@article {2022|2159, title = {Design {\textendash} a new way to look at old molecules}, journal = {Journal of Integrative Bioinformatics}, volume = {19}, year = {2022}, pages = {20220020}, doi = {doi:10.1515/jib-2022-0020}, url = {https://doi.org/10.1515/jib-2022-0020}, author = {Davide Spalvieri and Anne-Marine Mauviel and Matthieu Lambert and Nicolas F{\'e}rey and S Sacquin-Mora and Matthieu Chavent and Marc Baaden} } @article {2020|2130, title = {Direct Homologous dsDNA-dsDNA Pairing: How, Where, and Why?}, journal = {J Mol Biol}, volume = {432}, year = {2020}, month = {2020 Feb 07}, pages = {737-744}, abstract = {

The ability of homologous chromosomes (or selected chromosomal loci) to pair specifically in the apparent absence of DNA breakage and recombination represents a prominent feature of eukaryotic biology. The mechanism of homology recognition at the basis of such recombination-independent pairing has remained elusive. A number of studies have supported the idea that sequence homology can be sensed between intact DNA double helices in vivo. In particular, recent analyses of the two silencing phenomena in fungi, known as \"repeat-induced point mutation\" (RIP) and \"meiotic silencing by unpaired DNA\" (MSUD), have provided genetic evidence for the existence of the direct homologous dsDNA-dsDNA pairing. Both RIP and MSUD likely rely on the same search strategy, by which dsDNA segments are matched as arrays of interspersed base-pair triplets. This process is general and very efficient, yet it proceeds normally without the RecA/Rad51/Dmc1 proteins. Further studies of RIP and MSUD may yield surprising insights into the function of DNA in the cell.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2019.11.005}, author = {Mazur, Alexey K and Nguyen, Tinh-Suong and Gladyshev, Eugene} } @article {2019|2070, title = {Design games and game design: Relations between design, codesign and serious games in adult education}, journal = {From UXD to LivXD: Living eXperience Design}, year = {2019}, pages = {229{\textendash}253}, author = {Alvarez, Julian and Irrmann, Olivier and Djaouti, Damien and Antoine Taly and Rampnoux, Olivier and Sauv{\'e}, Louise} } @article {2018|2134, title = {DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43}, journal = {J Phys Chem Lett}, volume = {9}, year = {2018}, month = {Jul}, pages = {3800-3807}, abstract = {

Understanding the molecular mechanisms governing protein-nucleic acid interactions is fundamental to many nuclear processes. However, how nucleic acid binding affects the conformation and dynamics of the substrate protein remains poorly understood. Here we use a combination of single molecule force spectroscopy AFM and biochemical assays to show that the binding of TG-rich ssDNA triggers a mechanical switch in the RRM1 domain of TDP-43, toggling between an entropic spring devoid of mechanical stability and a shock absorber bound-form that resists unfolding forces of \∼40 pN. The fraction of mechanically resistant proteins correlates with an increasing length of the TG n oligonucleotide, demonstrating that protein mechanical stability is a direct reporter of nucleic acid binding. Steered molecular dynamics simulations on related RNA oligonucleotides reveal that the increased mechanical stability fingerprinting the holo-form is likely to stem from a unique scenario whereby the nucleic acid acts as a \"mechanical staple\" that protects RRM1 from mechanical unfolding. Our approach highlights nucleic acid binding as an effective strategy to control protein nanomechanics.

}, doi = {10.1021/acs.jpclett.8b01494}, author = {Wang, Yong Jian and Rico-Lastres, Palma and Lezamiz, Ainhoa and Mora, Marc and Solsona, Carles and Guillaume Stirnemann and Garcia-Manyes, Sergi} } @article {2018|2093, title = {Dystrophin{\textquoteright}s central domain forms a complex filament that becomes disorganized by in-frame deletions.}, journal = {J Biol Chem}, volume = {293}, year = {2018}, month = {2018 05 04}, pages = {6637-6646}, abstract = {

