@article {2022|2160, title = {Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation}, journal = {Nature Communications}, volume = {13}, year = {2022}, doi = {10.1038/s41467-022-34813-5}, url = {https://doi.org/10.1038/s41467-022-34813-5}, author = {John T. Petroff and Noah M. Dietzen and Ezry Santiago-McRae and Brett Deng and Maya S. Washington and Lawrence J. Chen and K. Trent Moreland and Zengqin Deng and Michael Rau and James A. J. Fitzpatrick and Peng Yuan and Thomas T. Joseph and J{\'e}r{\^o}me H{\'e}nin and Grace Brannigan and Wayland W. L. Cheng} } @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 {2018|2092, title = {Oriented chiral water wires in artificial transmembrane channels.}, journal = {Sci Adv}, volume = {4}, year = {2018}, month = {2018 03}, pages = {eaao5603}, abstract = {

Aquaporins (AQPs) feature highly selective water transport through cell membranes, where the dipolar orientation of structured water wires spanning the AQP pore is of considerable importance for the selective translocation of water over ions. We recently discovered that water permeability through artificial water channels formed by stacked imidazole I-quartet superstructures increases when the channel water molecules are highly organized. Correlating water structure with molecular transport is essential for understanding the underlying mechanisms of (fast) water translocation and channel selectivity. Chirality adds another factor enabling unique dipolar oriented water structures. We show that water molecules exhibit a dipolar oriented wire structure within chiral I-quartet water channels both in the solid state and embedded in supported lipid bilayer membranes (SLBs). X-ray single-crystal structures show that crystallographic water wires exhibit dipolar orientation, which is unique for chiral I-quartets. The integration of I-quartets into SLBs was monitored with a quartz crystal microbalance with dissipation, quantizing the amount of channel water molecules. Nonlinear sum-frequency generation vibrational spectroscopy demonstrates the first experimental observation of dipolar oriented water structures within artificial water channels inserted in bilayer membranes. Confirmation of the ordered confined water is obtained via molecular simulations, which provide quantitative measures of hydrogen bond strength, connectivity, and the stability of their dipolar alignment in a membrane environment. Together, uncovering the interplay between the dipolar aligned water structure and water transport through the self-assembled I-quartets is critical to understanding the behavior of natural membrane channels and will accelerate the systematic discovery for developing artificial water channels for water desalting.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aao5603}, author = {Kocsis, Istvan and Sorci, Mirco and Vanselous, Heather and Murail, Samuel and Sanders, Stephanie E and Licsandru, Erol and Legrand, Yves-Marie and van der Lee, Arie and Marc Baaden and Petersen, Poul B and Belfort, Georges and Barboiu, Mihail} } @article {2016|2027, title = {Orientational Dynamics of Water at an Extended Hydrophobic Interface}, journal = {J Am Chem Soc}, volume = {138}, year = {2016}, month = {May}, pages = {5551-60}, abstract = {

We report on the orientational dynamics of water at an extended hydrophobic interface with an octadecylsilane self-assembled monolayer on fused silica. The interfacial dangling OH stretch mode is excited with a resonant pump, and its evolution followed in time by a surface-specific, vibrationally resonant, infrared-visible sum-frequency probe. High sensitivity pump-probe anisotropy measurements and isotopic dilution clearly reveal that the decay of the dangling OH stretch excitation is almost entirely due to a jump to a hydrogen-bonded configuration that occurs in 1.61 $\pm$ 0.10 ps. This is more than twice as fast as the jump time from one hydrogen-bonded configuration to another in bulk H2O but about 50\% slower than the reported out-of-plane reorientation at the air/water interface. In contrast, the intrinsic population lifetime of the dangling OH stretch in the absence of such jumps is found to be \>10 ps. Molecular dynamics simulations of air/water and hexane/water interfaces reproduce the fast jump dynamics of interfacial dangling OH with calculated jump times of 1.4 and 1.7 ps for the air and hydrophobic interfaces, respectively. The simulations highlight that while the air/water and hydrophobic/water surfaces exhibit great structural similarities, a small stabilization of the OH groups by the hydrophobic interface produces the pronounced difference in the dynamics of dangling bonds.

