@article {2020|2117, title = {Aggregation of disease-related peptides.}, journal = {Prog Mol Biol Transl Sci}, volume = {170}, year = {2020}, month = {2020}, pages = {435-460}, abstract = {

Protein misfolding and aggregation of amyloid proteins is the fundamental cause of more than 20 diseases. Molecular mechanisms of the self-assembly and the formation of the toxic aggregates are still elusive. Computer simulations have been intensively used to study the aggregation of amyloid peptides of various amino acid lengths related to neurodegenerative diseases. We review atomistic and coarse-grained simulations of short amyloid peptides aimed at determining their transient oligomeric structures and the early and late aggregation steps.

}, issn = {1878-0814}, doi = {10.1016/bs.pmbts.2019.12.002}, author = {Phuong Hoang Nguyen and Sterpone, Fabio and Philippe Derreumaux} } @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 = {

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.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.9b11881}, author = {Ngo, Son Tung and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2020|2125, title = {Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ Peptide.}, journal = {J Chem Inf Model}, volume = {60}, year = {2020}, month = {2020 Mar 23}, pages = {1399-1408}, abstract = {

There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ trimer from the U-shape conformation and MD simulations starting from Aβ dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ peptide.

}, issn = {1549-960X}, doi = {10.1021/acs.jcim.9b01074}, author = {Minh Hung, Huynh and Nguyen, Minh Tho and Tran, Phuong-Thao and Truong, Vi Khanh and Chapman, James and Quynh Anh, Le Huu and Philippe Derreumaux and Vu, Van V and Ngo, Son Tung} } @article {2020|2116, title = {Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation}, journal = {The Journal of Physical Chemistry B}, year = {2020}, author = {Ngo, Son Tung and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2020|2131, title = {Tau R3-R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations.}, journal = {J Phys Chem B}, year = {2020}, month = {2020 Mar 27}, abstract = {

In Alzheimer\&$\#$39;s disease, neurofibrillary lesions correlate with cognitive deficits and consist of inclusions of tau protein with cross-β structure. A stable dimeric form of soluble tau has been evidenced in the cells, but its high-resolution structure is missing in solution. We know, however, that cryo-electron microscopy (c-EM) of full-length tau in the brain of an individual with AD displays a core of eight β-sheets with a C-shaped architecture spanning the R3-R4 repeat domain, while the rest of the protein is very flexible. To address the conformational ensemble of the dimer, we performed atomistic replica exchange molecular dynamics simulations on the tau R3-R4 domain starting from the c-EM configuration. We find that the wild type tau R3-R4 dimer explores elongated, U-shaped, V-shaped and globular forms rather than the C-shape. Phosphorylation of Ser356, pSer356, is known to block the interaction between the tau protein and the amyloid-β42 peptide. Standard molecular dynamics simulations of this phosphorylated sequence for a total of 5 microseconds compared to its wild type counterpart show a modulation of the population of β-helices and accessible topologies, and a decrease of intermediates near the fibril like conformers.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.0c00574}, author = {Philippe Derreumaux and Man, Viet Hoang and Wang, Junmei and Phuong Hoang Nguyen} } @article {2019|2109, title = {Amyloid-β (29{\textendash}42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids}, journal = {The Journal of Physical Chemistry B}, volume = {123}, year = {2019}, pages = {2687{\textendash}2696}, author = {Lu, Yan and Shi, Xiao-Feng and Phuong Hoang Nguyen and Sterpone, Fabio and Salsbury Jr, Freddie R and Philippe Derreumaux} } @article {2019|2127, title = {C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ Tetramer in Solution: Intensive MD Study.}, journal = {ACS Omega}, volume = {4}, year = {2019}, month = {2019 Jun 30}, pages = {11066-11073}, abstract = {

Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer\&$\#$39;s disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms \→ oligomers \→ photofibrils \→ mature fibrils \→ plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ tetramer (S4Aβ) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is \∼42 \± 3\%. Furthermore, the dissociation free energy of the S4Aβ peptide was predicted using a biased sampling method. The obtained free energy is Δ = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ peptide. We anticipate that the obtained S4Aβ structures could be used as targets for AD inhibitor screening over the in silico study.

}, issn = {2470-1343}, doi = {10.1021/acsomega.9b00992}, author = {Tung, Nguyen Thanh and Philippe Derreumaux and Vu, Van V and Nam, Pham Cam and Ngo, Son Tung} } @article {2019|2110, title = {Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16{\textendash}22 dimer}, journal = {Journal of chemical theory and computation}, volume = {15}, year = {2019}, pages = {1440{\textendash}1452}, author = {Man, Viet Hoang and He, Xibing and Philippe Derreumaux and Ji, Beihong and Xie, Xiang-Qun and Phuong Hoang Nguyen and Wang, Junmei} } @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 {2019|2118, title = {Mesoscale biosimulations within a unified framework: from proteins to plasmids}, year = {2019}, pages = {1-12}, author = {P. Maiocchi and Philippe Derreumaux and F. Sterpone and S. Melchionna} } @article {2019|2122, title = {Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics}, journal = {Scientific Reports}, volume = {9}, year = {2019}, pages = {16450}, abstract = {

In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.

}, isbn = {2045-2322}, doi = {10.1038/s41598-019-52760-y}, url = {https://doi.org/10.1038/s41598-019-52760-y}, author = {F. Brandner, Astrid and Timr, Stepan and Melchionna, Simone and Philippe Derreumaux and Marc Baaden and Sterpone, Fabio} } @article {2019|2120, title = {Multiscale Aggregation of the Amyloid Aβ16{\textendash}22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils}, journal = {The Journal of Physical Chemistry Letters}, volume = {10}, year = {2019}, pages = {1594-1599}, doi = {10.1021/acs.jpclett.9b00423}, url = {https://doi.org/10.1021/acs.jpclett.9b00423}, author = {Chiricotto, Mara and Melchionna, Simone and Philippe Derreumaux and Sterpone, Fabio} } @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 {2019|2121, title = {OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field}, journal = {Journal of Chemical Theory and Computation}, volume = {15}, year = {2019}, pages = {3875-3888}, doi = {10.1021/acs.jctc.9b00202}, url = {https://doi.org/10.1021/acs.jctc.9b00202}, author = {Barroso da Silva, Fernando Luis and Sterpone, Fabio and Philippe Derreumaux} } @article {2019|2128, title = {Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca Ions.}, journal = {J Phys Chem B}, volume = {123}, year = {2019}, month = {2019 Mar 28}, pages = {2645-2653}, abstract = {

Amyloid β (Aβ) peptides are considered the major causative agents of Alzheimer\&$\#$39;s disease (AD). In a widely accepted mechanism for AD pathogenesis, Aβ peptides are proposed to play multiple roles in damaging brain cells and their synaptic communications. Due to the heterogeneous nature of Aβ oligomers, their in vivo structures have not been understood. Most experimental and computational studies favored β-rich structures of Aβ as observed in Aβ fibrils. In this in silico study, we investigated an alternative perspective on the structures and function of Aβ oligomers in the cell membrane. Transmembrane α-helix bundles of the Aβ tetramer and trimer were observed in extensive temperature replica exchange molecular dynamics (REMD) simulations. We observed three minima on the free-energy landscape of each oligomer, namely, A, B, and C for the tetramer and D, E, and F for the trimer. Except for F, the minima consist of 4 or 3 parallel helices spanning across the membrane model dipalmitoylphosphatidylcholine. Replica exchange molecular dynamics-umbrella sampling (REMD-US) simulation was applied to study the process of a Ca crossing the pore formed by the α-helix bundles in A-E in comparison to that in a calcium channel and a proton channel. REMD-US reveals that A, C, and D allow Ca to cross their pore with a free-energy barrier comparable to that found for the calcium channel. In contrast, the free-energy barrier of a Ca ion crossing B, E, and the proton channel is significantly higher. This result suggests that Aβ peptide oligomers could form transmembrane α-helix bundles that provide feasible pathways for Ca transport. This is an intriguing observation that will stimulate further studies.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.8b10792}, author = {Ngo, Son Tung and Philippe Derreumaux and Vu, Van V} } @article {2019|2105, title = {Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.}, journal = {J Phys Chem B}, volume = {123}, year = {2019}, month = {2019 Aug 08}, pages = {6750-6756}, abstract = {

Alzheimer\&$\#$39;s disease (AD) is characterized by the accumulation of extracellular Aβ42 and Aβ40 oligomers and plaques. In a recent computational study, we found that the presence of the residues I41 and A42 increases significantly the propensity of Aβ to form a tetrameric β-barrel structure in a bilayer mimicking a neuronal membrane. In this work, we have determined the propensity of the two Aβ proteins to form tetrameric β-barrel structures in aqueous solution using four atomistic protein fields, that is, Amber99SB-ILDN/TIP3P, OPLS/TIP3P, CHARMM36m/TIP3P-modified, and Amber99SB/DISP. Extensive replica exchange molecular dynamics simulations make it clear that a β-barrel, made of two distinct β-hairpin motifs and an asymmetric arrangement of eight antiparallel β-strands with an inner pore diameter of 0.7 nm, exists transiently for Aβ42 peptide, but this is less the case for Aβ40 peptide, due to the change of the CHC-CHC and the Cter-Cter interfaces. This study has several implications in AD.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.9b05288}, author = {Phuong Hoang Nguyen and Campanera, Josep M and Ngo, Son Tung and Loquet, Antoine and Philippe Derreumaux} } @article {2019|2106, title = {Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.}, journal = {J Phys Chem B}, volume = {123}, year = {2019}, month = {2019 May 02}, pages = {3643-3648}, abstract = {

The amyloid-β (Aβ) 42 oligomers are much more toxic than Aβ40 oligomers in Alzheimer\&$\#$39;s disease. Numerous experiments indicate that toxicity could involve the formation of pores in membranes, but experimental high-resolution structure determination of these pore-forming Aβ oligomers has been impeded by aggregate heterogeneity. Using extensive atomistic simulations, low-resolution data obtained in lipid bilayers, and other theoretical factors, we proposed atomic structures of Aβ40 and Aβ42 β-barrels in a bilayer mimicking a neuronal membrane. The 3D model, which consists of tetramer subunits, two distinct β-hairpin motifs and an asymmetric arrangement of eight antiparallel β-strands, is drastically destabilized for Aβ40 compared to its Aβ42 counterpart. Our computational modeling has several implications in Alzheimer\&$\#$39;s disease, sheds light on the amyloid pore hypothesis, and explains the higher deleterious property of Aβ42.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.9b01206}, author = {Phuong Hoang Nguyen and Campanera, Josep M and Ngo, Son Tung and Loquet, Antoine and Philippe Derreumaux} } @article {2018|2113, title = {Amyloid-β/drug interactions from computer simulations and cell-based assays}, journal = {Journal of Alzheimer{\textquoteright}s Disease}, volume = {64}, year = {2018}, pages = {S659{\textendash}S672}, author = {Phuong Hoang Nguyen and Del Castillo-Frias, Maria P and Berthoumieux, Olivia and Faller, Peter and Doig, Andrew J and Philippe Derreumaux} } @article {2018|2112, title = {Breaking down cellulose fibrils with a mid-infrared laser}, journal = {Cellulose}, volume = {25}, year = {2018}, pages = {5553{\textendash}5568}, author = {Domin, Dominik and Man, Viet Hoang and Van-Oanh, Nguyen-Thi and Wang, Junmei and Kawasaki, Takayasu and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2018|2034, title = {Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer.}, journal = {J Chem Phys}, volume = {148}, year = {2018}, month = {2018 Jan 28}, pages = {045105}, abstract = {

Alzheimer\&$\#$39;s disease is linked to various types of aggregates of amyloid-β (Aβ) peptide and their interactions with protein receptors and neuronal cell membranes. Little is known on the impact of the electric field on membrane-embedded Aβ. Here we use atomistic molecular dynamics simulations to study the effects of a constant electric field on the conformations of Aβdimer inside a membrane, where the electric field has a strength of 20 mV/nm which exists across the membrane of a human neuron. Starting from α-helix peptides, the transmembrane electric field (TMEF) accelerates the conversion from the Gly-out substate to the Gly-side and Gly-in substates. Starting from β-sheet peptides, TMEF induces changes of the kink and tilt angles at Gly33 and Gly37. Overall, in the simulations totaling 10 μs, TMEF establishes new ground states for the dimer, similar to induced-fit in ligand binding. Our findings indicate that TMEF can stabilize rare conformations of amyloid peptides, and this could influence the cleavage of the amyloid precursor protein and the formation of β-sheet oligomers in membrane bilayers.

