@article {2024|2167, title = {NP-collabs: Investigating counterion-mediated bridges in the multiply phosphorylated tau-R2 repeat}, journal = {J. Chem. Inf. Model.}, volume = {64}, year = {2024}, pages = {6570{\textendash}6582}, abstract = {

Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer\&$\#$39;s disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.

}, author = {Marien, Jules and Pr{\'e}vost, Chantal and S Sacquin-Mora} } @article {2019|2107, title = {Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion}, journal = {The Journal of chemical physics}, volume = {151}, year = {2019}, pages = {024103}, author = {Man, Viet Hoang and Li, Mai Suan and Wang, Junmei and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2017|2028, title = {New Coarse Variables for the Accurate Determination of Standard Binding Free Energies}, journal = {J Chem Theory Comput}, volume = {13}, year = {2017}, month = {2017 Nov 14}, pages = {5173-5178}, abstract = {

To improve sampling of the configurational entropy change upon protein-ligand binding, we have introduced a new set of coarse variables describing the relative orientation and position of the ligand via a global macromolecular orientational procedure, onto which geometrical restraints are applied. Evaluating the potential of mean force for the different coarse variables, the experimental standard binding free energy for three decapeptides associated with the SH3 domain of the Abl kinase is reproduced quantitatively.

}, issn = {1549-9626}, doi = {10.1021/acs.jctc.7b00791}, author = {Fu, Haohao and Cai, Wensheng and J{\'e}r{\^o}me H{\'e}nin and Roux, Beno{\^\i}t and Chipot, Christophe} } @article {2016|1703, title = {Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils}, journal = {J. Chem. Phys.}, volume = {145}, number = {17}, year = {2016}, month = {nov}, abstract = {The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an A beta fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis. Published by AIP Publishing.}, issn = {0021-9606}, doi = {10.1063/1.4966263}, author = {Man Hoang Viet and Philippe Derreumaux and Phuong Hoang Nguyen} } @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|1672, title = {A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of gamma-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes.}, journal = {J. Biol. Chem}, volume = {291}, year = {2016}, month = {sep}, pages = {20473{\textendash}86}, abstract = {

Propofol, an intravenous anesthetic, is a positive modulator of the GABAA receptor, but the mechanistic details, including the relevant binding sites and alternative targets, remain disputed. Here we undertook an in-depth study of alkylphenol-based anesthetic binding to synaptic membranes. We designed, synthesized, and characterized a chemically active alkylphenol anesthetic (2-((prop-2-yn-1-yloxy)methyl)-5-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenol, AziPm-click (1)), for affinity-based protein profiling (ABPP) of propofol-binding proteins in their native state within mouse synaptosomes. The ABPP strategy captured approximately 4\% of the synaptosomal proteome, including the unbiased capture of five alpha or beta GABAA receptor subunits. Lack of gamma2 subunit capture was not due to low abundance. Consistent with this, independent molecular dynamics simulations with alchemical free energy perturbation calculations predicted selective propofol binding to interfacial sites, with higher affinities for alpha/beta than gamma-containing interfaces. The simulations indicated hydrogen bonding is a key component leading to propofol-selective binding within GABAA receptor subunit interfaces, with stable hydrogen bonds observed between propofol and alpha/beta cavity residues but not gamma cavity residues. We confirmed this by introducing a hydrogen bond-null propofol analogue as a protecting ligand for targeted-ABPP and observed a lack of GABAA receptor subunit protection. This investigation demonstrates striking interfacial GABAA receptor subunit selectivity in the native milieu, suggesting that asymmetric occupancy of heteropentameric ion channels by alkylphenol-based anesthetics is sufficient to induce modulation of activity.

