@article {2024, title = {A Perspective on the Prospective Use of AI in Protein Structure Prediction}, journal = {J Chem Inf Model}, volume = {64}, year = {2024}, month = {Jan}, pages = {26{\textendash}41}, author = {Versini, R. and Sritharan, S. and Aykac Fas, B. and Tubiana, T. and Aimeur, S. Z. and Henri, J. and Erard, M. and N{\"u}sse, O. and Andreani, J. and Baaden, M. and Fuchs, P. and Galochkina, T. and Chatzigoulas, A. and Cournia, Z. and Santuz, H. and S Sacquin-Mora and Taly, A.} } @article {2020|2143, title = {A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.}, journal = {J Chem Phys}, volume = {153}, year = {2020}, month = {2020 Aug 07}, pages = {050901}, abstract = {

Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.

}, issn = {1089-7690}, doi = {10.1063/5.0017775}, author = {Dubou{\'e}-Dijon, E and Javanainen, M and Delcroix, P and Jungwirth, P and Martinez-Seara, H} } @article {2020, title = {Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.}, journal = {J Mol Biol}, volume = {432}, year = {2020}, month = {2020 Feb 14}, pages = {1183-1198}, abstract = {

In the crowded cell, a strong selective pressure operates on the proteome to limit the competition between functional and non-functional protein-protein interactions. We developed an original theoretical framework in order to interrogate how this competition constrains the behavior of proteins with respect to their partners or random encounters. Our theoretical framework relies on a two-dimensional (2D) representation of interaction energy landscapes, with 2D energy maps, which reflect in a synthetic way the spatial distribution of the interaction propensity of a protein surface for another protein. We realized the interaction propensity mapping of proteins\&$\#$39; surfaces in interaction with functional and arbitrary partners and asked whether the distribution of their interaction propensity is conserved during evolution. Therefore, we performed several thousands of cross-docking simulations to systematically characterize the energy landscapes of 103 proteins interacting with different sets of homologs, corresponding to their functional partner\&$\#$39;s family or arbitrary protein families. Then, we systematically compared the energy maps resulting from the docking of each protein with the different protein families of the dataset. Strikingly, we show that the interaction propensity not only of the binding sites but also of the rest of the surface is conserved for docking partners belonging to the same protein family. Interestingly, this observation holds for docked proteins corresponding to true but also arbitrary partners. Our theoretical framework enables the characterization of the energy behavior of a protein in interaction with hundreds of proteins and opens the way for the characterization of the behavior of proteins in a specific environment.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2019.12.047}, author = {Schweke, Hugo and Mucchielli, Marie-H{\'e}l{\`e}ne and S Sacquin-Mora and Bei, Wanying and Lopes, Anne} } @inbook {2020|2123, title = {Protein thermal stability}, booktitle = {Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly}, year = {2020}, author = {S. Timr and D. Madern and F. Sterpone} } @article {2019|2072, title = {Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking}, journal = {Mitochondrion}, volume = {49}, year = {2019}, pages = {234{\textendash}244}, author = {Brandner, Astrid and De Vecchis, Dario and Marc Baaden and Cohen, Micka{\"e}l M and Antoine Taly} } @article {2019|2062, title = {The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements}, journal = {Nucleic Acids Res}, volume = {47}, year = {2019}, month = {02}, pages = {1836-1846}, abstract = {

Bacterial recombinational repair of double-strand breaks often begins with creation of initiating 3\&$\#$39; single-stranded DNA (ssDNA) tails on each side of a double-strand break (DSB). Importantly, if the RecBCD pathway is followed, RecBCD creates a gap between the sequences at 3\&$\#$39; ends of the initiating strands. The gap flanks the DSB and extends at least to the nearest Chi site on each strand. Once the initiating strands form ssDNA-RecA filaments, each ssDNA-RecA filament searches for homologous double-stranded DNA (dsDNA) to use as a template for the DNA synthesis needed to fill the gap created by RecBCD. Our experimental results show that the DNA synthesis requires formation of a heteroduplex dsDNA that pairs \>20 contiguous bases in the initiating strand with sequence matched bases in a strand from the original dsDNA. To trigger synthesis, the heteroduplex must be near the 3\&$\#$39; end of the initiating strand. Those experimentally determined requirements for synthesis combined with the Chi site dependence of the function of RecBCD and the distribution of Chi sites in bacterial genomes could allow the RecBCD pathway to avoid some genomic rearrangements arising from directly induced DSBs; however, the same three factors could promote other rearrangements.

