@article {2017|2031,
	title = {High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.},
	journal = {J Phys Chem B},
	volume = {121},
	year = {2017},
	month = {2017 Jun 22},
	pages = {5977-5987},
	abstract = {<p>The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in Alzheimer\&$\#$39;s disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn, and AMBERsb14 force fields with the TIP3P water model. On the basis of 144 μs replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties, and small-angle X-ray scattering profiles independent of the force field. There are, however, marked differences in secondary structure, with the AMBERsb14 and CHARMM22* ensembles overestimating the CD-derived helix content, and the OPLS-AA and AMBER99sb-ildn secondary structure contents in agreement with CD data. Also the intramolecular beta-hairpin content spanning residues 17-21 and 30-36 varies between 1.5\% and 13\%. Overall, there are significant differences in tertiary and quaternary conformations among all force fields, and the key finding, irrespective of the force field, is that the dimer is stabilized by nonspecific interactions, explaining therefore its possible transient binding to multiple cellular partners and, in part, its toxicity.</p>
},
	issn = {1520-5207},
	doi = {10.1021/acs.jpcb.7b04689},
	author = {Man, Viet Hoang and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@conference {2016|1607,
	title = {Hydrodynamic Effects on Amyloid-beta Aggregation},
	booktitle = {Biophys. J.},
	volume = {110},
	number = {3, 1},
	year = {2016},
	note = {60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016},
	month = {feb},
	pages = {219A},
	publisher = {Biophys Soc},
	organization = {Biophys Soc},
	issn = {0006-3495},
	author = {Chiricotto, Mara and Melchionna, Simone and Philippe Derreumaux and Fabio Sterpone}
}
@article {2016|1702,
	title = {Hydrodynamic effects on beta-amyloid (16-22) peptide aggregation},
	journal = {J. Chem. Phys.},
	volume = {145},
	number = {3},
	year = {2016},
	month = {jul},
	abstract = {Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid A beta(16-22) peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned the essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 A beta(16-22) peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 A beta(16-22) peptide system, the simulation of similar to 300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 A beta(16-22) peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally. Published by AIP Publishing.},
	issn = {0021-9606},
	doi = {10.1063/1.4958323},
	author = {Chiricotto, Mara and Melchionna, Simone and Philippe Derreumaux and Fabio Sterpone}
}
@article {2010|1917,
	title = {HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA},
	journal = {J. Phys. Chem. B},
	volume = {114},
	number = {37},
	year = {2010},
	month = {sep},
	pages = {11957{\textendash}11966},
	doi = {10.1021/jp102497y},
	author = {Pasquali, Samuela and Philippe Derreumaux}
}
@article {2006|1943,
	title = {Hfq variant with altered RNA binding functions},
	journal = {Nucleic Acids Res.},
	volume = {34},
	number = {2},
	year = {2006},
	pages = {709{\textendash}720},
	doi = {10.1093/nar/gkj464},
	author = {Ziolkowska, K and Philippe Derreumaux and Folichon, M and Pellegrini, O and Regnier, P and Boni, IV and Hajnsdorf, E}
}
@article {2004|1791,
	title = {Helix H1 of the prion protein is rather stable against environmental perturbations: molecular dynamics of mutation and deletion variants of PrP(90-231)},
	journal = {Cell. Mol. Life Sci.},
	volume = {61},
	number = {7-8},
	year = {2004},
	month = {apr},
	pages = {951{\textendash}960},
	doi = {10.1007/s00018-003-3455-3},
	author = {Santini, S and Philippe Derreumaux}
}
@article {1993|1908,
	title = {HARMONIC AND MOLECULAR-DYNAMICS OF N-OCTANE - COMPARISON BETWEEN THE AMBER AND SPASIBA FORCE-FIELDS},
	journal = {J. Mol. Struct.},
	volume = {295},
	year = {1993},
	month = {may},
	pages = {233{\textendash}244},
	doi = {10.1016/0022-2860(93)85023-N},
	author = {Philippe Derreumaux and VERGOTEN, G}
}
