@article {2024|2168, title = {The characterization of ancient Methanococcales malate dehydrogenases reveals that strong thermal stability prevents unfolding under intense γ-irradiation}, journal = {Mol. Biol. Evol.}, volume = {41}, year = {2024}, abstract = {

Malate dehydrogenases (MalDHs) (EC.1.1.1.37), which are involved in the conversion of oxaloacetate to pyruvate in the tricarboxylic acid cycle, are a relevant model for the study of enzyme evolution and adaptation. Likewise, a recent study showed that Methanococcales, a major lineage of Archaea, is a good model to study the molecular processes of proteome thermoadaptation in prokaryotes. Here, we use ancestral sequence reconstruction and paleoenzymology to characterize both ancient and extant MalDHs. We observe a good correlation between inferred optimal growth temperatures and experimental optimal temperatures for activity (A-Topt). In particular, we show that the MalDH present in the ancestor of Methanococcales was hyperthermostable and had an A-Topt of 80 \°C, consistent with a hyperthermophilic lifestyle. This ancestor gave rise to two lineages with different thermal constraints: one remained hyperthermophilic, while the other underwent several independent adaptations to colder environments. Surprisingly, the enzymes of the first lineage have retained a thermoresistant behavior (i.e. strong thermostability and high A-Topt), whereas the ancestor of the second lineage shows a strong thermostability, but a reduced A-Topt. Using mutants, we mimic the adaptation trajectory toward mesophily and show that it is possible to significantly reduce the A-Topt without altering the thermostability of the enzyme by introducing a few mutations. Finally, we reveal an unexpected link between thermostability and the ability to resist γ-irradiation-induced unfolding.

}, keywords = {ancestral sequence reconstruction, COaLA evolutionary model, extremophiles, irradiation, reactive oxygen species, thermal adaptation}, author = {Madern, Dominique and Halgand, Fr{\'e}d{\'e}ric and Hou{\'e}e-Levin, Chantal and Dufour, Anne-B{\'e}atrice and Coquille, Sandrine and Ansanay-Alex, Salom{\'e} and S Sacquin-Mora and Brochier-Armanet, C{\'e}line} } @article {2023, title = {Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator}, journal = {Frontiers in Microbiology}, volume = {13}, year = {2023}, abstract = {

Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel\–iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes.

}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.1073315}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1073315}, author = {Dragelj, Jovan and Karafoulidi-Retsou, Chara and Katz, Sagie and Lenz, Oliver and Zebger, Ingo and Caserta, Giorgio and S Sacquin-Mora and Mroginski, Maria Andrea} } @article {2022|2157, title = {Consistent Picture of Phosphate{\textendash}Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization}, journal = {J. Phys. Chem. B}, volume = {126}, year = {2022}, month = {05/2022}, pages = {4022-4034}, doi = {10.1021/acs.jpcb.2c01158}, url = {https://pubs.acs.org/doi/full/10.1021/acs.jpcb.2c01158}, author = {Julie Puyo-Fourtine and Marie Juill{\'e} and J{\'e}r{\^o}me H{\'e}nin and Carine Clavagu{\'e}ra and Elise Dubou{\'e}-Dijon} } @article {2020|2075, title = {Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study.}, journal = {Phys Chem Chem Phys}, volume = {22}, year = {2020}, month = {2020 Jan 21}, pages = {1611-1623}, abstract = {

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

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

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

}, keywords = {Model building, molecular dynamics, Molecular mechanisms of disease}, isbn = {9789811358593}, doi = {10.1007/978-981-13-5859-3_47}, author = {Marc Baaden}, editor = {Van Toi, Vo and Le, Trung Quoc and Ngo, Hoan Thanh and Nguyen, Thi-Hiep} } @article {2019|2061, title = {Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.}, journal = {J R Soc Interface}, volume = {16}, year = {2019}, month = {2019 Jul 26}, pages = {20190075}, abstract = {

Dynamics are a key feature of protein function, and this is especially true of gating residues, which occupy cavity or tunnel lining positions in the protein structure, and will reversibly switch between open and closed conformations in order to control the diffusion of small molecules within a protein\&$\#$39;s internal matrix. Earlier work on globins and hydrogenases have shown that these gating residues can be detected using a multiscale scheme combining all-atom classic molecular dynamics simulations and coarse-grain calculations of the resulting conformational ensemble mechanical properties. Here, we show that the structural variations observed in the conformational ensembles produced by NMR spectroscopy experiments are sufficient to induce noticeable mechanical changes in a protein, which in turn can be used to identify residues important for function and forming a mechanical nucleus in the protein core. This new approach, which combines experimental data and rapid coarse-grain calculations and no longer needs to resort to time-consuming all-atom simulations, was successfully applied to five different protein families.

