuong-Thao and Truong, Vi Khanh and Chapman, James and Quynh Anh, Le Huu and Philippe Derreumaux and Vu, Van V and Ngo, Son Tung} } @inbook {2020|2123, title = {Protein thermal stability}, booktitle = {Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly}, year = {2020}, author = {S. Timr and D. Madern and F. Sterpone} } @article {2020|2142, title = {Scalable molecular dynamics on CPU and GPU architectures with NAMD}, journal = {The Journal of Chemical Physics}, volume = {153}, year = {2020}, chapter = {044130}, abstract = {

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

}, keywords = {NAMD}, doi = {10.1063/5.0014475}, url = {https://aip.scitation.org/doi/10.1063/5.0014475}, author = {James Phillips and David Hardy and Julio Maia and John Stone and Joao Ribeiro and Rafael Bernardi and Ronak Buch and Giacomo Fiorin and J{\'e}r{\^o}me H{\'e}nin and Wei Jiang and Ryan McGreevy and Melo, Marcelo Cardoso dos Reis and Brian Radak and Robert Skeel and Abhishek Singharoy and Yi Wang and Benoit Roux and Aleksei Aksimentiev and Zan Luthey-Schulten and Laxmikant Kale and Klaus Schulten and Christophe Chipot and Emad Tajkhorshid} } @article {2019|2060, title = {Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand.}, journal = {Biochemistry}, volume = {58}, year = {2019}, month = {2019 May 21}, pages = {2463-2473}, abstract = {

The double-stranded RNA-binding domain (dsRBD) is a broadly distributed domain among RNA-maturing enzymes. Although this domain recognizes dsRNA\&$\#$39;s structures via a conserved canonical structure adopting an α-βββ-α topology, several dsRBDs can accommodate discrete structural extensions expanding further their functional repertoire. How these structural elements engage cooperative communications with the canonical structure and how they contribute to the dsRBD\&$\#$39;s overall folding are poorly understood. Here, we addressed these issues using the dsRBD of human dihydrouridine synthase-2 (hDus2) (hDus2-dsRBD) as a model. This dsRBD harbors N- and C-terminal extensions, the former being directly involved in the recognition of tRNA substrate of hDus2. These extensions engage residues that form a long-range hydrophobic network (LHN) outside the RNA-binding interface. We show by coarse-grain Brownian dynamics that the Nt-extension and its residues F359 and Y364 rigidify the major folding nucleus of the canonical structure via an indirect effect. hDus2-dsRBD unfolds following a two-state cooperative model, whereas both F359A and Y364A mutants, designed to destabilize this LHN, unfold irreversibly. Structural and computational analyses show that these mutants are unstable due to an increase in the dynamics of the two extensions favoring solvent exposure of α2-helix and weakening the main folding nucleus rigidity. This LHN appears essential for maintaining a thermodynamic stability of the overall system and eventually a functional conformation for tRNA recognition. Altogether, our findings suggest that functional adaptability of extended dsRBDs is promoted by a cooperative hydrophobic coupling between the extensions acting as effectors and the folding nucleus of the canonical structure.

}, issn = {1520-4995}, doi = {10.1021/acs.biochem.9b00111}, author = {Bou-Nader, Charles and Pecqueur, Ludovic and Barraud, Pierre and Fontecave, Marc and Tisn{\'e}, Carine and S Sacquin-Mora and Hamdane, Djemel} } @article {2019|2127, title = {C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ Tetramer in Solution: Intensive MD Study.}, journal = {ACS Omega}, volume = {4}, year = {2019}, month = {2019 Jun 30}, pages = {11066-11073}, abstract = {

Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer\&$\#$39;s disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms \→ oligomers \→ photofibrils \→ mature fibrils \→ plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ tetramer (S4Aβ) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is \∼42 \± 3\%. Furthermore, the dissociation free energy of the S4Aβ peptide was predicted using a biased sampling method. The obtained free energy is Δ = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ peptide. We anticipate that the obtained S4Aβ structures could be used as targets for AD inhibitor screening over the in silico study.

}, issn = {2470-1343}, doi = {10.1021/acsomega.9b00992}, author = {Tung, Nguyen Thanh and Philippe Derreumaux and Vu, Van V and Nam, Pham Cam and Ngo, Son Tung} } @article {2019|2070, title = {Design games and game design: Relations between design, codesign and serious games in adult education}, journal = {From UXD to LivXD: Living eXperience Design}, year = {2019}, pages = {229{\textendash}253}, author = {Alvarez, Julian and Irrmann, Olivier and Djaouti, Damien and Antoine Taly and Rampnoux, Olivier and Sauv{\'e}, Louise} } @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|2067, title = {An inter-dimer allosteric switch controls NMDA receptor activity}, journal = {The EMBO journal}, volume = {38}, year = {2019}, author = {Esmenjaud, Jean-Baptiste and Stroebel, David and Chan, Kelvin and Grand, Teddy and David, M{\'e}lissa and Wollmuth, Lonnie P and Antoine Taly and Paoletti, Pierre} } @article {2019|2071, title = {Involvement of the GABAA receptor α subunit in the mode of action of etifoxine}, journal = {Pharmacological research}, volume = {145}, year = {2019}, pages = {104250}, author = {Mattei, C{\'e}sar and Antoine Taly and Soualah, Zineb and Saulais, Oph{\'e}lie and Henrion, Daniel and Gu{\'e}rineau, Nathalie C and Verleye, Marc and Legros, Christian} } @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|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} } @article {2019|2062, title = {The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements}, journal = {Nucleic Acids Res}, volume = {47}, year = {2019}, month = {02}, pages = {1836-1846}, abstract = {

Bacterial recombinational repair of double-strand breaks often begins with creation of initiating 3\&$\#$39; single-stranded DNA (ssDNA) tails on each side of a double-strand break (DSB). Importantly, if the RecBCD pathway is followed, RecBCD creates a gap between the sequences at 3\&$\#$39; ends of the initiating strands. The gap flanks the DSB and extends at least to the nearest Chi site on each strand. Once the initiating strands form ssDNA-RecA filaments, each ssDNA-RecA filament searches for homologous double-stranded DNA (dsDNA) to use as a template for the DNA synthesis needed to fill the gap created by RecBCD. Our experimental results show that the DNA synthesis requires formation of a heteroduplex dsDNA that pairs \>20 contiguous bases in the initiating strand with sequence matched bases in a strand from the original dsDNA. To trigger synthesis, the heteroduplex must be near the 3\&$\#$39; end of the initiating strand. Those experimentally determined requirements for synthesis combined with the Chi site dependence of the function of RecBCD and the distribution of Chi sites in bacterial genomes could allow the RecBCD pathway to avoid some genomic rearrangements arising from directly induced DSBs; however, the same three factors could promote other rearrangements.

}, doi = {10.1093/nar/gky1252}, author = {Li, Chastity and Danilowicz, Claudia and Tashjian, Tommy F and Godoy, Veronica G and Chantal Pr{\'e}vost and Prentiss, Mara} } @article {2019|2063, title = {Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair}, journal = {J Biol Chem}, volume = {294}, year = {2019}, month = {May}, pages = {7588-7600}, abstract = {

The evolutionarily conserved Escherichia coli translesion DNA polymerase IV (DinB) is one of three enzymes that can bypass potentially deadly DNA lesions on the template strand during DNA replication. Remarkably, however, DinB is the only known translesion DNA polymerase active in RecA-mediated strand exchange during error-prone double-strand break repair. In this process, a single-stranded DNA (ssDNA)-RecA nucleoprotein filament invades homologous dsDNA, pairing the ssDNA with the complementary strand in the dsDNA. When exchange reaches the 3\&$\#$39; end of the ssDNA, a DNA polymerase can add nucleotides onto the end, using one strand of dsDNA as a template and displacing the other. It is unknown what makes DinB uniquely capable of participating in this reaction. To explore this topic, we performed molecular modeling of DinB\&$\#$39;s interactions with the RecA filament during strand exchange, identifying key contacts made with residues in the DinB fingers domain. These residues are highly conserved in DinB, but not in other translesion DNA polymerases. Using a novel FRET-based assay, we found that DinB variants with mutations in these conserved residues are less effective at stabilizing RecA-mediated strand exchange than native DinB. Furthermore, these variants are specifically deficient in strand displacement in the absence of RecA filament. We propose that the amino acid patch of highly conserved residues in DinB-like proteins provides a mechanistic explanation for DinB\&$\#$39;s function in strand exchange and improves our understanding of recombination by providing evidence that RecA plays a role in facilitating DinB\&$\#$39;s activity during strand exchange.