Dystrophin, encoded by the gene, is critical for maintaining plasma membrane integrity during muscle contraction events. Mutations in the gene disrupting the reading frame prevent dystrophin production and result in severe Duchenne muscular dystrophy (DMD); in-frame internal deletions allow production of partly functional internally deleted dystrophin and result in less severe Becker muscular dystrophy (BMD). Many known BMD deletions occur in dystrophin\&$\#$39;s central domain, generally considered to be a monotonous rod-shaped domain based on the knowledge of spectrin family proteins. However, the effects caused by these deletions, ranging from asymptomatic to severe BMD, argue against the central domain serving only as a featureless scaffold. We undertook structural studies combining small-angle X-ray scattering and molecular modeling in an effort to uncover the structure of the central domain, as dystrophin has been refractory to characterization. We show that this domain appears to be a tortuous and complex filament that is profoundly disorganized by the most severe BMD deletion (loss of exons 45-47). Despite the preservation of large parts of the binding site for neuronal nitric oxide synthase (nNOS) in this deletion, computational approaches failed to recreate the association of dystrophin with nNOS. This observation is in agreement with a strong decrease of nNOS immunolocalization in muscle biopsies, a parameter related to the severity of BMD phenotypes. The structural description of the whole dystrophin central domain we present here is a first necessary step to improve the design of microdystrophin constructs toward the goal of a successful gene therapy for DMD.

}, keywords = {Binding Sites, Dystrophin, Exons, Gene Deletion, Humans, Molecular Docking Simulation, Muscular Dystrophy, Duchenne, Nitric Oxide Synthase Type I, Protein Domains, Reading Frames, Scattering, Small Angle, Solutions, X-Ray Diffraction}, issn = {1083-351X}, doi = {10.1074/jbc.M117.809798}, author = {Delalande, Olivier and Molza, Anne-Elisabeth and Dos Santos Morais, Raphael and Ch{\'e}ron, Ang{\'e}lique and Pollet, {\'E}meline and Raguenes-Nicol, C{\'e}line and Tascon, Christophe and Giudice, Emmanuel and Guilbaud, Marine and Nicolas, Aur{\'e}lie and Bondon, Arnaud and Leturcq, France and Nicolas F{\'e}rey and Marc Baaden and Perez, Javier and Roblin, Pierre and Pi{\'e}tri-Rouxel, France and Hubert, Jean-Fran{\c c}ois and Czjzek, Mirjam and Le Rumeur, Elisabeth} } @article {2017|2020, title = {Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {May}, pages = {1858}, author = {Colloc{\textquoteright}h, N. and S Sacquin-Mora and Avella, G. and Dhaussy, A. C. and Prange, T. and Vallone, B. and Girard, E.} } @article {2016|1712, title = {Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation}, journal = {J. Phys. Chem. B}, volume = {120}, number = {47}, year = {2016}, pages = {12111{\textendash}12126}, abstract = {Amyloid beta (A beta) oligomerization is associated with the origin and progression of Alzheimer{\textquoteright}s disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T A beta(40) dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V A beta(40) dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel beta-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded beta-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded beta-sheet or inhibiting the formation of an interpeptide beta-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of A beta species.}, issn = {1520-6106}, doi = {10.1021/acs.jpcp.6b10722}, author = {Phuong Hoang Nguyen and Fabio Sterpone and Pouplana, Ramon and Philippe Derreumaux and Campanera, Josep M.} } @article {2015|1766, title = {Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key}, journal = {Structure}, volume = {23}, number = {8}, year = {2015}, month = {aug}, pages = {1373{\textendash}1374}, doi = {10.1016/j.str.2015.07.004}, author = {S Sacquin-Mora and Chantal Pr{\'e}vost} } @article {2014|1951, title = {DNA flexibility on short length scales probed by atomic force microscopy}, journal = {Phys. Rev. Lett.}, volume = {112}, year = {2014}, pages = {068104}, author = {Alexey K Mazur and Mounir Maaloum} } @article {2013|1904, title = {Density functional conformational study of 2-O-sulfated 3,6 anhydro-alpha-D-galactose and of neo-kappa- and iota-carrabiose molecules in gas phase and water}, journal = {J. Mol. Model.}, volume = {19}, number = {2}, year = {2013}, month = {feb}, pages = {893{\textendash}904}, doi = {10.1007/s00894-012-1621-y}, author = {Bestaoui-Berrekhchi-Berrahma, Noreya and Philippe Derreumaux and Sekkal-Rahal, Majda and Springborg, Michael and Sayede, Adlane and Yousfi, Noureddine and Kadoun, Abd-Ed-Daim} } @article {2012|1911, title = {Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts}, journal = {J. Pept. Sci.}, volume = {18}, number = {1}, year = {2012}, month = {sep}, pages = {S38}, author = {Thevenet, P. and Shen, Y. and Maupetit, J. and Guyon, F. and Padilla, A. and Philippe Derreumaux and Pierre Tuffery} } @article {2012|1922, title = {Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N)}, journal = {J. Phys. Chem. B}, volume = {116}, number = {13}, year = {2012}, month = {apr}, pages = {4043{\textendash}4055}, doi = {10.1021/jp2126366}, author = {Cote, Sebastien and Laghaei, Rozita and Philippe Derreumaux and Mousseau, Normand} } @article {2011|1857, title = {{D}iscrimination of agonists versus antagonists of nicotinic ligands based on docking onto {A}{C}h{B}{P} structures}, journal = {J. Mol. Graph. Model.}, volume = {30}, year = {2011}, month = {sep}, pages = {100{\textendash}109}, author = {Antoine Taly and Colas, C. and Malliavin, T. and Blondel, A. and Nilges, M. and Corringer, P. J. and Joseph, D.} } @article {2011|1890, title = {Distinct Morphologies for Amyloid Beta Protein Monomer: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N)}, journal = {J. Chem. Theory Comput.}, volume = {7}, number = {8}, year = {2011}, month = {aug}, pages = {2584{\textendash}2592}, doi = {10.1021/ct1006967}, author = {Cote, Sebastien and Philippe Derreumaux and Mousseau, Normand} } @article {2011|1690, title = {Dynamics of water in concentrated solutions of amphiphiles: Key roles of local structure and aggregation}, journal = {J. Phys. Chem. B}, volume = {115}, year = {2011}, pages = {3254{\textendash}3262}, abstract = {

