@article {2022|2151, title = {Symmetry-Adapted Restraints for Binding Free Energy Calculations.}, journal = {J Chem Theory Comput}, year = {2022}, month = {2022 Mar 01}, abstract = {

Binding free energy calculations rely critically on a precise definition of the bound state and well-designed ligand restraints to ensure that binding free energy calculations converge rapidly and yield estimates of well-defined thermodynamic quantities. The distance-to-bound-configuration (DBC) is a single variable that can precisely delineate the bound state of a ligand including translational, rotational and conformational degrees of freedom and has been successfully used to capture binding modes with complex geometries. DBC is defined as the root-mean-square deviation (RMSD) of ligand coordinates in the frame of reference of the binding site. In the special case where the ligand features symmetry-equivalent atoms, a standard RMSD arbitrarily distinguishes equivalent poses, mixing equivalent and nonequivalent degrees of freedom, and preventing the precise delineation of the bound state ensemble, which negates the benefits of defining a flat-bottom binding restraint. To remedy this, we introduce a symmetry-adapted DBC coordinate where the RMSD is minimized over permutations of equivalent ligand atoms. This coordinate is implemented in a portable software library, the Collective Variables Module. We tested the approach by computing the absolute binding free energy of benzene to the engineered site of a mutant lysozyme (L99A/M102H) using alchemical free energy perturbation. We found that the symmetry-adapted restraint leads to well-behaved convergence of both the decoupling free energy in the binding site and the restrained free energy in the gas phase, recovering the affinity computed using a classic center-of-mass restraint. Thus, symmetry-adapted DBC seamlessly generalizes the benefits of DBC restraints to the case of symmetric ligands. The underlying symmetric RMSD coordinate can also be used for analyzing or biasing simulations in other contexts than affinity predictions.

}, issn = {1549-9626}, doi = {10.1021/acs.jctc.1c01235}, author = {Ebrahimi, Mina and J{\'e}r{\^o}me H{\'e}nin} } @article {2020|2142, title = {Scalable molecular dynamics on CPU and GPU architectures with NAMD}, journal = {The Journal of Chemical Physics}, volume = {153}, year = {2020}, chapter = {044130}, abstract = {

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

}, keywords = {NAMD}, doi = {10.1063/5.0014475}, url = {https://aip.scitation.org/doi/10.1063/5.0014475}, author = {James Phillips and David Hardy and Julio Maia and John Stone and Joao Ribeiro and Rafael Bernardi and Ronak Buch and Giacomo Fiorin and J{\'e}r{\^o}me H{\'e}nin and Wei Jiang and Ryan McGreevy and Melo, Marcelo Cardoso dos Reis and Brian Radak and Robert Skeel and Abhishek Singharoy and Yi Wang and Benoit Roux and Aleksei Aksimentiev and Zan Luthey-Schulten and Laxmikant Kale and Klaus Schulten and Christophe Chipot and Emad Tajkhorshid} } @article {2020|2098, title = {Scruter les mol{\'e}cules en r{\'e}alit{\'e} virtuelle, pour quoi faire ?}, journal = {L{\textquoteright}Actualit{\'e} Chimique}, year = {2020}, pages = {23{\textendash}26}, abstract = {

Les repr{\'e}sentations des mol{\'e}cules ont pris une place importante dans la communication d\’id{\'e}es, la g{\'e}n{\'e}ration d\’hypoth{\`e}ses sur les m{\'e}canismes biologiques et l\’analyse de simulations mol{\'e}culaires. Pourtant, les dispositifs pour les observer et les manipuler restent souvent cantonn{\'e}s aux deux dimensions des {\'e}crans et {\`a} l\’interaction limit{\'e}e d\’une souris et d\’un clavier. D\’autres solutions plus performantes et {\`a} port{\'e}e de tous existent, notamment avec les derni{\`e}res {\'e}volutions de la r{\'e}alit{\'e} virtuelle pour le grand public. Des adaptations sont n{\'e}anmoins n{\'e}cessaires pour b{\'e}n{\'e}ficier pleinement des avantages li{\'e}s {\`a} l\’utilisation de la r{\'e}alit{\'e} virtuelle pour la visualisation scientifique. Cet article pr{\'e}sente quelques exemples r{\'e}alis{\'e}s avec le logiciel UnityMol. En plus des applications directes dans l\’enseignement, le changement de paradigme d\’interaction et la perception accrue de la profondeur et des formes des mol{\'e}cules biologiques facilitent d{\`e}s {\`a} pr{\'e}sent la compr{\'e}hension de ces syst{\`e}mes complexes et am{\`e}neront certainement {\`a} la d{\'e}couverte de nouveaux savoirs scientifiques.