}, issn = {1742-5662}, doi = {10.1098/rsif.2019.0075}, author = {S Sacquin-Mora} } @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 {2018|2137, title = {Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis}, journal = {Proc Natl Acad Sci U S A}, volume = {115}, year = {2018}, month = {11}, pages = {11525-11530}, abstract = {

An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.

}, keywords = {enzymology, mechanics, proteases, single molecule, torsional free energy}, doi = {10.1073/pnas.1803872115}, author = {Guerin, Marcelo E and Guillaume Stirnemann and Giganti, David} } @article {2018|2046, title = {Controlling Redox Enzyme Orientation at Planar Electrodes}, journal = {Catalysts}, volume = {8}, year = {2018}, abstract = {

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

}, issn = {2073-4344}, doi = {10.3390/catal8050192}, url = {http://www.mdpi.com/2073-4344/8/5/192}, author = {Hitaishi, Vivek Pratap and Clement, Romain and Bourassin, Nicolas and Marc Baaden and de Poulpiquet, Anne and S Sacquin-Mora and Ciaccafava, Alexandre and Lojou, Elisabeth} } @article {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|2033, title = {Configurational Disorder of Water Hydrogen Bond Network at the Protein Dynamical Transition}, volume = {121}, year = {2017}, pages = {6792-6798}, author = {O. Rahaman and M. Kalimeri and M. Katava and A. Paciaroni and F. Sterpone} } @article {2017|2032, title = {Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.}, journal = {J Phys Chem B}, volume = {121}, year = {2017}, month = {2017 Mar 23}, pages = {2434-2442}, abstract = {

We characterized the dimer of the amyloid-β wild-type (WT) peptide, Aβ, of 42 residues and its disulfide-bond-locked double mutant (S8C) by replica exchange molecular dynamics simulations. Aβ dimers are known to be the smallest toxic species in Alzheimer\&$\#$39;s disease, and the S8C mutant has been shown experimentally to form an exclusive homogeneous and neurotoxic dimer. Our 50 μs all-atom simulations reveal similar secondary structures and collision cross-sections but very different intramolecular and intermolecular conformations upon double S8C mutation. Both dimers are very dynamic with hundreds of free-energy minima that differ from the U-shape and S-shape conformations of the peptides in the fibrils. The only common structural feature, shared by both species with a probability of 4\% in WT and 12\% in S8C-S8C, is a three-stranded β-sheet spanning the 17-23, 29-36, and 39-41 residues, which does not exist in the Aβ40 WT dimers.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.7b00267}, author = {Man, Viet Hoang and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2017|2025, title = {Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion}, journal = {Proc Natl Acad Sci U S A}, volume = {114}, year = {2017}, month = {Aug}, pages = {9361-9366}, abstract = {

Internal subnanosecond timescale motions are key for the function of proteins, and are coupled to the surrounding solvent environment. These fast fluctuations guide protein conformational changes, yet their role for protein stability, and for unfolding, remains elusive. Here, in analogy with the Lindemann criterion for the melting of solids, we demonstrate a common scaling of structural fluctuations of lysozyme protein embedded in different environments as the thermal unfolding transition is approached. By combining elastic incoherent neutron scattering and advanced molecular simulations, we show that, although different solvents modify the protein melting temperature, a unique dynamical regime is attained in proximity of thermal unfolding in all solvents that we tested. This solvation shell-independent dynamical regime arises from an equivalent sampling of the energy landscape at the respective melting temperatures. Thus, we propose that a threshold for the conformational entropy provided by structural fluctuations of proteins exists, beyond which thermal unfolding is triggered.

