Dynamique des structures protéiques et son impact sur les comportements structuraux locaux

Protein structures are highly dynamic in nature contrary to their depiction in crystal structures. A major component of structural dynamics is the inherent protein flexibility. The prime objective of this thesis is to understand the role of the inherent dynamics in protein structures and its propagation. Protein flexibility is analyzed at various levels of structural complexity, from primary to quaternary levels of organization. Each of the first five chapters’ deal with a different level of local structural organization with first chapter dealing with classical secondary structures while the second one analysis the same using a structural alphabet - Protein Blocks. The third chapter focuses on the impact of special physiological events like post-translational modifications and disorder to order transitions on protein flexibility. These three chapters indicate towards a context dependent implementation of structural flexibility in their local environment. In subsequent chapters, more complex structures are taken under investigation. Chapter 4 deals with integrin αIIbβ3 that is involved in rare genetic disorders. Impact of the pathological mutations on the local flexibility is studied in two rigid domains of integrin αIIbβ3 ectodomain. Inherent flexibility in these domains is shown to modulate the impact of mutations towards the loops. Chapter 5 deals with the structural modelling and dynamics of a more complex protein structure of Duffy Antigen Chemokine Receptor embedded in an erythrocyte mimic membrane system. The model is supported by the most comprehensive phylogenetic analysis on chemokine receptors till date as explained in the last chapter of the thesis.Les structures protéiques sont de nature hautement dynamique contrairement à leur représentation dans les structures cristallines. Une composante majeure de la dynamique structurelle est la flexibilité des protéines inhérentes. L'objectif principal de cette thèse est de comprendre le rôle de la dynamique inhérente dans les structures protéiques et leur propagation. La flexibilité des protéines est analysée à différents niveaux de complexité structurelle, du niveau d'organisation primaire au niveau quaternaire. Chacun des cinq premiers chapitres traite un niveau différent d'organisation structurelle locale avec le premier chapitre traitant des structures secondaires classiques tandis que le second analyse la même chose en utilisant un alphabet structurel - les blocs protéiques. Le troisième chapitre se concentre sur l'impact d'événements physiologiques spéciaux comme les modifications post-traductionnelles et le désordre sur les transitions d'ordre sur la flexibilité des protéines. Ces trois chapitres indiquent une mise en œuvre dépendante du contexte de la flexibilité structurelle dans leur environnement local. Dans les chapitres suivants, des structures plus complexes sont prises en compte. Le chapitre 4 traite de l'intégrine αIIbβ3 impliquée dans des troubles génétiques rares. L'impact des mutations pathologiques sur la flexibilité locale est étudié dans deux domaines rigides de l'intégrine αIIbβ3 ectodomaine. La flexibilité inhérente dans ces domaines est montrée pour moduler l'impact des mutations vers les boucles. Le chapitre 5 traite de la modélisation structurelle et de la dynamique d'une structure protéique plus complexe du récepteur des chimiokines des antigènes du groupe Duffy incorporé dans un système de membrane mimétique érythrocytaire. Le modèle est soutenu par l'analyse phylogénétique la plus complète sur les récepteurs de chimiokines jusqu'à ce jour, comme expliqué dans le dernier chapitre de la thèse

Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus.

Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria

Investigating the Product Profiles and Structural Relationships of New Levansucrases with Conventional and Non-Conventional Substrates

International audienceThe synthesis of complex oligosaccharides is desired for their potential as prebiotics, and their role in the pharmaceutical and food industry. Levansucrase (LS, EC 2.4.1.10), a fructosyl-transferase, can catalyze the synthesis of these compounds. LS acquires a fructosyl residue from a donor molecule and performs a non-Lenoir transfer to an acceptor molecule, via β-(2→6)-glycosidic linkages. Genome mining was used to uncover new LS enzymes with increased transfructosylating activity and wider acceptor promiscuity, with an initial screening revealing five LS enzymes. The product profiles and activities of these enzymes were examined after their incubation with sucrose. Alternate acceptor molecules were also incubated with the enzymes to study their consumption. LSs from Gluconobacter oxydans and Novosphingobium aromaticivorans synthesized fructooligosaccharides (FOSs) with up to 13 units in length. Alignment of their amino acid sequences and substrate docking with homology models identified structural elements causing differences in their product spectra. Raffinose, over sucrose, was the preferred donor molecule for the LS from Vibrio natriegens, N. aromaticivorans, and Paraburkolderia graminis. The LSs examined were found to have wide acceptor promiscuity, utilizing monosaccharides, disaccharides, and two alcohols to a high degree

A binary map depicting cluster of homologous proteins among all genomes.

