X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins.

Membrane proteins are distinguished from soluble proteins by their insertion into biological membranes. This insertion is achieved via a noticeable arrangement of hydrophobic amino acids that are exposed at the surface of the protein, and renders the interaction with the aliphatic tails of lipids more energetically favorable. This important difference between these two categories of proteins is the source of the need for a specific handling of membrane proteins, which transpired in the creation of new tools for their recombinant expression, purification and even crystallization. Following this line, we show here that crystals of membrane proteins display systematically higher diffraction anisotropy than those of soluble proteins. This phenomenon dramatically hampers structure solution and refinement, and has a strong impact on the quality of electron-density maps. A farther search for origins of this phenomenon showed that the type of crystallization, and thus the crystal packing, has no impact on anisotropy, nor does the nature or function of the membrane protein. Membrane proteins fully embedded within the membrane display equal anisotropy compared to the ones with extra membranous domains or fusions with soluble proteins. Overall, these results overturn common beliefs and call for a specific handling of their diffraction data

Au courant computation of the PDB to audit diffraction anisotropy of soluble and membrane proteins.

This data article makes available the informed computation of the whole Protein Data Bank (PDB) to investigate diffraction anisotropy on a large scale and to perform statistics. This data has been investigated in detail in "X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins" [1]. Diffraction anisotropy is traditionally associated with absence of contacts in-between macromolecules within the crystals in a given direction of space. There are however many case that do not follow this empirical rule. To investigate and sort out this discrepancy, we computed diffraction anisotropy for every entry of the PDB, and put them in context of relevant metrics to compare X-ray diffraction in reciprocal space to the crystal packing in real space. These metrics were either extracted from PDB files when available (resolution, space groups, cell parameters, solvent content), or calculated using standard procedures (anisotropy, crystal contacts, presence of ligands). More specifically, we separated entries to compare soluble vs membrane proteins, and further separated the later in subcategories according to their insertion in the membrane, function, or type of crystallization (Type I vs Type II crystal packing). This informed database is being made available to investigators in the raw and curated formats that can be re-used for further downstream studies. This dataset is useful to test ideas and to ascertain hypothesis based on statistical analysis

Etudes structurales et fonctionnelles de l'HPr Kinase/Phosphorylase, de sa voie de signalisation et de sa nouvelle famille de protéine-kinases à P-loop

Mon travail de thèse s'articule autour de l'étude d'une protéine-kinase bactérienne d'un nouveau genre, l'HPr Kinase/Phosphorylase (HPrK/P). Cette enzyme bifonctionnelle régule chez les bactéries à Gram positif la répression cataabolique du carbone, qui permet aux bactéries de s'adapter rapidement à la disponibilité en source de carbone. HPrK/P ne présente aucune similarité structurale avec les protéine-kinases eucaryotes. Elle phosphoryle la serine 46 des protéines HPr et Crh, qui activent alors le régulateur transcriptionnel CcpA. La conformation phosphorylase de l'enzyme est connue depuis 2001. Lors de ma thèse, l'étude cristallographique du mutant V267F du domaine catalytique de l'HPrK/P de L. casei a permis de résoudre sa conformation kinase. L'analyse structurale des interactions entre CcpA et les formes phosphorylées de HPr et Crh a également été réalisée. Enfin, j'ai étudié les protéines Fap7 et YFH7 de S. cerevisiae dans le cadre d'un projet d'analyse systématique des protéines à P-loop de fonction inconnue chez la levure.My PhD work concerns the study of a new type of bacterial protein-kinase, the HPr Kinase/Phosphorylase (HPrK/P). This bifunctional enzyme is a key sensor of the Carbon catabolite regulation mechanism in low G+C Gram positive bacteria. HPrK/P exhibits no similiarity with eukaryotic protein kinases. HPrK/P phosphorylates residue serine 46 of the HPr and Crh proteins, allowing them to activate the transcriptional regulator CcpA, and to regulate the expression of carbon catabolism genes. This mechanism enables bacteria to adapt to their environment. The structure of the phosphorylase conformation of HPrK/P was known. My work on mutant V267F of L. casei HPrK/P catalytic domain allowed me to gain insights into the kinase conformation. I also performed structural analysis of the interactions between CcpA and the phosphorylated forms of HPr and Crh. Finally, I analysed the proteins Fap7 and YFH7 of S. cerevisiae in a project of systematic study of yeast P-loop containing proteins of unknown function.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Leishmania tarentolae as a Promising Tool for Expressing Polytopic and Multi-Transmembrane Spans Eukaryotic Membrane Proteins: The Case of the ABC Pump ABCG6

International audienceThis chapter includes a practical method of membrane protein production in Leishmania tarentolae cells. We routinely use it to express membrane proteins of the ABC (adenosine triphosphate-binding cassette) family, here exemplified with ABCG6 from L. braziliensis, implicated in phospholipid trafficking and drug efflux. The pLEXSY system used here allows membrane protein production with a mammalian-like N-glycosylation pattern, at high levels and at low costs. Also the effects of an N-terminal truncation of the protein are described. The method is described to allow any kind of membrane protein production

Architectures de convertisseurs DC/DC basse tension et fort courant avec commande numérique

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

CryoEM reconstructions of membrane proteins solved in several amphipathic solvents, nanodisc, amphipol and detergents, yield amphipathic belts of similar sizes corresponding to a common ordered solvent layer

International audienc

Structure, function, and inhibition of catalytically asymmetric ABC transporters: Lessons from the PDR subfamily

International audienceATP-binding cassette (ABC) superfamily comprises a large group of ubiquitous transmembrane proteins that play a crucial role in transporting a diverse spectrum of substrates across cellular membranes. They participate in a wide array of physiological and pathological processes including nutrient uptake, antigen presentation, toxin elimination, and drug resistance in cancer and microbial cells. ABC transporters couple ATP binding and hydrolysis to undergo conformational changes allowing substrate translocation. Within this superfamily, a set of ABC transporters has lost the capacity to hydrolyze ATP at one of their nucleotide-binding sites (NBS), called the non-catalytic NBS, whose importance became evident with extensive biochemistry carried out on yeast pleiotropic drug resistance (PDR) transporters. Recent single-particle cryogenic electron microscopy (cryo-EM) advances have further catapulted our understanding of the architecture of these pumps. We provide here a comprehensive overview of the structural and functional aspects of catalytically asymmetric ABC pumps with an emphasis on the PDR subfamily. Furthermore, given the increasing evidence of efflux-mediated antifungal resistance in clinical settings, we also discuss potential grounds to explore PDR transporters as therapeutic targets

The non-Newtonian behavior of detergents during concentration is increased by macromolecules, in trans, and results in their over-concentration

International audienceConcentration of pure membrane proteins in detergent solution results in detergent concentration, albeit in unknown amounts. This phenomenon is observed in every lab working on membrane proteins, but has seldom been investigated. In this study, we explored the behavior of detergents mixed with membrane proteins during the step of sample concentration using centrifugal devices. We show that detergent over-concentrate with the presence of polymers, typically membrane or soluble proteins but also polysaccharides. The over-concentration of detergents depends on centrifugal force applied to the device. With the use of a specific dye, we observed the formation of a mesh on the concentrator device. Importantly, reducing the centrifugal speed allows to reduce the concentration of detergents when mixed to macromolecules, as tested with 3 different membrane proteins. All together, these results highlight the non-Newtonian behavior of detergents and provides a solid framework to investigators to improve drastically biochemical and structural studies of membrane proteins