}, issn = {1089-7690}, doi = {10.1063/1.5018459}, author = {Lu, Yan and Shi, Xiao-Feng and Salsbury, Freddie R and Philippe Derreumaux} } @article {2018|2035, title = {Molecular Mechanism of Protein Unfolding under Shear: A Lattice Boltzmann Molecular Dynamics Study.}, journal = {J Phys Chem B}, volume = {122}, year = {2018}, month = {2018 Feb 08}, pages = {1573-1579}, abstract = {

Proteins are marginally stable soft-matter entities that can be disrupted using a variety of perturbative stresses, including thermal, chemical, or mechanical ones. Fluid under extreme flow conditions is a possible route to probe the weakness of biomolecules and collect information on the molecular cohesive interactions that secure their stability. Moreover, in many cases, physiological flow triggers the functional response of specialized proteins as occurring in blood coagulation or cell adhesion. We deploy the Lattice Boltzmann molecular dynamics technique based on the coarse-grained model for protein OPEP to study the mechanism of protein unfolding under Couette flow. Our simulations provide a clear view of how structural elements of the proteins are affected by shear, and for the simple study case, the β-hairpin, we exploited the analogy to pulling experiments to quantify the mechanical forces acting on the protein under shear.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.7b10796}, author = {Sterpone, Fabio and Philippe Derreumaux and Melchionna, Simone} } @article {2018|2111, title = {Molecular mechanism of the cell membrane pore formation induced by bubble stable cavitation}, journal = {The Journal of Physical Chemistry B}, volume = {123}, year = {2018}, pages = {71{\textendash}78}, author = {Man, Viet Hoang and Truong, Phan Minh and Li, Mai Suan and Wang, Junmei and Van-Oanh, Nguyen-Thi and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2018|2129, title = {Probing the quality control mechanism of the twin-arginine translocase with folding variants of a -designed heme protein.}, journal = {J Biol Chem}, volume = {293}, year = {2018}, month = {2018 05 04}, pages = {6672-6681}, abstract = {

Protein transport across the cytoplasmic membrane of bacterial cells is mediated by either the general secretion (Sec) system or the twin-arginine translocase (Tat). The Tat machinery exports folded and cofactor-containing proteins from the cytoplasm to the periplasm by using the transmembrane proton motive force as a source of energy. The Tat apparatus apparently senses the folded state of its protein substrates, a quality-control mechanism that prevents premature export of nascent unfolded or misfolded polypeptides, but its mechanistic basis has not yet been determined. Here, we investigated the innate ability of the model Tat system to recognize and translocate -designed protein substrates with experimentally determined differences in the extent of folding. Water-soluble, four-helix bundle maquette proteins were engineered to bind two, one, or no heme cofactors, resulting in a concomitant reduction in the extent of their folding, assessed with temperature-dependent CD spectroscopy and one-dimensional H NMR spectroscopy. Fusion of the archetypal N-terminal Tat signal peptide of the trimethylamine--oxide (TMAO) reductase (TorA) to the N terminus of the protein maquettes was sufficient for the Tat system to recognize them as substrates. The clear correlation between the level of Tat-dependent export and the degree of heme -induced folding of the maquette protein suggested that the membrane-bound Tat machinery can sense the extent of folding and conformational flexibility of its substrates. We propose that these artificial proteins are ideal substrates for future investigations of the Tat system\&$\#$39;s quality-control mechanism.

}, keywords = {Amino Acid Sequence, Bacterial Proteins, Circular Dichroism, Escherichia coli, Escherichia coli Proteins, Heme-Binding Proteins, Hemeproteins, Membrane Transport Proteins, Methylamines, Models, Molecular, Oxidoreductases, N-Demethylating, Periplasm, Protein Folding, Protein Sorting Signals, Protein Stability, Protein Transport, Proton Magnetic Resonance Spectroscopy, Substrate Specificity, Temperature}, issn = {1083-351X}, doi = {10.1074/jbc.RA117.000880}, author = {Sutherland, George A and Grayson, Katie J and Adams, Nathan B P and Mermans, Daphne M J and Jones, Alexander S and Robertson, Angus J and Auman, Dirk B and Brindley, Amanda A and Sterpone, Fabio and Tuffery, Pierre and Philippe Derreumaux and Dutton, P Leslie and Robinson, Colin and Hitchcock, Andrew and Hunter, C Neil} } @article {2018|2114, title = {Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study}, journal = {The Journal of Chemical Physics}, volume = {148}, year = {2018}, pages = {094505}, author = {Man, Viet Hoang and Li, Mai Suan and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2018|2138, title = {Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses}, journal = {J Phys Chem B}, volume = {122}, year = {2018}, month = {Dec}, pages = {11922-11930}, abstract = {

The perturbation of a protein conformation by a physiological fluid flow is crucial in various biological processes including blood clotting and bacterial adhesion to human tissues. Investigating such mechanisms by computer simulations is thus of great interest, but it requires development of ad hoc strategies to mimic the complex hydrodynamic interactions acting on the protein from the surrounding flow. In this study, we apply the Lattice Boltzmann Molecular Dynamics (LBMD) technique built on the implicit solvent coarse-grained model for protein Optimized Potential for Efficient peptide structure Prediction (OPEP) and a mesoscopic representation of the fluid solvent, to simulate the unfolding of a small globular cold-shock protein in shear flow and to compare it to the unfolding mechanisms caused either by mechanical or thermal perturbations. We show that each perturbation probes a specific weakness of the protein and causes the disruption of the native fold along different unfolding pathways. Notably, the shear flow and the thermal unfolding exhibit very similar pathways, while because of the directionality of the perturbation, the unfolding under force is quite different. For force and thermal disruption of the native state, the coarse-grained simulations are compared to all-atom simulations in explicit solvent, showing an excellent agreement in the explored unfolding mechanisms. These findings encourage the use of LBMD based on the OPEP model to investigate how a flow can affect the function of larger proteins, for example, in catch-bond systems.

}, doi = {10.1021/acs.jpcb.8b08711}, author = {Languin-Catto{\"e}n, Olivier and Melchionna, Simone and Philippe Derreumaux and Guillaume Stirnemann and Sterpone, Fabio} } @article {2017|2039, title = {A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against.}, journal = {Bioinform Biol Insights}, volume = {11}, year = {2017}, month = {2017}, pages = {1177932217712471}, abstract = {

We present an approach for detecting enzymes that are specific ofcompared withand provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific forcompared with, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific ofand 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with. Among the 40 strictly specific enzymes, we identified sterol 24-C-methyltransferase, pyruvate phosphate dikinase, trypanothione synthetase, and RNA-editing ligase as 4 essential enzymes forthat may serve as targets for drug development.

}, issn = {1177-9322}, doi = {10.1177/1177932217712471}, author = {Catharina, Larissa and Lima, Carlyle Ribeiro and Franca, Alexander and Guimar{\~a}es, Ana Carolina Ramos and Alves-Ferreira, Marcelo and Tuffery, Pierre and Philippe Derreumaux and Carels, Nicolas} } @article {2017|2032, title = {Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.}, journal = {J Phys Chem B}, volume = {121}, year = {2017}, month = {2017 Mar 23}, pages = {2434-2442}, abstract = {

We characterized the dimer of the amyloid-β wild-type (WT) peptide, Aβ, of 42 residues and its disulfide-bond-locked double mutant (S8C) by replica exchange molecular dynamics simulations. Aβ dimers are known to be the smallest toxic species in Alzheimer\&$\#$39;s disease, and the S8C mutant has been shown experimentally to form an exclusive homogeneous and neurotoxic dimer. Our 50 μs all-atom simulations reveal similar secondary structures and collision cross-sections but very different intramolecular and intermolecular conformations upon double S8C mutation. Both dimers are very dynamic with hundreds of free-energy minima that differ from the U-shape and S-shape conformations of the peptides in the fibrils. The only common structural feature, shared by both species with a probability of 4\% in WT and 12\% in S8C-S8C, is a three-stranded β-sheet spanning the 17-23, 29-36, and 39-41 residues, which does not exist in the Aβ40 WT dimers.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.7b00267}, author = {Man, Viet Hoang and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2017|2041, title = {Fast coarse-grained model for RNA titration.}, journal = {J Chem Phys}, volume = {146}, year = {2017}, month = {2017 Jan 21}, pages = {035101}, abstract = {

A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-H{\"u}ckel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKshifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

}, keywords = {Azotobacter vinelandii, Introns, Models, Chemical, Molecular Dynamics Simulation, Monte Carlo Method, Protein Structure, Secondary, Protons, RNA, RNA, Catalytic, Titrimetry}, issn = {1089-7690}, doi = {10.1063/1.4972986}, author = {Barroso da Silva, Fernando Luis and Philippe Derreumaux and Pasquali, Samuela} } @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 = {

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.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.7b04689}, author = {Man, Viet Hoang and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2017|2037, title = {Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.}, journal = {J Chem Phys}, volume = {147}, year = {2017}, month = {2017 Oct 21}, pages = {152715}, abstract = {

We explore the energy landscape for a four-fold telomere repeat, obtaining interconversion pathways between six experimentally characterised G-quadruplex topologies. The results reveal a multi-funnel system, with a variety of intermediate configurations and misfolded states. This organisation is identified with the intrinsically multi-functional nature of the system, suggesting a new paradigm for the classification of such biomolecules and clarifying issues regarding apparently conflicting experimental results.

}, issn = {1089-7690}, doi = {10.1063/1.4997377}, author = {Cragnolini, Tristan and Chakraborty, Debayan and Sponer, Jiri and Philippe Derreumaux and Pasquali, Samuela and Wales, David J} } @article {2017|2029, title = {Multi-scale simulations of biological systems using the OPEP coarse-grained model.}, journal = {Biochem Biophys Res Commun}, year = {2017}, month = {2017 Sep 14}, abstract = {

Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.

}, issn = {1090-2104}, doi = {10.1016/j.bbrc.2017.08.165}, author = {Sterpone, Fabio and Doutreligne, S{\'e}bastien and Tran, Thanh Thuy and Melchionna, Simone and Marc Baaden and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2017|2038, title = {Protein-RNA complexation driven by the charge regulation mechanism.}, journal = {Biochem Biophys Res Commun}, year = {2017}, month = {2017 Jul 12}, abstract = {

Electrostatic interactions play a pivotal role in many (bio)molecular association processes. The molecular organization and function in biological systems are largely determined by these interactions from pure Coulombic contributions to more peculiar mesoscopic forces due to ion-ion correlation and proton fluctuations. The latter is a general electrostatic mechanism that gives attraction particularly at low electrolyte concentrations. This charge regulation mechanism due to titrating amino acid and nucleotides residues is discussed here in a purely electrostatic framework. By means of constant-pH Monte Carlo simulations based on a fast coarse-grained titration proton scheme, a new computer molecular model was devised to study protein-RNA interactions. The complexation between the RNA silencing suppressor p19 viral protein and the 19-bp small interfering RNA was investigated at different solution pH and salt conditions. The outcomes illustrate the importance of the charge regulation mechanism that enhances the association between these macromolecules in a similar way as observed for other protein-polyelectrolyte systems typically found in colloidal science. Due to the highly negative charge of RNA, the effect is more pronounced in this system as predicted by the Kirkwood-Shumaker theory. Our results contribute to the general physico-chemical understanding of macromolecular complexation and shed light on the extensive role of RNA in the cell\&$\#$39;s life.

