@article {2016|1703,
	title = {Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer{\textquoteright}s peptides},
	journal = {J. Chem. Phys.},
	volume = {144},
	number = {20},
	year = {2016},
	month = {may},
	abstract = {Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments A beta(16-22) and A beta(37-42) of the full length A beta(1-42) Alzheimer{\textquoteright}s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the A beta(16-22) dimer by fitting its equilibrium parallel and anti-parallel beta-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of A beta(16-22) and the dimer and trimer of A beta(37-42). Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the A beta(16-22) decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the A beta(37-42) decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases. Published by AIP Publishing.},
	issn = {0021-9606},
	doi = {10.1063/1.4951739},
	author = {Thanh-Thuy Tran and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2015|1975,
	title = {{A}llosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure},
	journal = {Proc. Natl. Acad. Sci. U.s.a.},
	volume = {112},
	number = {9},
	year = {2015},
	month = {mar},
	pages = {2865{\textendash}2870},
	author = {Moraga-Cid, G. and Sauguet, L. and Huon, C. and Malherbe, L. and Girard-Blanc, C. and Petres, S. and Murail, S. and Antoine Taly and Marc Baaden and Delarue, M. and Corringer, P. J.}
}
@article {2014|1637,
	title = {{L}ong distance effect on ligand-gated ion channels extracellular domain may affect interactions with the intracellular machinery},
	journal = {Commun. Integr. Biol.},
	volume = {7},
	year = {2014},
	pages = {e27984},
	author = {Garret, M. and Boue-Grabot, E. and Antoine Taly}
}
@article {2014|1717,
	title = {Lipid concentration and molar ratio boundaries for the use of isotropic bicelles.},
	journal = {Langmuir},
	volume = {30},
	number = {21},
	year = {2014},
	month = {jun},
	pages = {6162{\textendash}6170},
	publisher = {Department of Chemistry, Universit{\'e} du Qu{\'e}bec {\`a} Montr{\'e}al and Centre Qu{\'e}b{\'e}cois sur les Mat{\'e}riaux Fonctionnels , P.O. Box 8888, Downtown Station, Montreal, Canada H3C 3P8.},
	abstract = {Bicelles are model membranes generally made of long-chain dimyristoylphosphatidylcholine (DMPC) and short-chain dihexanoyl-PC (DHPC). They are extensively used in the study of membrane interactions and structure determination of membrane-associated peptides, since their composition and morphology mimic the widespread PC-rich natural eukaryotic membranes. At low DMPC/DHPC (q) molar ratios, fast-tumbling bicelles are formed in which the DMPC bilayer is stabilized by DHPC molecules in the high-curvature rim region. Experimental constraints imposed by techniques such as circular dichroism, dynamic light scattering, or microscopy may require the use of bicelles at high dilutions. Studies have shown that such conditions induce the formation of small aggregates and alter the lipid-to-detergent ratio of the bicelle assemblies. The objectives of this work were to determine the exact composition of those DMPC/DHPC isotropic bicelles and study the lipid miscibility. This was done using (31)P nuclear magnetic resonance (NMR) and exploring a wide range of lipid concentrations (2-400 mM) and q ratios (0.15-2). Our data demonstrate how dilution modifies the actual DMPC/DHPC molar ratio in the bicelles. Care must be taken for samples with a total lipid concentration <=250 mM and especially at q \~{} 1.5-2, since moderate dilutions could lead to the formation of large and slow-tumbling lipid structures that could hinder the use of solution NMR methods, circular dichroism or dynamic light scattering studies. Our results, supported by infrared spectroscopy and molecular dynamics simulations, also show that phospholipids in bicelles are largely segregated only when q > 1. Boundaries are presented within which control of the bicelles{\textquoteright} q ratio is possible. This work, thus, intends to guide the choice of q ratio and total phospholipid concentration when using isotropic bicelles.},