}, keywords = {DinB, DNA damage, DNA polymerase, DNA polymerase IV, DNA repair, DNA synthesis, homologous recombination, RecA}, doi = {10.1074/jbc.RA118.006233}, author = {Tashjian, Tommy F and Danilowicz, Claudia and Molza, Anne-Elizabeth and Nguyen, Brian H and Chantal Pr{\'e}vost and Prentiss, Mara and Godoy, Veronica G} } @article {2019|2064, title = {Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology}, journal = {J Biol Chem}, volume = {294}, year = {2019}, month = {May}, pages = {8606-8616}, abstract = {

DNA recombination resulting from RecA-mediated strand exchange aided by RecBCD proteins often enables accurate repair of DNA double-strand breaks. However, the process of recombinational repair between short DNA regions of accidental similarity can lead to fatal genomic rearrangements. Previous studies have probed how effectively RecA discriminates against interactions involving a short similar sequence that is embedded in otherwise dissimilar sequences but have not yielded fully conclusive results. Here, we present results of in vitro experiments with fluorescent probes strategically located on the interacting DNA fragments used for recombination. Our findings suggest that DNA synthesis increases the stability of the recombination products. Fluorescence measurements can also probe the homology dependence of the extension of invading DNA strands in D-loops formed by RecA-mediated strand exchange. We examined the slow extension of the invading strand in a D-loop by DNA polymerase (Pol) IV and the more rapid extension by DNA polymerase LF-Bsu We found that when DNA Pol IV extends the invading strand in a D-loop formed by RecA-mediated strand exchange, the extension afforded by 82 bp of homology is significantly longer than the extension on 50 bp of homology. In contrast, the extension of the invading strand in D-loops by DNA LF-Bsu Pol is similar for intermediates with \≥50 bp of homology. These results suggest that fatal genomic rearrangements due to the recombination of small regions of accidental homology may be reduced if RecA-mediated strand exchange is immediately followed by DNA synthesis by a slow polymerase.

}, keywords = {cooperativity, DNA damage, DNA polymerase, DNA recombination, double-strand break (DSB), fluorescence resonance energy transfer (FRET), heteroduplex formation, molecular dynamics, RecA, strand displacement synthesis}, doi = {10.1074/jbc.RA119.007554}, author = {Lu, Daniel and Danilowicz, Claudia and Tashjian, Tommy F and Chantal Pr{\'e}vost and Godoy, Veronica G and Prentiss, Mara} } @article {2019|2119, title = {Stability Effect of Quinary Interactions Reversed by Single Point Mutations}, journal = {Journal of the American Chemical Society}, volume = {141}, year = {2019}, pages = {4660-4669}, doi = {10.1021/jacs.8b13025}, url = {https://doi.org/10.1021/jacs.8b13025}, author = {Gnutt, David and Timr, Stepan and Ahlers, Jonas and K{\"o}nig, Benedikt and Manderfeld, Emily and Heyden, Matthias and Sterpone, Fabio and Ebbinghaus, Simon} } @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} } @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} } @conference {2018|2069, title = {Is the boundary of fun redefined in a mixed-reality serious game?}, year = {2018}, author = {Antoine Taly} } @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|2111, title = {Molecular mechanism of the cell membrane pore formation induced by bubble stable cavitation}, journal = {The Journal of Physical Chemistry B}, volume = {123}, year = {2018}, pages = {71{\textendash}78}, author = {Man, Viet Hoang and Truong, Phan Minh and Li, Mai Suan and Wang, Junmei and Van-Oanh, Nguyen-Thi and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2018|2129, title = {Probing the quality control mechanism of the twin-arginine translocase with folding variants of a -designed heme protein.}, journal = {J Biol Chem}, volume = {293}, year = {2018}, month = {2018 05 04}, pages = {6672-6681}, abstract = {

Protein transport across the cytoplasmic membrane of bacterial cells is mediated by either the general secretion (Sec) system or the twin-arginine translocase (Tat). The Tat machinery exports folded and cofactor-containing proteins from the cytoplasm to the periplasm by using the transmembrane proton motive force as a source of energy. The Tat apparatus apparently senses the folded state of its protein substrates, a quality-control mechanism that prevents premature export of nascent unfolded or misfolded polypeptides, but its mechanistic basis has not yet been determined. Here, we investigated the innate ability of the model Tat system to recognize and translocate -designed protein substrates with experimentally determined differences in the extent of folding. Water-soluble, four-helix bundle maquette proteins were engineered to bind two, one, or no heme cofactors, resulting in a concomitant reduction in the extent of their folding, assessed with temperature-dependent CD spectroscopy and one-dimensional H NMR spectroscopy. Fusion of the archetypal N-terminal Tat signal peptide of the trimethylamine--oxide (TMAO) reductase (TorA) to the N terminus of the protein maquettes was sufficient for the Tat system to recognize them as substrates. The clear correlation between the level of Tat-dependent export and the degree of heme -induced folding of the maquette protein suggested that the membrane-bound Tat machinery can sense the extent of folding and conformational flexibility of its substrates. We propose that these artificial proteins are ideal substrates for future investigations of the Tat system\&$\#$39;s quality-control mechanism.

}, keywords = {Amino Acid Sequence, Bacterial Proteins, Circular Dichroism, Escherichia coli, Escherichia coli Proteins, Heme-Binding Proteins, Hemeproteins, Membrane Transport Proteins, Methylamines, Models, Molecular, Oxidoreductases, N-Demethylating, Periplasm, Protein Folding, Protein Sorting Signals, Protein Stability, Protein Transport, Proton Magnetic Resonance Spectroscopy, Substrate Specificity, Temperature}, issn = {1083-351X}, doi = {10.1074/jbc.RA117.000880}, author = {Sutherland, George A and Grayson, Katie J and Adams, Nathan B P and Mermans, Daphne M J and Jones, Alexander S and Robertson, Angus J and Auman, Dirk B and Brindley, Amanda A and Sterpone, Fabio and Tuffery, Pierre and Philippe Derreumaux and Dutton, P Leslie and Robinson, Colin and Hitchcock, Andrew and Hunter, C Neil} } @article {2018, title = {RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro}, journal = {Nucleic Acids Res}, volume = {ahead of print}, year = {2018}, month = {Jan}, abstract = {

Mg2+ ion stimulates the DNA strand exchange reaction catalyzed by RecA, a key step in homologous recombination. To elucidate the molecular mechanisms underlying the role of Mg2+ and the strand exchange reaction itself, we investigated the interaction of RecA with Mg2+ and sought to determine which step of the reaction is affected. Thermal stability, intrinsic fluorescence, and native mass spectrometric analyses of RecA revealed that RecA binds at least two Mg2+ ions with KD \‚{\^a}{\`a} 2 mM and 5 mM. Deletion of the C-terminal acidic tail of RecA made its thermal stability and fluorescence characteristics insensitive to Mg2+ and similar to those of full-length RecA in the presence of saturating Mg2+. These observations, together with the results of a molecular dynamics simulation, support the idea that the acidic tail hampers the strand exchange reaction by interacting with other parts of RecA, and that binding of Mg2+ to the tail prevents these interactions and releases RecA from inhibition. We observed that binding of the first Mg2+ stimulated joint molecule formation, whereas binding of the second stimulated progression of the reaction. Thus, RecA is actively involved in the strand exchange step as well as bringing the two DNAs close to each other.

}, doi = {10.1093/nar/gky048}, author = {Kim, Raeyeong and Kanamaru, Shuji and Mikawa, Tsutomu and Chantal Pr{\'e}vost and Ishii, Kentaro and Ito, Kentaro and Uchiyama, Susumu and Oda, Masayuki and Iwasaki, Hiroshi and Kim, Seog K and Takahashi, Masayuki} } @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 {2017|2039, title = {A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against.}, journal = {Bioinform Biol Insights}, volume = {11}, year = {2017}, month = {2017}, pages = {1177932217712471}, abstract = {

We present an approach for detecting enzymes that are specific ofcompared withand provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific forcompared with, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific ofand 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with. Among the 40 strictly specific enzymes, we identified sterol 24-C-methyltransferase, pyruvate phosphate dikinase, trypanothione synthetase, and RNA-editing ligase as 4 essential enzymes forthat may serve as targets for drug development.

}, issn = {1177-9322}, doi = {10.1177/1177932217712471}, author = {Catharina, Larissa and Lima, Carlyle Ribeiro and Franca, Alexander and Guimar{\~a}es, Ana Carolina Ramos and Alves-Ferreira, Marcelo and Tuffery, Pierre and Philippe Derreumaux and Carels, Nicolas} } @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} } @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|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} } @article {2017|2030, title = {Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer{\textquoteright}s Disease?}, journal = {ACS Chem Neurosci}, volume = {8}, year = {2017}, month = {2017 Jul 19}, pages = {1435-1437}, abstract = {

The two hallmarks of Alzheimer\&$\#$39;s disease (AD) are the presence of neurofibrillary tangles (NFT) made of aggregates of the hyperphosphorylated tau protein and of amyloid plaques composed of amyloid-β (Aβ) peptides, primarily Aβ1-40 and Aβ1-42. Targeting the production, aggregation, and toxicity of Aβ with small molecule drugs or antibodies is an active area of AD research due to the general acceptance of the amyloid cascade hypothesis, but thus far all drugs targeting Aβ have failed. From a review of the recent literature and our own experience based on in vitro, in silico, and in vivo studies, we present some reasons to explain this repetitive failure.