Water translational and reorientational dynamics in concentrated solutions of amphiphiles are investigated through molecular dynamics simulations and analytic modeling. We evidence the critical importance of the solute concentration in determining the magnitude of the slowdown in water dynamics compared to the bulk situation. The comparison of concentrated aqueous solutions of tetramethylurea, which tends to aggregate, and of trimethylamine N-oxide, which does not, shows the dramatic impact of solute clustering on the water dynamics. No significant decoupling of the reorientation and translation dynamics of water is observed, even at very high solute concentrations. The respective roles of energetic and topological disorders in determining the translational subdiffusive water dynamics in these confining environments are discussed. The water reorientational dynamics is shown to be quantitatively described by an extended jump model which combines two factors determined by the local structure: the transition-state excluded volume and the transition-state hydrogen-bond strength.

}, issn = {15206106}, author = {Guillaume Stirnemann and Fabio Sterpone and Laage, Damien} } @article {2010|1510, title = {{D}{N}{A} structures from phosphate chemical shifts}, journal = {Nucleic Acids Res.}, volume = {38}, year = {2010}, month = {jan}, pages = {e18}, author = {Abi-Ghanem, J. and Heddi, B. and Foloppe, N. and Hartmann, B.} } @article {2010|1696, title = {Direct evidence of angular jumps during water reorientation through two-dimensional infrared anisotropy}, journal = {J. Phys. Chem. Lett.}, volume = {1}, year = {2010}, pages = {1511{\textendash}1516}, abstract = {

Water reorientation was recently suggested via simulations to proceed through large angular jumps, but direct experimental evidence has so far remained elusive. Here we show that both infrared pump-probe and photon echo spectroscopies can provide such evidence through the measurement of the two-dimensional anisotropy decay. We calculate these two-dimensional anisotropies from simulations and show they can be interpreted as a vibrational frequency-dependent resolved orientation time-correlation function. We develop a frequency-dependent extended jump model to predict the nature of the angular jump signature in these anisotropies. This model provides a rigorous and unambiguous connection between ultrafast infrared experimental results and the presence of angular jumps in bulk water, and calls for new experiments.