}, keywords = {cell thermal stability, Lindemann criterion, Molecular Dynamics Simulation, neutron scattering, protein dynamics}, doi = {10.1073/pnas.1707357114}, author = {Katava, Marina and Guillaume Stirnemann and Zanatta, Marco and Capaccioli, Simone and Pachetti, Maria and Ngai, K L and Sterpone, Fabio and Paciaroni, Alessandro} } @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|1707, title = {Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes}, journal = {J. Chem. Theory Comput.}, volume = {12}, number = {12}, year = {2016}, month = {dec}, pages = {6077{\textendash}6097}, abstract = {G-quadruplexes are the most important non canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)(n), have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite the availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradictory models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach thermodynamic equilibrium. Based on atomistic simulations of diverse classes of intermediates in G-quadruplex folding, we have suggested that the folding is an extremely multipathway process combining a kinetic partitioning mechanism with conformational diffusion. However, complete G-quadruplex folding is far beyond the time scale of atomistic simulations. Here we use high-resolution coarse-grained simulations to investigate potential unfolding intermediates, whose structural dynamics are then further explored with all-atom simulations. This multiscale approach indicates how various pathways are interconnected in a complex network. Spontaneous conversions between different folds are observed. We demonstrate the inability of simple order parameters, such as radius of gyration or the number of native H-bonds, to describe the folding landscape of the G-quadruplexes. Our study also provides information relevant to further development of the coarse grained force field.}, issn = {1549-9618}, doi = {10.1021/acs.jctc.6b00667}, author = {Stadlbauer, Petr and Mazzanti, Liuba and Cragnolini, Tristan and Wales, David J. and Philippe Derreumaux and Pasquali, Samuela and Sponer, Jiri} } @article {2015|1657, title = {Changes in protein structure at the interface accompanying complex formation.}, journal = {Iucrj}, volume = {2}, number = {Pt 6}, year = {2015}, month = {nov}, pages = {643{\textendash}652}, publisher = {Department of Biochemistry, Bose Institute , P-1/12 CIT Scheme VIIM, Kolkata 700 054, India.}, abstract = {Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69\%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16\% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.}, doi = {10.1107/S2052252515015250}, author = {Chakravarty, Devlina and Janin, Jo{\"e}l and Charles H. Robert and Chakrabarti, Pinak} } @article {2015|1708, title = {Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings}, journal = {J. Chem. Theory Comput.}, volume = {11}, number = {7}, year = {2015}, pages = {3510{\textendash}3522}, doi = {10.1021/acs.jctc.5b00200}, author = {Cragnolini, Tristan and Laurin, Yoann and Philippe Derreumaux and Pasquali, Samuela} } @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} } @article {2015|1704, title = {Communication: Multiple atomistic force fields in a single enhanced sampling simulation}, journal = {J. Chem. Phys.}, volume = {143}, number = {2}, year = {2015}, month = {jul}, pages = {021101}, doi = {10.1063/1.4926535}, author = {Man Hoang Viet and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2015|1768, title = {Communication: Multiple atomistic force fields in a single enhanced sampling simulation.}, journal = {The Journal of Chemical Physics}, volume = {143}, number = {2}, year = {2015}, month = {jul}, pages = {021101{\textendash}021101}, doi = {10.1063/1.4926535}, author = {Hoang Viet, Man and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2015|1679, title = {Conformational ensembles and sampled landscapes: analysis and comparison}, journal = {J. Comp. Chem.}, volume = {36}, year = {2015}, pages = {1213{\textendash}31}, author = {Fr{\'e}d{\'e}ric Cazals and A Roth and T Dreyfus and D Mazauric and Charles H. Robert} } @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 {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|1784, title = {Coarse-Grain RNA Folding: Towards More Complex Structures}, booktitle = {Biophys. J.}, volume = {106}, number = {2, 1}, year = {2014}, note = {58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014}, month = {jan}, pages = {283A}, author = {Cragnolini, Tristan and Laurin, Yoann and Philippe Derreumaux and Pasquali, Samuela} } @conference {2014|1385, title = {Content-guided Navigation in Multimeric Molecular Complexes}, booktitle = {{BIOIMAGING} 2014 - Proceedings of the International Conference on Bioimaging, ESEO, Angers, Loire Valley, France, 3-6 March, 2014}, year = {2014}, pages = {76{\textendash}81}, doi = {10.5220/0004914300760081}, author = {M. Trellet and Nicolas F{\'e}rey and Marc Baaden and P. Bourdot} } @article {2014|1433, title = {{A} cooperative mechanism of clotrimazoles in {P}450 revealed by the dissociation picture of clotrimazole from {P}450}, journal = {J. Chem. Inf. Model.}, volume = {54}, number = {4}, year = {2014}, note = {[DOI:\href{http://dx.doi.org/10.1021/ci400660e}{10.1021/ci400660e}] [PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/24611729}{24611729}]}, month = {apr}, pages = {1218{\textendash}1225}, author = {Wang, M. and Marc Baaden and Wang, J. and Liang, Z.} } @article {2013|1403, title = {{C}oarse-grain modelling of protein-protein interactions}, journal = {Curr. Opin. Struct. Biol.}, volume = {23}, number = {6}, year = {2013}, pages = {878{\textendash}886}, author = {Marc Baaden and Marrink, S. J.} } @article {2013|1498, title = {coarse-grained models for protein folding ang aggregation}, journal = {Methods Mol. Biol.}, volume = {924}, year = {2013}, pages = {585{\textendash}600}, author = {Philippe Derreumaux} } @article {2013|1923, title = {Coarse-Grained Simulations of RNA and DNA Duplexes}, journal = {J. Phys. Chem. B}, volume = {117}, number = {27}, year = {2013}, month = {jul}, pages = {8047{\textendash}8060}, doi = {10.1021/jp400786b}, author = {Cragnolini, Tristan and Philippe Derreumaux and Pasquali, Samuela} } @article {2013|1743, title = {Comment on {\textquoteright}Length scale dependence of DNA mechanical properties{\textquoteright}}, journal = {Phys. Rev. Lett.}, volume = {111}, year = {2013}, pages = {179801}, author = {Alexey K Mazur} } @article {2013|1523, title = {Comment on {\textquoteleft}{\textquoteleft}Length Scale Dependence of DNA Mechanical Properties{{\textquoteright}{\textquoteright}}}, journal = {Phys. Rev. Lett.}, volume = {111}, number = {17}, year = {2013}, month = {oct}, author = {Alexey K Mazur} } @article {2013|1887, title = {Communication: Simulated tempering with fast on-the-fly weight determination}, journal = {J. Chem. Phys.}, volume = {138}, number = {6}, year = {2013}, month = {feb}, pages = {061102}, doi = {10.1063/1.4792046}, author = {Phuong Hoang Nguyen and Okamoto, Yuko and Philippe Derreumaux} } @article {2013|1924, title = {Conformational Ensemble and Polymorphism of the All-Atom Alzheimer{\textquoteright}s A beta(37-42) Amyloid Peptide Oligomers}, journal = {J. Phys. Chem. B}, volume = {117}, number = {19}, year = {2013}, month = {may}, pages = {5831{\textendash}5840}, doi = {10.1021/jp401563n}, author = {Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2012|1920, title = {The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins}, journal = {J. Phys. Chem. B}, volume = {116}, number = {30}, year = {2012}, month = {aug}, pages = {8741{\textendash}8752}, doi = {10.1021/jp301665f}, author = {Y Chebaro and Pasquali, Samuela and Philippe Derreumaux} } @article {2012|1676, title = {Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics}, journal = {J. Chem. Phys.}, volume = {137}, year = {2012}, abstract = {