}, keywords = {anesthesia, anesthetic, click chemistry, GABA receptor, photoaffinity labeling}, doi = {10.1074/jbc.M116.736975}, author = {Woll, Kellie A. and Murlidaran, Sruthi and Pinch, Benika J. and J{\'e}r{\^o}me H{\'e}nin and Wang, Xiaoshi and Salari, Reza and Covarrubias, Manuel and Dailey, William P. and Grace Brannigan and Garcia, Benjamin A. and Roderic G Eckenhoff} } @article {2015|1549, title = {{N}othing to sneeze at: a dynamic and integrative computational model of an influenza {A} virion}, journal = {Structure}, volume = {23}, number = {3}, year = {2015}, month = {mar}, pages = {584{\textendash}597}, author = {Reddy, T. and Shorthouse, D. and Parton, D. L. and Jefferys, E. and Fowler, P. W. and Matthieu Chavent and Marc Baaden and Sansom, M. S.} } @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 {2012|1506, title = {A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel}, journal = {Nature Structural \& Molecular Biology}, year = {2012}, month = {apr}, author = {M. Prevost and L. Sauguet and H. Nury and C. Van Renterghem and C. Huon and F. Poitevin and Marc Baaden and M. Delarue and P.-J. Corringer} } @article {2011|1738, title = {Non-monotonic dependence of water reorientation dynamics on surface hydrophilicity: competing effects of the hydration structure and hydrogen-bond strength}, journal = {Phys. Chem. Chem. Phys.}, volume = {13}, year = {2011}, pages = {19911}, abstract = {

The reorientation dynamics of interfacial water molecules was recently shown to change non-monotonically next to surfaces of increasing hydrophilicity, with slower dynamics next to strongly hydrophobic (apolar) and very hydrophilic surfaces, and faster dynamics next to surfaces of intermediate hydrophilicities. Through a combination of molecular dynamics simulations and analytic modeling, we provide a molecular interpretation of this behavior. We show that this non-monotonic dependence arises from two competing effects induced by the increasing surface hydrophilicity: first a change in the hydration structure with an enhanced population of water OH bonds pointing toward the surface and second a strengthening of the water-surface interaction energy. The extended jump model, including the effects due to transition-state excluded volume and transition-state hydrogen-bond strength, provides a quasi-quantitative description of the non-monotonic changes in the water reorientation dynamics with surface hydrophilicity.