}, issn = {1090-2104}, doi = {10.1016/j.bbrc.2017.07.027}, author = {Barroso da Silva, Fernando Luis and Philippe Derreumaux and Pasquali, Samuela} } @article {2017|2040, title = {Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).}, journal = {J Chem Phys}, volume = {146}, year = {2017}, month = {2017 Apr 14}, pages = {145101}, abstract = {

The formation of senile plaques in central neural system resulting from the aggregation of the amyloid β (Aβ) of 40 and 42 residues is one of the two hallmarks of Alzheimer\&$\#$39;s disease. Numerous experiments and computational studies have shown that the aggregation of Aβ peptides in vitro is very complex and depends on many factors such as pH, agitation, temperature, and peptide concentration. The impact of a static electric field (EF) on amyloid peptide aggregation has been much less studied, although EFs may have some applications to treat Parkinson\&$\#$39;s disease symptoms. Here, we study the influence of an EF strength of 20 mV/nm, present in the human brains, on the conformation of the Aβdimer. Our 7 μs non-equilibrium atomistic simulations in aqueous solution show that this field-strength promotes substantially the formation of β-hairpins, believed to be a very important intermediate state during aggregation. This work also suggests that structural biology experiments conducted under appropriate EF strengths may help reduce the conformational heterogeneity of Aβ/Aβdimers and provide significant insights into their structures that may be disease-causing.

}, issn = {1089-7690}, doi = {10.1063/1.4979866}, author = {Lu, Yan and Shi, Xiao-Feng and Salsbury, Freddie R and Philippe Derreumaux} } @article {2017|2036, title = {VLITL is a major cross-β-sheet signal for fibrinogen Aα-chain frameshift variants.}, journal = {Blood}, volume = {130}, year = {2017}, month = {2017 12 21}, pages = {2799-2807}, abstract = {

The first case of hereditary fibrinogen Aα-chain amyloidosis was recognized \>20 years ago, but disease mechanisms still remain unknown. Here we report detailed clinical and proteomics studies of a French kindred with a novel amyloidogenic fibrinogen Aα-chain frameshift variant, Phe521Leufs, causing a severe familial form of renal amyloidosis. Next, we focused our investigations to elucidate the molecular basis that render this Aα-chain variant amyloidogenic. We show that a 49-mer peptide derived from the C-terminal part of the Phe521Leufs chain is deposited as fibrils in the patient\&$\#$39;s kidneys, establishing that only a small portion of Phe521Leufs directly contributes to amyloid formation in vivo. In silico analysis indicated that this 49-mer Aα-chain peptide contained a motif (VLITL), with a high intrinsic propensity for β-aggregation at residues 44 to 48 of human renal fibrils. To experimentally verify the amyloid propensity of VLITL, we generated synthetic Phe521Leufs-derived peptides and compared their capacity for fibril formation in vitro with that of their VLITL-deleted counterparts. We show that VLITL forms typical amyloid fibrils in vitro and is a major signal for cross-β-sheet self-association of the 49-mer Phe521Leufs peptide identified in vivo, whereas its absence abrogates fibril formation. This study provides compelling evidence that VLITL confers amyloidogenic properties to Aα-chain frameshift variants, yielding a previously unknown molecular basis for the pathogenesis of Aα-chain amyloidosis.

}, keywords = {Amino Acid Motifs, Amino Acid Sequence, Amyloid, Amyloidosis, Familial, Fibrinogen, Frameshift Mutation, Humans, Kidney, Protein Conformation, beta-Strand}, issn = {1528-0020}, doi = {10.1182/blood-2017-07-796185}, author = {Garnier, Cyrille and Briki, Fatma and Nedelec, Brigitte and Le Pogamp, Patrick and Dogan, Ahmet and Rioux-Leclercq, Nathalie and Goude, Renan and Beugnet, Caroline and Martin, Laurent and Delpech, Marc and Bridoux, Frank and Grateau, Gilles and Doucet, Jean and Philippe Derreumaux and Valleix, Sophie} } @article {2017|2042, title = {What Can Human-Guided Simulations Bring to RNA Folding?}, journal = {Biophys J}, volume = {113}, year = {2017}, month = {2017 Jul 25}, pages = {302-312}, abstract = {

Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.

}, keywords = {Access to Information, Computer Simulation, Feedback, Psychological, Humans, Internet, Models, Genetic, Models, Molecular, RNA, RNA Folding, Software, Solvents}, issn = {1542-0086}, doi = {10.1016/j.bpj.2017.05.047}, author = {Mazzanti, Liuba and Doutreligne, S{\'e}bastien and Gageat, Cedric and Philippe Derreumaux and Antoine Taly and Marc Baaden and Pasquali, Samuela} } @article {2017|2030, title = {Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer{\textquoteright}s Disease?}, journal = {ACS Chem Neurosci}, volume = {8}, year = {2017}, month = {2017 Jul 19}, pages = {1435-1437}, abstract = {

The two hallmarks of Alzheimer\&$\#$39;s disease (AD) are the presence of neurofibrillary tangles (NFT) made of aggregates of the hyperphosphorylated tau protein and of amyloid plaques composed of amyloid-β (Aβ) peptides, primarily Aβ1-40 and Aβ1-42. Targeting the production, aggregation, and toxicity of Aβ with small molecule drugs or antibodies is an active area of AD research due to the general acceptance of the amyloid cascade hypothesis, but thus far all drugs targeting Aβ have failed. From a review of the recent literature and our own experience based on in vitro, in silico, and in vivo studies, we present some reasons to explain this repetitive failure.

