@article {2020|2126,
	title = {Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics.},
	journal = {J Phys Chem B},
	volume = {124},
	year = {2020},
	month = {2020 Feb 20},
	pages = {1175-1182},
	abstract = {<p>In Alzheimer\&$\#$39;s disease (AD), many experimental and computational studies support the amyloid pore hypothesis of the Aβ42 peptide. We recently designed a β-barrel tetramer in a membrane-mimicking environment consistent with some low-resolution experimental data. In this earlier study, by using extensive replica exchange molecular dynamics simulations, we found that the wild-type (WT) Aβ42 peptides have a high propensity to form β-barrels, while the WT Aβ40 peptides do not. In this work, we have investigated the effect of mutations D23N and A2T on the Aβ42 barrel tetramer by using the same enhanced conformational sampling technique. It is known that the D23N mutation leads to early onset AD, while the A2T mutation protects from AD. This computational study in a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer membrane shows that the WT sequence and its A2T variant have similar β-barrel populations and the three-dimensional model is slightly destabilized for D23N compared to its WT sequence. These extensive modeling calculations indicate that the lower and higher induced toxicity of these two mutations in AD cannot be correlated to their β-barrel tetramer stabilities in a DPPC lipid bilayer membrane.</p>
},
	issn = {1520-5207},
	doi = {10.1021/acs.jpcb.9b11881},
	author = {Ngo, Son Tung and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2019|2108,
	title = {Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level},
	journal = {The Journal of chemical physics},
	volume = {150},
	year = {2019},
	pages = {215101},
	author = {Man, Viet Hoang and Li, Mai Suan and Wang, Junmei and Philippe Derreumaux and Phuong Hoang Nguyen}
}
@article {2016|1578,
	title = {Impact of the A2V Mutation on the Heterozygous and Homozygous A beta 1-40 Dimer Structures from Atomistic Simulations},
	journal = {Acs Chem. Neurosci.},
	volume = {7},
	number = {6},
	year = {2016},
	month = {jun},
	pages = {823{\textendash}832},
	abstract = {The A2V mutation was reported to protect from Alzheimer{\textquoteright}s disease in its heterozygous form and cause an early Alzheimer{\textquoteright}s disease type dementia in its homozygous form. Experiments showed that the aggregation rate follows the order A2V > WT (wild-type) > A2V-WT. To understand the impact of this mutation, we carried out replica exchange molecular dynamics simulations of A beta 1-40 WT-A2V and A2V-A2V dimers and compared to the WT dimer. Our atomistic simulations reveal that the mean secondary structure remains constant, but there are substantial differences in the intramolecular and intermolecular conformations upon single and double A2V mutation. Upon single mutation, the intrinsic disorder is reduced, the intermolecular potential energies are reduced, the population of intramolecular three-stranded beta-sheets is increased, and the number of all a dimer topologies is decreased. Taken together, these results offer an explanation for the reduced aggregation rate of the A beta 1-40 A2V-WT peptides and the protective effect of A2V in heterozygotes.},
	issn = {1948-7193},
	doi = {10.1021/acschemneuro.6b00053},
	author = {Phuong Hoang Nguyen and Fabio Sterpone and Campanera, Josep M. and Nasica-Labouze, Jessica and Philippe Derreumaux}
}
@article {2013|1892,
	title = {Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation},
	journal = {J. Chem. Theory Comput.},
	volume = {9},
	number = {10},
	year = {2013},
	month = {oct},
	pages = {4574{\textendash}4584},
	doi = {10.1021/ct4003493},
	author = {Sterpone, Fabio and Phuong Hoang Nguyen and Kalimeri, Maria and Philippe Derreumaux}
}
@article {2010|1470,
	title = {Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study},
	journal = {J. Chem. Phys.},
	volume = {133},
	number = {3},
	year = {2010},
	month = {jul},
	author = {Kobus, Maja and Phuong Hoang Nguyen and Stock, Gerhard}
}
@article {2006|1466,
	title = {Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces},
	journal = {J. Chem. Phys.},
	volume = {124},
	number = {15},
	year = {2006},
	month = {apr},
	author = {Phuong Hoang Nguyen and Mittag, E and Torda, AE and Stock, G}
}