}, issn = {1463-9076}, author = {Guillaume Stirnemann and Castrillon, Santiago Romero-Vargas and Hynes, James T. and Rossky, Peter J. and Debenedetti, Pablo G. and Laage, Damien} } @article {2010|1685, title = {Non adiabatic simulations of exciton dissociation in poly-p-phenylenevinylene oligomers}, journal = {J. Phys. Chem. A}, volume = {114}, year = {2010}, pages = {7661{\textendash}7670}, author = {M. Bedard-Hearn and Fabio Sterpone and P.J. Rossky} } @article {2010|1472, title = {Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix}, journal = {J. Chem. Phys.}, volume = {132}, number = {2}, year = {2010}, month = {jan}, author = {Phuong Hoang Nguyen and Park, Sang-Min and Stock, Gerhard} } @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|1438, title = {{A}n optimized extended {D}{N}{A} kappa {B} site that enhances plasmid {D}{N}{A} nuclear import and gene expression}, journal = {J. Gene Med.}, volume = {11}, year = {2009}, month = {may}, pages = {401{\textendash}411}, author = {Goncalves, C. and Ardourel, M. Y. and Decoville, M. and Breuzard, G. and Midoux, P. and Hartmann, B. and Pichon, C.} } @article {2009|1384, title = {New Insight into the interaction between erbin and smad3: a non-classical binding interface for the erbin PDZ domain}, journal = {Biochem. Biophys. Res. Commun.}, volume = {378}, number = {3}, year = {2009}, pages = {360{\textendash}365}, author = {N Deliot and Matthieu Chavent and C Nourry and P Lecine and C Arnaud and A Hermant and B Maigret and J.-P. Borg} } @article {2009|1440, title = {Nonadiabatic mixed quantum-classical dynamic simulation of pi-stacked oligophenylenevinylenes}, journal = {J. Phys. Chem. A}, volume = {113}, number = {15}, year = {2009}, pages = {3427{\textendash}30}, author = {Sterpone, Fabio and Bedard-Hearn, Michael J and Rossky, Peter J} } @inbook {2009|1568, title = {Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment}, year = {2009}, publisher = {CRC Press}, organization = {CRC Press}, author = {Phuong Hoang Nguyen and P. Hamm and G. Stock}, editor = {D. Leitner and J. Straub} } @article {2009|1521, title = {Numerical studies of Lifshitz interactions between dielectrics}, journal = {Phys. Rev. A}, volume = {79}, year = {2009}, pages = {020102(R)}, author = {S. Pasquali and A.C. Maggs} } @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} } @article {2008|1397, title = {Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description}, journal = {Chem. Phys.}, volume = {347}, number = {1-3}, year = {2008}, month = {may}, pages = {208{\textendash}217}, author = {Kobus, Maja and Gorbunov, Roman D. and Phuong Hoang Nguyen and Stock, Gerhard} } @article {2008|1519, title = {Numerical methods for fluctuation driven interactions between dielectrics}, journal = {Phys. Rev. E}, volume = {77}, year = {2008}, pages = {016705}, author = {S. Pasquali and F. Nitti and A.C. Maggs} } @article {2006|1396, title = {Nonequilibrium molecular dynamics simulation of a photoswitchable peptide}, journal = {Chem. Phys.}, volume = {323}, number = {1}, year = {2006}, month = {mar}, pages = {36{\textendash}44}, author = {Phuong Hoang Nguyen and Stock, G} } @article {2006|1810, title = {Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors}, journal = {Febs Lett.}, volume = {580}, number = {22}, year = {2006}, month = {oct}, pages = {5130{\textendash}5136}, abstract = {We demonstrate the utility of normal mode analysis in correctly predicting the binding modes of inhibitors in the active sites of matrix metalloproteinases (MMPs). We show the accuracy in predicting the positions of MMP-3 inhibitors is strongly dependent on which structure is used as the target, especially when it has been energy minimized. This dependency can be overcome by using intermediate structures generated along one of the normal modes previously calculated for a given target. These results may be of prime importance for further in silico drug discovery.}, doi = {10.1016/j.febslet.2006.08.037}, author = {Nicolas Floquet and Jean-Didier Mar{\'e}chal and Marie-Ange Badet-Denisot and Charles H Robert and Manuel Dauchez and David Perahia} } @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} } @article {2005|1952, title = {Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique}, journal = {Phys. Biol.}, volume = {2}, number = {4, Sp. Iss. SI}, year = {2005}, month = {dec}, pages = {S101-S107}, doi = {10.1088/1478-3975/2/4/S04}, author = {Mousseau, N and Philippe Derreumaux and Gilbert, G} } @article {2003|1957, title = {Nanoscopic liquid bridges exposed to a torsional strain}, journal = {Physical Review E}, volume = {68}, number = {6, Part 2}, year = {2003}, month = {dec}, pages = {066103}, doi = {10.1103/PhysRevE.68.066103}, author = {S Sacquin-Mora and Fuchs, AH and Schoen, M} } @article {2003|1464, title = {Nonequilibrium molecular-dynamics study of the vibrational energy relaxation of peptides in water}, journal = {J. Chem. Phys.}, volume = {119}, number = {21}, year = {2003}, month = {dec}, pages = {11350{\textendash}11358}, author = {Phuong Hoang Nguyen and Stock, G} } @article {2002|1599, title = {New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations}, journal = {Biophys. J.}, volume = {82}, number = {6}, year = {2002}, month = {jun}, pages = {3224{\textendash}3245}, author = {Mouawad, Liliane and Perahia, David and Charles H. Robert and Guilbert, Christophe} } @article {1995|1869, title = {A NEW SPECTROSCOPIC MOLECULAR MECHANICS FORCE-FIELD - PARAMETERS FOR PROTEINS}, journal = {J. Chem. Phys.}, volume = {102}, number = {21}, year = {1995}, month = {jun}, pages = {8586{\textendash}8605}, doi = {10.1063/1.468848}, author = {Philippe Derreumaux and VERGOTEN, G} } @article {1991|1719, title = {NMR and conformational studies of the cyclobutane ring involved in the bicyclo [4.2. 0] octane system of a tetracyclic diterpene structure}, journal = {Magn. Reson. Chem.}, volume = {29}, year = {1991}, pages = {870{\textendash}877}, abstract = {

