Reverse transition to hydrodynamic stability through the Schwarzschild line in a supercritical fluid layer.

We consider a fluid close to its gas-liquid critical point in a bottom-heated cavity. Due to strong density stratification, both the Schwarzschild and the Rayleigh stability criteria are relevant at the same space scale. Taking advantage of the competition between these two limits of the convection-onset criterion, we numerically exhibit striking non-Boussinesq effects: the reverse transition to stability through the Schwarzschild line of a heat diffusing layer subjected to convection, and the convection onset inside a few-millimeters-thick layer according to the Schwarzschild criterion.

[Structural disorder within the replicative complex of measles virus: functional implications].

Measles virus belongs to the Paramyxoviridae family within the Mononegavirales order. Its non segmented, single stranded, negative sense RNA genome is encapsidated by the nucleoprotein (N) to form a helical nucleocapsid. This ribonucleoproteic complex is the substrate for both transcription and replication.

The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded.

Measles virus is a negative-sense, single-stranded RNA virus within the Mononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. The measles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, N(TAIL) (aa 401-525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459-507) of the viral phosphoprotein. With in N(TAIL), an alpha-helical molecular recognition element (alpha-MoRE, aa 488-499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD.

Contribution of the Nernst potential to stiffness constants: the asymmetrical case.

Inside biological membranes, one of the fundamental functions of active proteins such as pumps is to generate some electrochemical gradient across the membrane and then, to establish a new stationary state. The membrane electric potential generated by activity modifies the stiffness constants of the membrane. A spontaneous curvature appears if the inner and outer Debye lengths are different.

Diastereoselective synthesis and ESR study of 4-phenylDEPMPO spin traps.

[reaction: see text] The cis and trans diastereoisomers of 5-(diethoxyphosphoryl)-5-methyl-4-phenylpyrroline N-oxide (4-PhDEPMPOt 8 and 4-PhDEPMPOc 9) were prepared stereoselectively and used as spin traps for hydroxyl and superoxide radicals. The spin adduct formed by reaction of the cis stereoisomer 9with superoxide radical anion exhibited an 8-line ESR spectrum, showing only a reduced alternating line width phenomenon. This spectrum is simpler than the 12-line spectrum of DEPMPO-OOH, which exhibits a strong alternating line width phenomenon.

VaZyMolO: a tool to define and classify modularity in viral proteins.

Viral structural genomic projects aim at unveiling the function of unknown viral proteins by employing high-throughput approaches to determine their 3D structure and to identify their function through fold-homology studies. The 'viral enzyme module localization' (VaZyMolO) tool has been developed, which aims at defining viral protein modules that might be expressed in a soluble and functionally active form, thereby identifying candidates for crystallization studies. VaZyMolO includes 114 complete viral genome sequences of both negative- and positive-sense, single-stranded RNA viruses available from NCBI.

Sheath liquid interface for the coupling of normal-phase liquid chromatography with electrospray mass spectrometry and its application to the analysis of neoflavonoids.

A novel interface that allows normal-phase liquid chromatography to be coupled with electrospray ionization (ESI) is reported. A make-up solution of 60 mM ammonium acetate in methanol, infused at a 5 microl min(-1) flow-rate at the tip of the electrospray probe, provides a sheath liquid which is poorly miscible with the chromatographic effluent, but promotes efficient ionization of the targeted analytes. Protonated molecules generated in the ESI source were subjected to tandem mass spectrometric experiments in a triple-quadrupole mass spectrometer.

Curvature induced periodic attractor on growth interface.

We experimentally address the long-time dynamics of an artificially curved growth interface in directional solidification. Repetitive cell nucleations are found to appear in a disordered way but to eventually organize themselves coherently, at long times. This behavior is recovered by simulation of a nonlinear advection-diffusion model for the phase dynamics.

Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.

As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively.

Pattern formation of stationary transcellular ionic currents in Fucus.

Stationary and nonstationary spatiotemporal pattern formations emerging from the cellular electric activity are a common feature of biological cells and tissues. The nonstationary ones are well explained in the framework of the cable model. Inversely, the formation of the widespread self-organized stationary patterns of transcellular ionic currents remains elusive, despite their importance in cell polarization, apical growth, and morphogenesis.

Structural aspects of sexual attraction and chemical communication in insects.

In the animal kingdom, the relationship between individuals and the environment is often modulated by chemical communication. In the olfaction of insects, small antennary proteins--such as odorant- and pheromone-binding proteins (OBPs and PBPs, respectively) and chemosensory proteins (CSP)--have been proposed to carry their ligand from the air-fluid interface to the olfactory receptors. Binding experiments and recent structural studies of three PBPs, an OBP and a CSP have illustrated their versatility and ability to accommodate ligands of different shapes and chemical structures.

Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.

Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. The structure of the inactive mutant beta-agarase A-E147S in complex with agaro-octaose has been solved at 1.

The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding.

Lipocalins form a large multifunctional family of small proteins (15-25 kDa) first discovered in eukaryotes. More recently, several types of bacterial lipocalins have been reported, among which Blc from Escherichia coli is an outer membrane lipoprotein. As part of our structural genomics effort on proteins from E.

The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world.

The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-A resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins.

Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis.

Fucosylated glycoconjugates are involved in numerous biological events, and alpha-l-fucosidases, the enzymes responsible for their processing, are therefore of crucial importance. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterized by rapid neurodegeneration, resulting in severe mental and motor deterioration. To gain insight into alpha-l-fucosidase function at the molecular level, we have determined the crystal structure of Thermotoga maritima alpha-l-fucosidase.

Why are there so many carbohydrate-active enzyme-related genes in plants?

Plants contain far more carbohydrate-active enzyme-encoding genes than any other organism sequenced to date. The extremely large number of glycosidase and glycosyltransferase-related genes in plant genomes can be explained by the complex structure of the plant cell wall, by ancient genome duplication and by recent local duplications, but also by the recent emergence of novel and unrelated protein functions based on widely available pre-existing scaffolds.

Sulfur single-wavelength anomalous diffraction crystal structure of a pheromone-binding protein from the honeybee Apis mellifera L.

Pheromone binding proteins (PBPs) are small helical proteins ( approximately 13-17 kDa) present in several sensory organs from moth and other insect species. They are involved in the transport of pheromones from the sensillar lymph to the olfactory receptors. We report here the crystal structure of a PBP (Amel-ASP1) originating from the honey-bee (Apis mellifera) antennae and expressed as recombinant protein in the yeast Pichia pastoris.

The three-dimensional structures of two beta-agarases.

Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized.

Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein.

The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive-stranded RNA virus (SARS-CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS-CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains.

The crystal structure of the Escherichia coli YfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases.

Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium.

Optimization of crystals from nanodrops: crystallization and preliminary crystallographic study of a pheromone-binding protein from the honeybee Apis mellifera L.

Pheromone-binding proteins (PBPs) are small helical proteins ( approximately 13-17 kDa) present in various sensory organs from moths and other insect species. They are involved in the transport of pheromones from the sensillar lymph to the olfactory receptors. Here, crystals of a PBP (Amel-ASP1) originating from honeybee (Apis mellifera L.

Crystallization and preliminary crystallographic study of a pheromone-binding protein from the cockroach Leucophaea maderae.

Pheromone-binding proteins (PBPs) are small helical proteins (13-18 kDa) present in various sensory organs of moths and other insect species. An antennal protein from the cockroach Leucophaea maderae (LmaPBP) has been found to share all the hallmarks of the PBP family and is expressed specifically in the female adult antennae, the gender that perceives the sex pheromone. Here, the crystallization of LmaPBP expressed as a recombinant protein in Escherichia coli periplasm is reported.

The crystal structure of a cockroach pheromone-binding protein suggests a new ligand binding and release mechanism.

Pheromone-binding proteins (PBPs) are small helical proteins found in sensorial organs, particularly in the antennae, of moth and other insect species. They were proposed to solubilize and carry the hydrophobic pheromonal compounds through the antennal lymph to receptors, participating thus in the peri-receptor events of signal transduction. The x-ray structure of Bombyx mori PBP (BmorPBP), from male antennae, revealed a six-helix fold forming a cavity that contains the pheromone bombykol.

Medium-scale structural genomics: strategies for protein expression and crystallization.

While high-throughput methods of protein production and crystallization are beginning to be well documented, owing to the output of large structural genomics programs, medium-throughput methods at the laboratory scale lag behind. In this paper, we report a possible way for an academic laboratory to adapt high-throughput to medium-throughput methods, on the basis of the first results of two projects aimed at solving the 3D structures of Escherichia coli and Mycobacterium tuberculosis (Tb) proteins of unknown function. We have developed sequential and iterative procedures as well as new technical processes for these programs.

A medium-throughput crystallization approach.

The first results of a medium-scale structural genomics program clearly demonstrate the value of using a medium-throughput crystallization approach based on a two-step procedure: a large screening step employing robotics, followed by manual or automated optimization of the crystallization conditions. The structural genomics program was based on cloning in the Gateway vectors pDEST17, introducing a long 21-residue tail at the N-terminus. So far, this tail has not appeared to hamper crystallization.