}, issn = {19487185}, doi = {10.1021/jz100385r}, author = {Guillaume Stirnemann and Laage, Damien} } @article {2009|1636, title = {Deforming DNA: from physics to biology}, journal = {Chemphyschem}, volume = {10}, year = {2009}, month = {jul}, pages = {1399{\textendash}404}, abstract = {

The DNA double helix has become a modern icon which symbolizes our understanding of the molecular basis of life. It is less widely recognized that the double helix proposed by Watson and Crick more than half a century ago is a remarkably adaptable molecule that can undergo major conformational rearrangements without being irreversibly damaged. Indeed, DNA deformation is an intrinsic feature of many of the biological processes in which it is involved. Over the last two decades, single-molecule experiments coupled with molecular modeling have transformed our understanding of DNA flexibility, while the accumulation of high-resolution structures of DNA-protein complexes have demonstrated how organisms can exploit this property as a useful feature for preserving, reading, replicating, and packaging the genetic message. In this Minireview we summarize the information now available on the extreme\–and the less extreme\–deformations of the double helix.

}, doi = {10.1002/cphc.200900253}, author = {Chantal Pr{\'e}vost and M. Takahashi and Richard Lavery} } @article {2009|1394, title = {Disulfide bond substitution by directed evolution in an engineered binding-protein scaffold.}, journal = {Chembiochem}, volume = {10}, year = {2009}, pages = {1349{\textendash}1359}, author = {Antoine Drevelle and Agathe Urvoas and M{\'e}riam Ben Hamida-Rebai and G{\'e}rard Van Vooren and Magali Nicaise and Marie Valerio-Lepiniec and Michel Desmadril and Charles H. Robert and Philippe Minard} } @article {2008|1603, title = {Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF}, journal = {Biophys. J.}, volume = {94}, number = {3}, year = {2008}, pages = {832{\textendash}839}, abstract = {The glycerol uptake facilitator, GlpF, a major intrinsic protein found in Escherichia coli, selectively conducts water and glycerol across the inner membrane. The free energy landscape characterizing the assisted transport of glycerol by this homotetrameric aquaglyceroporin has been explored by means of equilibrium molecular dynamics over a timescale spanning 0.12 micros. To overcome the free energy barriers of the conduction pathway, an adaptive biasing force is applied to the glycerol molecule confined in each of the four channels. The results illuminate the critical role played by intramolecular relaxation on the diffusion properties of the permeant. These free energy calculations reveal that glycerol tumbles and isomerizes on a timescale comparable to that spanned by its adaptive-biasing-force-assisted conduction in GlpF. As a result, reorientation and conformational equilibrium of glycerol in GlpF constitute a bottleneck in the molecular simulations of the permeation event. A profile characterizing the position-dependent diffusion of the permeant has been determined, allowing reaction rate theory to be applied for investigating conduction kinetics based on the measured free energy landscape.