}, keywords = {Alzheimer Disease, Amyloid beta-Peptides, Animals, Drug Discovery, Humans, Neuroprotective Agents}, issn = {1948-7193}, doi = {10.1021/acschemneuro.7b00188}, author = {Doig, Andrew J and Del Castillo-Frias, Maria P and Berthoumieu, Olivia and Tarus, Bogdan and Nasica-Labouze, Jessica and Sterpone, Fabio and Phuong Hoang Nguyen and Hooper, Nigel M and Faller, Peter and Philippe Derreumaux} } @conference {2016|1606, title = {Alzheimer{\textquoteright}s Disease: Insights into Amyloid Fibril Formation from Lattice Monte Carlo Simulations}, booktitle = {Biophys. J.}, volume = {110}, number = {3, 1}, year = {2016}, note = {60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016}, month = {feb}, pages = {219A}, publisher = {Biophys Soc}, organization = {Biophys Soc}, issn = {0006-3495}, author = {Thanh-Thuy Tran and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2016|2115, title = {Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study}, journal = {The Journal of Physical Chemistry B}, volume = {120}, year = {2016}, pages = {7371{\textendash}7379}, author = {Nguyen, Hoang Linh and Thi Minh Thu, Tran and Truong, Phan Minh and Lan, Pham Dang and Man, Viet Hoang and Phuong Hoang Nguyen and Tu, Ly Anh and Chen, Yi-Cheng and Li, Mai Suan} } @article {2016|1656, title = {Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation}, journal = {Isr. J. Chem.}, volume = {DOI: 10.1002/ijch.201600048.}, year = {2016}, author = {M. Chiricotto and Thanh-Thuy Tran and Phuong Hoang Nguyen and S. Melchionna and Fabio Sterpone and Philippe Derreumaux} } @article {2016|1746, title = {Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.}, journal = {Plos One}, volume = {11}, year = {2016}, pages = {e0151934}, abstract = {

Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such \"Cys-less\" receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the \"Cys-loop\" proline is absolutely conserved, suggesting the more fitting name \"Pro loop\" for that motif, and \"Pro-loop receptors\" for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0151934}, author = {Jaiteh, Mariama and Antoine Taly and J{\'e}r{\^o}me H{\'e}nin} } @article {2016|1711, title = {In silico structural characterization of protein targets for drug development against Trypanosoma cruzi}, journal = {J. Mol. Model.}, volume = {22}, number = {10}, year = {2016}, month = {oct}, abstract = {Trypanosoma cruzi is the protozoan pathogen responsible for Chagas disease, which is a major public health problem in tropical and subtropical regions of developing countries and particularly in Brazil. Despite many studies, there is no efficient treatment against Chagas disease, and the search for new therapeutic targets specific to T. cruzi is critical for drug development. Here, we have revisited 41 protein sequences proposed by the analogous enzyme pipeline, and found that it is possible to provide structures for T. cruzi sequences with clear homologs or analogs in H. sapiens and likely associated with trypanothione reductase, cysteine synthase, and ATPase functions, and structures for sequences specific to T. cruzi and absent in H. sapiens associated with 2,4-dienoyl-CoA reductase, and leishmanolysin activities. The implications of our structures refined by atomistic molecular dynamics (monomer or dimer states) in their in vitro environments (aqueous solution or membrane bilayers) are discussed for drug development and suggest that all protein targets, except cysteine synthase, merit further investigation.}, issn = {1610-2940}, doi = {10.1007/s00894-016-3115-9}, author = {Lima, Carlyle Ribeiro and Carels, Nicolas and Ramos Guimaraes, Ana Carolina and Pierre Tuffery and Philippe Derreumaux} } @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|1703, title = {Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer{\textquoteright}s peptides}, journal = {J. Chem. Phys.}, volume = {144}, number = {20}, year = {2016}, month = {may}, abstract = {Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments A beta(16-22) and A beta(37-42) of the full length A beta(1-42) Alzheimer{\textquoteright}s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the A beta(16-22) dimer by fitting its equilibrium parallel and anti-parallel beta-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of A beta(16-22) and the dimer and trimer of A beta(37-42). Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the A beta(16-22) decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the A beta(37-42) decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases. Published by AIP Publishing.}, issn = {0021-9606}, doi = {10.1063/1.4951739}, author = {Thanh-Thuy Tran and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2016|1750, title = {Non-equivalent binding sites for Abeta1-40 on PrP determine the oligomerisation pathway}, journal = {Prion}, volume = {10}, number = {1}, year = {2016}, pages = {S40}, issn = {1933-6896}, author = {Grznarova, Katarina and Torrent, Joan and Munoz-Montesino, Carola and Nasica, Jessica and Philippe Derreumaux and Beringue, Vincent and Deslys, Jean-Philippe and Rezaei, Human} } @article {2016|1733, title = {PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex}, journal = {Nucleic Acids Res.}, volume = {44}, number = {W1}, year = {2016}, pages = {W449-W454}, abstract = {Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80\% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3 angstrom from the experimental conformation and return a native-like pose in the first 10 clusters for 52\% of the targets. PEP-FOLD3 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.}, issn = {0305-1048}, doi = {10.1093/nar/gkw329}, author = {Lamiable, Alexis and Thevenet, Pierre and Rey, Julien and Vavrusa, Marek and Philippe Derreumaux and Pierre Tuffery} } @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|1763, title = {Structure of ring-shaped Aβ42 oligomers determined by conformational selection}, journal = {Sci. Rep.}, volume = {6}, year = {2016}, pages = {21429}, abstract = {

The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a critical role in the pathogenesis of Alzheimer\&$\#$39;s disease. However, it has been challenging to characterize the tertiary and quaternary structures of Aβ peptides due to their disordered nature and high aggregation propensity. In this work, replica exchange molecular dynamics simulations were used to explore the conformational space of Aβ42 monomer. Among the most populated transient states, we identified a particular conformation which was able to generate ring-shaped pentamers and hexamers, when docked onto itself. The structures of these aggregates were stable during microsecond all-atom MD simulations in explicit solvent. In addition to high resolution models of these oligomers, this study provides support for the conformational selection mechanism of Aβ peptide self-assembly.

}, issn = {2045-2322}, doi = {10.1038/srep21429}, author = {Tran, Linh and Basdevant, Nathalie and Chantal Pr{\'e}vost and Ha-Duong, T{\^a}p} } @article {2015|1634, title = {Amyloid beta Protein and Alzheimer{\textquoteright}s Disease: When Computer Simulations Complement Experimental Studies}, journal = {Chem. Rev.}, volume = {115}, number = {9}, year = {2015}, month = {may}, pages = {3518{\textendash}3563}, doi = {10.1021/cr500638n}, author = {Nasica-Labouze, Jessica and Phuong Hoang Nguyen and Fabio Sterpone and Berthoumieu, Olivia and Buchete, Nicolae-Viorel and Cote, Sebastien and De Simone, Alfonso and Doig, Andrew J. and Faller, Peter and Garcia, Angel and Laio, Alessandro and Li, Mai Suan and Melchionna, Simone and Mousseau, Normand and Mu, Yuguang and Paravastu, Anant and Pasquali, Samuela and Rosenman, David J. and Strodel, Birgit and Tarus, Bogdan and Viles, John H. and Zhang, Tong and Wang, Chunyu and Philippe Derreumaux} } @article {2015|1635, title = {Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp}, journal = {Chemistry-a European Journal}, volume = {21}, number = {36}, year = {2015}, pages = {12657{\textendash}12666}, doi = {10.1002/chem.201500888}, author = {Berthoumieu, Olivia and Phuong Hoang Nguyen and del Castillo-Frias, Maria P. and Ferre, Sabrina and Tarus, Bogdan and Nasica-Labouze, Jessica and Noel, Sabrina and Saurel, Olivier and Rampon, Claire and Doig, Andrew J. and Philippe Derreumaux and Faller, Peter} } @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|1586, title = {Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin}, journal = {Biochemistry}, volume = {54}, number = {23}, year = {2015}, month = {jun}, pages = {3660{\textendash}3669}, doi = {10.1021/acs.biochem5b00146}, author = {Laurin, Y. and Savarin, P. and Charles H. Robert and M. Takahashi and Eyer, J. and Chantal Pr{\'e}vost and S Sacquin-Mora} } @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|1664, title = {Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.}, journal = {J. Membr. Biol.}, volume = {248}, year = {2015}, publisher = {Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece, zcournia@bioacademy.gr.}, chapter = {611}, abstract = {

Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.