}, keywords = {Alzheimer Disease, Amyloid beta-Peptides, Animals, Drug Discovery, Humans, Neuroprotective Agents}, issn = {1948-7193}, doi = {10.1021/acschemneuro.7b00188}, author = {Doig, Andrew J and Del Castillo-Frias, Maria P and Berthoumieu, Olivia and Tarus, Bogdan and Nasica-Labouze, Jessica and Sterpone, Fabio and Phuong Hoang Nguyen and Hooper, Nigel M and Faller, Peter and Philippe Derreumaux} } @conference {2016|1606, title = {Alzheimer{\textquoteright}s Disease: Insights into Amyloid Fibril Formation from Lattice Monte Carlo Simulations}, 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 = {Thanh-Thuy Tran and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2016|1656, title = {Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation}, journal = {Isr. J. Chem.}, volume = {DOI: 10.1002/ijch.201600048.}, year = {2016}, author = {M. Chiricotto and Thanh-Thuy Tran and Phuong Hoang Nguyen and S. Melchionna and Fabio Sterpone and Philippe Derreumaux} } @article {2016|1707, title = {Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes}, journal = {J. Chem. Theory Comput.}, volume = {12}, number = {12}, year = {2016}, month = {dec}, pages = {6077{\textendash}6097}, abstract = {G-quadruplexes are the most important non canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)(n), have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite the availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradictory models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach thermodynamic equilibrium. Based on atomistic simulations of diverse classes of intermediates in G-quadruplex folding, we have suggested that the folding is an extremely multipathway process combining a kinetic partitioning mechanism with conformational diffusion. However, complete G-quadruplex folding is far beyond the time scale of atomistic simulations. Here we use high-resolution coarse-grained simulations to investigate potential unfolding intermediates, whose structural dynamics are then further explored with all-atom simulations. This multiscale approach indicates how various pathways are interconnected in a complex network. Spontaneous conversions between different folds are observed. We demonstrate the inability of simple order parameters, such as radius of gyration or the number of native H-bonds, to describe the folding landscape of the G-quadruplexes. Our study also provides information relevant to further development of the coarse grained force field.}, issn = {1549-9618}, doi = {10.1021/acs.jctc.6b00667}, author = {Stadlbauer, Petr and Mazzanti, Liuba and Cragnolini, Tristan and Wales, David J. and Philippe Derreumaux and Pasquali, Samuela and Sponer, Jiri} } @article {2016|1712, title = {Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation}, journal = {J. Phys. Chem. B}, volume = {120}, number = {47}, year = {2016}, pages = {12111{\textendash}12126}, abstract = {Amyloid beta (A beta) oligomerization is associated with the origin and progression of Alzheimer{\textquoteright}s disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T A beta(40) dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V A beta(40) dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel beta-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded beta-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded beta-sheet or inhibiting the formation of an interpeptide beta-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of A beta species.}, issn = {1520-6106}, doi = {10.1021/acs.jpcp.6b10722}, author = {Phuong Hoang Nguyen and Fabio Sterpone and Pouplana, Ramon and Philippe Derreumaux and Campanera, Josep M.} } @article {2016|1765, title = {Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin}, journal = {Soft Matter}, volume = {12}, number = {25}, year = {2016}, pages = {5600{\textendash}5612}, abstract = {Spider silk is a fascinating material combining mechanical properties such as maximum strength and high toughness comparable or better than man-made materials, with biocompatible degradability characteristics. Experimental measurements have shown that pH triggers the dimer formation of the N-terminal domain (NTD) of the major ampullate spidroin 1 (MaSp 1). A coarse-grained model accounting for electrostatics, van der Waals and pH-dependent charge-fluctuation interactions, by means of Monte Carlo simulations, gave us a more comprehensive view of the NTD dimerization process. A detailed analysis of the electrostatic properties and free energy derivatives for the NTD homoassociation was carried out at different pH values and salt concentrations for the protein wild type and for several mutants. We observed an enhancement of dipole-dipole interactions at pH 6 due to the ionization of key amino acids, a process identified as the main driving force for dimerization. Analytical estimates based on the DVLO theory framework corroborate our findings. Molecular dynamics simulations using the OPEP coarse-grained force field for proteins show that the mutant E17Q is subject to larger structural fluctuations when compared to the wild type. Estimates of the association rate constants for this mutant were evaluated by the Debye-Smoluchowski theory and are in agreement with the experimental data when thermally relaxed structures are used instead of the crystallographic data. Our results can contribute to the design of new mutants with specific association properties.}, issn = {1744-683X}, doi = {10.1039/c6sm00860g}, author = {Barroso da Silva, Fernando Luis and Pasquali, Samuela and Philippe Derreumaux and Dias, Luis Gustavo} } @article {2016|1630, title = {Evaluation of the coarse-grained OPEP force field for protein-protein docking}, journal = {Bmc Biophysics}, volume = {9}, year = {2016}, month = {apr}, abstract = {Background: Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature. Methods: In this work, we rescore rigid body protein-protein predictions using the optimized potential for efficient structure prediction (OPEP), which is a coarse-grained force field. Using a force field based on continuous functions rather than a grid-based scoring function allows the introduction of protein flexibility during the docking procedure. First, we produce protein-protein predictions using ZDOCK, and after energy minimization via OPEP we rank them using an OPEP-based soft rescoring function. We also train the rescoring function for different complex classes and demonstrate its improved performance for an independent dataset. Results: The trained rescoring function produces a better ranking than ZDOCK for more than 50 \% of targets, rising to over 70 \% when considering only enzyme/inhibitor complexes. Conclusions: This study demonstrates for the first time that energy functions derived from the coarse-grained OPEP force field can be employed to rescore predictions for protein-protein complexes.}, issn = {2046-1682}, doi = {10.1186/s13628-016-0029-y}, author = {Kynast, Philipp and Philippe Derreumaux and Strodel, Birgit} } @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 {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 {2016|1711, title = {In silico structural characterization of protein targets for drug development against Trypanosoma cruzi}, journal = {J. Mol. Model.}, volume = {22}, number = {10}, year = {2016}, month = {oct}, abstract = {Trypanosoma cruzi is the protozoan pathogen responsible for Chagas disease, which is a major public health problem in tropical and subtropical regions of developing countries and particularly in Brazil. Despite many studies, there is no efficient treatment against Chagas disease, and the search for new therapeutic targets specific to T. cruzi is critical for drug development. Here, we have revisited 41 protein sequences proposed by the analogous enzyme pipeline, and found that it is possible to provide structures for T. cruzi sequences with clear homologs or analogs in H. sapiens and likely associated with trypanothione reductase, cysteine synthase, and ATPase functions, and structures for sequences specific to T. cruzi and absent in H. sapiens associated with 2,4-dienoyl-CoA reductase, and leishmanolysin activities. The implications of our structures refined by atomistic molecular dynamics (monomer or dimer states) in their in vitro environments (aqueous solution or membrane bilayers) are discussed for drug development and suggest that all protein targets, except cysteine synthase, merit further investigation.}, issn = {1610-2940}, doi = {10.1007/s00894-016-3115-9}, author = {Lima, Carlyle Ribeiro and Carels, Nicolas and Ramos Guimaraes, Ana Carolina and Pierre Tuffery and Philippe Derreumaux} } @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 {2016|1639, title = {MP2 and DFT studies of beta-D-neocarrabiose and beta-D-neocarrabiose monohydrate}, journal = {Comput. Theor. Chem.}, volume = {1091}, year = {2016}, month = {sep}, pages = {24{\textendash}30}, abstract = {MP2 and density functional theory calculations have been carried out on beta-D-neocarrabiose and its mono hydrate in order to determine the conformational preferences of these molecules in the gas phase and in solvent. Relaxed iso-energetic maps were first obtained using B3LYP/6-31G(d). Then, the lower energy conformers were further fully optimized using B3LYP, B3PW91 and MP2 methods. Overall, it was demonstrated that a lower energy conformer corresponding to the couple of dihedral angles (Phi,Psi)= (69 degrees,-117 degrees) is detected either in the gas phase or in solvent provided that full optimizations are performed on the conformers corresponding to the minima detected from the iso-energetic maps. (C) 2016 Elsevier B.V. All rights reserved.}, issn = {2210-271X}, doi = {10.1016/j.comptc.2016.07.009}, author = {Bestaoui-Berrekhchi-Berrahma, N. and Sekkal-Rahal, M. and Philippe Derreumaux and Yousfi, N.} } @article {2016|1735, title = {Multiscale simulation of molecular processes in cellular environments}, journal = {Philosophical Transactions of the Royal Society A-mathematical Physical and Engineering Sciences}, volume = {374}, number = {2080}, year = {2016}, abstract = {We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated. This article is part of the themed issue {\textquoteleft}Multiscale modelling at the physics-chemistry-biology interface{\textquoteright}.}, issn = {1364-503X}, doi = {10.1098/rsta.2016.0225}, author = {Chiricotto, Mara and Fabio Sterpone and Philippe Derreumaux and Melchionna, Simone} } @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|1733, title = {PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex}, journal = {Nucleic Acids Res.}, volume = {44}, number = {W1}, year = {2016}, pages = {W449-W454}, abstract = {Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80\% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3 angstrom from the experimental conformation and return a native-like pose in the first 10 clusters for 52\% of the targets. PEP-FOLD3 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.}, issn = {0305-1048}, doi = {10.1093/nar/gkw329}, author = {Lamiable, Alexis and Thevenet, Pierre and Rey, Julien and Vavrusa, Marek and Philippe Derreumaux and Pierre Tuffery} } @article {2016|1744, title = {Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses}, journal = {Phys. Chem. Chem. Phys.}, volume = {18}, number = {17}, year = {2016}, month = {may}, pages = {11951{\textendash}11958}, abstract = {Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibriummolecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.}, issn = {1463-9076}, doi = {10.1039/c5cp07711g}, author = {Viet Hoang Man and Van-Oanh, Nguyen-Thi and Philippe Derreumaux and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and Phuong Hoang Nguyen} } @conference {2016|1608, title = {Toward Microscopic Simulations of Proteins in Cell-Like Environments}, 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 = {386A}, publisher = {Biophys Soc}, organization = {Biophys Soc}, issn = {0006-3495}, author = {Fabio Sterpone and Philippe Derreumaux and Melchionna, Simone} } @article {2015|1716, title = {Ab initio RNA folding}, journal = {Journal of Physics-condensed Matter}, volume = {27}, number = {23}, year = {2015}, month = {jun}, pages = {233102}, doi = {10.1088/0953-8984/27/23/233102}, author = {Cragnolini, Tristan and Philippe Derreumaux and Pasquali, Samuela} } @article {2015|1634, title = {Amyloid beta Protein and Alzheimer{\textquoteright}s Disease: When Computer Simulations Complement Experimental Studies}, journal = {Chem. Rev.}, volume = {115}, number = {9}, year = {2015}, month = {may}, pages = {3518{\textendash}3563}, doi = {10.1021/cr500638n}, author = {Nasica-Labouze, Jessica and Phuong Hoang Nguyen and Fabio Sterpone and Berthoumieu, Olivia and Buchete, Nicolae-Viorel and Cote, Sebastien and De Simone, Alfonso and Doig, Andrew J. and Faller, Peter and Garcia, Angel and Laio, Alessandro and Li, Mai Suan and Melchionna, Simone and Mousseau, Normand and Mu, Yuguang and Paravastu, Anant and Pasquali, Samuela and Rosenman, David J. and Strodel, Birgit and Tarus, Bogdan and Viles, John H. and Zhang, Tong and Wang, Chunyu and Philippe Derreumaux} } @article {2015|1910, title = {Are coarse-grained models apt to detect protein thermal stability? The case of \{OPEP\} force field}, journal = {J. Non-cryst. Solids}, volume = {407}, year = {2015}, note = {7th IDMRCS: Relaxation in Complex Systems}, pages = {494{\textendash}501}, keywords = {Conformational substates network}, doi = {10.1016/j.jnoncrysol.2014.07.005}, url = {http://www.sciencedirect.com/science/article/pii/S0022309314002889}, author = {Maria Kalimeri and Philippe Derreumaux and Fabio Sterpone} } @article {2015|1708, title = {Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings}, journal = {J. Chem. Theory Comput.