}, keywords = {Aquaporins, Chemical, Computer Simulation, Diffusion, Escherichia coli Proteins, Glycerol, Ion Channel Gating, Models, Molecular, Molecular Conformation, Porosity}, doi = {10.1529/biophysj.107.115105}, author = {J{\'e}r{\^o}me H{\'e}nin and Emad Tajkhorshid and Klaus Schulten and Christophe Chipot} } @article {2008|1434, title = {Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach}, journal = {J Chem Theo Comp}, volume = {4}, number = {9}, year = {2008}, pages = {1428{\textendash}1434}, author = {Sterpone, Fabio and Spanu, Leonardo and Ferraro, Luca and Sorella, Sandro and Guidoni, Leonardo} } @article {2008|1695, title = {Does water condense in hydrophobic cavities? A molecular simulation study of hydration in heterogeneous nanopores}, journal = {J. Phys. Chem. C}, volume = {112}, year = {2008}, pages = {10435{\textendash}10445}, author = {Cailliez, Fabien and Guillaume Stirnemann and Boutin, Anne and Demachy, Isabelle and Fuchs, Alain H.} } @article {2007|2001, title = {{D}ocking of alpha-cobratoxin suggests a basal conformation of the nicotinic receptor}, journal = {Biochem. Biophys. Res. Commun.}, volume = {359}, number = {3}, year = {2007}, month = {aug}, pages = {413{\textendash}418}, publisher = {Academic Press}, author = {Konstantakaki, M. and Jean-Pierre Changeux and Antoine Taly} } @article {2007, title = {Dihedral angle principal component analysis of molecular dynamics simulations}, journal = {J. Chem. Phys.}, volume = {126}, number = {24}, year = {2007}, month = {jun}, author = {Altis, Alexandros and Phuong Hoang Nguyen and Hegger, Rainer and Stock, Gerhard} } @article {2005|1979, title = {Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {61}, number = {4}, year = {2005}, month = {dec}, pages = {732{\textendash}740}, doi = {10.1002/prot.20698}, author = {Pierre Tuffery and Philippe Derreumaux} } @conference {2004|1420, title = {A Distributed Multimedia Database Visualization within An Immersive Environment for Bioinformatics}, booktitle = {International Symposium on Multimedia Software Engineering (ISMSE 2004 - IEEE)}, year = {2004}, month = {dec}, pages = {156{\textendash}159}, address = {Miami - USA}, author = {Nicolas F{\'e}rey and P.-E. Gros and J. H{\'e}risson and R. Gherbi} } @conference {2004|1425, title = {DNA in Virtuo: Visualization and Exploration of 3D Genomic Structures}, booktitle = {International Conference on Virtual Reality, Computer Graphics, Visualization and Interaction (Afrigraph 2005 - ACM-SIGRAPH sponsored)}, year = {2004}, month = {nov}, address = {Stellenbosch (Cap town), South Africa}, author = {J. H{\'e}risson and P.-E. Gros and Nicolas F{\'e}rey and O. Magneau and R. Gherbi} } @conference {2004|1419, title = {DNA in Virtuo: Visualization and Virtual Manipulation of 3D Genomic Structures}, booktitle = {International CODATA Conference, The Information Society: New Horizons for Science}, year = {2004}, month = {nov}, address = {Berlin, Germany}, author = {J. H{\'e}risson and P.-E. Gros and Nicolas F{\'e}rey and O. Magneau and R. Gherbi} } @article {2003|1663, title = {Docking macromolecules with flexible segments}, journal = {J. Comput. Chem.}, volume = {24}, year = {2003}, month = {nov}, pages = {1910{\textendash}20}, abstract = {