}, doi = {10.1021/jacs.6b01820}, author = {Xiao, Shunhao and Figge, Florian and Guillaume Stirnemann and Laage, Damien and McGuire, John A} } @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} } @conference {2014|1760, title = {Optogating a powerful approach to control an ion-channel gate}, booktitle = {PURINERGIC SIGNALLING}, volume = {10}, number = {4}, year = {2014}, pages = {762{\textendash}762}, publisher = {SPRINGER VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, organization = {SPRINGER VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, author = {Lemoine, Damien and Habermacher, Chlo{\'e} and Martz, Adeline and M{\'e}ry, Pierre-Fran\c cois and Bouquier, Nathalie and Diverchy, Fanny and Antoine Taly and Rassendren, Fran\c cois and Specht, Alexandre and Grutter, Thomas} } @article {2013|1973, title = {{O}ptical control of an ion channel gate}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {110}, number = {51}, year = {2013}, month = {dec}, pages = {20813{\textendash}20818}, author = {Lemoine, D. and Habermacher, C. and Martz, A. and Mery, P. F. and Bouquier, N. and Diverchy, F. and Antoine Taly and Rassendren, F. and Specht, A. and Grutter, T.} } @article {2013|1688, title = {On the origin of thermal untwisting of DNA}, journal = {J. Phys. Chem. B}, volume = {117}, year = {2013}, pages = {1857{\textendash}1861}, author = {Alexey K Mazur} } @article {2011|1748, title = {Optimizing the design of oligonucleotides for homology directed gene targeting}, journal = {Plos One}, volume = {6}, year = {2011}, pages = {e14795}, abstract = {

BACKGROUND: Gene targeting depends on the ability of cells to use homologous recombination to integrate exogenous DNA into their own genome. A robust mechanistic model of homologous recombination is necessary to fully exploit gene targeting for therapeutic benefit. METHODOLOGY/PRINCIPAL FINDINGS: In this work, our recently developed numerical simulation model for homology search is employed to develop rules for the design of oligonucleotides used in gene targeting. A Metropolis Monte-Carlo algorithm is used to predict the pairing dynamics of an oligonucleotide with the target double-stranded DNA. The model calculates the base-alignment between a long, target double-stranded DNA and a probe nucleoprotein filament comprised of homologous recombination proteins (Rad51 or RecA) polymerized on a single strand DNA. In this study, we considered different sizes of oligonucleotides containing 1 or 3 base heterologies with the target; different positions on the probe were tested to investigate the effect of the mismatch position on the pairing dynamics and stability. We show that the optimal design is a compromise between the mean time to reach a perfect alignment between the two molecules and the stability of the complex. CONCLUSION AND SIGNIFICANCE: A single heterology can be placed anywhere without significantly affecting the stability of the triplex. In the case of three consecutive heterologies, our modeling recommends using long oligonucleotides (at least 35 bases) in which the heterologous sequences are positioned at an intermediate position. Oligonucleotides should not contain more than 10\% consecutive heterologies to guarantee a stable pairing with the target dsDNA. Theoretical modeling cannot replace experiments, but we believe that our model can considerably accelerate optimization of oligonucleotides for gene therapy by predicting their pairing dynamics with the target dsDNA.