}, issn = {0151-9093}, url = {http://www.lactualitechimique.org/Scruter-les-molecules-en-realite-virtuelle-pour-quoi-faire}, author = {Martinez, Xavier and Marc Baaden} } @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|2140, title = {Structural transitions in the RNA 7SK 5{\textquoteright} hairpin and their effect on HEXIM binding}, journal = {Nucleic Acids Res}, volume = {48}, year = {2020}, month = {01}, pages = {373-389}, abstract = {

7SK RNA, as part of the 7SK ribonucleoprotein complex, is crucial to the regulation of transcription by RNA-polymerase II, via its interaction with the positive transcription elongation factor P-TEFb. The interaction is induced by binding of the protein HEXIM to the 5\&$\#$39; hairpin (HP1) of 7SK RNA. Four distinct structural models have been obtained experimentally for HP1. Here, we employ computational methods to investigate the relative stability of these structures, transitions between them, and the effects of mutations on the observed structural ensembles. We further analyse the results with respect to mutational binding assays, and hypothesize a mechanism for HEXIM binding. Our results indicate that the dominant structure in the wild type exhibits a triplet involving the unpaired nucleotide U40 and the base pair A43-U66 in the GAUC/GAUC repeat. This conformation leads to an open major groove with enough potential binding sites for peptide recognition. Sequence mutations of the RNA change the relative stability of the different structural ensembles. Binding affinity is consequently lost if these changes alter the dominant structure.

}, doi = {10.1093/nar/gkz1071}, author = {R{\"o}der, Konstantin and Guillaume Stirnemann and Dock-Bregeon, Anne-Catherine and Wales, David J and Pasquali, Samuela} } @article {2019|2064, title = {Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology}, journal = {J Biol Chem}, volume = {294}, year = {2019}, month = {May}, pages = {8606-8616}, abstract = {

DNA recombination resulting from RecA-mediated strand exchange aided by RecBCD proteins often enables accurate repair of DNA double-strand breaks. However, the process of recombinational repair between short DNA regions of accidental similarity can lead to fatal genomic rearrangements. Previous studies have probed how effectively RecA discriminates against interactions involving a short similar sequence that is embedded in otherwise dissimilar sequences but have not yielded fully conclusive results. Here, we present results of in vitro experiments with fluorescent probes strategically located on the interacting DNA fragments used for recombination. Our findings suggest that DNA synthesis increases the stability of the recombination products. Fluorescence measurements can also probe the homology dependence of the extension of invading DNA strands in D-loops formed by RecA-mediated strand exchange. We examined the slow extension of the invading strand in a D-loop by DNA polymerase (Pol) IV and the more rapid extension by DNA polymerase LF-Bsu We found that when DNA Pol IV extends the invading strand in a D-loop formed by RecA-mediated strand exchange, the extension afforded by 82 bp of homology is significantly longer than the extension on 50 bp of homology. In contrast, the extension of the invading strand in D-loops by DNA LF-Bsu Pol is similar for intermediates with \≥50 bp of homology. These results suggest that fatal genomic rearrangements due to the recombination of small regions of accidental homology may be reduced if RecA-mediated strand exchange is immediately followed by DNA synthesis by a slow polymerase.

}, keywords = {cooperativity, DNA damage, DNA polymerase, DNA recombination, double-strand break (DSB), fluorescence resonance energy transfer (FRET), heteroduplex formation, molecular dynamics, RecA, strand displacement synthesis}, doi = {10.1074/jbc.RA119.007554}, author = {Lu, Daniel and Danilowicz, Claudia and Tashjian, Tommy F and Chantal Pr{\'e}vost and Godoy, Veronica G and Prentiss, Mara} } @article {2019|2119, title = {Stability Effect of Quinary Interactions Reversed by Single Point Mutations}, journal = {Journal of the American Chemical Society}, volume = {141}, year = {2019}, pages = {4660-4669}, doi = {10.1021/jacs.8b13025}, url = {https://doi.org/10.1021/jacs.8b13025}, author = {Gnutt, David and Timr, Stepan and Ahlers, Jonas and K{\"o}nig, Benedikt and Manderfeld, Emily and Heyden, Matthias and Sterpone, Fabio and Ebbinghaus, Simon} } @article {2019|2078, title = {Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.}, journal = {Data Brief}, volume = {26}, year = {2019}, month = {2019 Oct}, pages = {104460}, abstract = {