}, doi = {10.1007/s00232-015-9802-0}, author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Grace Brannigan and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and Del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and J{\'e}r{\^o}me H{\'e}nin and Kasimova, Marina A. and Kolocouris, Antonios and Michael L Klein and Khalid, Syma and Lemieux, M Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Mounir Tarek and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta} } @article {2015|1646, title = {Molecular structure of the NQTrp inhibitor with the Alzheimer A beta 1-28 monomer}, journal = {Eur. J. Med. Chem.}, volume = {91}, year = {2015}, month = {feb}, pages = {43{\textendash}50}, doi = {10.1016/j.ejmech.2014.07.002}, author = {Tarus, Bogdan and Phuong Hoang Nguyen and Berthoumieu, Olivia and Faller, Peter and Doig, Andrew J. and Philippe Derreumaux} } @article {2015|1745, title = {Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study}, journal = {Phys. Chem. Chem. Phys.}, volume = {17}, number = {41}, year = {2015}, pages = {27275{\textendash}27280}, doi = {10.1039/c5cp04401d}, author = {Viet, Man Hoang and Phan Minh Truong and Philippe Derreumaux and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and Phuong Hoang Nguyen} } @article {2015|1769, title = {Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins}, journal = {The Journal of Physical Chemistry B}, volume = {119}, number = {40}, year = {2015}, pages = {12760{\textendash}12770}, publisher = {American Chemical Society}, author = {Chakraborty, Debashree and Antoine Taly and Fabio Sterpone} } @article {2015|1714, title = {Structures of the Alzheimer{\textquoteright}s Wild-Type A beta 1-40 Dimer from Atomistic Simulations}, journal = {J. Phys. Chem. B}, volume = {119}, number = {33}, year = {2015}, pages = {10478{\textendash}10487}, doi = {10.1021/acs.jpcb.5b05593}, author = {Tarus, Bogdan and Thanh-Thuy Tran and Nasica-Labouze, Jessica and Fabio Sterpone and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2015|2000, title = {{T}he plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology}, journal = {Annu. Rev. Plant Biol.}, volume = {66}, number = {1}, year = {2015}, pages = {49{\textendash}74}, publisher = {Annual Reviews}, author = {Nawrocki, W. J. and Tourasse, N. J. and Antoine Taly and Rappaport, F. and Wollman, F. A.} } @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|1609, title = {What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers}, booktitle = {Biophys. J.}, volume = {108}, number = {2}, year = {2015}, pages = {204A-204A}, author = {Nasica-Labouze, Jessica and Tarus, Bogdan and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2014|1792, title = {Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective}, journal = {Channels}, volume = {8}, number = {4}, year = {2014}, pages = {350{\textendash}360}, keywords = {Allosteric Regulation, Animals, chemistry/metabolism, Humans, Ion Channel Gating, Ligand-Gated Ion Channels, metabolism, Models, Molecular, Protein Multimerization, Small Molecule Libraries}, author = {Antoine Taly and J{\'e}r{\^o}me H{\'e}nin and Changeux, Jean-Pierre and Cecchini, Marco} } @article {2014|1669, title = {CHARMM36 united atom chain model for lipids and surfactants.}, journal = {J. Phys. Chem. B}, volume = {118}, number = {2}, year = {2014}, month = {jan}, pages = {547{\textendash}556}, publisher = {, Maryland 20742, United States.}, abstract = {Molecular simulations of lipids and surfactants require accurate parameters to reproduce and predict experimental properties. Previously, a united atom (UA) chain model was developed for the CHARMM27/27r lipids (H{\'e}nin, J., et al. J. Phys. Chem. B. 2008, 112, 7008-7015) but suffers from the flaw that bilayer simulations using the model require an imposed surface area ensemble, which limits its use to pure bilayer systems. A UA-chain model has been developed based on the CHARMM36 (C36) all-atom lipid parameters, termed C36-UA, and agreed well with bulk, lipid membrane, and micelle formation of a surfactant. Molecular dynamics (MD) simulations of alkanes (heptane and pentadecane) were used to test the validity of C36-UA on density, heat of vaporization, and liquid self-diffusion constants. Then, simulations using C36-UA resulted in accurate properties (surface area per lipid, X-ray and neutron form factors, and chain order parameters) of various saturated- and unsaturated-chain bilayers. When mixed with the all-atom cholesterol model and tested with a series of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/cholesterol mixtures, the C36-UA model performed well. Simulations of self-assembly of a surfactant (dodecylphosphocholine, DPC) using C36-UA suggest an aggregation number of 53 {\textpm} 11 DPC molecules at 0.45 M of DPC, which agrees well with experimental estimates. Therefore, the C36-UA force field offers a useful alternative to the all-atom C36 lipid force field by requiring less computational cost while still maintaining the same level of accuracy, which may prove useful for large systems with proteins.}, keywords = {analogs /\&/ derivatives/chemistry, chemistry, Cholesterol, Dimyristoylphosphatidylcholine, Lipid Bilayers, Lipids, Micelles, Molecular Dynamics Simulation, Phosphorylcholine, Surface-Active Agents}, doi = {10.1021/jp410344g}, author = {Lee, Sarah and Tran, Alan and Allsopp, Matthew and Lim, Joseph B. and J{\'e}r{\^o}me H{\'e}nin and Klauda, Jeffery B.} } @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|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.} } @article {2014|1927, title = {Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A beta 1-28 Monomer}, journal = {J. Phys. Chem. B}, volume = {118}, number = {2}, year = {2014}, month = {jan}, pages = {501{\textendash}510}, doi = {10.1021/jp4115404}, author = {Phuong Hoang Nguyen and Tarus, Bogdan and Philippe Derreumaux} } @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|1893, title = {Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction}, journal = {J. Chem. Theory Comput.}, volume = {10}, number = {10}, year = {2014}, month = {oct}, pages = {4745{\textendash}4758}, doi = {10.1021/ct500592m}, author = {Shen, Yimin and Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @article {2014|1637, title = {{L}ong distance effect on ligand-gated ion channels extracellular domain may affect interactions with the intracellular machinery}, journal = {Commun. Integr. Biol.}, volume = {7}, year = {2014}, pages = {e27984}, author = {Garret, M. and Boue-Grabot, E. and Antoine Taly} } @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} } @conference {2014|1760, title = {Optogating a powerful approach to control an ion-channel gate}, booktitle = {PURINERGIC SIGNALLING}, volume = {10}, number = {4}, year = {2014}, pages = {762{\textendash}762}, publisher = {SPRINGER VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, organization = {SPRINGER VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, author = {Lemoine, Damien and Habermacher, Chlo{\'e} and Martz, Adeline and M{\'e}ry, Pierre-Fran\c cois and Bouquier, Nathalie and Diverchy, Fanny and Antoine Taly and Rassendren, Fran\c cois and Specht, Alexandre and Grutter, Thomas} } @article {2013|1699, title = {Agonist-dependent endocytosis of $\gamma$-aminobutyric acid type A (GABAA) receptors revealed by a $\gamma$2 (R43Q) epilepsy mutation}, journal = {J. Biol. Chem.}, volume = {288}, number = {39}, year = {2013}, pages = {28254{\textendash}28265}, publisher = {American Society for Biochemistry and Molecular Biology}, author = {Chaumont, Severine and Andr{\'e}, Caroline and Perrais, David and Bou{\'e}-Grabot, Eric and Antoine Taly and Garret, Maurice} } @article {2013|1938, title = {Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, number = {4}, year = {2013}, pages = {477{\textendash}485}, publisher = {Nature Publishing Group}, author = {Zhu, Shujia and Stroebel, David and Yao, C Andrea and Antoine Taly and Paoletti, Pierre} } @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|1974, title = {{A} gating mechanism of pentameric ligand-gated ion channels}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {110}, number = {42}, year = {2013}, month = {oct}, pages = {E3987{\textendash}3996}, author = {Calimet, N. and Simoes, M. and Changeux, J. P. and Karplus, M. and Antoine Taly and Cecchini, M.} } @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|1998, title = {{M}oving through the gate in {A}{T}{P}-activated {P}2{X} receptors}, journal = {Trends Biochem. Sci.}, volume = {38}, number = {1}, year = {2013}, month = {jan}, pages = {20{\textendash}29}, author = {Jiang, R. and Antoine Taly and Grutter, T.} } @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} } @article {2013|1770, title = {Moving through the gate in ATP-activated P2X receptors}, journal = {Trends Biochem. Sci.}, volume = {38}, number = {1}, year = {2013}, pages = {20{\textendash}29}, publisher = {Elsevier Current Trends}, author = {Jiang, Ruotian and Antoine Taly and Grutter, Thomas} } @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|1648, title = {Novel approaches to drug design for the treatment of schizophrenia}, journal = {Expert Opin. Drug Discovery}, volume = {8}, number = {10}, year = {2013}, pages = {1285{\textendash}1296}, publisher = {Informa UK, Ltd. London}, author = {Antoine Taly} } @article {2013|1973, title = {{O}ptical control of an ion channel gate}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {110}, number = {51}, year = {2013}, month = {dec}, pages = {20813{\textendash}20818}, author = {Lemoine, D. and Habermacher, C. and Martz, A. and Mery, P. F. and Bouquier, N. and Diverchy, F. and Antoine Taly and Rassendren, F. and Specht, A. and Grutter, T.} } @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.} } @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|1642, title = {$\alpha$7 nicotinic acetylcholine receptors: a therapeutic target in the structure era}, journal = {Curr. Drug Targets}, volume = {13}, number = {5}, year = {2012}, pages = {695{\textendash}706}, publisher = {Bentham Science Publishers}, author = {Antoine Taly and Charon, S{\'e}bastien} } @article {2012|1911, title = {Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts}, journal = {J. Pept. Sci.}, volume = {18}, number = {1}, year = {2012}, month = {sep}, pages = {S38}, author = {Thevenet, P. and Shen, Y. and Maupetit, J. and Guyon, F. and Padilla, A. and Philippe Derreumaux and Pierre Tuffery} } @article {2012|1932, title = {Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches}, journal = {Journal of the Royal Society Interface}, volume = {9}, number = {66}, year = {2012}, month = {jan}, pages = {20{\textendash}33}, doi = {10.1098/rsif.2011.0584}, author = {Pierre Tuffery and Philippe Derreumaux} } @article {2012|1793, title = {{I}ntermediate closed channel state(s) precede(s) activation in the {A}{T}{P}-gated {P}2{X}2 receptor}, journal = {Channels (austin)}, volume = {6}, number = {5}, year = {2012}, pages = {398{\textendash}402}, author = {Jiang, R. and Antoine Taly and Lemoine, D. and Martz, A. and Specht, A. and Grutter, T.} } @article {2012|1756, title = {Involvement of the cysteine-rich head domain in activation and desensitization of the P2X1 receptor}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {28}, year = {2012}, pages = {11396{\textendash}11401}, publisher = {National Acad Sciences}, author = {L{\"o}rinczi, {\'E}va and Bhargava, Yogesh and Marino, Stephen F and Antoine Taly and Kaczmarek-H{\'a}jek, Karina and Barrantes-Freer, Alonso and Dutertre, S{\'e}bastien and Grutter, Thomas and Rettinger, J{\"u}rgen and Nicke, Annette} } @article {2012|2004, title = {Ligand-gated ion channels: new insights into neurological disorders and ligand recognition}, journal = {Chem. Rev.}, volume = {112}, number = {12}, year = {2012}, month = {sep}, pages = {6285{\textendash}6318}, publisher = {American Chemical Society}, author = {Lemoine, Damien and Jiang, Ruotian and Antoine Taly and Chataigneau, Thierry and Specht, Alexandre and Grutter, Thomas} } @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|1944, title = {PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides}, journal = {Nucleic Acids Res.}, volume = {40}, number = {W1}, year = {2012}, month = {jul}, pages = {W288-W293}, doi = {10.1093/nar/gks419}, author = {Thevenet, Pierre and Shen, Yimin and Maupetit, Julien and Guyon, Frederic and Philippe Derreumaux and Pierre Tuffery} } @article {2012|1527, title = {{S}tructure-function analysis of the {NFL}-{TBS}.40-63 peptide corresponding to the binding site of tubulin on the light neurofilament subunit}, journal = {Plos One}, volume = {7}, year = {2012}, pages = {e49436}, author = {Berges, R. and Balzeau, J. and Takahashi, M. and Chantal Pr{\'e}vost and Eyer, J.} } @article {2012|1805, title = {{T}ightening of the {A}{T}{P}-binding sites induces the opening of {P}2{X} receptor channels}, journal = {Embo J.}, volume = {31}, number = {9}, year = {2012}, month = {may}, pages = {2134{\textendash}2143}, author = {Jiang, R. and Antoine Taly and Lemoine, D. and Martz, A. and Cunrath, O. and Grutter, T.} } @article {2012|2005, title = {α7-{N}icotinic acetylcholine receptors: an old actor for new different roles}, journal = {Curr. Drug Targets}, volume = {13}, number = {5}, year = {2012}, month = {may}, pages = {574{\textendash}578}, publisher = {Bentham Science Publishers}, author = {Russo, P. and Antoine Taly} } @article {2011|1834, title = {{B}inding modes of noncompetitive {G}{A}{B}{A}-channel blockers revisited using engineered affinity-labeling reactions combined with new docking studies}, journal = {J. Agric. Food Chem.}, volume = {59}, number = {7}, year = {2011}, month = {apr}, pages = {2803{\textendash}2807}, author = {Charon, S. and Antoine Taly and Rodrigo, J. and Perret, P. and Goeldner, M.} } @article {2011|1665, title = {Community-wide assessment of protein-interface modeling suggests improvements to design methodology.}, journal = {J. Mol. Biol.}, volume = {414}, year = {2011}, month = {nov}, pages = {289{\textendash}302}, abstract = {