We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water{\textquoteright}s reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.

}, issn = {00219606}, author = {Guillaume Stirnemann and Laage, Damien} } @article {2012|1955, title = {Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature}, journal = {Phys. Chem. Chem. Phys.}, volume = {14}, number = {20}, year = {2012}, pages = {877{\textendash}886}, doi = {10.1039/c1cp21779h}, author = {Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2011|1610, title = {Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer{\textquoteright}s Amyloid-beta(16-22) Peptide}, journal = {Biophys. J.}, volume = {101}, number = {9}, year = {2011}, month = {nov}, pages = {2267{\textendash}2276}, doi = {10.1016/j.bpj.2011.09.046}, author = {Li, Huiyu and Luo, Yin and Philippe Derreumaux and Wei, Guanghong} } @article {2011|1653, title = {On the characterization and selection of diverse conformational ensembles with applications to flexible docking}, journal = {Ieee/acm Trans. Comput. Biol. Bioinform.}, volume = {8}, year = {2011}, pages = {487{\textendash}98}, abstract = {

To address challenging flexible docking problems, a number of docking algorithms pregenerate large collections of candidate conformers. To remove the redundancy from such ensembles, a central problem in this context is to report a selection of conformers maximizing some geometric diversity criterion. We make three contributions to this problem. First, we resort to geometric optimization so as to report selections maximizing the molecular volume or molecular surface area (MSA) of the selection. Greedy strategies are developed, together with approximation bounds. Second, to assess the efficacy of our algorithms, we investigate two conformer ensembles corresponding to a flexible loop of four protein complexes. By focusing on the MSA of the selection, we show that our strategy matches the MSA of standard selection methods, but resorting to a number of conformers between one and two orders of magnitude smaller. This observation is qualitatively explained using the Betti numbers of the union of balls of the selection. Finally, we replace the conformer selection problem in the context of multiple-copy flexible docking. On the aforementioned systems, we show that using the loops selected by our strategy can improve the result of the docking process.