In this work we present a novel set of possible auto-oligomerisation states of yeast protein Fzo1 in the context of membrane docking. The dataset reports atomistic models and trajectories derived from a molecular dynamics study of the yeast mitofusin Fzo1, residues 101-855. The initial modelling was followed by coarse-grained molecular dynamics simulation to evaluate the stability and the dynamics of each structural model in a solvated membrane environment. Simulations were run for 1\ μs and collected with GROMACS v5.0.4 using the martini v2.1 force field. For each structural model, the dataset comprises the production phase under semi-isotropic condition at 1\ bar, 310 K and 150 mn NaCl. The integration step is 20 fs and coordinates have been saved every 1 ns. Each trajectory is associated with a ready-available visualization state for the VMD software. These structural detailed informations are a ready-available platform to plan integrative studies on the mitofusin Fzo1 and will aid the community to further elucidate the mitochondrial tethering process during membrane fusion. This dataset is based on the publication \"Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking.\" (Brandner and De Vecchis et\ al., 2019)\".

}, issn = {2352-3409}, doi = {10.1016/j.dib.2019.104460}, author = {Brandner, Astrid and De Vecchis, Dario and Marc Baaden and Cohen, Micka{\"e}l M and Antoine Taly} } @article {2018|2135, title = {Segmentation and the Entropic Elasticity of Modular Proteins}, journal = {J Phys Chem Lett}, volume = {9}, year = {2018}, month = {Aug}, pages = {4707-4713}, abstract = {

Single-molecule force spectroscopy utilizes polyproteins, which are composed of tandem modular domains, to study their mechanical and structural properties. Under the application of external load, the polyproteins respond by unfolding and refolding domains to acquire the most favored extensibility. However, unlike single-domain proteins, the sequential unfolding of the each domain modifies the free energy landscape (FEL) of the polyprotein nonlinearly. Here we use force-clamp (FC) spectroscopy to measure unfolding and collapse-refolding dynamics of polyubiquitin and poly(I91). Their reconstructed unfolding FEL involves hundreds of kB T in accumulating work performed against conformational entropy, which dwarfs the \∼30 kB T that is typically required to overcome the free energy difference of unfolding. We speculate that the additional entropic energy caused by segmentation of the polyprotein to individual proteins plays a crucial role in defining the \"shock absorber\" properties of elastic proteins such as the giant muscle protein titin.

}, doi = {10.1021/acs.jpclett.8b01925}, author = {Berkovich, Ronen and Fernandez, Vicente I and Guillaume Stirnemann and Valle-Orero, Jessica and Fernandez, Julio M} } @article {2018|2089, title = {Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.}, journal = {J Integr Bioinform}, volume = {15}, year = {2018}, month = {2018 Jul 09}, abstract = {

The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.

}, keywords = {Computer Graphics, Humans, Imaging, Three-Dimensional, Models, Structural, Semantics, Software, Statistics as Topic, User-Computer Interface}, issn = {1613-4516}, doi = {10.1515/jib-2018-0004}, author = {Trellet, Mikael and Nicolas F{\'e}rey and Floty{\'n}ski, Jakub and Marc Baaden and Bourdot, Patrick} } @article {2018|2059, title = {A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.}, journal = {Journal of Chemical Theory and Computation}, volume = {14}, year = {2018}, pages = {6560{\textendash}6573}, abstract = {

The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making quantitative predictions of binding probabilities in environments other than dilute isotropic solution. Existing techniques, ranging from simple automated docking procedures to sophisticated thermodynamics-based methods, have been developed with soluble proteins in mind. Biologically and pharmacologically relevant protein-ligand interactions often occur in complex environments, including lamellar phases like membranes and crowded, nondilute solutions. Here, we revisit the theoretical bases of ligand binding equilibria, avoiding overly specific assumptions that are nearly always made when describing receptor-ligand binding. Building on this formalism, we extend the asymptotically exact Alchemical Free Energy Perturbation technique to quantifying occupancies of sites on proteins in a complex bulk, including phase-separated, anisotropic, or nondilute solutions, using a thermodynamically consistent and easily generalized approach that resolves several ambiguities of current frameworks. To incorporate the complex bulk without overcomplicating the overall thermodynamic cycle, we simplify the common approach for ligand restraints by using a single distance-from-bound-configuration (DBC) ligand restraint during AFEP decoupling from protein. DBC restraints should be generalizable to binding modes of most small molecules, even those with strong orientational dependence. We apply this approach to compute the likelihood that membrane cholesterol binds to known crystallographic sites on three GPCRs (β -adrenergic, 5HT-2B, and μ-opioid) at a range of concentrations. Nonideality of cholesterol in a binary cholesterol:phosphatidylcholine (POPC) bilayer is characterized and consistently incorporated into the interpretation. We find that the three sites exhibit very different affinities for cholesterol: The site on the adrenergic receptor is predicted to be high affinity, with 50\% occupancy for 1:10 CHOL:POPC mixtures. The sites on the 5HT-2B and μ-opioid receptor are predicted to be lower affinity, with 50\% occupancy for 1:10 CHOL:POPC and 1:10 CHOL:POPC, respectively. These results could not have been predicted from the crystal structures alone.

