On the Characterization and Selection of Diverse Conformational Ensembles, with Applications to Flexible Docking

To address challenging flexible docking problems, a number of docking algorithms pre-generate large collections of candidate conformers. To remove the redundancy from such ensembles, a central problem in this context is to report a selection of conformers maximizing some geometric diversity criterion. We make three contributions to this problem. First, we resort to geometric optimization so as to report selections maximizing the molecular volume or molecular surface area (MSA) of the selection. Greedy strategies are developed, together with approximation bounds. Second, to assess the efficacy of our algorithms, we investigate two conformer ensembles corresponding to a flexible loop of four protein complexes. By focusing on the MSA of the selection, we show that our strategy matches the MSA of standard selection methods, but resorting to a number of conformers between one and two orders of magnitude smaller. This observation is qualitatively explained using the Betti numbers of the union of balls of the selection. Finally, we replace the conformer selection problem in the context of multiple-copy flexible docking. On the afore-mentioned systems, we show that using the loops selected by our strategy can improve the result of the docking process

Optimizing the Design of Oligonucleotides for Homology Directed Gene Targeting

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

Etude physico-chimique de nouveaux tensioactifs fonctionnalisés complexants au comportement démixant thermoréversible (application à l'extraction de l'uranyle)

De nouveaux tensioactifs fonctionnalisés associant un bloc complexant dérivé d'acide aminé et un bloc tensioactif thermoréversible polyéthoxylé (CiEj) ont été synthétisés et étudiés. En solution aqueuse, ces molécules conservent les propriétés de tensioactif thermoréversible du bloc CiEj, et la propriété de complexation du cation uranyle par le ligand diamide.Le bloc complexant apporte une contribution hydrophile aux composés avec une augmentation de leur surface par tête. En solution aqueuse diluée, ces composés s auto-associent en micelles sphériques, caractérisées par diffusion de rayons X et de neutrons aux petits angles. A forte concentration, l auto-association conduit à des structures de courbures plus faibles que les CiEj précurseurs.Le complexe formé avec le nitrate d'uranyle en solution aqueuse a été caractérisé par RMN et spectrométrie de masse electrospray : il est de stœchiométrie 1:1 et possède deux ligands nitrate ; la constante de complexation associée, très faible, a été évaluée. L'effet de sels de nitrate à fortes concentrations a été étudié notamment avec LiNO3 utilisé pour déplacer l'équilibre de complexation. Les nitrates d'alcalins induisent des variations de point de trouble semblables pour les tensioactifs fonctionnalisés et les CiEj.La complexation du nitrate d uranyle provoque une diminution du point de trouble associée à une diminution de surface par tête. L effet diminue quand le volume polaire du CiEj précurseur augmente. Les tests d'extractions par point de trouble démontrent l'efficacité des tensioactifs fonctionnalisés et l'intérêt du couplage covalent d'un bloc complexant et d'un bloc tensioactif.New thermosensitive functionalized surfactants with metal-chelating properties have been developed and their physical-chemistry studied. They associate a polyethoxylated nonionic surfactant (CiEj) block and a amino-acid residue as a chelating group. Functionalization preserves both properties of the thermosensitive surfactant moiety and the chelating group, a diamide closed to uranyl ionophore.The complexing group participates to the polar head group of the surfactant, increasing the area per molecule. As a result, functionalized surfactants form spherical micelles when diluted in water, and the concentrated part of their phase diagrams exhibits structures having higher curvatures than the nonionic precursor CiEj.The structure of the uranyl - diamide complex has been elucidated by NMR and ESI-MS and is of the type UO2(NO3)2.L; the associated complexation constant, which is very low, has been evaluated by 1H NMR.A nitrate salt, LiNO3, is added at high concentration to improve complexation. The effect of this salt has been analyzed, and was found to be rather similar to the effect on classical CiEj.When uranyl nitrate complexation occurs, the cloud point decreases dramatically, together with the reduction of the area per head group at micelle / solution interface. This effect can be minimized by using a nonionic precursor having a larger polar head group. The functionalized surfactants have been tested in the cloud point extraction of uranyl nitrate, and have proved their efficiency. Those results demonstrate the viability of the functionalized surfactants design, with a covalent link between a thermosensitive surfactant block and a chelating group.VERSAILLES-BU Sciences et IUT (786462101) / SudocSudocFranceF

Assemblage flexible de macromolécules (la théorie du champ moyen appliquée au remodelage des boucles protéiques)

PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination

International audienc

Chemical analysis of vegetable oils obtained from commercial frying process

International audienc

Identification of linoleic acid geometrical isomers in frying oils

International audienc

Etat d'alteration de quelques huiles de friture prelevees en restauration

National audienc

Chemical analysis of vegetable oils obtained from commercial frying process

International audienc