}, doi = {10.1109/TCBB.2009.59}, author = {Loriot, S{\'e}bastien and Sachdeva, Sushant and Bastard, Karine and Chantal Pr{\'e}vost and Fr{\'e}d{\'e}ric Cazals} } @conference {2011|1611, title = {Characterization of the Aggregation Pathway for a 20-mer of GNNQQNY using Coarse-Grained and All-Atom Representations}, booktitle = {Biophys. J.}, volume = {100}, number = {3}, year = {2011}, month = {feb}, pages = {Biophys Soc}, author = {Nasica-Labouze, Jessica and Meli, Massimiliano and Philippe Derreumaux and Colombo, Giorgio and Mousseau, Normand} } @mastersthesis {2011|1574, title = {Coarse-grain models for proteins: Mechanical properties and interactions}, year = {2011}, note = {HDR d{\'e}livr{\'e}e par l{\textquoteright}UFR Sciences du Vivant}, month = {dec}, school = {Universit{\'e} Paris-Diderot - Paris VII}, type = {phdHabilitation {\`a} diriger des recherches}, keywords = {Computational biology, docking, elastic networks, interactions prot{\'e}iques, m{\'e}canique des prot{\'e}ines, Mod{\'e}lisation mol{\'e}culaire, protein interactions, protein mechanics, r{\'e}seau {\'e}lastique}, url = {https://tel.archives-ouvertes.fr/tel-00652917}, author = {S Sacquin-Mora} } @article {2011|1771, title = {Coherent Excitation Transfer Driven by Torsional Dynamics: a Model Hamiltonian for PPV Type Systems}, journal = {Zeitschrift F{\"u}r Physikalische Chemie}, volume = {255}, year = {2011}, pages = {541{\textendash}551}, author = {Fabio Sterpone and R. Martinazzo and A.N. Panda and I. Burghardt} } @article {2011|1473, title = {Coherent vibrational energy transfer along a peptide helix}, journal = {J. Chem. Phys.}, volume = {134}, number = {12}, year = {2011}, month = {mar}, author = {Kobus, Maja and Phuong Hoang Nguyen and Stock, Gerhard} } @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 {2010|1749, title = {A computational study of a recreated {G} protein-{GEF} reaction intermediate competent for nucleotide exchange: fate of the {M}g ion}, journal = {Plos One}, volume = {5}, number = {2}, year = {2010}, month = {feb}, pages = {e9142}, publisher = {Public Library of Science}, abstract = {

Small G-proteins of the superfamily Ras function as molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs). Large conformational changes accompany the exchange reaction, and our understanding of the mechanism is correspondingly incomplete. However, much knowledge has been derived from structural studies of blocked or inactive mutant GEFs, which presumably closely represent intermediates in the exchange reaction and yet which are by design incompetent for carrying out the nucleotide exchange reaction. In this study we have used comparative modelling to recreate an exchange-competent form of a late, pre-GDP-ejection intermediate species in Arf1, a well-characterized small G-protein. We extensively characterized three distinct models of this intermediate using molecular dynamics simulations, allowing us to address ambiguities related to the mutant structural studies. We observed in particular the unfavorable nature of Mg2+ associated forms of the complex and the establishment of closer Arf1-GEF contacts in its absence. The results of this study shed light on GEF-mediated activation of this small G protein and on predicting the fate of the Mg ion at a critical point in the exchange reaction. The structural models themselves furnish additional targets for interfacial inhibitor design, a promising direction for exploring potentially druggable targets with high biological specificity.

}, doi = {10.1371/journal.pone.0009142}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0009142}, author = {M{\'e}riam Ben Hamida{\textendash}Reba\"{\i} and Charles H. Robert} } @article {2010|1736, title = {Consensus {M}odes, a robust description of protein collective motions from multiple-minima normal mode analysis{\textendash}application to the {HIV}-1 protease.}, journal = {Phys. Chem. Chem. Phys.}, volume = {12}, year = {2010}, month = {mar}, pages = {2850{\textendash}2859}, abstract = {

Protein flexibility is essential for enzymatic function, ligand binding, and protein-protein or protein-nucleic acid interactions. Normal mode analysis has increasingly been shown to be well suited for studying such flexibility, as it can be used to identify favorable structural deformations that correspond to functional motions. However, normal modes are strictly relevant to a single structure, reflecting a particular minimum on a complex energy surface, and are thus susceptible to artifacts. We describe a new theoretical framework for determining \"consensus\" normal modes from a set of related structures, such as those issuing from a short molecular dynamics simulation. This approach is more robust than standard normal mode analysis, and provides higher collectivity and symmetry properties. In an application to HIV-1 protease, the low-frequency consensus modes describe biologically relevant motions including flap opening and closing that can be used in interpreting structural changes accompanying the binding of widely differing inhibitors.