}, issn = {1549-9626}, doi = {10.1021/acs.jctc.8b00447}, author = {Salari, Reza and Joseph, Thomas and Lohia, Ruchi and J{\'e}r{\^o}me H{\'e}nin and Brannigan, Grace} } @inbook {2018|2083, title = {Structure and function of natural proteins for water transport: general discussion.}, booktitle = {Faraday Discuss}, volume = {209}, year = {2018}, month = {2018 09 28}, pages = {83-95}, keywords = {Molecular Structure, Proteins, Water}, issn = {1364-5498}, doi = {10.1039/c8fd90019a}, author = {Marc Baaden and Barboiu, Mihail and Bill, Roslyn M and Casanova, Serena and Chen, Chun-Long and Conner, Matthew and Freger, Viatcheslav and Gong, Bing and G{\'o}ra, Artur and Hinds, Bruce and Horner, Andreas and Hummer, Gerhard and Kumar, Manish and Lokesh, Mahesh and Mitra, Sushanta and Noy, Aleksandr and Pohl, Peter and Sadet, Aude and Sansom, Mark and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish} } @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|1686, title = {Smoothed biasing forces yield unbiased free energies with the extended-system Adaptive Biasing Force method}, journal = {J. Phys. Chem. B}, volume = {121}, year = {2017}, month = {dec}, pages = {3676{\textendash}3685}, doi = {10.1021/acs.jpcb.6b10055}, author = {Lesage, A. and Leli{\`e}vre, T. and Stoltz, G. and J{\'e}r{\^o}me H{\'e}nin} } @article {2017|2096, title = {String method solution of the gating pathways for a pentameric ligand-gated ion channel.}, journal = {Proc Natl Acad Sci U S A}, volume = {114}, year = {2017}, month = {2017 05 23}, pages = {E4158-E4167}, abstract = {

Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.

}, keywords = {Computer Simulation, Ligand-Gated Ion Channels, Models, Biological, Models, Chemical}, issn = {1091-6490}, doi = {10.1073/pnas.1617567114}, author = {Lev, Bogdan and Murail, Samuel and Poitevin, Fr{\'e}d{\'e}ric and Cromer, Brett A and Marc Baaden and Delarue, Marc and Allen, Toby W} } @article {2016|1447, title = {{S}alt-{E}xcluding {A}rtificial {W}ater {C}hannels {E}xhibiting {E}nhanced {D}ipolar {W}ater and {P}roton {T}ranslocation}, journal = {J. Am. Chem. Soc.}, volume = {138}, number = {16}, year = {2016}, month = {apr}, pages = {5403{\textendash}5409}, author = {Licsandru, E. and Kocsis, I. and Shen, Y. X. and Murail, S. and Legrand, Y. M. and van der Lee, A. and Tsai, D. and Marc Baaden and Kumar, M. and Barboiu, M.} } @article {2016|1550, title = {{S}ites of {A}nesthetic {I}nhibitory {A}ction on a {C}ationic {L}igand-{G}ated {I}on {C}hannel}, journal = {Structure}, volume = {24a}, number = {4}, year = {2016}, month = {apr}, pages = {595{\textendash}605}, author = {Laurent, B. and Murail, S. and Shahsavar, A. and Sauguet, L. and Delarue, M. and Marc Baaden} } @article {2016|1687, title = {Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue}, journal = {J. Phys. Chem. B}, volume = {120}, year = {2016}, pages = {2721{\textendash}2730}, abstract = {

Comparing homologous enzymes adapted to different thermal environments aids to shed light on their delicate stability/function trade-off. Protein mechanical rigidity was postulated to secure stability and high-temperature functionality of thermophilic proteins. In this work, we challenge the corresponding-state principle for a pair of homologous GTPase domains by performing extensive molecular dynamics simulations, applying conformational and kinetic clustering, as well as exploiting an enhanced sampling technique (REST2). While it was formerly shown that enhanced protein flexibility and high temperature stability can coexist in the apo hyperthermophilic variant, here we focus on the holo states of both homologues by mimicking the enzymatic turnover. We clearly show that the presence of the ligands affects the conformational landscape visited by the proteins, and that the corresponding state principle applies for some functional modes. Namely, in the hyperthermophilic species, the flexibility of the effec...