<p>A binary map depicting cluster of homologous proteins among all genomes.</p

Investigation of the impact of PTMs on the protein backbone conformation

International audiencePost-Translational Modifications (PTMs) are known to play a critical role in the regulation of the protein functions. Their impact on protein structures, and their link to disorder regions have already been spotted on the past decade. Nonetheless, the high diversity of PTMs types, and the multiple schemes of protein modifications (multiple PTMs, of different types, at different time, etc) make difficult the direct confrontation of PTM annotations and protein structures data.We so analyzed the impact of the residue modifications on the protein structures at local level. Thanks to a dedicated structure database, namely PTM-SD, a large screen of PTMs have been done and analyze at a local protein conformation levels using the structural alphabet Protein Blocks (PBs). We investigated the relation between PTMs and the backbone conformation of modified residues, of their local environment, and at the level of the complete protein structure. The two main PTM types (N-glycosylation and phosphorylation) have been studied in non-redundant datasets, and then, 4 different proteins were focused, covering 3 types of PTMs: N-glycosylation in renin endopeptidase and liver carboxylesterase, phosphorylation in cyclin-dependent kinase 2 (CDK2), and methylation in actin. We observed that PTMs could either stabilize or destabilize the backbone structure, at a local and global scale, and that these effects depend on the PTM types

Proliferation and apoptosis in testicular tissue after / / experimental damage

Carbohydrate-degrading enzymes, arranged by GH family. (XLS 67 kb

Comparative representation of homologous protein distribution within the genomes.

<p>Proteome dataset from each genome was subjected to BLASTp to identify homologous proteins between the genomes with an E-value cutoff of 1e-5, query coverage of 50% and identity of 35%. Protein distribution between different combinations of genomes was identified and is represented as a 3D-graph. X, Y and Z-axis respectively denote genome name, the number of proteins and the genome combination.</p

Venn diagram of comparative annotations of <i>Myxococcus xanthus</i> DK1622 using RAST, Glimmer, xBASE and the original NCBI annotation.

<p>All genome annotations were mapped to each other using BLASTp [E-value cutoff: 1e^-5]. The diagram depicts the homologous proteins shared between two or more annotations (overlapping area) along with unique proteins (yellow shade). RAST, Glimmer, xBASE and the original NCBI annotations are shown in brick red, green, orange and blue colors respectively. The number of annotated proteins using the respective annotation pipeline is shown in the box.</p

Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

International audiencePlasmodium vivax malaria affects 14 million people each year. Its invasion requires interactions between the parasitic Duffy-binding protein (PvDBP) and the N-terminal extracellular domain (ECD1) of the host’s Duffy antigen/receptor for chemokines (DARC). ECD1 is highly flexible and intrinsically disordered, therefore it can adopt different conformations. We computationally modeled the challenging ECD1 local structure. With T-REMD simulations, we sampled its dynamic behavior and collected its most representative conformations. Our results suggest that most of the DARC ECD1 domain remains in a disordered state during the simulated time. Globular local conformations are found in the analyzed local free-energy minima. These globular conformations share an α-helix spanning residues Ser18 to Ser29 and in many cases they comprise an antiparallel β-sheet, whose β-strands are formed around residues Leu10 and Ala49. The formation of a parallel β-sheet is almost negligible. So far, progress in understanding the mechanisms forming the basis of the P. vivax malaria infection of reticulocytes has been hampered by experimental difficulties, along with a lack of DARC structural information. Our collection of the most probable ECD1 structural conformations will help to advance modeling of the DARC structure and to explore DARC–ECD1 interactions with a range of physiological and pathological ligands

Circular representation of the <i>M</i>. <i>hansupus</i> complete genome.

<p><b>Circles</b> (from inside to outside) <b>1 and 2</b> (GC content; black line and GC skew; magenta and green lines), <b>circle 3</b> (<i>M</i>. <i>hansupus</i>; red circle); <b>circle 4</b> (mapped <i>Myxococcus fulvus</i> HW-1 genome with <i>M</i>. <i>hansupus</i> genome; green circle); <b>circle 5</b> (mapped <i>Myxococcus xanthus</i> DK1622 genome with <i>M</i>. <i>hansupus</i> genome; purple circle); <b>circle 6</b> (mapped <i>Myxococcus xanthus</i> DZF1 genome with <i>M</i>. <i>hansupus</i> genome; Orange circle); <b>circle 7</b> (mapped <i>Myxococcus xanthus</i> DZ2 genome with <i>M</i>. <i>hansupus</i> genome; blue circle); <b>circle 8</b> (mapped <i>Myxococcus stipitatus</i> genome with <i>M</i>. <i>hansupus</i> genome; yellow circle). BRIG 0.95 was used to build the circular representation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148593#pone.0148593.ref053" target="_blank">53</a>]. Mapping studies were done using BLASTn with an E-value cut-off 1e^-5.</p