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.

}, keywords = {Binding Sites, Models, Molecular, Protein Binding, Proteins}, issn = {1089-8638}, doi = {10.1016/j.jmb.2011.09.031}, author = {Fleishman, Sarel J and Whitehead, Timothy A and Strauch, Eva-Maria and Corn, Jacob E and Qin, Sanbo and Zhou, Huan-Xiang and Mitchell, Julie C and Demerdash, Omar N A and Takeda-Shitaka, Mayuko and Terashi, Genki and Moal, Iain H and Li, Xiaofan and Bates, Paul A and Martin Zacharias and Park, Hahnbeom and Ko, Jun-su and Lee, Hasup and Seok, Chaok and Bourquard, Thomas and Bernauer, Julie and Poupon, Anne and Az{\'e}, J{\'e}r{\^o}me and Soner, Seren and Ovali, Sefik Kerem and Ozbek, Pemra and Tal, Nir Ben and Haliloglu, T{\"u}rkan and Hwang, Howook and Vreven, Thom and Pierce, Brian G and Weng, Zhiping and P{\'e}rez-Cano, Laura and Pons, Carles and Fern{\'a}ndez-Recio, Juan and Jiang, Fan and Yang, Feng and Gong, Xinqi and Cao, Libin and Xu, Xianjin and Liu, Bin and Wang, Panwen and Li, Chunhua and Wang, Cunxin and Charles H. Robert and Guharoy, Mainak and Liu, Shiyong and Huang, Yangyu and Li, Lin and Guo, Dachuan and Chen, Ying and Xiao, Yi and London, Nir and Itzhaki, Zohar and Schueler-Furman, Ora and Inbar, Yuval and Potapov, Vladimir and Cohen, Mati and Schreiber, Gideon and Tsuchiya, Yuko and Kanamori, Eiji and Standley, Daron M and Nakamura, Haruki and Kinoshita, Kengo and Driggers, Camden M and Hall, Robert G and Morgan, Jessica L and Hsu, Victor L and Zhan, Jian and Yang, Yuedong and Zhou, Yaoqi and Kastritis, Panagiotis L and Bonvin, Alexandre M J J and Zhang, Weiyi and Camacho, Carlos J and Kilambi, Krishna P and Sircar, Aroop and Gray, Jeffrey J and Ohue, Masahito and Uchikoga, Nobuyuki and Matsuzaki, Yuri and Ishida, Takashi and Akiyama, Yutaka and Khashan, Raed and Bush, Stephen and Fouches, Denis and Tropsha, Alexander and Esquivel-Rodr{\'\i}guez, Juan and Kihara, Daisuke and Stranges, P Benjamin and Jacak, Ron and Kuhlman, Brian and Huang, Sheng-You and Zou, Xiaoqin and Wodak, Shoshana J and Janin, Jo{\"e}l and Baker, David} } @article {2011|1857, title = {{D}iscrimination of agonists versus antagonists of nicotinic ligands based on docking onto {A}{C}h{B}{P} structures}, journal = {J. Mol. Graph. Model.}, volume = {30}, year = {2011}, month = {sep}, pages = {100{\textendash}109}, author = {Antoine Taly and Colas, C. and Malliavin, T. and Blondel, A. and Nilges, M. and Corringer, P. J. and Joseph, D.} } @article {2011|2014, title = {{F}rom toxins targeting ligand gated ion channels to therapeutic molecules}, journal = {Toxins (basel)}, volume = {3}, number = {3}, year = {2011}, month = {mar}, pages = {260{\textendash}293}, publisher = {Molecular Diversity Preservation International}, author = {Nasiripourdori, A. and Taly, V. and Grutter, T. and Antoine Taly} } @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|1972, title = {{A}gonist trapped in {A}{T}{P}-binding sites of the {P}2{X}2 receptor}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {108}, number = {22}, year = {2011}, month = {may}, pages = {9066{\textendash}9071}, author = {Jiang, R. and Lemoine, D. and Martz, A. and Antoine Taly and Gonin, S. and Prado de Carvalho, L. and Specht, A. and Grutter, T.} } @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|1691, title = {On the reorientation and hydrogen-bond dynamics of Alcohols}, journal = {J. Phys. Chem. B}, volume = {115}, year = {2011}, pages = {12173{\textendash}12178}, abstract = {

The mechanism of the OH bond reorientation in liquid methanol and ethanol is examined. It is found that the extended jump model, recently developed for water, describes the OH reorientation in these liquids. The slower reorientational dynamics in these alcohols compared to water can be explained by two key factors. The alkyl groups on the alcohol molecules exclude potential partners for hydrogen bonding exchanges, an effect that grows with the size of the alkyl chain. This increases the importance of the reorientation of intact hydrogen bonds, which also slows with increasing size of the alcohol and becomes the dominant reorientation pathway.

}, issn = {15206106}, author = {Vartia, Anthony A. and Mitchell-Koch, Katie R. and Guillaume Stirnemann and Laage, Damien and Thompson, Ward H.} } @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|1901, title = {A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction}, journal = {J. Comput. Chem.}, volume = {31}, number = {4}, year = {2010}, month = {mar}, pages = {726{\textendash}738}, doi = {10.1002/jcc.21365}, author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @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|2007, title = {{A} putative extracellular salt bridge at the subunit interface contributes to the ion channel function of the {A}{T}{P}-gated {P}2{X}2 receptor}, journal = {J. Biol. Chem.}, volume = {285}, number = {21}, year = {2010}, month = {may}, pages = {15805{\textendash}15815}, publisher = {American Society for Biochemistry and Molecular Biology}, author = {Jiang, R. and Martz, A. and Gonin, S. and Antoine Taly and de Carvalho, L. P. and Grutter, T.} } @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} } @article {2009|1636, title = {Deforming DNA: from physics to biology}, journal = {Chemphyschem}, volume = {10}, year = {2009}, month = {jul}, pages = {1399{\textendash}404}, abstract = {

The DNA double helix has become a modern icon which symbolizes our understanding of the molecular basis of life. It is less widely recognized that the double helix proposed by Watson and Crick more than half a century ago is a remarkably adaptable molecule that can undergo major conformational rearrangements without being irreversibly damaged. Indeed, DNA deformation is an intrinsic feature of many of the biological processes in which it is involved. Over the last two decades, single-molecule experiments coupled with molecular modeling have transformed our understanding of DNA flexibility, while the accumulation of high-resolution structures of DNA-protein complexes have demonstrated how organisms can exploit this property as a useful feature for preserving, reading, replicating, and packaging the genetic message. In this Minireview we summarize the information now available on the extreme\–and the less extreme\–deformations of the double helix.