}, volume = {11}, number = {7}, year = {2015}, pages = {3510{\textendash}3522}, doi = {10.1021/acs.jctc.5b00200}, author = {Cragnolini, Tristan and Laurin, Yoann and Philippe Derreumaux and Pasquali, Samuela} } @article {2015|1635, title = {Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp}, journal = {Chemistry-a European Journal}, volume = {21}, number = {36}, year = {2015}, pages = {12657{\textendash}12666}, doi = {10.1002/chem.201500888}, author = {Berthoumieu, Olivia and Phuong Hoang Nguyen and del Castillo-Frias, Maria P. and Ferre, Sabrina and Tarus, Bogdan and Nasica-Labouze, Jessica and Noel, Sabrina and Saurel, Olivier and Rampon, Claire and Doig, Andrew J. and Philippe Derreumaux and Faller, Peter} } @article {2015|1768, title = {Communication: Multiple atomistic force fields in a single enhanced sampling simulation.}, journal = {The Journal of Chemical Physics}, volume = {143}, number = {2}, year = {2015}, month = {jul}, pages = {021101{\textendash}021101}, doi = {10.1063/1.4926535}, author = {Hoang Viet, Man and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2015|1704, title = {Communication: Multiple atomistic force fields in a single enhanced sampling simulation}, journal = {J. Chem. Phys.}, volume = {143}, number = {2}, year = {2015}, month = {jul}, pages = {021101}, doi = {10.1063/1.4926535}, author = {Man Hoang Viet and Philippe Derreumaux and Phuong Hoang Nguyen} } @article {2015|1780, title = {{E}pock: rapid analysis of protein pocket dynamics}, journal = {Bioinformatics}, volume = {31}, number = {9}, year = {2015}, month = {may}, pages = {1478{\textendash}1480}, doi = {10.1093/bioinformatics/btu822}, author = {Laurent, Benoist and Matthieu Chavent and Cragnolini, Tristan and Dahl, Anna Caroline E. and Pasquali, Samuela and Philippe Derreumaux and Sansom, Mark S. P. and Marc Baaden} } @article {2015|1713, title = {Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering}, journal = {J. Phys. Chem. B}, volume = {119}, number = {23}, year = {2015}, month = {jun}, pages = {6941{\textendash}6951}, author = {Zhang, Tong and Phuong Hoang Nguyen and Nasica-Labouze, Jessica and Mu, Yuguang and Philippe Derreumaux} } @article {2015|1643, title = {Inhibition of protein aggregation and amyloid formation by small molecules}, journal = {Curr. Opin. Struct. Biol.}, volume = {30}, year = {2015}, month = {feb}, pages = {50{\textendash}56}, doi = {10.1016/j.sbi.2014.12.004}, author = {Doig, Andrew J. and Philippe Derreumaux} } @article {2015|1646, title = {Molecular structure of the NQTrp inhibitor with the Alzheimer A beta 1-28 monomer}, journal = {Eur. J. Med. Chem.}, volume = {91}, year = {2015}, month = {feb}, pages = {43{\textendash}50}, doi = {10.1016/j.ejmech.2014.07.002}, author = {Tarus, Bogdan and Phuong Hoang Nguyen and Berthoumieu, Olivia and Faller, Peter and Doig, Andrew J. and Philippe Derreumaux} } @article {2015|1449, title = {{P}redicting and exploring complex nucleic acids architectures through a coarse-grained model}, journal = {J. Biomol. Struct. Dyn.}, volume = {33 Suppl 1}, year = {2015}, pages = {30{\textendash}31}, author = {Cragnolini, T. and Doutreligne, S. and Marc Baaden and Philippe Derreumaux and Pasquali, S.} } @article {2015|1705, title = {Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study}, journal = {J. Chem. Phys.}, volume = {143}, number = {15}, year = {2015}, month = {oct}, pages = {155101}, doi = {10.1063/1.4933207}, author = {Man Hoang Viet and Philippe Derreumaux and Mai Suan Li and Roland, Christopher and Sagui, Celeste and Phuong Hoang Nguyen} } @article {2015|1745, title = {Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study}, journal = {Phys. Chem. Chem. Phys.}, volume = {17}, number = {41}, year = {2015}, pages = {27275{\textendash}27280}, doi = {10.1039/c5cp04401d}, author = {Viet, Man Hoang and Phan Minh Truong and Philippe Derreumaux and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and Phuong Hoang Nguyen} } @article {2015|1701, title = {Predicting and exploring complex nucleic acids architectures through a coarse-grained model}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {33}, year = {2015}, pages = {30{\textendash}31}, doi = {10.1080/07391102.2015.1032593}, author = {Cragnolini, T. and Doutreligne, S. and Marc Baaden and Philippe Derreumaux and Pasquali, S.} } @article {2015|1709, title = {Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics}, journal = {J. Chem. Theory Comput.}, volume = {11}, number = {4}, year = {2015}, month = {apr}, pages = {1843{\textendash}1853}, doi = {10.1021/ct501015h}, author = {Fabio Sterpone and Philippe Derreumaux and Melchionna, Simone} } @article {2015|1727, title = {Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation}, journal = {Mol. Simul.}, volume = {41}, number = {10-12}, year = {2015}, month = {aug}, pages = {1041{\textendash}1044}, author = {Nishikawa, Naohiro and Phuong Hoang Nguyen and Philippe Derreumaux and Okamoto, Yuko} } @article {2015|1714, title = {Structures of the Alzheimer{\textquoteright}s Wild-Type A beta 1-40 Dimer from Atomistic Simulations}, journal = {J. Phys. Chem. B}, volume = {119}, number = {33}, year = {2015}, pages = {10478{\textendash}10487}, doi = {10.1021/acs.jpcb.5b05593}, author = {Tarus, Bogdan and Thanh-Thuy Tran and Nasica-Labouze, Jessica and Fabio Sterpone and Phuong Hoang Nguyen and Philippe Derreumaux} } @conference {2015|1555, title = {UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules}, booktitle = {Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on}, year = {2015}, month = {mar}, pages = {1{\textendash}6}, keywords = {biomolecular systems, coarse-grained RNA, collaborative research applications, data visualisation, feature extracti, HireRNA physics engine, interactive systems, Ludic visual manipulation, molecular biophysics, RNA, software architecture, teaching, UnityMol framework}, author = {S. Doutreligne and C. Gageat and T. Cragnolini and Antoine Taly and S. Pasquali and Philippe Derreumaux and Marc Baaden} } @conference {2015|1609, title = {What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers}, booktitle = {Biophys. J.}, volume = {108}, number = {2}, year = {2015}, pages = {204A-204A}, author = {Nasica-Labouze, Jessica and Tarus, Bogdan and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2014|1888, title = {Amyloid oligomer structure characterization from simulations: A general method}, journal = {J. Chem. Phys.}, volume = {140}, number = {9}, year = {2014}, month = {mar}, pages = {094105}, doi = {10.1063/1.4866902}, author = {Phuong Hoang Nguyen and Li, Mai Suan and Philippe Derreumaux} } @article {2014|1380, title = {Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-L-tryptophan Inhibitor on Alzheimer{\textquoteright}s A beta 1-42 Dimer in Terms of Aggregation and Toxicity}, journal = {Acs Chem. Neurosci.}, volume = {5}, number = {2}, year = {2014}, month = {feb}, pages = {148{\textendash}159}, author = {Zhang, Tong and Xu, Weixin and Mu, Yuguang and Philippe Derreumaux} } @conference {2014|1784, title = {Coarse-Grain RNA Folding: Towards More Complex Structures}, booktitle = {Biophys. J.}, volume = {106}, number = {2, 1}, year = {2014}, note = {58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014}, month = {jan}, pages = {283A}, author = {Cragnolini, Tristan and Laurin, Yoann and Philippe Derreumaux and Pasquali, Samuela} } @article {2014|1379, title = {Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42}, journal = {Acs Chem. Neurosci.}, volume = {5}, number = {8}, year = {2014}, month = {aug}, pages = {646{\textendash}657}, author = {Man Hoang Viet and Phuong Hoang Nguyen and Philippe Derreumaux and Li, Mai Suan} } @article {2014|1927, title = {Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A beta 1-28 Monomer}, journal = {J. Phys. Chem. B}, volume = {118}, number = {2}, year = {2014}, month = {jan}, pages = {501{\textendash}510}, doi = {10.1021/jp4115404}, author = {Phuong Hoang Nguyen and Tarus, Bogdan and Philippe Derreumaux} } @article {2014|1893, title = {Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction}, journal = {J. Chem. Theory Comput.}, volume = {10}, number = {10}, year = {2014}, month = {oct}, pages = {4745{\textendash}4758}, doi = {10.1021/ct500592m}, author = {Shen, Yimin and Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @article {2014|1798, title = {The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems}, journal = {Chem. Soc. Rev.}, volume = {43}, number = {13}, year = {2014}, pages = {4871{\textendash}4893}, doi = {10.1039/c4cs00048j}, author = {F. Sterpone and S. Melchionna and Pierre Tuffery and S. Pasquali and N. Mousseau and T. Cragnolini and Y Chebaro and J.-F. St-Pierre and M. Kalimeri and A. Barducci and Y. Laurin and A. Tek and Marc Baaden and Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2014|1905, title = {Theoretical study of the NLO responses of some natural and unnatural amino acids used as probe molecules}, journal = {J. Mol. Model.}, volume = {20}, number = {8}, year = {2014}, month = {aug}, pages = {2388}, doi = {10.1007/s00894-014-2388-0}, author = {Derrar, S. N. and Sekkal-Rahal, M. and Philippe Derreumaux and Springborg, M.} } @article {2014, title = {Understanding Amyloid Fibril Nucleation and A beta Oligomer/Drug Interactions from Computer Simulations}, journal = {Acc. Chem. Res.}, volume = {47}, number = {2}, year = {2014}, pages = {603{\textendash}611}, author = {Nguyent, Phuong and Philippe Derreumaux} } @conference {2014|1496, title = {UnityMol: Interactive scientific visualization for integrative biology}, booktitle = {Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium on}, year = {2014}, month = {nov}, pages = {109{\textendash}110}, keywords = {biology computing, biomolecular system visualization, data analysis, data exploration, data representation, data visualisation, information extraction, integrative biology, interactive scientific visualization, interactive virtual lab, molecular biophysics, UnityMol}, author = {S. Doutreligne and T. Cragnolini and S. Pasquali and Philippe Derreumaux and Marc Baaden} } @conference {2014|1783, title = {Wide Exploration of OPEP Protein Energy Landscapes using Advanced Monte Carlo Methods}, booktitle = {Biophys. J.}, volume = {106}, number = {2, 1}, year = {2014}, note = {58th Annual Meeting of the Biophysical-Society, San Francisco, CA, FEB 15-19, 2014}, month = {jan}, pages = {256A}, author = {Cragnolini, Tristan and Sutherland-Cash, Kyle H. and Wales, David and Pasquali, Samuela and Philippe Derreumaux} } @article {2013|1498, title = {coarse-grained models for protein folding ang aggregation}, journal = {Methods Mol. Biol.}, volume = {924}, year = {2013}, pages = {585{\textendash}600}, author = {Philippe Derreumaux} } @article {2013|1923, title = {Coarse-Grained Simulations of RNA and DNA Duplexes}, journal = {J. Phys. Chem. B}, volume = {117}, number = {27}, year = {2013}, month = {jul}, pages = {8047{\textendash}8060}, doi = {10.1021/jp400786b}, author = {Cragnolini, Tristan and Philippe Derreumaux and Pasquali, Samuela} } @article {2013|1887, title = {Communication: Simulated tempering with fast on-the-fly weight determination}, journal = {J. Chem. Phys.}, volume = {138}, number = {6}, year = {2013}, month = {feb}, pages = {061102}, doi = {10.1063/1.4792046}, author = {Phuong Hoang Nguyen and Okamoto, Yuko and Philippe Derreumaux} } @article {2013|1924, title = {Conformational Ensemble and Polymorphism of the All-Atom Alzheimer{\textquoteright}s A beta(37-42) Amyloid Peptide Oligomers}, journal = {J. Phys. Chem. B}, volume = {117}, number = {19}, year = {2013}, month = {may}, pages = {5831{\textendash}5840}, doi = {10.1021/jp401563n}, author = {Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2013|1904, title = {Density functional conformational study of 2-O-sulfated 3,6 anhydro-alpha-D-galactose and of neo-kappa- and iota-carrabiose molecules in gas phase and water}, journal = {J. Mol. Model.}, volume = {19}, number = {2}, year = {2013}, month = {feb}, pages = {893{\textendash}904}, doi = {10.1007/s00894-012-1621-y}, author = {Bestaoui-Berrekhchi-Berrahma, Noreya and Philippe Derreumaux and Sekkal-Rahal, Majda and Springborg, Michael and Sayede, Adlane and Yousfi, Noureddine and Kadoun, Abd-Ed-Daim} } @article {2013, title = {Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42)}, journal = {Acs Chem. Neurosci.