We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA.

}, doi = {10.1002/jcc.10329}, author = {Bastard, Karine and Thureau, Aur{\'e}lien and Richard Lavery and Chantal Pr{\'e}vost} } @article {2002|1790, title = {Differential core histone binding behavior: {R}{N}{A} polymerase {I} promoter region vs 5{S} r{D}{N}{A} positioning {D}{N}{A} sequences}, journal = {Cell Biochem. Biophys.}, volume = {37}, number = {1}, year = {2002}, pages = {1{\textendash}13}, author = {Georgel, Philippe T and Robert, Charles H} } @article {2002|1402, title = {The direct correlation function in nematic liquid crystals from computer simulation}, journal = {Comput. Phys. Commun.}, volume = {147}, number = {1-2}, year = {2002}, note = {Europhysics Conference on Computational Physics (CCP 2001), AACHEN, GERMANY, SEP 05-08, 2001}, month = {aug}, pages = {350{\textendash}353}, author = {Phuong, NH and Germano, G and Schmid, F} } @article {2002|1837, title = {{DNA} dynamics in a water drop without counterions}, journal = {J. Am. Chem. Soc.}, volume = {124}, number = {49}, year = {2002}, pages = {14707{\textendash}14715}, author = {Alexey K Mazur} } @article {2001|1823, title = {Dynamics of hydration in hen egg white lysozyme}, journal = {J. Mol. Biol.}, volume = {311}, number = {2}, year = {2001}, month = {aug}, pages = {409{\textendash}19}, abstract = {We investigate the hydration dynamics of a small globular protein, hen egg-white lysozyme. Extensive simulations (two trajectories of 9 ns each) were carried out to identify the time-scales and mechanism of water attachment to this protein. The location of the surface and integral water molecules in lysozyme was also investigated. Three peculiar temporal scales of the hydration dynamics can be discerned: two among these, with sub-nanosecond mean residence time, tau(w), are characteristic of surface hydration water; the slower time-scale (tau(w) approximately 2/3 ns) is associated with buried water molecules in hydrophilic pores and in superficial clefts. The computed tau(w) values in the two independent runs fall in a similar range and are consistent with each other, thus adding extra weight to our result. The tau(w) of surface water obtained from the two independent trajectories is 20 and 24 ps. In both simulations only three water molecules are bound to lysozyme for the entire length of the trajectories, in agreement with nuclear magnetic relaxation dispersion estimates. Locations other than those identified in the protein crystal are found to be possible for these long-residing water molecules. The dynamics of the hydration water molecules observed in our simulations implies that each water molecule visits a multitude of residues during the lifetime of its bound with the protein. The number of residues seen by a single water molecule increases with the time-scale of its residence time and, on average, is equal to one only for the water molecules with shorter residence time. Thus, tau(w) values obtained from inelastic neutron scattering and based on jump-diffusion models are likely not to account for the contribution of water molecules with longer residence time.}, doi = {10.1006/jmbi.2001.4860}, author = {Sterpone, F and Ceccarelli, M and Marchi, M} } @article {2000|1501, title = {Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X}, journal = {Mol. Phys.}, volume = {98}, number = {6}, year = {2000}, month = {mar}, pages = {329{\textendash}342}, author = {Marc Baaden and Granger, P and Strich, A} } @article {1999|1455, title = {{D}{N}{A} structure and polymerase fidelity}, journal = {J. Mol. Biol.}, volume = {293}, year = {1999}, month = {nov}, pages = {835{\textendash}853}, author = {Y Timsit} } @article {1998|1454, title = {{D}{N}{A} crossovers and type {I}{I} {D}{N}{A} topoisomerases: {A} thermodynamical study}, journal = {J. Mol. Biol.}, volume = {284}, year = {1998}, month = {dec}, pages = {1279{\textendash}1287}, author = {Sikorav, J.L. and Duplantier, B. and Jannink, G. and Y Timsit} } @article {1997|1871, title = {A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain .1. Formulation and test on a hexadecapeptide}, journal = {J. Chem. Phys.}, volume = {106}, number = {12}, year = {1997}, month = {mar}, pages = {5260{\textendash}5270}, doi = {10.1063/1.473525}, author = {Philippe Derreumaux} } @article {1997|1819, title = {Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: An internal coordinate molecular modeling study}, journal = {J. Biomol. Struct. Dyn.}, volume = {14}, number = {6}, year = {1997}, month = {jun}, pages = {703{\textendash}714}, abstract = {

A trans-diamminedichloroplatinum(II) (trans-DDP) intrastrand adduct within the sequence d(TCTG*TG*TC).d(GACACAGA) (where G* represents a platinated guanine) is modeled on the basis of qualitative experimental data concerning global unwinding and curvature as well as information on base pairing. Modeling is performed using the internal coordinate JUMNA program, specific to nucleic acids, and modified to include the possibility of covalently bound ligands. Calibration of the energy functions representing the Pt-N7 bond with guanine is described. The platinum atom and the platinum-nitrogen bonds are parameterized for use in the H{\"u}ckel Del Re method to calculate monopoles at each atom. These monopoles are consistent with the Flex force field included in Jumna. By developing an appropriate minimization protocol we are able to generate stable, distorted three-dimensional structures compatible with the experimental data and including an unusually high global unwinding. No a priori geometric assumptions are made in generating these structures.

}, doi = {10.1080/07391102.1997.10508173}, author = {Chantal Pr{\'e}vost and Boudvillain, M and Beudaert, P and Leng, M and Lavery, R and Vovelle, F} } @article {1994, title = {{D}{N}{A} self-fitting: the double helix directs the geometry of its supramolecular assembly}, journal = {Embo J.}, volume = {13}, year = {1994}, month = {jun}, pages = {2737{\textendash}2746}, author = {Y Timsit and Moras, D.} } @article {1991|1683, title = {Derivation and testing of explicit equations of motion for polymers described by internal coordinates}, journal = {J. Comput. Phys.}, volume = {92}, year = {1991}, pages = {261{\textendash}272}, author = {Alexey K Mazur and Vladimir E. Dorofeyev and Ruben A. Abagyan} } @article {1985|1855, title = {Dry deposition of nitric acid to grass}, journal = {J. Geophys. Res.}, volume = {90}, year = {1985}, pages = {2085{\textendash}2090}, author = {B. A. Huebert and C. H. Robert} }