}, doi = {10.1371/journal.pone.0014795}, author = {Min{\'e}-Hattab, Judith and Fleury, Genevi{\`e}ve and Chantal Pr{\'e}vost and Dutreix, Marie and Viovy, Jean-Louis} } @article {2010|1529, title = {{O}ne-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {107}, year = {2010}, month = {apr}, pages = {6275{\textendash}6280}, author = {Nury, H. and Poitevin, F. and Van Renterghem, C. and Changeux, J. P. and Corringer, P. J. and Delarue, M. and Marc Baaden} } @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} } @inbook {2008|1566, title = {Order-disorder transitions in ribosome assembly}, booktitle = {Ribosomal proteins,}, year = {2008}, publisher = {Nova publishers, Hauppauge NY}, organization = {Nova publishers, Hauppauge NY}, author = {Y Timsit and F Allemand and Chiaruttini C and M Springer}, editor = {Colombus} } @article {2008|1409, title = {Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers}, journal = {European Biophysics Journal with Biophysics Letters}, volume = {37}, number = {2}, year = {2008}, month = {feb}, pages = {131{\textendash}141}, author = {Cox, Katherine and Bond, Peter J. and Grottesi, Alessandro and Marc Baaden and Sansom, Mark S. P.} } @article {2007|2006, title = {{O}pened by a twist: a gating mechanism for the nicotinic acetylcholine receptor}, journal = {Eur. Biophys. J.}, volume = {36}, number = {8}, year = {2007}, month = {nov}, pages = {911{\textendash}918}, publisher = {Springer-Verlag}, author = {Antoine Taly} } @article {2006|1658, title = {Odorant Binding and Conformational Dynamics in the Odorant-binding Protein}, journal = {J. Biol. Chem.}, volume = {281}, number = {40}, year = {2006}, month = {oct}, pages = {29929{\textendash}29937}, abstract = {In mammals, the olfactory epithelium secretes odorant-binding proteins (OBPs), which are lipocalins found freely dissolved in the mucus layer protecting the olfactory neurons. OBPs may act as passive transporters of predominantly hydrophobic odorant molecules across the aqueous mucus layer, or they may play a more active role in which the olfactory neuronal receptor recognizes the OBP-ligand complex. To better understand the molecular events accompanying the initial steps in the olfaction process, we have performed molecular dynamics studies of rat and pig OBPs with the odorant molecule thymol. These calculations provide an atomic level description of conformational changes and pathway intermediates that remain difficult to study directly. A series of eight independent molecular dynamics trajectories of rat OBP permitted the observation of a consensus pathway for ligand unbinding and the calculation of the potential of mean force (PMF) along this path. Titration microcalorimetry confirmed the specific binding of thymol to this protein with a strong hydrophobic component. In both rat and pig OBPs we observed lipocalin strand pair opening in the presence of ligand, consistent with potential roles of these proteins in olfactive receptor recognition.}, doi = {10.1074/jbc.M604869200}, author = {Eric Hajjar and David Perahia and Helene D{\'e}bat and Claude Nespoulous and Charles H. Robert} } @article {2004, title = {OmpT: Molecular dynamics simulations of an outer membrane enzyme}, journal = {Biophys. J.}, volume = {87}, number = {5}, year = {2004}, month = {nov}, pages = {2942{\textendash}2953}, author = {Marc Baaden and Sansom, MSP} } @article {2004|1846, title = {Overcoming free energy barriers using unconstrained molecular dynamics simulations}, journal = {J. Chem. Phys.}, volume = {121}, year = {2004}, pages = {2904{\textendash}2914}, author = {J{\'e}r{\^o}me H{\'e}nin and Christophe Chipot} } @article {1993|1682, title = {Optimization of numerical algorithms for internal coordinate molecular dynamics}, journal = {J. Comput. Phys.}, volume = {107}, year = {1993}, pages = {359{\textendash}366}, author = {Vladimir E. Dorofeyev and Alexey K Mazur} } @article {1987|1592, title = {Oxygen binding constants for human hemoglobin tetramers}, journal = {Biochemistry}, volume = {26}, number = {13}, year = {1987}, month = {jun}, pages = {3995{\textendash}4002}, author = {Gill, S J and Di Cera, E and Doyle, M L and Bishop, G A and Charles H. Robert} } @article {1985, title = {Oligomer distribution of depolymerase digests: Comparison of theory and experiments}, journal = {Febs Lett.}, volume = {192}, year = {1985}, pages = {43{\textendash}46}, author = {Alexey K Mazur and N. I. Nazarova and L. A. Elyakova} }