}, doi = {10.1093/nar/gky1252}, author = {Li, Chastity and Danilowicz, Claudia and Tashjian, Tommy F and Godoy, Veronica G and Chantal Pr{\'e}vost and Prentiss, Mara} } @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 {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 {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 {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} } @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|1732, title = {The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo}, journal = {Nucleic Acids Res.}, volume = {43}, year = {2015}, month = {jul}, pages = {6473{\textendash}85}, abstract = {

RecA family proteins are responsible for homology search and strand exchange. In bacteria, homology search begins after RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site, forming the presynaptic filament. Once the filament is formed, it interrogates double-stranded DNA (dsDNA). During the interrogation, bases in the dsDNA attempt to form Watson-Crick bonds with the corresponding bases in the initiating strand. Mismatch dependent instability in the base pairing in the heteroduplex strand exchange product could provide stringent recognition; however, we present experimental and theoretical results suggesting that the heteroduplex stability is insensitive to mismatches. We also present data suggesting that an initial homology test of 8 contiguous bases rejects most interactions containing more than 1/8 mismatches without forming a detectable 20 bp product. We propose that, in vivo, the sparsity of accidental sequence matches allows an initial 8 bp test to rapidly reject almost all non-homologous sequences. We speculate that once the initial test is passed, the mismatch insensitive binding in the heteroduplex allows short mismatched regions to be incorporated in otherwise homologous strand exchange products even though sequences with less homology are eventually rejected.