}, doi = {10.1039/b919148h}, author = {Paulo R. Batista and Charles H. Robert and Jean-Didier Mar{\'e}chal and M{\'e}riam Ben Hamida{\textendash}Reba\"{\i} and Paulo Pascutti and Paulo M. Bisch and David P. Perahia} } @article {2009|1442, title = {{C}harge {R}ecombination {K}inetics and {P}rotein {D}ynamics in {W}ild {T}ype and {C}arotenoid-less {B}acterial {R}eaction {C}enters: {S}tudies in {T}rehalose {G}lasses}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, month = {jul}, pages = {10389{\textendash}1398}, author = {Francia, F. and Malferrari, M. and S Sacquin-Mora and Venturoli, G.} } @article {2009|1399, title = {{C}oarse-grain simulations of the {R}-{S}{N}{A}{R}{E} fusion protein in its membrane environment detect long-lived conformational sub-states}, journal = {Chemphyschem}, volume = {10}, year = {2009}, month = {jul}, pages = {1548{\textendash}1552}, author = {Durrieu, M. P. and Bond, P. J. and Sansom, M. S. and Lavery, R. and Marc Baaden} } @article {2009|1435, title = {{C}omplex molecular assemblies at hand via interactive simulations}, journal = {J. Comput. Chem.}, volume = {30}, year = {2009}, month = {nov}, pages = {2375{\textendash}2387}, author = {Delalande, O. and Nicolas F{\'e}rey and Grasseau, G. and Marc Baaden} } @book {2009|1567, title = {Coarse-graining protein mechanics}, volume = {Coarse-Graining of Condensed Phase and Biomolecular Systems}, year = {2009}, publisher = {Taylor and Francis}, organization = {Taylor and Francis}, author = {R Lavery and S Sacquin-Mora}, editor = {G. Voth} } @article {2009|2017, title = {The Conversion of Helix H2 to beta-Sheet Is Accelerated in the Monomer and Dimer of the Prion Protein upon T183A Mutation}, journal = {J. Phys. Chem. B}, volume = {113}, number = {19}, year = {2009}, month = {may}, pages = {6942{\textendash}6948}, doi = {10.1021/jp900334s}, author = {Y Chebaro and Philippe Derreumaux} } @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|1884, title = {The complex folding pathways of protein A suggest a multiple-funnelled energy landscape}, journal = {J. Chem. Phys.}, volume = {128}, number = {4}, year = {2008}, month = {jan}, pages = {045101}, doi = {10.1063/1.2812562}, author = {St-Pierre, Jean-Francois and Mousseau, Normand and Philippe Derreumaux} } @article {2008|1468, title = {Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis}, journal = {J. Chem. Phys.}, volume = {128}, number = {24}, year = {2008}, month = {jun}, author = {Altis, Alexandros and Otten, Moritz and Phuong Hoang Nguyen and Hegger, Rainer and Stock, Gerhard} } @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|1882, title = {Coarse-grained protein molecular dynamics simulations}, journal = {J. Chem. Phys.}, volume = {126}, number = {2}, year = {2007}, month = {jan}, pages = {025101}, doi = {10.1063/1.2408414}, author = {Philippe Derreumaux and Mousseau, Normand} } @article {2007|2013, title = {Computational Simulations of the Early Steps of Protein Aggregation}, journal = {Prion}, volume = {1}, number = {1}, year = {2007}, month = {jan}, pages = {3{\textendash}8}, author = {Wei, Guanghong and Mousseau, Normand and Philippe Derreumaux} } @article {2007|1542, title = {Conformational states and folding pathways of peptides revealed by principal-independent component analyses}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {67}, number = {3}, year = {2007}, month = {may}, pages = {579{\textendash}592}, author = {Phuong Hoang Nguyen} } @article {2007|1776, title = {The conserved glycine/alanine residue of the active-site loop containing the putative acetylCoA-binding motif is essential for the overall structural integrity of Mesorhizobium loti arylamine N-acetyltransferase 1}, journal = {Biochem. Biophys. Res. Commun.}, volume = {361}, number = {1}, year = {2007}, month = {sep}, pages = {256{\textendash}262}, doi = {10.1016/j.bbrc.2007.07.034}, author = {Atmane, Noureddine and Dairou, Julien and Flatters, Delphine and Martins, Marta and Pluvinage, Benjamin and Philippe Derreumaux and Dupret, Jean-Marie and Rodrigues-Lima, Fernando} } @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|1843, title = {Comparison of different torsion angle approaches for NMR structure determination}, journal = {J. Biol. Nmr}, volume = {34}, number = {3}, year = {2006}, pages = {153{\textendash}166}, author = {B. Bardiaux and T. E. Malliavin and M. Nilges and Alexey K Mazur} } @article {2006|1541, title = {Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {65}, number = {4}, year = {2006}, month = {dec}, pages = {898{\textendash}913}, author = {Phuong Hoang Nguyen} } @article {2006|1860, title = {Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations}, journal = {J. Phys. Chem. B}, volume = {110}, number = {33}, year = {2006}, pages = {16718{\textendash}16723}, doi = {10.1021/jp0601116}, author = {J{\'e}r{\^o}me H{\'e}nin and Schulten, K. and Christophe Chipot} } @article {2006|1880, title = {The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution}, journal = {J. Chem. Phys.