}, doi = {10.1002/cphc.200900253}, author = {Chantal Pr{\'e}vost and M. Takahashi and Richard Lavery} } @article {2009|1436, title = {A fast method for large-scale De Novo peptide and miniprotein structure prediction.}, journal = {J. Comput. Chem.}, year = {2009}, month = {jun}, doi = {10.1002/jcc.21365}, author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery} } @article {2009|1605, title = {The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15 N chemical shifts}, journal = {Biophys. Chem.}, volume = {143}, number = {3}, year = {2009}, pages = {111{\textendash}123}, publisher = {Elsevier}, author = {Spichty, Martin and Antoine Taly and Hagn, Franz and Kessler, Horst and Barluenga, Sofia and Winssinger, Nicolas and Karplus, Martin} } @article {2009|1959, title = {Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling}, journal = {Plos Comput. Biol.}, volume = {5}, number = {1}, year = {2009}, month = {jan}, pages = {e1000267}, doi = {10.1371/journal.pcbi.1000267}, url = {http://dx.doi.org/10.1371\%2Fjournal.pcbi.1000267}, author = {Engelen, Stefan and Trojan, Ladislas A. and S Sacquin-Mora and Lavery, Richard and Carbone, Alessandra} } @article {2009|2010, title = {{N}icotinic receptors: allosteric transitions and therapeutic targets in the nervous system}, journal = {Nat. Rev. Drug Discov.}, volume = {8}, number = {9}, year = {2009}, month = {sep}, pages = {733{\textendash}750}, publisher = {Nature Publishing Group}, author = {Antoine Taly and Corringer, P. J. and Guedin, D. and Lestage, P. and Jean-Pierre Changeux} } @article {2009|1942, title = {PEP-FOLD: an online resource for de novo peptide structure prediction.}, journal = {Nucleic Acids Res.}, volume = {37}, number = {Web Server issue}, year = {2009}, month = {jul}, pages = {W498{\textendash}W503}, keywords = {Algorithms, Internet, Models, Molecular, Peptides, Protein, Protein Conformation, Reproducibility of Results, Sequence Analysis, Software, User-Computer Interface}, doi = {10.1093/nar/gkp323}, author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery} } @article {2009|1734, title = {PEP-FOLD: an online resource for de novo peptide structure prediction}, journal = {Nucleic Acids Res.}, volume = {37}, year = {2009}, month = {jul}, pages = {W498-W503}, doi = {10.1093/nar/gkp323}, author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @article {2008|1583, title = {{C}omparative models of {P}2{X}2 receptor support inter-subunit {A}{T}{P}-binding sites}, journal = {Biochem. Biophys. Res. Commun.}, volume = {375}, number = {3}, year = {2008}, month = {oct}, pages = {405{\textendash}409}, author = {Guerlet, G. and Antoine Taly and Prado de Carvalho, L. and Martz, A. and Jiang, R. and Specht, A. and Le Novere, N. and Grutter, T.} } @article {2008|1585, title = {Comparative models of P2X2 receptor support inter-subunit ATP-binding sites}, journal = {Biochem. Biophys. Res. Commun.}, volume = {375}, number = {3}, year = {2008}, pages = {405{\textendash}409}, publisher = {Academic Press}, author = {Guerlet, Guillaume and Antoine Taly and De Carvalho, Lia Prado and Martz, Adeline and Jiang, Ruotian and Specht, Alexandre and Le Novere, Nicolas and Grutter, Thomas} } @article {2008|1603, title = {Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF}, journal = {Biophys. J.}, volume = {94}, number = {3}, year = {2008}, pages = {832{\textendash}839}, abstract = {The glycerol uptake facilitator, GlpF, a major intrinsic protein found in Escherichia coli, selectively conducts water and glycerol across the inner membrane. The free energy landscape characterizing the assisted transport of glycerol by this homotetrameric aquaglyceroporin has been explored by means of equilibrium molecular dynamics over a timescale spanning 0.12 micros. To overcome the free energy barriers of the conduction pathway, an adaptive biasing force is applied to the glycerol molecule confined in each of the four channels. The results illuminate the critical role played by intramolecular relaxation on the diffusion properties of the permeant. These free energy calculations reveal that glycerol tumbles and isomerizes on a timescale comparable to that spanned by its adaptive-biasing-force-assisted conduction in GlpF. As a result, reorientation and conformational equilibrium of glycerol in GlpF constitute a bottleneck in the molecular simulations of the permeation event. A profile characterizing the position-dependent diffusion of the permeant has been determined, allowing reaction rate theory to be applied for investigating conduction kinetics based on the measured free energy landscape.}, keywords = {Aquaporins, Chemical, Computer Simulation, Diffusion, Escherichia coli Proteins, Glycerol, Ion Channel Gating, Models, Molecular, Molecular Conformation, Porosity}, doi = {10.1529/biophysj.107.115105}, author = {J{\'e}r{\^o}me H{\'e}nin and Emad Tajkhorshid and Klaus Schulten and Christophe Chipot} } @article {2008|1485, title = {Energy transport in peptide helices: A comparison between high- and low-energy excitations}, journal = {J. Phys. Chem. B}, volume = {112}, number = {30}, year = {2008}, month = {jul}, pages = {9091{\textendash}9099}, author = {Backus, Ellen H. G. and Phuong Hoang Nguyen and Botan, Virgiliu and Pfister, Rolf and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Stock, Gerhard and Hamm, Peter} } @article {2008|1999, title = {{F}unctional organization and conformational dynamics of the nicotinic receptor: a plausible structural interpretation of myasthenic mutations}, journal = {Ann. N. Y. Acad. Sci.}, volume = {1132}, number = {1}, year = {2008}, pages = {42{\textendash}52}, publisher = {Wiley Online Library}, author = {Antoine Taly and Jean-Pierre Changeux} } @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|2012, title = {Nicotinic receptors, allosteric proteins and medicine}, journal = {Trends Mol. Med.}, volume = {14}, number = {3}, year = {2008}, month = {mar}, pages = {93{\textendash}102}, publisher = {Elsevier}, author = {Jean-Pierre Changeux and Antoine Taly} } @inbook {2008|1566, title = {Order-disorder transitions in ribosome assembly}, booktitle = {Ribosomal proteins,}, year = {2008}, publisher = {Nova publishers, Hauppauge NY}, organization = {Nova publishers, Hauppauge NY}, author = {Y Timsit and F Allemand and Chiaruttini C and M Springer}, editor = {Colombus} } @article {2008|1484, title = {Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties}, journal = {J. Phys. Chem. B}, volume = {112}, number = {48}, year = {2008}, month = {dec}, pages = {15487{\textendash}15492}, author = {Backus, Ellen H. G. and Phuong Hoang Nguyen and Botan, Virgiliu and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Zerbe, Oliver and Stock, Gerhard and Hamm, Peter} } @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} } @article {2007|1985, title = {A coarse-grained protein force field for folding and structure prediction}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {69}, number = {2}, year = {2007}, month = {nov}, pages = {394{\textendash}408}, doi = {10.1002/prot.21505}, author = {Maupetit, Julien and Pierre Tuffery and Philippe Derreumaux} } @article {2007|2001, title = {{D}ocking of alpha-cobratoxin suggests a basal conformation of the nicotinic receptor}, journal = {Biochem. Biophys. Res. Commun.}, volume = {359}, number = {3}, year = {2007}, month = {aug}, pages = {413{\textendash}418}, publisher = {Academic Press}, author = {Konstantakaki, M. and Jean-Pierre Changeux and Antoine Taly} } @article {2007|1534, title = {Energy transport in peptide helices}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {104}, number = {31}, year = {2007}, month = {jul}, pages = {12749{\textendash}12754}, author = {Botan, Virgiliu and Backus, Ellen H. G. and Pfister, Rolf and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Phuong Hoang Nguyen and Stock, Gerhard and Hamm, Peter} } @article {2007|1535, title = {Monomer adds to preformed structured oligomers of A beta-peptides by a two-stage dock-lock mechanism}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {104}, number = {1}, year = {2007}, month = {jan}, pages = {111{\textendash}116}, author = {Phuong Hoang Nguyen and Li, Mai Suan and Stock, Gerhard and Straub, John E. and Thirumalai, D.} } @article {2007|2006, title = {{O}pened by a twist: a gating mechanism for the nicotinic acetylcholine receptor}, journal = {Eur. Biophys. J.}, volume = {36}, number = {8}, year = {2007}, month = {nov}, pages = {911{\textendash}918}, publisher = {Springer-Verlag}, author = {Antoine Taly} } @article {2007|1728, title = {{A} prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family}, journal = {Nature}, volume = {445}, number = {7123}, year = {2007}, month = {jan}, pages = {116{\textendash}119}, author = {Bocquet, N. and Prado de Carvalho, L. and Cartaud, J. and Neyton, J. and Le Poupon, C. and Antoine Taly and Grutter, T. and Jean-Pierre Changeux and Corringer, P. J.} } @conference {2007|1491, title = {REVIVOS: REalit{\'e} VIrtuelle pour la construction de VOcabulaires Sp{\'e}cialis{\'e}s}, booktitle = {Journ{\'e}es Francophones d{\textquoteright}Ing{\'e}nierie des Connaissances (AFIA-IC 2007)}, year = {2007}, month = {jul}, address = {Grenoble - France}, author = {Nicolas F{\'e}rey and Claire Toffano-Nioche and Oriane Matte-Taillez and Rachid Gherbi and William Turner} } @article {2007|1547, title = {{T}he 1.3 {A} resolution structure of the {R}{N}{A} tridecamer r({G}{C}{G}{U}{U}{U}{G}{A}{A}{A}{C}{G}{C}): metal ion binding correlates with base unstacking and groove contraction}, journal = {Rna}, volume = {13}, year = {2007}, month = {dec}, pages = {2098{\textendash}2107}, author = {Y Timsit and Bombard, S.} } @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 {2006|1407, title = {{C}oexistence of two protein folding states in the crystal structure of ribosomal protein {L}20}, journal = {Embo Rep.}, volume = {7}, year = {2006}, month = {oct}, pages = {1013{\textendash}1018}, author = {Y Timsit and Allemand, F. and Chiaruttini, C. and Springer, M.} } @article {2006|2008, title = {{I}dentification of two critical residues within the {C}ys-loop sequence that determine fast-gating kinetics in a pentameric ligand-gated ion channel}, journal = {J. Mol. Neurosci.}, volume = {30}, number = {1-2}, year = {2006}, pages = {63{\textendash}64}, publisher = {Springer}, author = {Grutter, T. and de Carvalho, L. P. and Dufresne, V. and Antoine Taly and Jean-Pierre Changeux} } @article {2006|1754, title = {{I}mplications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {103}, number = {45}, year = {2006}, month = {nov}, pages = {16965{\textendash}16970}, author = {Antoine Taly and Corringer, P. J. and Grutter, T. and Prado de Carvalho, L. and Karplus, M. and Jean-Pierre Changeux} } @article {2006|1757, title = {Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors}, journal = {Proceedings of the National Academy of Sciences}, volume = {103}, number = {45}, year = {2006}, pages = {16965{\textendash}16970}, publisher = {National Acad Sciences}, author = {Antoine Taly and Corringer, Pierre-Jean and Grutter, Thomas and De Carvalho, Lia Prado and Karplus, Martin and Jean-Pierre Changeux} } @article {2006|1466, title = {Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces}, journal = {J. Chem. Phys.}, volume = {124}, number = {15}, year = {2006}, month = {apr}, author = {Phuong Hoang Nguyen and Mittag, E and Torda, AE and Stock, G} } @article {2006|1604, title = {Probing a model of a {GPCR}/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor}, journal = {Biophys. J.}, volume = {90}, number = {4}, year = {2006}, pages = {1232{\textendash}1240}, abstract = {A three-dimensional model structure of a complex formed by a G-protein-coupled receptor (GPCR) and an agonist ligand is probed and refined using molecular-dynamics simulations and free energy calculations in a realistic environment. The model of the human receptor of cholecystokinin associated to agonist ligand CCK9 was obtained from a synergistic procedure combining site-directed mutagenesis experiments and in silico modeling. The 31-ns molecular-dynamics simulation in an explicit membrane environment indicates that both the structure of the receptor and its interactions with the ligand are robust. Whereas the secondary structure of the {alpha}-helix bundle is well preserved, the region of the intracellular loops exhibits a significant flexibility likely to be ascribed to the absence of G-protein subunits in the model. New insight into the structural features of the binding pocket is gained, in particular, the interplay of the ligand with both the receptor and internal water molecules. Water-mediated interactions are shown to participate in the binding, hence, suggesting additional site-directed mutagenesis experiments. Accurate free energy calculations on mutated ligands provide differences in the receptor-ligand binding affinity, thus offering a direct, quantitative comparison to experiment. We propose that this detailed consistency-checking procedure be used as a routine refinement step of in vacuo GPCR models, before further investigation and application to structure-based drug design.}, url = {http://www.biophysj.org/cgi/content/abstract/90/4/1232}, author = {J{\'e}r{\^o}me H{\'e}nin and Maigret, B. and Mounir Tarek and Escrieut, C. and Fourmy, D. and Christophe Chipot} } @article {2005|1631, title = {{A} chimera encoding the fusion of an acetylcholine-binding protein to an ion channel is stabilized in a state close to the desensitized form of ligand-gated ion channels}, journal = {C. R. Biol.}, volume = {328}, number = {3}, year = {2005}, month = {mar}, pages = {223{\textendash}234}, author = {Grutter, T. and Prado de Carvalho, L. and Virginie, D. and Antoine Taly and Fischer, M. and Jean-Pierre Changeux} } @article {2005|1979, title = {Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {61}, number = {4}, year = {2005}, month = {dec}, pages = {732{\textendash}740}, doi = {10.1002/prot.20698}, author = {Pierre Tuffery and Philippe Derreumaux} } @article {2005|1900, title = {Improved greedy algorithm for protein structure reconstruction}, journal = {J. Comput. Chem.}, volume = {26}, number = {5}, year = {2005}, month = {apr}, pages = {506{\textendash}513}, doi = {10.1002/jcc.20181}, author = {Pierre Tuffery and Guyon, F and Philippe Derreumaux} } @article {2005|2011, title = {{M}olecular tuning of fast gating in pentameric ligand-gated ion channels}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {102}, number = {50}, year = {2005}, month = {dec}, pages = {18207{\textendash}18212}, publisher = {National Acad Sciences}, author = {Grutter, T. and de Carvalho, L. P. and Dufresne, V. and Antoine Taly and Edelstein, S. J. and Jean-Pierre Changeux} } @article {2005|2003, title = {{N}ormal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism}, journal = {Biophys. J.}, volume = {88}, number = {6}, year = {2005}, month = {jun}, pages = {3954{\textendash}3965}, publisher = {Cell Press}, author = {Antoine Taly and Delarue, M. and Grutter, T. and Nilges, M. and Le Novere, N. and Corringer, P. J. and Jean-Pierre Changeux} } @inbook {2004|1730, title = {Conformational transitions in proteins and membranes}, booktitle = {Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations}, year = {2004}, pages = {485{\textendash}502}, publisher = {Springer Netherlands}, organization = {Springer Netherlands}, author = {Smith, Jeremy C and Cournia, Zoe and Antoine Taly and Tournier, Alexander L and Mihailescu, Dan and Ullmann, G Matthias} } @article {2004|1647, title = {Critical role of the C-terminal segment in the maturation and export to the cell surface of the homopentameric $\alpha$7{\textendash}5HT3A receptor}, journal = {Eur. J. Neurosci.}, volume = {20}, number = {8}, year = {2004}, pages = {2022{\textendash}2030}, publisher = {Wiley Online Library}, author = {Pons, S and Sallette, J and Bourgeois, JP and Antoine Taly and Jean-Pierre Changeux and Devillers-Thi{\'e}ry, A} } @article {2004|1825, title = {Identification of the subunit-subunit interface of Xenopus Rad51.1 protein: Similarity to RecA}, journal = {J. Mol. Biol.}, volume = {335}, number = {4}, year = {2004}, month = {jan}, pages = {895{\textendash}904}, abstract = {