}, doi = {10.1093/nar/gkv610}, author = {Danilowicz, Claudia and Yang, Darren and Kelley, Craig and Chantal Pr{\'e}vost and Prentiss, Mara} } @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 {2014|1598, title = {A predicted binding site for cholesterol on the GABAA receptor.}, journal = {Biophys. J.}, volume = {106}, number = {9}, year = {2014}, month = {may}, pages = {1938{\textendash}1949}, publisher = {Department of Physics, Rutgers University-Camden, Camden, New Jersey; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey. Electronic address: Grace.Brannigan@rutgers.edu.}, abstract = {Modulation of the GABA type A receptor (GABAAR) function by cholesterol and other steroids is documented at the functional level, yet its structural basis is largely unknown. Current data on structurally related modulators suggest that cholesterol binds to subunit interfaces between transmembrane domains of the GABAAR. We construct homology models of a human GABAAR based on the structure of the glutamate-gated chloride channel GluCl of Caenorhabditis elegans. The models show the possibility of previously unreported disulfide bridges linking the M1 and M3 transmembrane helices in the α and γ subunits. We discuss the biological relevance of such disulfide bridges. Using our models, we investigate cholesterol binding to intersubunit cavities of the GABAAR transmembrane domain. We find that very similar binding modes are predicted independently by three approaches: analogy with ivermectin in the GluCl crystal structure, automated docking by AutoDock, and spontaneous rebinding events in unbiased molecular dynamics simulations. Taken together, the models and atomistic simulations suggest a somewhat flexible binding mode, with several possible orientations. Finally, we explore the possibility that cholesterol promotes pore opening through a wedge mechanism.}, keywords = {Amino Acid, Binding Sites, Caenorhabditis elegans Proteins, chemistry, chemistry/metabolism, Chloride Channels, Cholesterol, GABA-A, Humans, Hydrogen Bonding, Ivermectin, metabolism, Molecular Docking Simulation, Molecular Dynamics Simulation, Porosity, Protein Binding, Protein Conformation, Receptors, Sequence Homology, Substrate Specificity}, doi = {10.1016/j.bpj.2014.03.024}, author = {J{\'e}r{\^o}me H{\'e}nin and Salari, Reza and Murlidaran, Sruthi and Grace Brannigan} } @article {2013|1961, title = {Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information}, journal = {Plos Comput. Biol.}, volume = {9}, number = {12}, year = {2013}, month = {dec}, pages = {e1003369}, doi = {10.1371/journal.pcbi.1003369}, url = {http://hal.inria.fr/hal-00875116}, author = {Lopes, Anne and S Sacquin-Mora and Dimitrova, Viktoriya and Laine, Elodie and Ponty, Yann and Carbone, Alessandra} } @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 {2010|1395, title = {{P}hotocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination}, journal = {Chembiochem}, volume = {11}, year = {2010}, month = {mar}, pages = {653{\textendash}663}, author = {Sinha, D. K. and Neveu, P. and Gagey, N. and Aujard, I. and Benbrahim-Bouzidi, C. and Le Saux, T. and Rampon, C. and Gauron, C. and Goetz, B. and Dubruille, S. and Marc Baaden and Volovitch, M. and Bensimon, D. and Vriz, S. and Jullien, L.} } @inbook {2010|1758, title = {Protein-Protein Docking}, booktitle = {Protein-Protein Complexes. Analysis, Modeling and Drug Design}, year = {2010}, pages = {147{\textendash}181}, publisher = {Imperial College Press}, organization = {Imperial College Press}, chapter = {6}, author = {A Saladin and Chantal Pr{\'e}vost}, editor = {Martin Zacharias} } @article {2010|2007, title = {{A} putative extracellular salt bridge at the subunit interface contributes to the ion channel function of the {A}{T}{P}-gated {P}2{X}2 receptor}, journal = {J. Biol. Chem.}, volume = {285}, number = {21}, year = {2010}, month = {may}, pages = {15805{\textendash}15815}, publisher = {American Society for Biochemistry and Molecular Biology}, author = {Jiang, R. and Martz, A. and Gonin, S. and Antoine Taly and de Carvalho, L. P. and Grutter, T.} } @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|1392, title = {{PT}ools: an opensource molecular docking library.}, journal = {Bmc Struct. Biol.}, volume = {9}, year = {2009}, pages = {27{\textendash}37}, doi = {10.1186/1472-6807-9-27}, author = {A Saladin and Fiorucci, S and Poulain, P and Chantal Pr{\'e}vost and Martin Zacharias} } @article {2008|1494, title = {Pressure-induced core packing and interfacial dehydration in nonionic C12E6 micelle in aqueous solution}, journal = {Langmuir}, volume = {24}, number = {12}, year = {2008}, pages = {6067{\textendash}71}, author = {Sterpone, Fabio and Briganti, G and Melchionna, S and Pierleoni, C} } @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|1588, title = {Probing the flexibility of the bacterial reaction center: The wild-type protein is more rigid than two site-specific mutants}, journal = {Biochemistry}, volume = {46}, number = {51}, year = {2007}, month = {dec}, pages = {14960{\textendash}14968}, doi = {10.1021/bi7004416}, author = {S Sacquin-Mora and Sebban, P. and Derrien, V. and Frick, B. and Richard Lavery and Alba-Simionesco, C.} } @article {2007|1728, title = {{A} prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family}, journal = {Nature}, volume = {445}, number = {7123}, year = {2007}, month = {jan}, pages = {116{\textendash}119}, author = {Bocquet, N. and Prado de Carvalho, L. and Cartaud, J. and Neyton, J. and Le Poupon, C. and Antoine Taly and Grutter, T. and Jean-Pierre Changeux and Corringer, P. J.} } @article {2007|1868, title = {Protein mechanics: a route from structure to function}, journal = {Journal of Biosciences}, volume = {32}, number = {5, Sp. Iss. SI}, year = {2007}, month = {aug}, pages = {891{\textendash}898}, doi = {10.1007/s12038-007-0089-x}, author = {Lavery, Richard and S Sacquin-Mora} } @article {2006|1389, title = {Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study}, journal = {Biophys. J.}, volume = {91}, number = {4}, year = {2006}, month = {aug}, pages = {1224{\textendash}1234}, author = {Phuong Hoang Nguyen and Gorbunov, Roman D. and Stock, Gerhard} } @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|1604, title = {Probing a model of a {GPCR}/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor}, journal = {Biophys. J.}, volume = {90}, number = {4}, year = {2006}, pages = {1232{\textendash}1240}, abstract = {A three-dimensional model structure of a complex formed by a G-protein-coupled receptor (GPCR) and an agonist ligand is probed and refined using molecular-dynamics simulations and free energy calculations in a realistic environment. The model of the human receptor of cholecystokinin associated to agonist ligand CCK9 was obtained from a synergistic procedure combining site-directed mutagenesis experiments and in silico modeling. The 31-ns molecular-dynamics simulation in an explicit membrane environment indicates that both the structure of the receptor and its interactions with the ligand are robust. Whereas the secondary structure of the {alpha}-helix bundle is well preserved, the region of the intracellular loops exhibits a significant flexibility likely to be ascribed to the absence of G-protein subunits in the model. New insight into the structural features of the binding pocket is gained, in particular, the interplay of the ligand with both the receptor and internal water molecules. Water-mediated interactions are shown to participate in the binding, hence, suggesting additional site-directed mutagenesis experiments. Accurate free energy calculations on mutated ligands provide differences in the receptor-ligand binding affinity, thus offering a direct, quantitative comparison to experiment. We propose that this detailed consistency-checking procedure be used as a routine refinement step of in vacuo GPCR models, before further investigation and application to structure-based drug design.}, url = {http://www.biophysj.org/cgi/content/abstract/90/4/1232}, author = {J{\'e}r{\^o}me H{\'e}nin and Maigret, B. and Mounir Tarek and Escrieut, C. and Fourmy, D. and Christophe Chipot} } @article {2006|1514, title = {Protein Peeling 2: a web server to convert protein structures into series of protein units}, journal = {Nucleic Acids Res.}, volume = {34}, number = {Sp. Iss. SI}, year = {2006}, month = {jul}, pages = {W75-W78}, author = {Gelly, J. -C. and Etchebest, C. and Hazout, S. and de Brevern, A. G.} } @article {2006|1386, title = {{\textquoteleft}Protein Peeling{\textquoteright}: an approach for splitting a 3D protein structure into compact fragments}, journal = {Bioinformatics}, volume = {22}, number = {2}, year = {2006}, pages = {129{\textendash}133}, author = {Gelly, JC and de Brevern, AG and Hazout, S} } @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 {2003|1621, title = {The position of Q B in the photosynthetic reaction center depends on pH: A theoretical analysis of the proton uptake upon Q B reduction}, journal = {Biophys. J.}, volume = {84}, number = {3}, year = {2003}, pages = {2090{\textendash}2098}, publisher = {Cell Press}, author = {Antoine Taly and Sebban, Pierre and Smith, Jeremy C and Ullmann, G Matthias} } @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 {1993|1628, title = {Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2}, journal = {Biopolymers}, volume = {33}, year = {1993}, month = {mar}, pages = {335{\textendash}50}, abstract = {