}, volume = {4}, number = {11}, year = {2013}, month = {nov}, pages = {1446{\textendash}1457}, author = {Man Hoang Viet and Phuong Hoang Nguyen and Son Tung Ngo and Li, Mai Suan 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 {2013|1925, title = {Molecular Mechanism of the Inhibition of EGCG on the Alzheimer A beta(1-42) Dimer}, journal = {J. Phys. Chem. B}, volume = {117}, number = {15}, year = {2013}, month = {apr}, pages = {3993{\textendash}4002}, doi = {10.1021/jp312573y}, author = {Zhang, Tong and Zhang, Jian and Philippe Derreumaux and Mu, Yuguang} } @article {2013|1806, title = {Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments}, journal = {European Biophysics Journal with Biophysics Letters}, volume = {42}, number = {1}, year = {2013}, note = {9th European-Biophysical-Societies-Association Congress, Lisbon, PORTUGAL, JUL 13-17, 2013}, month = {jul}, pages = {S68}, author = {Nishikawa, N. and Phuong Hoang Nguyen and Philippe Derreumaux and Okamoto, Y.} } @article {2012|1920, title = {The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins}, journal = {J. Phys. Chem. B}, volume = {116}, number = {30}, year = {2012}, month = {aug}, pages = {8741{\textendash}8752}, doi = {10.1021/jp301665f}, author = {Y Chebaro and Pasquali, Samuela and Philippe Derreumaux} } @article {2012|1955, title = {Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature}, journal = {Phys. Chem. Chem. Phys.}, volume = {14}, number = {20}, year = {2012}, pages = {877{\textendash}886}, doi = {10.1039/c1cp21779h}, author = {Phuong Hoang Nguyen and Philippe Derreumaux} } @article {2012|1911, title = {Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts}, journal = {J. Pept. Sci.}, volume = {18}, number = {1}, year = {2012}, month = {sep}, pages = {S38}, author = {Thevenet, P. and Shen, Y. and Maupetit, J. and Guyon, F. and Padilla, A. and Philippe Derreumaux and Pierre Tuffery} } @article {2012|1922, title = {Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N)}, journal = {J. Phys. Chem. B}, volume = {116}, number = {13}, year = {2012}, month = {apr}, pages = {4043{\textendash}4055}, doi = {10.1021/jp2126366}, author = {Cote, Sebastien and Laghaei, Rozita and Philippe Derreumaux and Mousseau, Normand} } @article {2012|1932, title = {Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches}, journal = {Journal of the Royal Society Interface}, volume = {9}, number = {66}, year = {2012}, month = {jan}, pages = {20{\textendash}33}, doi = {10.1098/rsif.2011.0584}, author = {Pierre Tuffery and Philippe Derreumaux} } @article {2012|1944, title = {PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides}, journal = {Nucleic Acids Res.}, volume = {40}, number = {W1}, year = {2012}, month = {jul}, pages = {W288-W293}, doi = {10.1093/nar/gks419}, author = {Thevenet, Pierre and Shen, Yimin and Maupetit, Julien and Guyon, Frederic and Philippe Derreumaux and Pierre Tuffery} } @article {2012|1886, title = {Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations}, journal = {J. Chem. Phys.}, volume = {137}, number = {2}, year = {2012}, month = {jul}, pages = {025101}, doi = {10.1063/1.4732761}, author = {Lu, Yan and Wei, Guanghong and Philippe Derreumaux} } @article {2012|1921, title = {Structures of A beta 17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure}, journal = {J. Phys. Chem. B}, volume = {116}, number = {29, SI}, year = {2012}, month = {jul}, pages = {8412{\textendash}8422}, doi = {10.1021/jp2118778}, author = {Y Chebaro and Jiang, Ping and Zang, Tong and Mu, Yuguang and Phuong Hoang Nguyen and Mousseau, Normand and Philippe Derreumaux} } @article {2012|1816, title = {Theoretical study on a series of push-pull molecules grafted on methacrylate copolymers serving for nonlinear optics}, journal = {Int. J. Quantum Chem.}, volume = {112}, number = {15}, year = {2012}, month = {aug}, pages = {2735{\textendash}2742}, doi = {10.1002/qua.23299}, author = {Derrar, S. N. and Sekkal-Rahal, M. and Guemra, K. and Philippe Derreumaux} } @article {2011|1891, title = {Assessing the Quality of the OPEP Coarse-Grained Force Field}, journal = {J. Chem. Theory Comput.}, volume = {7}, number = {6}, year = {2011}, month = {jun}, pages = {1928{\textendash}1934}, doi = {10.1021/ct100646f}, author = {Barducci, Alessandro and Bonomi, Massimiliano and Philippe Derreumaux} } @article {2011|1610, title = {Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer{\textquoteright}s Amyloid-beta(16-22) Peptide}, journal = {Biophys. J.}, volume = {101}, number = {9}, year = {2011}, month = {nov}, pages = {2267{\textendash}2276}, doi = {10.1016/j.bpj.2011.09.046}, author = {Li, Huiyu and Luo, Yin and Philippe Derreumaux and Wei, Guanghong} } @conference {2011|1611, title = {Characterization of the Aggregation Pathway for a 20-mer of GNNQQNY using Coarse-Grained and All-Atom Representations}, booktitle = {Biophys. J.}, volume = {100}, number = {3}, year = {2011}, month = {feb}, pages = {Biophys Soc}, author = {Nasica-Labouze, Jessica and Meli, Massimiliano and Philippe Derreumaux and Colombo, Giorgio and Mousseau, Normand} } @article {2011|1890, title = {Distinct Morphologies for Amyloid Beta Protein Monomer: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N)}, journal = {J. Chem. Theory Comput.}, volume = {7}, number = {8}, year = {2011}, month = {aug}, pages = {2584{\textendash}2592}, doi = {10.1021/ct1006967}, author = {Cote, Sebastien and Philippe Derreumaux and Mousseau, Normand} } @article {2011|1953, title = {Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer}, journal = {Phys. Chem. Chem. Phys.}, volume = {13}, number = {20}, year = {2011}, pages = {9778{\textendash}9788}, doi = {10.1039/c1cp20323a}, author = {Phuong Hoang Nguyen and Li, Mai Suan and Philippe Derreumaux} } @article {2011|1919, title = {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}, journal = {J. Phys. Chem. B}, volume = {115}, number = {5}, year = {2011}, month = {feb}, pages = {1282{\textendash}1288}, doi = {10.1021/jp110269a}, author = {Lu, Yan and Wei, Guanghong and Philippe Derreumaux} } @article {2011|1889, title = {Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model}, journal = {J. Chem. Theory Comput.}, volume = {7}, number = {5}, year = {2011}, month = {may}, pages = {1502{\textendash}1510}, doi = {10.1021/ct100619p}, author = {Spill, Yannick G. and Pasquali, Samuela and Philippe Derreumaux} } @article {2011|1966, title = {Intrinsic Determinants of A beta(12-24) pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies}, journal = {Plos One}, volume = {6}, number = {9}, year = {2011}, month = {sep}, pages = {e24329}, doi = {10.1371/journal.pone.0024329}, author = {Xu, Weixin and Zhang, Ce and Philippe Derreumaux and Graslund, Astrid and Morozova-Roche, Ludmilla and Mu, Yuguang} } @article {2011|1962, title = {A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35}, journal = {Plos Comput. Biol.}, volume = {7}, number = {5}, year = {2011}, month = {may}, pages = {e1002051}, doi = {10.1371/journal.pcbi.1002051}, author = {Nasica-Labouze, Jessica and Meli, Massimiliano and Philippe Derreumaux and Colombo, Giorgio and Mousseau, Normand} } @article {2011|1782, title = {Simulation of the Oligomerization Pathway for Different Alloforms of the Amyloid Beta Protein Related to Alzheimer{\textquoteright}s Disease}, journal = {Biophys. J.}, volume = {100}, number = {3, 1}, year = {2011}, note = {55th Annual Meeting of the Biophysical-Society, Baltimore, MD, MAR 05-09, 2011}, month = {feb}, pages = {401}, author = {Cote, Sebastien and Laghaei, Rozita and Philippe Derreumaux and Mousseau, Normand} } @article {2010|1918, title = {Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study}, journal = {J. Phys. Chem. B}, volume = {114}, number = {2}, year = {2010}, month = {jan}, pages = {1004{\textendash}1009}, doi = {10.1021/jp908889q}, author = {Li, Huiyu and Luo, Yin and Philippe Derreumaux and Wei, Guanghong} } @article {2010|1901, title = {A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction}, journal = {J. Comput. Chem.}, volume = {31}, number = {4}, year = {2010}, month = {mar}, pages = {726{\textendash}738}, doi = {10.1002/jcc.21365}, author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @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 {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 {2010, title = {The VLITL aggregation-prone motif might trigger amyloid fibril formation of fibrinogen A alpha-chain frameshift variants in vivo}, journal = {Amyloid-journal of Protein Folding Disorders}, volume = {17}, number = {Suppl. 1}, year = {2010}, note = {12th International Symposium on Amyloidosis from Molecular Mechanisms Toward the Cure of Systemic Amyloidoses, Rome, ITALY, APR 18-21, 2010}, pages = {96{\textendash}97}, author = {Valleix, S. and Philippe Derreumaux and Garnier, C. and Briki, F. and Boimard, M. and Doucet, J. and Rioux-Leclercq, N. and Martin, L. and Grateau, G. and Delpech, M. and Le Pogamp, P.} } @article {2009|2017, title = {The Conversion of Helix H2 to beta-Sheet Is Accelerated in the Monomer and Dimer of the Prion Protein upon T183A Mutation}, journal = {J. Phys. Chem. B}, volume = {113}, number = {19}, year = {2009}, month = {may}, pages = {6942{\textendash}6948}, doi = {10.1021/jp900334s}, author = {Y Chebaro and Philippe Derreumaux} } @article {2009|2018, title = {Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study}, journal = {J. Phys. Chem. B}, volume = {113}, number = {27}, year = {2009}, month = {jul}, pages = {9340{\textendash}9347}, keywords = {Binding Sites, Computer Simulation, Energy Transfer, Guanine, Ligands, Models, Molecular, Nucleic Acid Conformation, RNA, Temperature}, doi = {10.1021/jp902013s}, author = {Phuong Hoang Nguyen and Philippe Derreumaux and Stock, Gerhard} } @conference {2009, title = {Exploring amyloid aggregates with the OPEP coarse-grained force field}, booktitle = {Abstracts of Papers of the American Chemical Society}, volume = {238}, year = {2009}, author = {Philippe Derreumaux} } @article {2009|1436, title = {A fast method for large-scale De Novo peptide and miniprotein structure prediction.}, journal = {J. Comput. Chem.}, year = {2009}, month = {jun}, doi = {10.1002/jcc.21365}, author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery} } @article {2009|1614, title = {Induced beta-Barrel Formation of the Alzheimer{\textquoteright}s A beta 25-35 Oligomers on Carbon Nanotube Surfaces: Implication for Amyloid Fibril Inhibition}, journal = {Biophys. J.}, volume = {97}, number = {6}, year = {2009}, month = {sep}, pages = {1795{\textendash}1803}, doi = {10.1016/j.bpj.2009.07.014}, author = {Fu, Zhaoming and Luo, Yin and Philippe Derreumaux and Wei, Guanghong} } @article {2009|1387, title = {Induced beta-barrel formation of the Alzheimer{\textquoteright}s Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition.}, journal = {Biophys. J.}, volume = {97}, number = {6}, year = {2009}, month = {sep}, pages = {1795{\textendash}1803}, doi = {10.1016/j.bpj.2009.07.014}, author = {Zhaoming Fu and Yin Luo and Philippe Derreumaux and Guanghong Wei} } @article {2009|1734, title = {PEP-FOLD: an online resource for de novo peptide structure prediction}, journal = {Nucleic Acids Res.}, volume = {37}, year = {2009}, month = {jul}, pages = {W498-W503}, doi = {10.1093/nar/gkp323}, author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery} } @article {2009|1942, title = {PEP-FOLD: an online resource for de novo peptide structure prediction.}, journal = {Nucleic Acids Res.}, volume = {37}, number = {Web Server issue}, year = {2009}, month = {jul}, pages = {W498{\textendash}W503}, keywords = {Algorithms, Internet, Models, Molecular, Peptides, Protein, Protein Conformation, Reproducibility of Results, Sequence Analysis, Software, User-Computer Interface}, doi = {10.1093/nar/gkp323}, author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery} } @article {2009|1830, title = {Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.}, journal = {J. Phys. Chem. B}, volume = {113}, number = {1}, year = {2009}, month = {jan}, pages = {267{\textendash}274}, keywords = {Amino Acid Sequence, Computer Simulation, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Peptides, Protein Folding, Protein Structure, Proteins, Secondary, Solvents, Temperature, Thermodynamics}, doi = {10.1021/jp805309e}, author = {Y Chebaro and Xiao Dong and Rozita Laghaei and Philippe Derreumaux and Normand Mousseau} } @article {2009|2009, title = {Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations}, journal = {J. Chem. Phys.