}, issn = {15205207}, doi = {10.1021/acs.jpcb.6b00306}, author = {Katava, Marina and Kalimeri, Maria and Guillaume Stirnemann and Fabio Sterpone} } @article {2016|1763, title = {Structure of ring-shaped Aβ42 oligomers determined by conformational selection}, journal = {Sci. Rep.}, volume = {6}, year = {2016}, pages = {21429}, abstract = {

The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a critical role in the pathogenesis of Alzheimer\&$\#$39;s disease. However, it has been challenging to characterize the tertiary and quaternary structures of Aβ peptides due to their disordered nature and high aggregation propensity. In this work, replica exchange molecular dynamics simulations were used to explore the conformational space of Aβ42 monomer. Among the most populated transient states, we identified a particular conformation which was able to generate ring-shaped pentamers and hexamers, when docked onto itself. The structures of these aggregates were stable during microsecond all-atom MD simulations in explicit solvent. In addition to high resolution models of these oligomers, this study provides support for the conformational selection mechanism of Aβ peptide self-assembly.

}, issn = {2045-2322}, doi = {10.1038/srep21429}, author = {Tran, Linh and Basdevant, Nathalie and Chantal Pr{\'e}vost and Ha-Duong, T{\^a}p} } @article {2015|1769, title = {Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins}, journal = {The Journal of Physical Chemistry B}, volume = {119}, number = {40}, year = {2015}, pages = {12760{\textendash}12770}, publisher = {American Chemical Society}, author = {Chakraborty, Debashree and Antoine Taly and Fabio Sterpone} } @article {2015|1641, title = {Structure/function relationships in RecA protein-mediated homology recognition and strand exchange}, journal = {Crit. Rev. Biochem. Mol. Biol.}, volume = {50}, year = {2015}, pages = {453{\textendash}76}, abstract = {RecA family proteins include RecA, Rad51, and Dmc1. These recombinases are responsible for homology search and strand exchange. Homology search and strand exchange occur during double-strand break repair and in eukaryotes during meiotic recombination. In bacteria, homology search begins when RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site to form the presynaptic filament. The filament is a right-handed helix, where the initiating strand is bound deep within the filament. Once the presynaptic filament is formed, it interrogates nearby double-stranded DNA (dsDNA) to find a homologous sequence; therefore, we provide a detailed discussion of structural features of the presynaptic filament that play important functional roles. The discussion includes many diagrams showing multiple filament turns. These diagrams illustrate interactions that are not evident in single turn structures. The first dsDNA interactions with the presynaptic filament are insensitive to mismatches. The mismatch insensitive interactions lead to dsDNA deformation that triggers a homology testing process governed by kinetics. The first homology test involves {\^a}ˆ{\textonequarter}8 bases. Almost all interactions are rejected by this initial rapid test, leading to a new cycle of homology testing. Interactions that pass the initial rapid test proceed to a slower testing stage. That slower stage induces nonhomologous dsDNA to reverse strand exchange and begin a new cycle of homology testing. In contrast, homologous dsDNA continues to extend the heteroduplex strand-exchange product until ATP hydrolysis makes strand exchange irreversible.}, keywords = {Double-strand break repair, meiosis, meiotic recombination, Rad51, recombinase}, doi = {10.3109/10409238.2015.1092943}, author = {Prentiss, Mara and Chantal Pr{\'e}vost and Danilowicz, Claudia} } @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} } @article {2013|1406, title = {{S}tructural basis for ion permeation mechanism in pentameric ligand-gated ion channels}, journal = {Embo J.}, volume = {32}, number = {5}, year = {2013}, month = {mar}, pages = {728{\textendash}741}, author = {Sauguet, L. and Poitevin, F. and Murail, S. and Van Renterghem, C. and Moraga-Cid, G. and Malherbe, L. and Thompson, A. W. and Koehl, P. and Corringer, P. J. and Marc Baaden and Delarue, M.} } @booklet {2013|1576, title = {Structural basis for ion permeation in a pentameric ligand-gated ion channel revealed by x-ray crystallograph}, year = {2013}, note = {44-45}, author = {Marc Baaden and M. Delarue} } @article {2012|1527, title = {{S}tructure-function analysis of the {NFL}-{TBS}.40-63 peptide corresponding to the binding site of tubulin on the light neurofilament subunit}, journal = {Plos One}, volume = {7}, year = {2012}, pages = {e49436}, author = {Berges, R. and Balzeau, J. and Takahashi, M. and Chantal Pr{\'e}vost and Eyer, J.} } @article {2012|1995, title = {Structural and Spectroscopic Properties of Water around Small Hydrophobic Solutes}, journal = {The Journal of Physical Chemistry B}, volume = {116}, number = {38}, year = {2012}, pages = {11695{\textendash}11700}, doi = {10.1021/jp303213m}, author = {Montagna, Maria and Sterpone, Fabio and Guidoni, Leonardo} } @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|1813, title = {Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders}, journal = {Hum. Mol. Genet.}, volume = {21}, number = {26}, year = {2012}, month = {dec}, pages = {5417{\textendash}5428}, doi = {10.1093/hmg/dds377}, author = {Katell Peoc{\textquoteright}h and Etienne Levavasseur and Emilien Delmont and Alfonso De Simone Isabelle Laffont-Proust and Nicolas Privat and Y Chebaro and C{\'e}line Chapuis Pierre Bedoucha and Jean-Philippe Brandel and Annie Laquerriere and Jean-Louis Kemeny Jean-Jacques Hauw and Michel Borg and Human Rezaei and Philippe Derreumaux Jean-Louis Laplanche and St{\'e}phane Ha{\"\i}k} } @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 {2011|1474, title = {Simulation of transient infrared spectra of a photoswitchable peptide}, journal = {J. Chem. Phys.}, volume = {135}, number = {12}, year = {2011}, month = {dec}, author = {Kobus, Maja and Lieder, Martin and Phuong Hoang Nguyen and Stock, Gerhard} } @article {2010|1456, title = {{S}equence-dependent {D}{N}{A} flexibility mediates {D}{N}ase {I} cleavage}, journal = {J. Mol. Biol.}, volume = {395}, year = {2010}, month = {jan}, pages = {123{\textendash}133}, author = {Heddi, B. and Abi-Ghanem, J. and Lavigne, M. and Hartmann, B.} } @article {2010|1977, title = {Side-chain rotamer transitions at protein-protein interfaces}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {78}, year = {2010}, pages = {3219{\textendash}25}, author = {Mainak Guharoy and Jo\�el Janin and Charles H. Robert} } @mastersthesis {2010|1570, title = {Simulations num{\'e}riques de syst{\`e}mes biologiques complexes : dynamique, structure et fonction de transporteurs, canaux et enzymes}, year = {2010}, school = {Universit{\'e} Paris-Diderot - Paris VII (15/06/2010), Fr{\'e}d{\'e}ric Dardel (Pr.)}, type = {phd}, author = {Marc Baaden} } @article {2010|1789, title = {Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye?}, journal = {Cell Adh. Migr.}, volume = {4}, number = {2}, year = {2010}, month = {apr}, pages = {313{\textendash}324}, abstract = {