	keywords = {chemistry, Circular Dichroism, Detergents, Dimyristoylphosphatidylcholine, Fourier Transform Infrared, Light, Lipid Bilayers, Magnetic Resonance Spectroscopy, Materials Testing, Micelles, Molecular Dynamics Simulation, Phospholipid Ethers, Phospholipids, Radiation, Scattering, Solutions, Spectroscopy, Temperature},
	doi = {10.1021/la5004353},
	author = {Beaugrand, Ma\"{\i}wenn and Arnold, Alexandre A. and J{\'e}r{\^o}me H{\'e}nin and Warschawski, Dror E. and Williamson, Philip T F. and Marcotte, Isabelle}
}
@article {2012|2004,
	title = {Ligand-gated ion channels: new insights into neurological disorders and ligand recognition},
	journal = {Chem. Rev.},
	volume = {112},
	number = {12},
	year = {2012},
	month = {sep},
	pages = {6285{\textendash}6318},
	publisher = {American Chemical Society},
	author = {Lemoine, Damien and Jiang, Ruotian and Antoine Taly and Chataigneau, Thierry and Specht, Alexandre and Grutter, Thomas}
}
@article {2011|1741,
	title = {Local elasticity of strained DNA studied by all-atom simulations},
	journal = {Phys. Rev. E},
	volume = {84},
	year = {2011},
	pages = {021903},
	author = {Alexey K Mazur}
}
@article {2010|1885,
	title = {Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: A replica exchange molecular dynamics study in explicit solvent},
	journal = {J. Chem. Phys.},
	volume = {132},
	number = {16},
	year = {2010},
	month = {apr},
	pages = {165103},
	doi = {10.1063/1.3385470},
	author = {De Simone, Alfonso and Philippe Derreumaux}
}
@article {2007|1984,
	title = {Locating the active sites of enzymes using mechanical properties},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {67},
	number = {2},
	year = {2007},
	month = {may},
	pages = {350{\textendash}359},
	doi = {10.1002/prot.21353},
	author = {S Sacquin-Mora and Laforet, Emilie and Lavery, Richard}
}
@article {2003|1694,
	title = {Linear response and electron transfer in complex biomolecules systems and Reaction Center Protein},
	journal = {J. Phys. Chem. B},
	volume = {107},
	year = {2003},
	pages = {11208{\textendash}11215},
	author = {Fabio Sterpone and M. Ceccarelli and M. Marchi}
}
@article {2003|1465,
	title = {Local structure in nematic and isotropic liquid crystals},
	journal = {J. Chem. Phys.},
	volume = {119},
	number = {2},
	year = {2003},
	month = {jul},
	pages = {1214{\textendash}1222},
	author = {Phuong, NH and Schmid, F}
}
@article {2001|1520,
	title = {Lanthanide cation binding to a phosphoryl-calix{[}4]arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations},
	journal = {Phys. Chem. Chem. Phys.},
	volume = {3},
	number = {7},
	year = {2001},
	pages = {1317{\textendash}1325},
	author = {Marc Baaden and Burgard, M and Boehme, C and Wipff, G}
}
@article {1999,
	title = {{L}eft-handed {D}{N}{A} crossovers. {I}mplications for {D}{N}{A}-{D}{N}{A} recognition and structural alterations},
	journal = {J. Biomol. Struct. Dyn.},
	volume = {16},
	year = {1999},
	month = {feb},
	pages = {775{\textendash}785},
	author = {Y Timsit and Shatzky-Schwartz, M. and Shakked, Z.}
}
@article {1998|1624,
	title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
	journal = {Biophys. J.},
	volume = {74},
	number = {1},
	year = {1998},
	month = {jan},
	pages = {72{\textendash}81},
	author = {Philippe Derreumaux and Schlick, T.}
}
@article {1995|1988,
	title = {LONG TIMESTEP DYNAMICS OF PEPTIDES BY THE DYNAMICS DRIVER APPROACH},
	journal = {Proteins-structure Function and Genetics},
	volume = {21},
	number = {4},
	year = {1995},
	month = {apr},
	pages = {282{\textendash}302},
	doi = {10.1002/prot.340210403},
	author = {Philippe Derreumaux and SCHLICK, T}
}
@article {1988|1589,
	title = {Linkage of organic phosphates to oxygen binding in human hemoglobin at high concentrations},
	journal = {Biochemistry},
	volume = {27},
	number = {18},
	year = {1988},
	month = {sep},
	pages = {6835{\textendash}6843},
	author = {Charles H. Robert and Fall, L and Gill, S J}
}
