Parallel Processing of Complex Biomolecular Information: Combining Experimental and Computational Approaches

International audienc

Services publics en réseau : perspectives de concurrence et nouvelles régulations. Rapport du groupe présidé par Jean Bergougnoux

Organisé en quatre chapitres sectoriels consacrés respectivement à l'électricité, au gaz, au transport ferroviaire et au secteur postal, complétés par le retour d'expérience du secteur des télécommunications, cet ouvrage met en évidence, au-delà des spécificités, des similitudes dans les interrogations auxquelles ces divers secteurs vont devoir répondre au cours des prochaines années du fait de la fin des monopoles publics par l'introduction de la concurrence. Pour les secteurs considérés, le rapport identifie les facteurs déterminants de leur organisation, tente de dessiner ce que sera l'Europe pour chacun, formule les questions et problèmes posés pour leur régulation, évoque la question des relations de l'Etat avec ces entreprises publiques, celle des instruments de mesure de la performance.réseau de distribution d'électricité ; réseau de distribution de gaz ; réseau de transport ferroviaire ; services postaux ; service public ; réseau de télécommunications ; concurrence ; marché européen ; réforme; régulation ; libéralisation

TAILOR-MADE BIOCATALYSTS: COMBINING THERMODYNAMICS, ORGANIC SYNTHESIS, MOLECULAR BIOLOGY, BIOCHEMISTRY AND MICROBIOLOGY FOR THE DESIGN OF ENZYME SELECTIONS

A general strategy for the isolation of catalysts for given chemical reactions was designed. A first link between genes and their corresponding proteins was established by phage display: using Darwin's principles on evolution based on selection and amplification, rare protein molecules can then be selected for function from a large repertoire prior to their characterization by sequencing of their genes. A second link was created between enzymes and their products. By making use of the chelate effect and of Inovirus particles as a chemical, affinity chromatography for the reaction product is then sufficient to isolate among 106 to 1011 proteins and their genes, the rare ones coding for catalysts of interest. The strategy for the parallel processing of information on the catalytic activity of variants from a large protein repertoire is highlighted in this review

From genetic coding to protein folding

modelsA discrete classical mechanics (DCM) is established here. It consists of classical mechanics principles and equations, which are solved over the field of rational numbers Q, and not over the field of real numbers R. The need for a DCM results from observations of the genetic code. A DCM model for protein folding allows a set of folding nuclei to be derived for each protein. Applications in protein structure prediction are envisioned

Tailor-made biocatalysts: combining thermodynamics, organic synthesis, molecular biology, biochemistry and microbiology for the design of enzyme selections

A general strategy for the isolation of catalysts for given chemical reactions was designed.A first link between genes and their corresponding proteins was established by phage display: using Darwin’s principles on evolution based on selection and amplification, rare protein molecules can then be selected for function from a large repertoire prior to their characterization by sequencing of their genes.A second link was created between enzymes and their products. By making use of the chelate effect and of Inovirus particles as a chemical, affinity chromatography for the reaction product is then sufficient to isolate among 106 to 1011 proteins and their genes, the rare ones coding for catalysts of interest. The strategy for the parallel processing of information on the catalytic activity of variants from a large protein repertoire is highlighted in this review

Characterizing the topology of protein beta-sheets by an axis.

article complémentaire de : Guilloux A, Caudron B, Jestin JL (2013) A method to predict edge strands in beta-sheets from protein sequences. Computational and Structural Biotechnology Journal. 7 (9): e201305001. doi: http://dx.doi.org/10.5936/csbj.201305001Beta-sheets and alpha-helices are the most frequent structural elements composing protein structures. Beta-sheets typically highlight complex curved and sequence-dependent surfaces of parallel and/or anti-parallel beta-strands. The topology of these curved surfaces are described in this work by a unique axis crossing all beta-sheet's strands. The distribution of the distances of the alpha carbons in each strand which are the closest to the axis is given. The frequency of the twenty amino acids along the axis is provided. Applications in the field of protein structure prediction are mentioned

Geometrical criteria for left-handed twists within protein beta-strands

International audienceUsing a statistical analysis on beta-sheet structures from the Protein Data Bank, characteristic angles within beta-strands were correlated to the nature of the side chains. The twists were computed from the atomic coordinates of five consecutive amino acids' alpha carbons from single beta-strand sequences. Conditions on the angles for twists to be mainly left-handed are given together with the frequency of occurrence for these non-standard geometrical properties within protein beta-strands. Applications in protein structure prediction and CASP challenges in particular are envisioned by making use of the probabilities of occurrence in protein structures of angle value ranges for given amino acids