}, volume = {125}, number = {8}, year = {2006}, month = {aug}, pages = {084911}, doi = {10.1063/1.2337628}, author = {Chen, Wei and Mousseau, Normand and Philippe Derreumaux} } @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|1775, title = {Chromatin remodeling complexes: ATP-dependent machines in action.}, journal = {Biochem. Cell Biol.}, volume = {83}, number = {4}, year = {2005}, month = {aug}, pages = {405{\textendash}417}, publisher = {Division of Biological Sciences, Marshall University, Huntington, WV 25755, USA.}, abstract = {Since the initial characterization of chromatin remodeling as an ATP-dependent process, many studies have given us insight into how nucleosome-remodeling complexes can affect various nuclear functions. However, the multistep DNA-histone remodeling process has not been completely elucidated. Although new studies are published on a nearly weekly basis, the nature and roles of interactions of the individual SWI/SNF- and ISWI-based remodeling complexes and DNA, core histones, and other chromatin-associated proteins are not fully understood. In addition, the potential changes associated with ATP recruitment and its subsequent hydrolysis have not been fully characterized. This review explores possible mechanisms by which chromatin-remodeling complexes are recruited to specific loci, use ATP hydrolysis to achieve actual remodeling through disruption of DNA-histone interactions, and are released from their chromatin template. We propose possible roles for ATP hydrolysis in a chromatin-release/target-scanning process that offer an alternative to or complement the often overlooked function of delivering the energy required for sliding or dislodging specific subsets of core histones.}, keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Animals, Chromatin, Gene Expression Regulation, genetics/metabolism, Humans, metabolism, Nucleosomes, Transcription Factors}, doi = {10.1139/o05-115}, author = {Cotteka N Johnson and Nicholas L Adkins and Philippe Georgel} } @conference {2004|1815, title = {Combining Applications and Databases Integration Approaches in a Common Distributed Genomic Platform}, booktitle = {International CODATA Conference, The Information Society: New Horizons for Science}, year = {2004}, month = {nov}, publisher = {Tamkang University}, organization = {Tamkang University}, address = {Berlin, Germany}, author = {P.-E. Gros and J. H{\'e}risson and Nicolas F{\'e}rey and R. Gherbi} } @article {2004|1978, title = {Complex folding pathways in a simple beta-hairpin}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {56}, number = {3}, year = {2004}, month = {aug}, pages = {464{\textendash}474}, doi = {10.1002/prot.20127}, author = {Wei, GH and Mousseau, N and Philippe Derreumaux} } @article {2004|1537, title = {Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {57}, number = {4}, year = {2004}, month = {dec}, pages = {783{\textendash}791}, author = {Faraldo-Gomez, JD and Forrest, LR and Marc Baaden and Bond, PJ and Domene, C and Patargias, G and Cuthbertson, J and Sansom, MSP} } @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|1807, title = {The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer}, journal = {Eur. J. Biochem.}, volume = {271}, number = {7}, year = {2004}, month = {apr}, pages = {1258{\textendash}1265}, doi = {10.1111/j.1432-1033.2004.04026.x}, author = {Arluison, V and Folichon, M and Marco, S and Philippe Derreumaux and Pellegrini, O and Seguin, J and Hajnsdorf, E and Regnier, P} } @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|1946, title = {Comparative bending dynamics in DNA with and without regularly repeated adenine tracts}, journal = {Phys. Rev. E}, volume = {66}, number = {1}, year = {2002}, pages = {011917}, author = {Alexey K Mazur and Dimitri E. Kamashev} } @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|1479, title = {The chloroform TBP aqueous nitric acid interfacial system: a molecular dynamics investigation}, journal = {J. Mol. Liq.}, volume = {90}, number = {1-3, Sp. Iss. SI}, year = {2001}, note = {26th International Conference on Solution Chemistry (26 ICSC), FUKUOKA, JAPAN, JUL 26-31, 1999}, month = {feb}, pages = {1{\textendash}9}, author = {Marc Baaden and Berny, F and Wipff, G} } @article {2001|1989, title = {Computer simulations aimed at structure prediction of supersecondary motifs in proteins}, journal = {Proteins-structure Function and Genetics}, volume = {45}, number = {2}, year = {2001}, month = {nov}, pages = {159{\textendash}166}, doi = {10.1002/prot.1135}, author = {Forcellino, F and Philippe Derreumaux} } @article {2000, title = {Calix{[}4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes}, journal = {Inorg. Chem.