}, volume = {130}, number = {12}, year = {2009}, month = {mar}, pages = {125101}, keywords = {Amino Acid Sequence, Amyloid, Humans, Models, Molecular, Molecular Sequence Data, Peptide Fragments, Protein Multimerization, Protein Structure, Quaternary, Solubility, Solvents}, doi = {10.1063/1.3097982}, author = {Mo, Yuxiang and Lu, Yan and Wei, Guanghong and Philippe Derreumaux} } @article {2009|1916, title = {Structures and Thermodynamics of Alzheimer{\textquoteright}s Amyloid-beta A beta(16-35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length A beta Fibrillation}, journal = {J. Phys. Chem. B}, volume = {113}, number = {21}, year = {2009}, month = {may}, pages = {7668{\textendash}7675}, doi = {10.1021/jp900425e}, author = {Y Chebaro and Mousseau, Normand and Philippe Derreumaux} } @article {2009|1986, title = {Targeting the early steps of A beta 16-22 protofibril disassembly by N-methylated inhibitors: A numerical study}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {75}, number = {2}, year = {2009}, month = {may}, pages = {442{\textendash}452}, doi = {10.1002/prot.22254}, author = {Y Chebaro and Philippe Derreumaux} } @article {2009|2019, title = {Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {75}, number = {4}, year = {2009}, month = {jun}, pages = {954{\textendash}963}, keywords = {Amino Acid Sequence, Amyloid beta-Protein, beta 2-Microglobulin, Cluster Analysis, Computer Simulation, Models, Molecular, Peptide Fragments, Protein Multimerization, Protein Structure, Secondary, Structure-Activity Relationship, Thermodynamics}, doi = {10.1002/prot.22305}, author = {Lu, Yan and Philippe Derreumaux and Guo, Zhi and Mousseau, Normand and Wei, Guanghong} } @article {2008|1615, title = {The beta-strand-loop-beta-strand conformation is marginally populated in beta(2)-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations}, journal = {Biophys. J.}, volume = {95}, number = {2}, year = {2008}, month = {jul}, pages = {510{\textendash}517}, doi = {10.1529/biophysj.107.125054}, author = {Liang, Chungwen and Philippe Derreumaux and Mousseau, Normand and Wei, Guanghong} } @article {2008|1884, title = {The complex folding pathways of protein A suggest a multiple-funnelled energy landscape}, journal = {J. Chem. Phys.}, volume = {128}, number = {4}, year = {2008}, month = {jan}, pages = {045101}, doi = {10.1063/1.2812562}, author = {St-Pierre, Jean-Francois and Mousseau, Normand and Philippe Derreumaux} } @article {2008|1883, title = {Energy landscapes of the monomer and dimer of the Alzheimer{\textquoteright}s peptide A beta(1-28)}, journal = {J. Chem. Phys.}, volume = {128}, number = {12}, year = {2008}, month = {mar}, pages = {125108}, doi = {10.1063/1.2890033}, author = {Dong, Xiao and Chen, Wei and Mousseau, Normand and Philippe Derreumaux} } @article {2008|1811, title = {Exploring energy landscapes of protein folding and aggregation}, journal = {Front. Biosci.}, volume = {13}, year = {2008}, month = {may}, pages = {4495{\textendash}4516}, doi = {10.2741/3019}, author = {Mousseau, Normand and Philippe Derreumaux} } @conference {2008|1544, title = {Free energy surface of Abeta(16-22) complexed by N-methylated Abeta16-22 inhibitors}, booktitle = {Publication Series of the John von Neumann Institute for Computing NIC Series}, volume = {40}, year = {2008}, pages = {177{\textendash}179}, author = {Y Chebaro and Philippe Derreumaux} } @conference {2008|1545, title = {OPERA: An OPtimized coarsed-grained Energy model for RnA}, booktitle = {Publication Series of the John von Neumann Institute for Computing NIC Series}, volume = {40}, year = {2008}, pages = {185{\textendash}187}, author = {C. Colas and Phuong Hoang Nguyen and J-C. Gelly and Philippe Derreumaux} } @article {2008|1804, title = {Role of the region 23-28 in A beta fibril formation: Insights from simulations of the monomers and dimers of Alzheimer{\textquoteright}s peptides A beta 40 and A beta 42}, journal = {Curr. Alzheimer Res.}, volume = {5}, number = {3}, year = {2008}, month = {jun}, pages = {244{\textendash}250}, doi = {10.2174/156720508784533330}, author = {Melquiond, Adrien and Dong, Xiao and Mousseau, Normand and Philippe Derreumaux} } @article {2008|1812, title = {Self-assembly of amyloid-forming peptides by molecular dynamics simulations}, journal = {Front. Biosci.}, volume = {13}, year = {2008}, month = {may}, pages = {5681{\textendash}5692}, author = {Wei, Guanghong and Song, Wei and Philippe Derreumaux and Mousseau, Normand} } @article {2008|1915, title = {Self-assembly of the beta 2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals beta-barrel species}, journal = {J. Phys. Chem. B}, volume = {112}, number = {14}, year = {2008}, month = {apr}, pages = {4410{\textendash}4418}, doi = {10.1021/jp710592v}, author = {Song, Wei and Wei, Guanghong and Mousseau, Normand and Philippe Derreumaux} } @conference {2008|1543, title = {Simulating the early steps of amyloid fibril formation and disassembly}, booktitle = {Publication Series of the John von Neumann Institute for Computing NIC Series}, volume = {40}, year = {2008}, pages = {7{\textendash}12}, author = {Philippe Derreumaux} } @article {2007|1985, title = {A coarse-grained protein force field for folding and structure prediction}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {69}, number = {2}, year = {2007}, month = {nov}, pages = {394{\textendash}408}, doi = {10.1002/prot.21505}, author = {Maupetit, Julien and Pierre Tuffery and Philippe Derreumaux} } @article {2007|1882, title = {Coarse-grained protein molecular dynamics simulations}, journal = {J. Chem. Phys.}, volume = {126}, number = {2}, year = {2007}, month = {jan}, pages = {025101}, doi = {10.1063/1.2408414}, author = {Philippe Derreumaux and Mousseau, Normand} } @article {2007|2013, title = {Computational Simulations of the Early Steps of Protein Aggregation}, journal = {Prion}, volume = {1}, number = {1}, year = {2007}, month = {jan}, pages = {3{\textendash}8}, author = {Wei, Guanghong and Mousseau, Normand and Philippe Derreumaux} } @article {2007|1776, title = {The conserved glycine/alanine residue of the active-site loop containing the putative acetylCoA-binding motif is essential for the overall structural integrity of Mesorhizobium loti arylamine N-acetyltransferase 1}, journal = {Biochem. Biophys. Res. Commun.}, volume = {361}, number = {1}, year = {2007}, month = {sep}, pages = {256{\textendash}262}, doi = {10.1016/j.bbrc.2007.07.034}, author = {Atmane, Noureddine and Dairou, Julien and Flatters, Delphine and Martins, Marta and Pluvinage, Benjamin and Philippe Derreumaux and Dupret, Jean-Marie and Rodrigues-Lima, Fernando} } @article {2007|1954, title = {{P}robing amyloid fibril formation of the {N}{F}{G}{A}{I}{L} peptide by computer simulations}, journal = {J. Chem. Phys.}, volume = {126}, number = {6}, year = {2007}, month = {feb}, pages = {065101}, doi = {10.1063/1.2435358}, author = {Melquiond, A. and Gelly, J.C. and Mousseau, N. and Philippe Derreumaux} } @article {2007|1881, title = {Sampling small-scale and large-scale conformational changes in proteins and molecular complexes}, journal = {J. Chem. Phys.}, volume = {126}, number = {10}, year = {2007}, month = {mar}, pages = {105101}, doi = {10.1063/1.2710270}, author = {Yun, Mi-Ran and Mousseau, N. and Philippe Derreumaux} } @article {2007|1616, title = {Structural and hydration properties of the partially unfolded states of the prion protein}, journal = {Biophys. J.}, volume = {93}, number = {4}, year = {2007}, month = {aug}, pages = {1284{\textendash}1292}, doi = {10.1529/biophysj.107.108613}, author = {De Simone, Alfonso and Zagari, Adriana and Philippe Derreumaux} } @article {2007|1617, title = {Structure and aggregation mechanism of beta 2-microglobulin (83-99) peptides studied by molecular dynamics Simulations}, journal = {Biophys. J.}, volume = {93}, number = {10}, year = {2007}, month = {nov}, pages = {3353{\textendash}3362}, doi = {10.1529/biophysj.107.105585}, author = {Liang, Chungwen and Philippe Derreumaux and Wei, Guanghong} } @article {2006|1981, title = {Aggregating the amyloid A beta(11-25) peptide into a four-stranded beta-sheet structure}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {65}, number = {4}, year = {2006}, month = {dec}, pages = {877{\textendash}888}, doi = {10.1002/prot.21134}, author = {Boucher, Genevive and Mousseau, Normand and Philippe Derreumaux} } @article {2006|1983, title = {ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {63}, number = {4}, year = {2006}, month = {jun}, pages = {967{\textendash}975}, doi = {10.1002/prot.20938}, author = {Yun, MR and Lavery, R and Mousseau, N and Zakrzewska, K and Philippe Derreumaux} } @article {2006|1880, title = {The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution}, journal = {J. Chem. Phys.}, volume = {125}, number = {8}, year = {2006}, month = {aug}, pages = {084911}, doi = {10.1063/1.2337628}, author = {Chen, Wei and Mousseau, Normand 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 {2006|1618, title = {Impact of the mutation A21G (Flemish variant) on Alzheimer{\textquoteright}s beta-amyloid dimers by molecular dynamics simulations}, journal = {Biophys. J.}, volume = {91}, number = {10}, year = {2006}, month = {nov}, pages = {3829{\textendash}3840}, doi = {10.1526/biophysj.106.090993}, author = {Huet, Alexis and Philippe Derreumaux} } @conference {2006, title = {PHYS 4-Applications of activated methods to proteins and materials science}, booktitle = {Abstracts of Papers of the American Chemical Society}, volume = {232}, year = {2006}, author = {Mousseau, Normand and Barkema, Gerard T. and Chubynsky, Mykyta V. and Philippe Derreumaux and El-Mellouhi, Fedwa and Vocks, Henk} } @article {2006|1982, title = {Structures of soluble amyloid oligomers from computer simulations}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {65}, number = {1}, year = {2006}, month = {oct}, pages = {180{\textendash}191}, doi = {10.1002/prot.21100}, author = {Melquiond, Adrien and Mousseau, Normand and Philippe Derreumaux} } @article {2005|1980, title = {The beta alpha beta alpha beta alpha elementary Supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {60}, number = {4}, year = {2005}, month = {sep}, pages = {740{\textendash}745}, doi = {10.1002/prot.20507}, author = {Coincon, M and Heitz, A and Chiche, L and Philippe Derreumaux} } @article {2005|1979, title = {Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {61}, number = {4}, year = {2005}, month = {dec}, pages = {732{\textendash}740}, doi = {10.1002/prot.20698}, author = {Pierre Tuffery and Philippe Derreumaux} } @article {2005|1378, title = {Exploring the early steps of amyloid peptide aggregation by computers}, journal = {Acc. Chem. Res.}, volume = {38}, number = {11}, year = {2005}, pages = {885{\textendash}891}, author = {Mousseau, N and Philippe Derreumaux} } @article {2005|1879, title = {Following the aggregation of amyloid-forming peptides by computer simulations}, journal = {J. Chem. Phys.}, volume = {122}, number = {17}, year = {2005}, month = {may}, pages = {174904}, doi = {10.1063/1.1886725}, author = {Melquiond, A and Boucher, G and Mousseau, N and Philippe Derreumaux} } @conference {2005, title = {Following the aggregation of amyloid-forming peptides by computer simulations.}, booktitle = {Abstracts of Papers of the American Chemical Society}, volume = {229}, number = {Part 2}, year = {2005}, pages = {U735}, author = {Philippe Derreumaux} } @article {2005|1900, title = {Improved greedy algorithm for protein structure reconstruction}, journal = {J. Comput. Chem.}, volume = {26}, number = {5}, year = {2005}, month = {apr}, pages = {506{\textendash}513}, doi = {10.1002/jcc.20181}, author = {Pierre Tuffery and Guyon, F and Philippe Derreumaux} } @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 {2004|1867, title = {The antitumor properties of the alpha 3(IV)-(185-203) peptide from the NC1 domain of type IV collagen (tumstatin) are conformation-dependent}, journal = {J. Biol. Chem.}, volume = {279}, number = {3}, year = {2004}, month = {jan}, pages = {2091{\textendash}2100}, doi = {10.1074/jbc.M307736200}, author = {Floquet, N and Pasco, S and Ramont, L and Philippe Derreumaux and Laronze, JY and Nuzillard, JM and Maquart, FX and Alix, AJP and Monboisse, JC} } @article {2004|1978, title = {Complex folding pathways in a simple beta-hairpin}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {56}, number = {3}, year = {2004}, month = {aug}, pages = {464{\textendash}474}, doi = {10.1002/prot.20127}, author = {Wei, GH and Mousseau, N and Philippe Derreumaux} } @article {2004|1807, title = {The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer}, journal = {Eur. J. Biochem.}, volume = {271}, number = {7}, year = {2004}, month = {apr}, pages = {1258{\textendash}1265}, doi = {10.1111/j.1432-1033.2004.04026.x}, author = {Arluison, V and Folichon, M and Marco, S and Philippe Derreumaux and Pellegrini, O and Seguin, J and Hajnsdorf, E and Regnier, P} } @article {2004|1939, title = {Early steps of amyloid-petide oligomerisation explored by simulations}, journal = {Neurobiol. Aging}, volume = {25}, number = {Suppl. 2}, year = {2004}, month = {jul}, pages = {S143}, doi = {10.1016/S0197-4580(04)80481-0}, author = {Philippe Derreumaux and Wei, GH and Santini, S and Mousseau, NN} } @article {2004|1928, title = {Exploring the early steps of aggregation of amyloid-forming peptide KFFE}, journal = {Journal of Physics-condensed Matter}, volume = {16}, number = {44, Sp. Iss. SI}, year = {2004}, month = {nov}, pages = {S5047-S5054}, doi = {10.1088/0953-8984/16/44/002}, author = {Wei, GH and Mousseau, N and Philippe Derreumaux} } @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 {2004|1930, title = {In silico assembly of Alzheimer{\textquoteright}s A beta(16-22) peptide into beta-sheets}, journal = {J. Am. Chem. Soc.