As a whole, integral membrane proteins represent about one third of sequenced genomes, and more than 50\% of currently available drugs target membrane proteins, often cell surface receptors. Some membrane protein classes, with a defined number of transmembrane (TM) helices, are receiving much attention because of their great functional and pharmacological importance, such as G protein-coupled receptors possessing 7 TM segments. Although they represent roughly half of all membrane proteins, bitopic proteins (with only 1 TM helix) have so far been less well characterized. Though they include many essential families of receptors, such as adhesion molecules and receptor tyrosine kinases, many of which are excellent targets for biopharmaceuticals (peptides, antibodies, et al.). A growing body of evidence suggests a major role for interactions between TM domains of these receptors in signaling, through homo and heteromeric associations, conformational changes, assembly of signaling platforms, etc. Significantly, mutations within single domains are frequent in human disease, such as cancer or developmental disorders. This review attempts to give an overview of current knowledge about these interactions, from structural data to therapeutic perspectives, focusing on bitopic proteins involved in cell signaling.

}, keywords = {Animals, Biological, Humans, Membrane Proteins, Models, Protein Structure, Secondary, Signal Transduction, Tertiary}, issn = {1933-6926}, doi = {10.4161/cam.4.2.12430}, author = {Pierre Hubert and Paul Sawma and Jean-Pierre Duneau and Jonathan Khao and J{\'e}r{\^o}me H{\'e}nin and Dominique Bagnard and James Sturgis} } @article {2009|1495, title = {Sphere versus cylinder: the effect of packing on the structure of nonionic C12E6 micelles}, journal = {Langmuir}, volume = {25}, number = {16}, year = {2009}, pages = {8960{\textendash}7}, author = {Sterpone, Fabio and Briganti, G and Pierleoni, C} } @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} } @inbook {2008|1651, title = {Searching for Homology by Filaments of RecA-like Proteins}, booktitle = {Genome Dynamics \& Stability}, volume = {Recombination and Meiosis. Models, Means and Evolution}, number = {3}, year = {2008}, pages = {65{\textendash}89}, publisher = {Springer Verlag}, organization = {Springer Verlag}, edition = {Richard Egel and Dirk-Henner Lankenau}, address = {Berlin Heidelberg}, abstract = {