A theory and graphical presentation for the analysis of helix structure and deformations in oligonucleotides is presented. The parameters \"persistence\" and \"flexibility\" as defined in the configurational statistics of polymers of infinite length are reformulated at the oligonucleotide level in an extension of J. A. Schellman\&$\#$39;s method [(1974) Biopolymers, Vol. 17, pp. 217-226], and used as a basis for a systematic \"Persistence Analysis\" of the helix deformation properties for all possible subsequences in the structure. The basis for the analysis is a set of link vectors referenced to individual base pairs, and is limited to sequences exhibiting only perturbed rod-like behavior, i.e., below the threshold for supercoiling. The present application of the method is concerned with a physical model for the angular component of bending, so the link vectors are defined as the unit components of a global helix axis obtained by the procedure \"Curves\" of R. Lavery and H. Sklenar [(1988) J. Biomol. Struct. Dynam., Vol. 6, pp. 63-91; (1989) ibid., Vol. 6, pp. 655-667]. A discussion of the relationship between global bending and relative orientation of base pairs is provided. Our approach is illustrated by analysis of some model oligonucleotide structures with intrinsic kinks, the crystal structure of the dodecamer d(CGCGAATTCGCG)2, and the results of two molecular dynamics simulations on this dodecamer using two variations of the GROMOS force field. The results indicate that essentially all aspects of curvature in short oligonucleotides can be determined, such as the position and orientation of each bend, the sharpness or smoothness, and the location and linearity of subsequences. In the case of molecular dynamics simulations, where a Boltzmann ensemble of structures is analyzed, the spatial extent of the deformations (flexibility) is also considered.

}, doi = {10.1002/bip.360330303}, author = {Chantal Pr{\'e}vost and Louise-May, S and Ravishanker, G and Richard Lavery and Beveridge, D L} } @article {1991|1698, title = {A probabilistic view on steady state enzyme kinetics}, journal = {J. Theor. Biol.}, volume = {148}, year = {1991}, pages = {229{\textendash}242}, author = {Alexey K Mazur} } @article {1990, title = {Pore formation kinetics in membranes, determined from the release of marker molecules out of liposomes or cells}, journal = {Biophys. J.}, volume = {58}, year = {1990}, pages = {577{\textendash}583}, author = {Schwarz, Gerhard and Charles H. Robert} } @article {1985|1725, title = {On the possible mechanism of multiple enzyme attack in polysaccharide degradation}, journal = {Mol. Biol.}, volume = {19}, year = {1985}, pages = {1400{\textendash}1408}, author = {Alexey K Mazur} }