}, volume = {39}, number = {10}, year = {2000}, month = {may}, pages = {2033{\textendash}2041}, author = {Lambert, B and Jacques, V and Shivanyuk, A and Matthews, SE and Tunayar, A and Marc Baaden and Wipff, G and Bohmer, V and Desreux, JF} } @article {2000|1490, title = {Cation coordination by calix{[}4]arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs. Na+? A combined NMR and molecular dynamics study}, journal = {Journal of the Chemical Society-perkin Transactions 2}, number = {7}, year = {2000}, pages = {1315{\textendash}1321}, author = {Marc Baaden and Wipff, G and Yaftian, MR and Burgard, M and Matt, D} } @article {2000|1551, title = {Complexation of M3+ lanthanide cations by calix{[}4]arene-CMPO ligands: A molecular dynamics study in methanol solution and at a water/chloroform interface}, journal = {Supramol. Chem.}, volume = {12}, number = {1, Sp. Iss. SI}, year = {2000}, note = {International Symposium on Supramolecular Chemistry, FUKUOKA, JAPAN, 1997}, pages = {27+}, author = {Troxler, L and Marc Baaden and Bohmer, V and Wipff, G} } @article {1997|1680, title = {Collective-variable Monte Carlo simulation of DNA}, journal = {J. Comp. Chem.}, volume = {18}, year = {1997}, pages = {2001{\textendash}2011}, author = {H. Gabb and Chantal Pr{\'e}vost and G. Bertucat and Charles H. Robert and Richard Lavery} } @article {1997|1854, title = {Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of St{\H o}rmer-leapfrog integrators}, journal = {J. Comput. Phys.}, volume = {136}, number = {2}, year = {1997}, pages = {354{\textendash}365}, author = {Alexey K Mazur} } @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 {1994|1584, title = {The catalytic mechanism of {$\alpha$}-amylases based upon enzyme crystal structures and model building calculations}, journal = {Biochem. Biophys. Res. Commun.}, volume = {204}, year = {1994}, pages = {297{\textendash}302}, author = {Alexey K Mazur and R. Haser and F. Payan} } @article {1993|1907, title = {COMPARISON OF THE IR AND RAMAN VIBRATIONAL FREQUENCIES AND INTENSITIES OF ALKANES USING THE AMBER AND SPASIBA FORCE-FIELDS - APPLICATION TO ETHANE, AND GAUCHE-N-BUTANE AND TRANS-N-BUTANE}, journal = {J. Mol. Struct.}, volume = {295}, year = {1993}, month = {may}, pages = {223{\textendash}232}, doi = {10.1016/0022-2860(93)85022-M}, author = {Philippe Derreumaux and LAGANT, P and VERGOTEN, G} } @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|1593, title = {A combined study of aggregation, membrane affinity and pore activity of natural and modified melittin}, journal = {Biochim. Biophys. Acta}, volume = {1069}, number = {1}, year = {1991}, month = {oct}, pages = {77{\textendash}86}, author = {Stankowski, S and Pawlak, M and Kaisheva, E and Charles H. Robert and Schwarz, G} } @article {1990|1638, title = {Conformational energy derivatives for polypeptides with flexible proline rings}, journal = {Comput. \& Chem.}, volume = {14}, year = {1990}, pages = {169{\textendash}175}, author = {Ruben A. Abagyan and Alexey K Mazur} } @article {1989|1912, title = {CONFORMATIONAL STUDIES OF NEUROACTIVE LIGANDS .1. FORCE-FIELD AND VIBRATIONAL-SPECTRA OF CRYSTALLINE ACETYLCHOLINE}, journal = {J. Phys. Chem.}, volume = {93}, number = {4}, year = {1989}, month = {feb}, pages = {1338{\textendash}1350}, doi = {10.1021/j100341a033}, author = {Philippe Derreumaux and WILSON, KJ and VERGOTEN, G and PETICOLAS, WL} } @article {1989|1913, title = {CONFORMATIONAL STUDIES OF NEUROACTIVE LIGANDS .2. SOLUTION-STATE CONFORMATIONS OF ACETYLCHOLINE}, journal = {J. Phys. Chem.}, volume = {93}, number = {4}, year = {1989}, month = {feb}, pages = {1351{\textendash}1357}, doi = {10.1021/j100341a034}, author = {WILSON, KJ and Philippe Derreumaux and VERGOTEN, G and PETICOLAS, WL} } @inbook {1987, title = {Calorimetric analysis of oxygen binding to lobster hemocyanin}, booktitle = {Invertebrate Oxygen Carriers}, year = {1987}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin}, author = {Parody-Morreale, A. and Robert, C. H. and Gill, S. J.} } @article {1987|1818, title = {Calorimetric studies of oxygen and carbon monoxide binding to human hemoglobin. Sequential binding heats for oxygen}, journal = {J. Biol. Chem.}, volume = {262}, number = {23}, year = {1987}, month = {aug}, pages = {10994{\textendash}10999}, author = {Parody-Morreale, A and Robert, C H and Bishop, G A and Gill, S J} } @article {1987|1820, title = {Carbon dioxide and oxygen linkage in human hemoglobin tetramers}, journal = {J. Mol. Biol.}, volume = {196}, number = {4}, year = {1987}, month = {aug}, pages = {927{\textendash}934}, author = {Doyle, M L and Di Cera, E and Robert, C H and Gill, S J} } @article {1986|1602, title = {Cooperative free energies for nested allosteric models as applied to human hemoglobin}, journal = {Biophys. J.}, volume = {50}, number = {4}, year = {1986}, month = {oct}, pages = {747{\textendash}752}, author = {Gill, S J and Charles H. Robert and Coletta, M and Di Cera, E and Brunori, M} }