The recombinase proteins of the RecA family perform tasks that are essential for cell survival and for the maintenance of genetic diversity. They are able to rearrange genes in new combinations and to repair DNA double-strand breaks in an almost error-free fashion. Their function in homologous recombination is performed in an original way that has no equivalent in the DNA processing machinery: They form long helical filaments on a target DNA, capable of recognizing homologous DNA sequences in the genome and of exchanging DNA strands. How the DNA sequences are recognized during this process and how the DNA strands are exchanged remain matters of investigation. This chapter reviews the information that has been accumulated on recognition and strand exchange, together with the models that aim at organizing this data, viewed at different levels: that of the nucleus, the molecule, or the atom. Altogether, a picture begins to emerge on a multiscale dimension, which presents the search for homology as a complex process with important dynamic components.

}, author = {Chantal Pr{\'e}vost}, editor = {Richard Egel and Dirk Henner-Lankenau} } @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 {2008|1862, title = {Statistics of time-limited ensembles of bent DNA conformations}, journal = {J. Phys. Chem. B}, volume = {112}, number = {16}, year = {2008}, pages = {4975{\textendash}4982}, author = {Alexey K Mazur} } @article {2008|1484, title = {Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties}, journal = {J. Phys. Chem. B}, volume = {112}, number = {48}, year = {2008}, month = {dec}, pages = {15487{\textendash}15492}, author = {Backus, Ellen H. G. and Phuong Hoang Nguyen and Botan, Virgiliu and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Zerbe, Oliver and Stock, Gerhard and Hamm, Peter} } @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 {2007|1489, title = {Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study}, journal = {J. Am. Chem. Soc.}, volume = {129}, number = {5}, year = {2007}, month = {feb}, pages = {1179{\textendash}1189}, author = {Graf, Juergen and Phuong Hoang Nguyen and Stock, Gerhard and Schwalbe, Harald} } @article {2006|1842, title = {Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging}, journal = {J. Biol. Chem.}, volume = {281}, number = {4}, year = {2006}, pages = {2151{\textendash}2161}, author = {Severine Zirah and Sergey A. Kozin and Alexey K Mazur and Alain Blond and Michel Cheminant and Isabelle Segalas-Milazzo and Pascale Debey and Sylvie Rebuffat} } @article {2006|1827, title = {Structure and dynamics of hydrogen bonds in the interface of a C12E6 spherical micelle in water solution: a MD study at various temperatures}, journal = {J. Phys. Chem. B}, volume = {110}, number = {37}, year = {2006}, pages = {18254{\textendash}61}, author = {Sterpone, Fabio and Pierleoni, Carlo and Briganti, Giuseppe and Marchi, Massimo} } @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|1539, title = {Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {60}, number = {3}, year = {2005}, month = {aug}, pages = {485{\textendash}494}, author = {Phuong Hoang Nguyen and Mu, YG and Stock, G} } @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|1778, title = {Single-stranded breaks relax intrinsic curvature in {DNA}?}, journal = {Biochemistry}, volume = {43}, number = {25}, year = {2004}, pages = {8160{\textendash}8168}, author = {Dimitri E. Kamashev and Alexey K Mazur} } @article {2004|1404, title = {Squash inhibitors: From structural motifs to macrocyclic knottins}, journal = {Current Protein \& Peptide Science}, volume = {5}, number = {5}, year = {2004}, pages = {341{\textendash}349}, author = {Chiche, L and Heitz, A and Gelly, JC and Gracy, J and Chau, PTT and Ha, PT and Hernandez, JF and Le-Nguyen, D} } @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|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} } @conference {2002|1502, title = {Spatial order in liquid crystals: Computer simulations of systems of ellipsoids}, booktitle = {MORPHOLOGY OF CONDENSED MATTER: PHYSICS AND GEOMETRY OF SPATIALLY COMPLEX SYSTEMS}, series = {Lecture Notes in Physics}, volume = {600}, year = {2002}, note = {2nd International Wuppertal Workshop on Statistical Physics and Spatial Statistics, UNIV WUPPERTAL, WUPPERTAL, GERMANY, MAR 05-09, 2001}, pages = {172{\textendash}186}, author = {Schmid, F and Phuong, NH}, editor = {Mecke, K and Stoyan, D} } @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|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 {2001|1841, title = {Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution}, journal = {J. Biol. Chem.}, volume = {276}, number = {49}, year = {2001}, pages = {46364{\textendash}46370}, author = {S. A. Kozin and G. Bertho and Alexey K Mazur and H. Rabesona and J. P. Girault and T. Haertle and M. Takahashi and P. Debey and G. H. Hoa} } @conference {2000|1532, title = {Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores}, booktitle = {Proceedings of the Euradwaste 1999 conference}, year = {2000}, pages = {390{\textendash}393}, address = {EC, Luxembourg}, author = {Marc Baaden and F. Berny and N. Muzet and R. Schurhammer and G. Wipff}, editor = {C. Davies} } @article {1999|1845, title = {Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion}, journal = {J. Chem. Phys.}, volume = {111}, number = {4}, year = {1999}, pages = {1407{\textendash}1414}, author = {Alexey K Mazur} } @article {1998|1453, title = {{S}ymmetry and chirality in topoisomerase {I}{I}-{D}{N}{A} crossover recognition}, journal = {J. Mol. Biol.}, volume = {284}, year = {1998}, month = {dec}, pages = {1289{\textendash}1299}, author = {Y Timsit and Duplantier, B. and Jannink, G. and Sikorav, J.L.} } @article {1998|1822, title = {A soft, mean{\textendash}field potential derived from crystal contacts for predicting protein{\textendash}protein interactions}, journal = {J. Mol. Biol.}, volume = {283}, number = {5}, year = {1998}, month = {nov}, pages = {1037{\textendash}1047}, author = {Robert, C H and Janin, J} } @article {1995|1452, title = {{S}elf-fitting and self-modifying properties of the {B}-{D}{N}{A} molecule}, journal = {J. Mol. Biol.}, volume = {251}, year = {1995}, month = {sep}, pages = {629{\textendash}647}, author = {Y Timsit and Moras, D.} } @article {1995|1969, title = {Significance of bound water to local chain conformations in protein crystals}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {92}, number = {16}, year = {1995}, month = {aug}, pages = {7600{\textendash}7604}, author = {Robert, C H and Ho, P S} } @article {1995|1941, title = {Solution structure of oligonucleotides covalently linked to a psoralen derivative.}, journal = {Nucleic Acids Res.}, volume = {23}, number = {5}, year = {1995}, month = {mar}, pages = {788{\textendash}795}, abstract = {

