Publications

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2012
Laurent B., Murail S., Da Silva F., Corringer P.-J., Baaden M.  2012.  Modeling complex biological systems: From solution chemistry to membranes and channels. Pure Appl. Chem.. ASAP
Prevost M., Sauguet L., Nury H., Van Renterghem C., Huon C., Poitevin F., Baaden M, Delarue M., Corringer P.-J..  2012.  A novel Locally Closed Conformation of a Bacterial Pentameric Proton-gated Ion Channel. Nature Structural & Molecular Biology.
Thevenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tuffery P.  2012.  PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res.. 40:W288-W293.
Lu Y, Wei G, Derreumaux P.  2012.  Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations. J. Chem. Phys.. 137:025101.
Chebaro Y, Jiang P, Zang T, Mu Y, Nguyen PHoang, Mousseau N, Derreumaux P.  2012.  Structures of A beta 17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure. J. Phys. Chem. B. 116:8412–8422.
Peoc'h K, Levavasseur E, Delmont E, Laffont-Proust ADe Simone, Privat N, Chebaro Y, Bedoucha CChapuis Pi, Brandel J-P, Laquerriere A, Hauw J-LKemeny Jea et al..  2012.  Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders. Hum. Mol. Genet.. 21:5417–5428.
Stadler A.M, Garvey C.J, Bocahut A., Sacquin-Mora S, Digel I., Schneider G.J, Natali F., Artmann G.M, Zaccai G..  2012.  Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics. J. R. Soc. Interface. 9:2845–2855.
Derrar S.N, Sekkal-Rahal M., Guemra K., Derreumaux P.  2012.  Theoretical study on a series of push-pull molecules grafted on methacrylate copolymers serving for nonlinear optics. Int. J. Quantum Chem.. 112:2735–2742.
Derrar S.N, Sekkal-Rahal M., Guemra K., Derreumaux P.  2012.  Theoretical study on a series of push-pull molecules grafted on methacrylate copolymers serving for nonlinear optics. Int. J. Quantum Chem.. 112:2735–2742.
2011
Barducci A, Bonomi M, Derreumaux P.  2011.  Assessing the Quality of the OPEP Coarse-Grained Force Field. J. Chem. Theory Comput.. 7:1928–1934.
Li H, Luo Y, Derreumaux P, Wei G.  2011.  Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer’s Amyloid-beta(16-22) Peptide. Biophys. J.. 101:2267–2276.
Nasica-Labouze J, Meli M, Derreumaux P, Colombo G, Mousseau N.  2011.  Characterization of the Aggregation Pathway for a 20-mer of GNNQQNY using Coarse-Grained and All-Atom Representations. Biophys. J.. 100:BiophysSoc.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Cote S, Derreumaux P, Mousseau N.  2011.  Distinct Morphologies for Amyloid Beta Protein Monomer: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N). J. Chem. Theory Comput.. 7:2584–2592.
Nguyen PHoang, Li MSuan, Derreumaux P.  2011.  Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
Lu Y, Wei G, Derreumaux P.  2011.  Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
Catoire L.J, Damian M., Baaden M, Guittet E., Banères J.-L..  2011.  Electrostatically–driven fast association and perdeuteration allow transferred cross–relaxation detection for G protein–coupled receptor ligands with equilibrium dissociation constants in the high–to–low nanomolar range. J Biomolecular Nmr. 50:191–5.
Delalande O., Sacquin-Mora S, Baaden M.  2011.  Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase. Biophys. J.. 101:1440–1449.
Jiang R., Lemoine D., Martz A., Taly A, Gonin S., L. de Carvalho P, Specht A., Grutter T..  2011.  Agonist trapped in ATP-binding sites of the P2X2 receptor. Proc. Natl. Acad. Sci. U.s.a.. 108:9066–9071.
Spill YG, Pasquali S, Derreumaux P.  2011.  Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model. J. Chem. Theory Comput.. 7:1502–1510.
Xu W, Zhang C, Derreumaux P, Graslund A, Morozova-Roche L, Mu Y.  2011.  Intrinsic Determinants of A beta(12-24) pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies. Plos One. 6:e24329.
Nasica-Labouze J, Meli M, Derreumaux P, Colombo G, Mousseau N.  2011.  A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35. Plos Comput. Biol.. 7:e1002051.
Stirnemann G, Castrillon SRomero-Var, Hynes JT, Rossky PJ, Debenedetti PG, Laage D.  2011.  Non-monotonic dependence of water reorientation dynamics on surface hydrophilicity: competing effects of the hydration structure and hydrogen-bond strength. Phys. Chem. Chem. Phys.. 13:19911.
Miné-Hattab J, Fleury G, Prévost C, Dutreix M, Viovy J-L.  2011.  Optimizing the design of oligonucleotides for homology directed gene targeting. Plos One. 6:e14795.

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