AFMBioMed Conference: Paris, France, August 2011

International audienceThe fourth edition of the AFMBioMed Conference, Paris 2011 was organized by the Institut Curie, INSERM, and the Life Science Division of the CEA (DSV). The conference was held at the Institut Curie, Paris, France on 23–26 August and chaired by Dr Simon Scheuring

Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data

SummaryClassical structural biology techniques face a great challenge to determine the structure at the atomic level of large and flexible macromolecules. We present a novel methodology that combines high-resolution AFM topographic images with atomic coordinates of proteins to assemble very large macromolecules or particles. Our method uses a two-step protocol: atomic coordinates of individual domains are docked beneath the molecular surface of the large macromolecule, and then each domain is assembled using a combinatorial search. The protocol was validated on three test cases: a simulated system of antibody structures; and two experimentally based test cases: Tobacco mosaic virus, a rod-shaped virus; and Aquaporin Z, a bacterial membrane protein. We have shown that AFM-intermediate resolution topography and partial surface data are useful constraints for building macromolecular assemblies. The protocol is applicable to multicomponent structures connected in the polypeptide chain or as disjoint molecules. The approach effectively increases the resolution of AFM beyond topographical information down to atomic-detail structures

Modélisation moléculaire par homologie des protéines : ses applications en Biologie et en Bioinformatique

Mes activités de recherche se focalisent sur l’étude structurale de la fonction des protéines tant au point de vue expérimental que théorique et plus particulièrement l’aspect de la reconnaissance intermoléculaire. Notre système de référence est celui de la reconnaissance antigène-anticorps. Ce système est le prototype parfait, de part sa fonction, mais également grâce à la dynamique de ce processus lié au concept de maturation. Aucours de ma thèse de doctorat, nous avons mesuré les constantes d’affinité, à l’équilibre et en cinétique, entre des anticorps monoclonaux et un antigène multivalent (virus de la mosaïque du tabac, VMT). De manière inattendue, nos résultats ont démontré une coopérativité négative dans la liaison d’anticorps au VMT. A partir de mon premier stage postdoctoral et jusqu’à aujourd’hui, ma recherche s’est orientée vers l’aspect structuralde la reconnaissance ; incluant le développement de fonctions énergétiques et de techniques d’analyse des structures tridimensionnelles, la construction de modèles moléculaires et l’assemblage de ligand dans leur recepteur.Ce mémoire résume mes cinq dernières années d’activités scientifiques dans le domaine de la modélisation moléculaire, bien que la parution de publications ne reflète guère ce laps de temps. La modélisation moléculaire est une discipline récente qui nécessite, à mon sens, une introduction formelle. Dans ce mémoire on définit la modélisation moléculaire comme l’ensemble des techniques qui permettent d’étudier la fonction d’unemolécule grâce à la connaissance de sa structure tridimensionnelle. Ces techniques incluent la modélisation par homologie, les méthodes de simulations, les méthodes d’assemblage (docking), les méthodes d’étude du repliement ab-initio des protéines. Les approches spectroscopiques comme la résonance magnétique nucléaire (RMN) ou le dichroisme circulaire et la microscopie électronique (ME) sont également inclues. Au sens littéral notre définition intègre également la diffraction des rayons X (RX).L’objectif de ce mémoire est de décrire en détail une de ces techniques : la modélisation par homologie. Ce mémoire focalise principalement sur les protéines bien que la modélisation moléculaire s’applique aussi bien aux acides nucléiques, aux sucres ou aux lipides. En dépit de la jeunesse de cette discipline, il est pratiquement impossible de la couvrir en son intégralité. Malgré une recherche bibliographique approfondie, elle est certainement incomplète due à l’interdisciplinarité de cette technique qui couvre tous les champs de recherches, de la théorie fondamentale à la médecine. Ce mémoire espère présenter l’impact de la modélisation par homologie dans la biologie moderne de la manière la plus juste.Ce mémoire comprend quatre parties. Après une introduction générale, on présentera en détail les diverses approches employées pour la modélisation par homologie. Les contributions personnelles à cette discipline seront enfin exposées. La perspective d’évolution de la modélisation moléculaire sera finalement brièvement discutée

Pilot in vivo toxicological investigation of boron nitride nanotubes

Boron nitride nanotubes (BNNTs) have attracted huge attention in many different research fields thanks to their outstanding chemical and physical properties. During recent years, our group has pioneered the use of BNNTs for biomedical applications, first of all assessing their in vitro cytocompatibility on many different cell lines. At this point, in vivo investigations are necessary before proceeding toward realistic developments of the proposed applications. In this communication, we report a pilot toxicological study of BNNTs in rabbits. Animals were injected with a 1 mg/kg BNNT solution and blood tests were performed up to 72 hours after injection. The analyses aimed at evaluating any acute alteration of hematic parameters that could represent evidence of functional impairment in blood, liver, and kidneys. Even if preliminary, the data are highly promising, as they showed no adverse effects on all the evaluated parameters, and therefore suggest the possibility of the realistic application of BNNTs in the biomedical field

Conserved pseudoknots in lncRNA MEG3 are essential for stimulation of the p53 pathway

Funding Information: Work in the Marcia lab is partly funded by the Agence Nationale de la Recherche (ANR-15-CE11-0003-01), the Agence Nationale de Recherche sur le Sida et les H?patites Virales (ANRS, ECTZ18552), and ITMO Cancer (18CN047-00). The Marcia lab uses the platforms of the Grenoble Instruct Center (ISBG UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, CEA). This work acknowledges the AFM platform at the IBS.Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures (“kissing loops”). Mutations that disrupt these interactions impair MEG3-dependent p53 stimulation in vivo and disrupt MEG3 folding in vitro. These findings provide mechanistic insights into regulation of the p53 pathway by MEG3 and reveal how conserved motifs of tertiary structure can regulate lncRNA biological function.Publisher PDFPeer reviewe

Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature

<p>Abstract</p> <p>Background</p> <p>Antigen-antibody interactions are key events in immune system, which provide important clues to the immune processes and responses. In Antigen-antibody interactions, the specific sites on the antigens that are directly bound by the B-cell produced antibodies are well known as B-cell epitopes. The identification of epitopes is a hot topic in bioinformatics because of their potential use in the epitope-based drug design. Although most B-cell epitopes are discontinuous (or conformational), insufficient effort has been put into the conformational epitope prediction, and the performance of existing methods is far from satisfaction.</p> <p>Results</p> <p>In order to develop the high-accuracy model, we focus on some possible aspects concerning the prediction performance, including the impact of interior residues, different contributions of adjacent residues, and the imbalanced data which contain much more non-epitope residues than epitope residues. In order to address above issues, we take following strategies. Firstly, a concept of 'thick surface patch' instead of 'surface patch' is introduced to describe the local spatial context of each surface residue, which considers the impact of interior residue. The comparison between the thick surface patch and the surface patch shows that interior residues contribute to the recognition of epitopes. Secondly, statistical significance of the distance distribution difference between non-epitope patches and epitope patches is observed, thus an adjacent residue distance feature is presented, which reflects the unequal contributions of adjacent residues to the location of binding sites. Thirdly, a bootstrapping and voting procedure is adopted to deal with the imbalanced dataset. Based on the above ideas, we propose a new method to identify the B-cell conformational epitopes from 3D structures by combining conventional features and the proposed feature, and the random forest (RF) algorithm is used as the classification engine. The experiments show that our method can predict conformational B-cell epitopes with high accuracy. Evaluated by leave-one-out cross validation (LOOCV), our method achieves the mean AUC value of 0.633 for the benchmark bound dataset, and the mean AUC value of 0.654 for the benchmark unbound dataset. When compared with the state-of-the-art prediction models in the independent test, our method demonstrates comparable or better performance.</p> <p>Conclusions</p> <p>Our method is demonstrated to be effective for the prediction of conformational epitopes. Based on the study, we develop a tool to predict the conformational epitopes from 3D structures, available at <url>http://code.google.com/p/my-project-bpredictor/downloads/list</url>.</p

Role of conformational dynamics in sequence-specific autoantibody•ssDNA recognition

11F8 is a sequence-specific monoclonal anti-ssDNA autoantibody isolated from a lupus prone mouse that forms pathogenic complexes with ssDNA, resulting in kidney damage. Prior studies show that specificity is mediated by a somatic mutation from serine at 31 V H to arginine. Reversion back to serine in 11F8 resulted in >30-fold decrease in affinity and altered thermodynamic and kinetic parameters for sequence-specific recognition of its cognate ssDNA ligand. Mutagenesis and structural studies suggest that R31 V H contacts ssDNA via a salt bridge and a bidentate hydrogen bond and may further contribute to specificity by altering binding-site conformation. Fluorescence resonance energy transfer experiments were conducted to assess the kinetics of conformational change during 11F8•ssDNA association. The extent of rearrangement between the six complementary determining regions in the 11F8•ssDNA complex with germline serine or somatically mutated arginine at residue 31 of the heavy chain was examined. Our studies show that greater conformational change occurs in five of six complementarity determining regions after the heavy chain germline J558 sequence undergoes mutation to arginine at 31 V H . © 2007 Wiley Periodicals, Inc. Biopolymers 85: 481–489, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55985/1/20692_ftp.pd

The Role of PAS Kinase in PASsing the Glucose Signal

PAS kinase is an evolutionarily conserved nutrient responsive protein kinase that regulates glucose homeostasis. Mammalian PAS kinase is activated by glucose in pancreatic beta cells, and knockout mice are protected from obesity, liver triglyceride accumulation, and insulin resistance when fed a high-fat diet. Yeast PAS kinase is regulated by both carbon source and cell integrity stress and stimulates the partitioning of glucose toward structural carbohydrate biosynthesis. In our current model for PAS kinase regulation, a small molecule metabolite binds the sensory PAS domain and activates the enzyme. Although bona fide PAS kinase substrates are scarce, in vitro substrate searches provide putative targets for exploration

Standardized nanomechanical atomic force microscopy procedure (SNAP) for measuring soft and biological samples

We present a procedure that allows a reliable determination of the elastic (Young's) modulus of soft samples, including living cells, by atomic force microscopy (AFM). The standardized nanomechanical AFM procedure (SNAP) ensures the precise adjustment of the AFM optical lever system, a prerequisite for all kinds of force spectroscopy methods, to obtain reliable values independent of the instrument, laboratory and operator. Measurements of soft hydrogel samples with a well-defined elastic modulus using different AFMs revealed that the uncertainties in the determination of the deflection sensitivity and subsequently cantilever's spring constant were the main sources of error. SNAP eliminates those errors by calculating the correct deflection sensitivity based on spring constants determined with a vibrometer. The procedure was validated within a large network of European laboratories by measuring the elastic properties of gels and living cells, showing that its application reduces the variability in elastic moduli of hydrogels down to 1%, and increased the consistency of living cells elasticity measurements by a factor of two. The high reproducibility of elasticity measurements provided by SNAP could improve significantly the applicability of cell mechanics as a quantitative marker to discriminate between cell types and conditions