}, volume = {126}, number = {37}, year = {2004}, month = {sep}, pages = {11509{\textendash}11516}, doi = {10.1021/ja047286i}, author = {Santini, S and Mousseau, N and Philippe Derreumaux} } @article {2004|1994, title = {Pathway complexity of Alzheimer{\textquoteright}s beta-amyloid A beta(16-22) peptide assembly}, journal = {Structure}, volume = {12}, number = {7}, year = {2004}, month = {jul}, pages = {1245{\textendash}1255}, doi = {10.1016/j.str.2004.04.018}, author = {Santini, S and Wei, GH and Mousseau, N and Philippe Derreumaux} } @article {2004|1620, title = {Sampling the self-assembly pathways of KFFE hexamers}, journal = {Biophys. J.}, volume = {87}, number = {6}, year = {2004}, month = {dec}, pages = {3648{\textendash}3656}, doi = {10.1529/biophysj.104.047688}, author = {Wei, G. H. and Mousseau, N. and Philippe Derreumaux} } @article {2004|1787, title = {Structural characterization of VGVAPG, an elastin-derived peptide}, journal = {Biopolymers}, volume = {76}, number = {3}, year = {2004}, pages = {266{\textendash}280}, doi = {10.1002/bip.20029}, author = {Floquet, N and Hery-Huynh, S and Dauchez, M and Philippe Derreumaux and Tamburro, AM and Alix, AJP} } @article {2003|1428, title = {Exploring the folding pathways of proteins through energy landscape sampling: Application to Alzheimer{\textquoteright}s beta-amyloid peptide}, journal = {Internet Electron. J. Mol. Des.}, volume = {2}, year = {2003}, pages = {564{\textendash}577}, author = {S. Santini and G. Wei and N. Mousseau and Philippe Derreumaux} } @article {2003|1914, title = {Generating conformations for two zinc-binding sites of HIV-1 nucleocapsid protein from random conformations by a hierarchical procedure and polarizable force field}, journal = {J. Phys. Chem. B}, volume = {107}, number = {20}, year = {2003}, month = {may}, pages = {4862{\textendash}4870}, doi = {10.1021/jp022527z}, author = {Gresh, N and Philippe Derreumaux} } @article {2003|1990, title = {Impact of the tail and mutations G131V and M129V on prion protein flexibility}, journal = {Proteins-structure Function and Genetics}, volume = {51}, number = {2}, year = {2003}, month = {may}, pages = {258{\textendash}265}, doi = {10.1002/prot.10348}, author = {Santini, S and Claude, JB and Audic, S and Philippe Derreumaux} } @article {2003|1877, title = {Role of supersecondary structural elements in protein G folding}, journal = {J. Chem. Phys.}, volume = {119}, number = {9}, year = {2003}, month = {sep}, pages = {4940{\textendash}4944}, doi = {10.1063/1.1596891}, author = {Philippe Derreumaux} } @article {2003|1876, title = {Sampling the complex energy landscape of a simple beta-hairpin}, journal = {J. Chem. Phys.}, volume = {119}, number = {13}, year = {2003}, month = {oct}, pages = {6403{\textendash}6406}, doi = {10.1063/1.1613642}, author = {Wei, GH and Philippe Derreumaux and Mousseau, N} } @article {2002|1874, title = {Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique}, journal = {J. Chem. Phys.}, volume = {117}, number = {24}, year = {2002}, month = {dec}, pages = {11379{\textendash}11387}, doi = {10.1063/1.1522373}, author = {Wei, GH and Mousseau, N and Philippe Derreumaux} } @article {2002|1875, title = {Insight into protein topology from Monte Carlo simulations}, journal = {J. Chem. Phys.}, volume = {117}, number = {7}, year = {2002}, month = {aug}, pages = {3499{\textendash}3503}, doi = {10.1063/1.1494427}, author = {Philippe Derreumaux} } @article {2002|1902, title = {Structural modelling of the Sm-like protein Hfq from Escherichia coli}, journal = {J. Mol. Biol.}, volume = {320}, number = {4}, year = {2002}, month = {jul}, pages = {705{\textendash}712}, doi = {10.1016/S0022-2836(02)00548-X}, author = {Arluison, V and Philippe Derreumaux and Allemand, F and Folichon, M and Hajnsdorf, E and Regnier, P} } @article {2001|1989, title = {Computer simulations aimed at structure prediction of supersecondary motifs in proteins}, journal = {Proteins-structure Function and Genetics}, volume = {45}, number = {2}, year = {2001}, month = {nov}, pages = {159{\textendash}166}, doi = {10.1002/prot.1135}, author = {Forcellino, F and Philippe Derreumaux} } @article {2001|1623, title = {Evidence that the 127-164 region of prion proteins has two equi-energetic conformations with beta or alpha features}, journal = {Biophys. J.}, volume = {81}, number = {3}, year = {2001}, month = {sep}, pages = {1657{\textendash}1665}, author = {Philippe Derreumaux} } @article {2001|1903, title = {Sampling activated mechanisms in proteins with the activation-relaxation technique}, journal = {Journal of Molecular Graphics \& Modelling}, volume = {19}, number = {1}, year = {2001}, pages = {78{\textendash}86}, doi = {10.1016/S1093-3263(00)00134-0}, author = {Mousseau, N and Philippe Derreumaux and Barkema, GT and Malek, R} } @article {2000|1997, title = {Ab initio polypeptide structure prediction}, journal = {Theor. Chem. Acc.}, volume = {104}, number = {1}, year = {2000}, month = {may}, pages = {1{\textendash}6}, doi = {10.1007/s002149900095}, author = {Philippe Derreumaux} } @article {2000|1958, title = {Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations}, journal = {Phys. Rev. Lett.}, volume = {85}, number = {1}, year = {2000}, month = {jul}, pages = {206{\textendash}209}, doi = {10.1103/PhysRevLett.85.206}, author = {Philippe Derreumaux} } @article {2000|1899, title = {Predicting helical hairpins from sequences by Monte Carlo simulations}, journal = {J. Comput. Chem.}, volume = {21}, number = {7}, year = {2000}, month = {may}, pages = {582{\textendash}589}, doi = {10.1002/(SICI)1096-987X(200005)21:7<582}, author = {Philippe Derreumaux} } @article {1999|1803, title = {Ab initio prediction of polypeptide structure from its sequence}, journal = {Comput. Phys. Commun.}, volume = {122}, number = {Sp. Iss. SI}, year = {1999}, month = {sep}, pages = {139{\textendash}140}, doi = {10.1016/S0010-4655(99)00299-4}, author = {Philippe Derreumaux} } @article {1999|1873, title = {From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential}, journal = {J. Chem. Phys.}, volume = {111}, number = {5}, year = {1999}, month = {aug}, pages = {2301{\textendash}2310}, doi = {10.1063/1.479501}, author = {Philippe Derreumaux} } @article {1998|1872, title = {Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method}, journal = {J. Chem. Phys.}, volume = {109}, number = {4}, year = {1998}, month = {jul}, pages = {1567{\textendash}1574}, doi = {10.1063/1.476708}, author = {Philippe Derreumaux} } @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 {1997|1871, title = {A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain .1. Formulation and test on a hexadecapeptide}, journal = {J. Chem. Phys.}, volume = {106}, number = {12}, year = {1997}, month = {mar}, pages = {5260{\textendash}5270}, doi = {10.1063/1.473525}, author = {Philippe Derreumaux} } @article {1997|1870, title = {Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method}, journal = {J. Chem. Phys.}, volume = {107}, number = {6}, year = {1997}, month = {aug}, pages = {1941{\textendash}1947}, doi = {10.1063/1.474546}, author = {Philippe Derreumaux} } @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 {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 {1995|1898, title = {A VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGICAL INTEREST .4. PARAMETERS FOR THE DIFFERENT GLYCOSIDIC LINKAGES OF OLIGOSACCHARIDES}, journal = {J. Comput. Chem.}, volume = {16}, number = {2}, year = {1995}, month = {feb}, pages = {188{\textendash}199}, doi = {10.1002/jcc.540160206}, author = {Dauchez, M and Philippe Derreumaux and LAGANT, P and VERGOTEN, G} } @article {1994|1992, title = {FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .1. TREHALOSE DIHYDRATE, SOPHOROSE MONOHYDRATE AND LAMINARIBIOSE}, journal = {Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy}, volume = {50}, number = {1}, year = {1994}, month = {jan}, pages = {87{\textendash}104}, doi = {10.1016/0584-8539(94)80117-7}, author = {Dauchez, M and Philippe Derreumaux and LAGANT, P and VERGOTEN, G and SEKKAL, M and LEGRAND, P} } @article {1994|1993, title = {FORCE-FIELD AND VIBRATIONAL-SPECTRA OF OLIGOSACCHARIDES WITH DIFFERENT GLYCOSIDIC LINKAGES .2. MALTOSE MONOHYDRATE, CELLOBIOSE AND GENTIOBIOSE}, journal = {Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy}, volume = {50}, number = {1}, year = {1994}, month = {jan}, pages = {105{\textendash}118}, doi = {10.1016/0584-8539(94)80118-5}, author = {Dauchez, M and LAGANT, P and Philippe Derreumaux and VERGOTEN, G and SEKKAL, M and SOMBRET, B} } @article {1994|1897, title = {A TRUNCATED NEWTON MINIMIZER ADAPTED FOR CHARMM AND BIOMOLECULAR APPLICATIONS}, journal = {J. Comput. Chem.}, volume = {15}, number = {5}, year = {1994}, month = {may}, pages = {532{\textendash}552}, doi = {10.1002/jcc.540150506}, author = {Philippe Derreumaux and ZHANG, GH and SCHLICK, T and BROOKS, B} } @article {1994|1909, title = {THE USE OF THE SPASIBA SPECTROSCOPIC POTENTIAL FOR REPRODUCING THE STRUCTURES AND VIBRATIONAL FREQUENCIES OF A SERIES OF ACIDS - ACETIC-ACID, PIVALIC ACID, SUCCINIC ACID, ADIPIC ACID AND L-GLUTAMIC ACID}, journal = {J. Mol. Struct.}, volume = {317}, number = {1-2}, year = {1994}, month = {jan}, pages = {171{\textendash}184}, doi = {10.1016/0022-2860(93)07860-Y}, author = {CHHIBA, M and Philippe Derreumaux and VERGOTEN, G} } @article {1993|1907, title = {COMPARISON OF THE IR AND RAMAN VIBRATIONAL FREQUENCIES AND INTENSITIES OF ALKANES USING THE AMBER AND SPASIBA FORCE-FIELDS - APPLICATION TO ETHANE, AND GAUCHE-N-BUTANE AND TRANS-N-BUTANE}, journal = {J. Mol. Struct.}, volume = {295}, year = {1993}, month = {may}, pages = {223{\textendash}232}, doi = {10.1016/0022-2860(93)85022-M}, author = {Philippe Derreumaux and LAGANT, P and VERGOTEN, G} } @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} } @article {1993|1996, title = {INFLUENCE OF THE SPECTROSCOPIC POTENTIAL-ENERGY FUNCTION SPASIBA ON MOLECULAR-DYNAMICS OF PROTEINS - COMPARISON WITH THE AMBER POTENTIAL}, journal = {Theochem-journal of Molecular Structure}, volume = {105}, year = {1993}, month = {oct}, pages = {55{\textendash}64}, author = {Philippe Derreumaux and VERGOTEN, G} } @article {1993|1906, title = {THE STRUCTURES AND VIBRATIONAL FREQUENCIES OF A SERIES OF ALKANES USING THE SPASIBA FORCE-FIELD}, journal = {J. Mol. Struct.}, volume = {295}, year = {1993}, month = {may}, pages = {203{\textendash}221}, doi = {10.1016/0022-2860(93)85021-L}, author = {Philippe Derreumaux and Dauchez, M and VERGOTEN, G} } @article {1993|1896, title = {VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGIC INTEREST .2. HARMONIC DYNAMICS OF BOTH ANOMERS OF GLUCOSE IN THE CRYSTALLINE STATE}, journal = {J. Comput. Chem.}, volume = {14}, number = {3}, year = {1993}, month = {mar}, pages = {263{\textendash}277}, doi = {10.1002/jcc.540140303}, author = {Dauchez, M and Philippe Derreumaux and VERGOTEN, G} } @article {1991|1987, title = {EFFECT OF UREY-BRADLEY-SHIMANOUCHI FORCE-FIELD ON THE HARMONIC DYNAMICS OF PROTEINS}, journal = {Proteins-structure Function and Genetics}, volume = {11}, number = {2}, year = {1991}, pages = {120{\textendash}132}, doi = {10.1002/prot.340110205}, author = {Philippe Derreumaux and VERGOTEN, G} } @article {1991|1895, title = {THE USE OF ULTRAVIOLET RESONANCE RAMAN INTENSITIES TO TEST PROPOSED MOLECULAR-FORCE FIELDS FOR NUCLEIC-ACID BASES}, journal = {J. Comput. Chem.}, volume = {12}, number = {6}, year = {1991}, month = {jul}, pages = {731{\textendash}741}, doi = {10.1002/jcc.540120610}, author = {LAGANT, P and Philippe Derreumaux and VERGOTEN, G and PETICOLAS, W} } @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 {1990|1894, title = {A VIBRATIONAL MOLECULAR-FORCE FIELD OF MODEL COMPOUNDS WITH BIOLOGICAL INTEREST .1. HARMONIC DYNAMICS OF CRYSTALLINE UREA AT 123-K}, journal = {J. Comput. Chem.}, volume = {11}, number = {5}, year = {1990}, month = {jun}, pages = {560{\textendash}568}, doi = {10.1002/jcc.540110504}, author = {Philippe Derreumaux and VERGOTEN, G and LAGANT, P} } @article {1989|1912, title = {CONFORMATIONAL STUDIES OF NEUROACTIVE LIGANDS .1. FORCE-FIELD AND VIBRATIONAL-SPECTRA OF CRYSTALLINE ACETYLCHOLINE}, journal = {J. Phys. Chem.}, volume = {93}, number = {4}, year = {1989}, month = {feb}, pages = {1338{\textendash}1350}, doi = {10.1021/j100341a033}, author = {Philippe Derreumaux and WILSON, KJ and VERGOTEN, G and PETICOLAS, WL} } @article {1989|1913, title = {CONFORMATIONAL STUDIES OF NEUROACTIVE LIGANDS .2. SOLUTION-STATE CONFORMATIONS OF ACETYLCHOLINE}, journal = {J. Phys. Chem.}, volume = {93}, number = {4}, year = {1989}, month = {feb}, pages = {1351{\textendash}1357}, doi = {10.1021/j100341a034}, author = {WILSON, KJ and Philippe Derreumaux and VERGOTEN, G and PETICOLAS, WL} } @article {1989|1796, title = {RAMAN-SPECTROSCOPY, MOLECULAR-FORCE FIELDS, AND THE DYNAMICS OF BIOLOGICAL MOLECULES}, journal = {Chemica Scripta}, volume = {29A}, year = {1989}, month = {sep}, pages = {113{\textendash}122}, author = {PETICOLAS, WL and WILSON, KJ and Philippe Derreumaux and VERGOTEN, G} } @article {1988|1625, title = {Uv Resonance Raman-spectra and Solution State Conformations of Cholinergic Neurotransmitters}, journal = {Biophys. J.}, volume = {53}, number = {2}, year = {1988}, month = {feb}, pages = {A287-A287}, author = {WILSON, K. J. and Philippe Derreumaux and VERGOTEN, G. and W. L. Peticolas} }