Psoralen (pso) was attached via its C-5 position to the 5\&$\#$39;-phosphate group of an oligodeoxynucleotide d(TAAGCCG) by a hexamethylene linker (m6). Complex formation between pso-m6-d(TAAGCCG) and the complementary strands d(CGGCTTA)[7-7mer] or d(CGGCTTAT)[7-8mer] was investigated by nuclear magnetic resonance in aqueous solution. Structural informations derived from DQF-COSY and NOESY maps, revealed that the mini double helix adopts a B-form conformation and that the deoxyriboses preferentially adopt a C2\&$\#$39;-endo conformation. The nOe connectivities observed between the protons of the bases or the sugars in each duplex, and the protons of the psoralen and the hexamethylene chain, led us to propose a model involving an equilibrium between two conformations due to different locations of the psoralen. Upon UV-irradiation, the psoralen moiety cross-linked the two DNA strands at the level of 5\&$\#$39;TpA3\&$\#$39; sequences. NMR studies of the single major photo-cross-linked duplex pso-m6-d(TAAGCCG) and d(CGGCTTA) were performed. The stereochemistry of the diadduct is indeed cis-syn at both cyclobutane rings. In addition, the effects of this diadduct on the helical structure are analyzed in detail.

}, keywords = {Base Sequence, chemistry, chemistry/radiation effects, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Psoralens, Solutions}, author = {O. Bornet and Chantal Pr{\'e}vost and F. Vovelle and M. Chassignol and N. T. Thuong and G. Lancelot} } @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 {1992|1697, title = {Schematic methods for probabilistic enzyme kinetics}, journal = {J. Theor. Biol.}, volume = {155}, year = {1992}, pages = {387{\textendash}407}, author = {Alexey K Mazur and A. V. Kuchinski} } @inbook {1989|1579, title = {Stereospecific Ion-Molecule reactions in the collision cell induced by nucleophilic gas phase reagents on CI/NH4+ protonated diastereoisomeric tetracyclic terpenes.}, booktitle = {Advances in Mass Spectrometry}, volume = {11}, year = {1989}, pages = {1056}, edition = {P. Longevialle, Heyden and Son, Ed, New York}, author = {Cole, RB and Chantal Pr{\'e}vost and Tabet, JC} } @article {1986|1595, title = {A study of interaction of an O-specific polysaccharide from Pseudomonas fluorescense with antibodies}, journal = {Bioorg. Chem.}, volume = {12}, year = {1986}, pages = {265{\textendash}272}, author = {T. F. Solovjeva and G. A. Naberezhnykh and Alexey K Mazur and V. A. Khomenko and Yu. S. Ovodov} }