Rad51, like its prokaryotic homolog RecA, forms a helical filament for homologous DNA recombination and recombinational DNA repair. Comparison of the three-dimensional structures of human Rad51 and Escherichia coli RecA indicated that the tyrosine residue at position 191 in human Rad51 lies at the centre of a putative subunit-subunit contact interface. We inserted a tryptophan residue as a fluorescent probe at the corresponding position in Xenopus Rad51.1 and found that its fluorescence depended upon the protein concentration, indicating that the residue is truly in the subunit-subunit interface. We also found that 3 M urea, which promoted the dissociation of Rad51 filament without complete unfolding of the protein, exposed the tryptophan residue to solvent. The fluorescence was not modified by binding to DNA and only slightly modified by ATP, indicating that the same site is used for formation of the active ATP-Rad51-DNA filament. The slight changes in fluorescence caused by ATP and ADP suggest that the subunit-subunit contact is altered, leading to the elongation of the filament by these nucleotides, as with the RecA filament. Thus, Rad51 forms filaments by subunit-subunit contact much like RecA does.

}, author = {Selmane, T and Camadro, JM and Conilleau, S and Fleury, F and Tran, V and Chantal Pr{\'e}vost and Takahashi, M} } @article {2004|1787, title = {Structural characterization of VGVAPG, an elastin-derived peptide}, journal = {Biopolymers}, volume = {76}, number = {3}, year = {2004}, pages = {266{\textendash}280}, doi = {10.1002/bip.20029}, author = {Floquet, N and Hery-Huynh, S and Dauchez, M and Philippe Derreumaux and Tamburro, AM and Alix, AJP} } @article {2003|1663, title = {Docking macromolecules with flexible segments}, journal = {J. Comput. Chem.}, volume = {24}, year = {2003}, month = {nov}, pages = {1910{\textendash}20}, abstract = {

We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA.

}, doi = {10.1002/jcc.10329}, author = {Bastard, Karine and Thureau, Aur{\'e}lien and Richard Lavery and Chantal Pr{\'e}vost} } @article {2003|1761, title = {Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination}, journal = {Q. Rev. Biophys.}, volume = {36}, year = {2003}, month = {nov}, pages = {429{\textendash}53}, abstract = {

Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell\&$\#$39;s genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50\% and unwound by 40\% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.