Conformational studies were performed on the bicyclo [4.2.0] octane system of a series of related tetracyclic diterpenes, using molecular mechanics and 1H NMR. Both methods gave compatible results, but did not permit the deduction of any quantitative relationship linking the vicinal coupling constants to the cyclobutane dihedral angles. Nevertheless, the Karplus relationship allowed a qualitative interpretation of the coupling constants in terms of conformation. A set of characteristic 1H NMR coupling constants was obtained which allows the interpretation of the 1H NMR spectrum of any compound presenting a similar system.

}, doi = {DOI: 10.1002/mrc.1260290903}, url = {http://onlinelibrary.wiley.com/doi/10.1002/mrc.1260290903/full}, author = {Do Khac Manh, Duc and Fetizon, Marcel and Chantal Pr{\'e}vost and Roy, Pierre} } @article {1990|1723, title = {A new method for analysing of kinetic graphs in enzymatic catalysis}, journal = {Mol. Biol.}, volume = {24}, year = {1990}, pages = {209{\textendash}213}, author = {Alexey K Mazur} } @article {1990|1929, title = {NORMAL-COORDINATE TREATMENT OF A NUCLEIC BASE PAIR MODEL IN ITS CRYSTALLINE STATE - 1-METHYLCYTOSINE-9-ETHYLGUANINE}, journal = {J. Raman Spectrosc.}, volume = {21}, number = {4}, year = {1990}, month = {apr}, pages = {215{\textendash}226}, doi = {10.1002/jrs.1250210402}, author = {LAGANT, P and VERGOTEN, G and Philippe Derreumaux and DHENNIN, R} } @article {1989|1644, title = {A new approach to the modelling of the structure and dynamics of biomacromolecules and their complexes}, journal = {Doklady. Biophysics}, volume = {304}, year = {1989}, pages = {456{\textendash}460}, author = {Alexey K Mazur and R. A. Abagyan and G. B. Elyakov} } @article {1989|1674, title = {New methodology for computer-aided modelling of biomolecular structure and dynamics: 2. Local deformations and cycles}, journal = {J. Biomol. Struct. Dyn.}, volume = {6}, year = {1989}, pages = {833{\textendash}845}, author = {Ruben A. Abagyan and Alexey K Mazur} } @article {1989|1675, title = {New methodology for computer-aided modelling of biomolecular structure and dynamics: 1. Non-cyclic structures}, journal = {J. Biomol. Struct. Dyn.}, volume = {6}, year = {1989}, pages = {815{\textendash}832}, author = {Alexey K Mazur and Ruben A. Abagyan} } @article {1988|1590, title = {Nested allosteric interaction in tarantula hemocyanin revealed through the binding of oxygen and carbon monoxide}, journal = {Biochemistry}, volume = {27}, number = {18}, year = {1988}, month = {sep}, pages = {6901{\textendash}6908}, author = {Decker, H and Connelly, P R and Charles H. Robert and Gill, S J} } @inbook {1987|1429, title = {Nesting- An extension of the MWC model and its application to tarantula hemocyanin}, booktitle = {Invertebrate Oxygen Carriers}, year = {1987}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin}, author = {Decker, H. and Robert, C. H. and Gill, S. J.} } @article {1987|1967, title = {Nesting: hierarchies of allosteric interactions}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {84}, number = {7}, year = {1987}, month = {apr}, pages = {1891{\textendash}1895}, author = {Robert, C H and Decker, H and Richey, B and Gill, S J and Wyman, J} }