}, author = {Chantal Pr{\'e}vost and M. Takahashi} } @article {2003|1621, title = {The position of Q B in the photosynthetic reaction center depends on pH: A theoretical analysis of the proton uptake upon Q B reduction}, journal = {Biophys. J.}, volume = {84}, number = {3}, year = {2003}, pages = {2090{\textendash}2098}, publisher = {Cell Press}, author = {Antoine Taly and Sebban, Pierre and Smith, Jeremy C and Ullmann, G Matthias} } @conference {2002|1622, title = {Cd2+ binding effect on bacterial reaction center mutants: The proton penetration involves interdependent pathways}, booktitle = {BIOPHYSICAL JOURNAL}, volume = {82}, number = {1}, year = {2002}, pages = {518A-518A}, publisher = {BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA}, organization = {BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA}, author = {Gerencser, L and Antoine Taly and Baciou, L and Maroti, P and Sebban, P} } @article {2002|2002, title = {{E}ffect of binding of {C}d2+ on bacterial reaction center mutants: proton-transfer uses interdependent pathways}, journal = {Biochemistry}, volume = {41}, number = {29}, year = {2002}, month = {jul}, pages = {9132{\textendash}9138}, publisher = {ACS Publications}, author = {Gerencser, L. and Antoine Taly and Baciou, L. and Maroti, P. and Sebban, P.} } @article {2002|1650, title = {{T}he {D}{M}{P}{C} lipid phase transition influences differently the first and the second electron transfer reactions in bacterial reaction centers}, journal = {Febs Lett.}, volume = {532}, number = {1-2}, year = {2002}, month = {dec}, pages = {91{\textendash}96}, author = {Antoine Taly and Baciou, L. and Sebban, P.} } @article {2001|1448, title = {{C}onvergent evolution of {M}ut{S} and topoisomerase {I}{I} for clamping {D}{N}{A} crossovers and stacked {H}olliday junctions}, journal = {J. Biomol. Struct. Dyn.}, volume = {19}, year = {2001}, month = {oct}, pages = {215{\textendash}218}, author = {Y Timsit} } @article {2001, title = {{H}ydration and structural alterations of {A}-{D}{N}{A}. {I}mplications for the accuracy of {D}{N}{A} replication}, journal = {Cell. Mol. Biol. (noisy-le-grand)}, volume = {47}, year = {2001}, pages = {815{\textendash}822}, author = {Mayer, C. and Y Timsit} } @article {2001|1841, title = {Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution}, journal = {J. Biol. Chem.}, volume = {276}, number = {49}, year = {2001}, pages = {46364{\textendash}46370}, author = {S. A. Kozin and G. Bertho and Alexey K Mazur and H. Rabesona and J. P. Girault and T. Haertle and M. Takahashi and P. Debey and G. H. Hoa} } @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|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} } @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 {1999|1455, title = {{D}{N}{A} structure and polymerase fidelity}, journal = {J. Mol. Biol.}, volume = {293}, year = {1999}, month = {nov}, pages = {835{\textendash}853}, author = {Y Timsit} } @article {1999, title = {{L}eft-handed {D}{N}{A} crossovers. {I}mplications for {D}{N}{A}-{D}{N}{A} recognition and structural alterations}, journal = {J. Biomol. Struct. Dyn.}, volume = {16}, year = {1999}, month = {feb}, pages = {775{\textendash}785}, author = {Y Timsit and Shatzky-Schwartz, M. and Shakked, Z.} } @article {1998|1454, title = {{D}{N}{A} crossovers and type {I}{I} {D}{N}{A} topoisomerases: {A} thermodynamical study}, journal = {J. Mol. Biol.}, volume = {284}, year = {1998}, month = {dec}, pages = {1279{\textendash}1287}, author = {Sikorav, J.L. and Duplantier, B. and Jannink, G. and Y Timsit} } @article {1998|1530, title = {Folding and Aggregation of Designed Protein Chains}, journal = {Proc. Natl. Acad. Sci. Usa}, volume = {95}, year = {1998}, pages = {12930{\textendash}1293}, author = {R.A. Broglia and G. Tiana and S. Pasquali and H. E. Roman and E. Vigezzi} } @article {1998, title = {{H}ydration and recognition of methylated {C}p{G} steps in {D}{N}{A}}, journal = {Embo J.}, volume = {17}, year = {1998}, month = {may}, pages = {2709{\textendash}2718}, author = {Mayer-Jung, C. and Moras, D. and Y Timsit} } @article {1998|1453, title = {{S}ymmetry and chirality in topoisomerase {I}{I}-{D}{N}{A} crossover recognition}, journal = {J. Mol. Biol.}, volume = {284}, year = {1998}, month = {dec}, pages = {1289{\textendash}1299}, author = {Y Timsit and Duplantier, B. and Jannink, G. and Sikorav, J.L.} } @article {1997, title = {{E}ffect of cytosine methylation on {D}{N}{A}-{D}{N}{A} recognition at {C}p{G} steps}, journal = {J. Mol. Biol.}, volume = {270}, year = {1997}, month = {jul}, pages = {328{\textendash}335}, author = {Mayer-Jung, C. and Moras, D. and Y Timsit} } @article {1996, title = {{C}ruciform structures and functions}, journal = {Q. Rev. Biophys.}, volume = {29}, year = {1996}, month = {dec}, pages = {279{\textendash}307}, author = {Y Timsit and Moras, D.} } @article {1995|1452, title = {{S}elf-fitting and self-modifying properties of the {B}-{D}{N}{A} molecule}, journal = {J. Mol. Biol.}, volume = {251}, year = {1995}, month = {sep}, pages = {629{\textendash}647}, author = {Y Timsit and Moras, D.} } @article {1995|1941, title = {Solution structure of oligonucleotides covalently linked to a psoralen derivative.}, journal = {Nucleic Acids Res.}, volume = {23}, number = {5}, year = {1995}, month = {mar}, pages = {788{\textendash}795}, abstract = {

Psoralen (pso) was attached via its C-5 position to the 5\&$\#$39;-phosphate group of an oligodeoxynucleotide d(TAAGCCG) by a hexamethylene linker (m6). Complex formation between pso-m6-d(TAAGCCG) and the complementary strands d(CGGCTTA)[7-7mer] or d(CGGCTTAT)[7-8mer] was investigated by nuclear magnetic resonance in aqueous solution. Structural informations derived from DQF-COSY and NOESY maps, revealed that the mini double helix adopts a B-form conformation and that the deoxyriboses preferentially adopt a C2\&$\#$39;-endo conformation. The nOe connectivities observed between the protons of the bases or the sugars in each duplex, and the protons of the psoralen and the hexamethylene chain, led us to propose a model involving an equilibrium between two conformations due to different locations of the psoralen. Upon UV-irradiation, the psoralen moiety cross-linked the two DNA strands at the level of 5\&$\#$39;TpA3\&$\#$39; sequences. NMR studies of the single major photo-cross-linked duplex pso-m6-d(TAAGCCG) and d(CGGCTTA) were performed. The stereochemistry of the diadduct is indeed cis-syn at both cyclobutane rings. In addition, the effects of this diadduct on the helical structure are analyzed in detail.

}, keywords = {Base Sequence, chemistry, chemistry/radiation effects, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Psoralens, Solutions}, author = {O. Bornet and Chantal Pr{\'e}vost and F. Vovelle and M. Chassignol and N. T. Thuong and G. Lancelot} } @article {1994, title = {{D}{N}{A} self-fitting: the double helix directs the geometry of its supramolecular assembly}, journal = {Embo J.}, volume = {13}, year = {1994}, month = {jun}, pages = {2737{\textendash}2746}, author = {Y Timsit and Moras, D.} } @article {1992, title = {{C}rystallization of {D}{N}{A}}, journal = {Meth. Enzymol.}, volume = {211}, year = {1992}, pages = {409{\textendash}429}, author = {Y Timsit and Moras, D.} } @article {1991|1503, title = {{B}ase-pairing shift in the major groove of ({C}{A})n tracts by {B}-{D}{N}{A} crystal structures}, journal = {Nature}, volume = {354}, year = {1991}, month = {nov}, pages = {167{\textendash}170}, author = {Y Timsit and Vilbois, E. and Moras, D.} } @article {1991, title = {{G}roove-backbone interaction in {B}-{D}{N}{A}. {I}mplication for {D}{N}{A} condensation and recombination}, journal = {J. Mol. Biol.}, volume = {221}, year = {1991}, month = {oct}, pages = {919{\textendash}940}, author = {Y Timsit and Moras, D.} } @inbook {1989|1579, title = {Stereospecific Ion-Molecule reactions in the collision cell induced by nucleophilic gas phase reagents on CI/NH4+ protonated diastereoisomeric tetracyclic terpenes.}, booktitle = {Advances in Mass Spectrometry}, volume = {11}, year = {1989}, pages = {1056}, edition = {P. Longevialle, Heyden and Son, Ed, New York}, author = {Cole, RB and Chantal Pr{\'e}vost and Tabet, JC} } @article {1989, title = {{U}nusual helical packing in crystals of {D}{N}{A} bearing a mutation hot spot}, journal = {Nature}, volume = {341}, year = {1989}, month = {oct}, pages = {459{\textendash}462}, author = {Y Timsit and Westhof, E. and Fuchs, R.P. and Moras, D.} } @article {1986|1652, title = {Ion-Molecule reaction in the gas phase part VI Regioselective SN2 reaction from terpenoid diastereoisomeric diols using CI/NH 4+}, journal = {Helv. Chim. Acta}, volume = {69}, year = {1986}, pages = {806{\textendash}815}, abstract = {

A stereospecific and regioselective SN2 mechanism (Walden inversion) is observed during studies involving modified terpenoid epimeric diols in a high-pressure ion source using ammonia as a reagent gas.

}, doi = {10.1002/hlca.19860690408}, author = {Tabet, Jean-Claude and Chantal Pr{\'e}vost and Bouillot, Anne and Bastard, Josette and Manh, Due Do Khae and Tondeur, Yves} }