Automating the application of smart materials for protein crystallization

The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as 'smart materials') for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials. © 2015, IUCR. All rights reserved

STABILIZATION OF NON ISOTHERMAL CHEMICAL REACTORS USING TWO THERMODYNAMIC LYAPUNOV FUNCTIONS

The main goal of this paper is to introduce a link between the thermodynamics and control systems theory. More precisely, the paper focuses on Lyapunov based control of process systems, specially the non isothermal Continuous Stirred Tank Reactors in a thermodynamic framework, using either the jacket temperature or the inlet molar flow rate as the only control input. As soon as the constraint on the total mass is considered and the reaction kinetics is a Lipschitz continuous function with respect to the temperature, it shows that the stabilization of thermal solicitations reciprocally entails the one of matter using La Salle’s invariance principle. As a consequence, these control problems can be solved if the closed loop Lyapunov functions are chosen to be proportional to the thermal part or material part of the so called thermodynamic availability function. Some numerical simulations for a first order chemical reaction with multiple steady states are given to validate our theoretical developments. The performance of the obtained nonlinear controllers with regard to the conversion rate is also discussed.The main goal of this paper is to introduce a link between the thermodynamics and control systems theory. More precisely, the paper focuses on Lyapunov based control of process systems, specially the non isothermal Continuous Stirred Tank Reactors in a thermodynamic framework, using either the jacket temperature or the inlet molar flow rate as the only control input. As soon as the constraint on the total mass is considered and the reaction kinetics is a Lipschitz continuous function with respect to the temperature, it shows that the stabilization of thermal solicitations reciprocally entails the one of matter using La Salle’s invariance principle. As a consequence, these control problems can be solved if the closed loop Lyapunov functions are chosen to be proportional to the thermal part or material part of the so called thermodynamic availability function. Some numerical simulations for a first order chemical reaction with multiple steady states are given to validate our theoretical developments. The performance of the obtained nonlinear controllers with regard to the conversion rate is also discussed

Lectin-like bacteriocins from pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor

Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins

Dynamic modeling of the reactive twin-screw co-rotating extrusion process: experimental validation by using inlet glass fibers injection response and application to polymers degassing

International audienceIn this paper is described an original dynamic model of a reactive co-rotating twinscrew extrusion (TSE) process operated by the Rhodia company for the Nylon-66 degassing finishing step. In order to validate the model, dynamic experiments have been performed on a small-scale pilot plant. These experiments consist in a temporary injection of glass fibers at the inlet of the extruder after it has reached a given operating point. The outlet glass fibers mass fraction time variation is then measured. This experiment does not lead to the RTD measurement. As a matter of fact, due to the high quantity of glass fibers that is introduced, the behavior of the flow through the extruder is perturbed so that the glass fibers cannot be considered as an inert tracer. The dynamic model that we have published elsewhere (Choulak et al., Ind. Eng. Chem. Res., 2004, 43(23), 7373-7382) is adapted to take into account this nonlinear behavior of the extruder with respect to the glass fibers injection and is favorably compared to experimental results. The description of the degassing operation is also included in the model. The model allows simulations of the complete dynamic behavior of the process. When the steady state is reached, the good position of the degassing vent with respect to the partially and fully filled zones positions can also be checked, thus illustrating the way the model can be used for design purposes

Comparison of the structure and activity of glycosylated and asglycosylated human carboxylesterase 1

Human Carboxylesterase 1 (hCES1) is the key liver microsomal enzyme responsible for detoxification and metabolism of a variety of clinical drugs. To analyse the role of the single N-linked glycan on the structure and activity of the enzyme, authentically glycosylated and aglycosylated hCES1, generated by mutating asparagine 79 to glutamine, were produced in human embryonic kidney cells. Purified enzymes were shown to be predominantly trimeric in solution by analytical ultracentrifugation. The purified aglycosylated enzyme was found to be more active than glycosylated hCES1 and analysis of enzyme kinetics revealed that both enzymes exhibit positive cooperativity. Crystal structures of hCES1 a catalytically inactive mutant (S221A) and the aglycosylated enzyme were determined in the absence of any ligand or substrate to high resolutions (1.86 Å, 1.48 Å and 2.01 Å, respectively). Superposition of all three structures showed only minor conformational differences with a root mean square deviations of around 0.5 Å over all Cα positions. Comparison of the active sites of these un-liganded enzymes with the structures of hCES1-ligand complexes showed that side-chains of the catalytic triad were pre-disposed for substrate binding. Overall the results indicate that preventing N-glycosylation of hCES1 does not significantly affect the structure or activity of the enzyme

Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains

The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation

Study of a driven self oscillating electrochemical reaction near Hopf bifurcation

Abstract The Schuhmann dissolution-passivation (Sdp) model is one of the simplest electrochemical model explaining potential oscillations under galvanostatic conditions. The potential oscillations are due to a Hopf bifurcation. The nonlinear dynamic behaviour of the Sdp model is studied numerically near the Hopf bifurcation. The classical behaviour for forced self oscillating systems such as periodic or quasi periodic behaviours may occur when the current density is modulated by a sinusoidal signal. A phase portrait shows the main Arnol'd tongues where phase locking occurs

Distributed port-Hamiltonian modelling for irreversible processes

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Study of the forced Ni|1 M H₂SO₄ oscillator

International audienceThe Ni|H2SO4 system is a well-known oscillator under galvanostatic conditions. New experimental results obtained forcing the Ni|1 M H2SO4 electrochemical oscillator under galvanostatic conditions are presented. First a simple dissolution–passivation model explaining potential oscillations under galvanostatic conditions is used to predict the possible behaviour of experimental systems. The non-linear dynamic behaviour of the model is studied numerically near the Hopf bifurcation. The classical behaviour for forced self-oscillating systems, such as periodic or quasi-periodic behaviour, may occur when the current density is modulated by a sinusoidal signal. A phase portrait showing the main Arnold tongues where phase locking occurs is plotted. Next, several types of behaviour theoretically predicted for forced oscillators are observed experimentally for the Ni|1 M H2SO4 system, for example phase locking, bi-periodic behaviour, etc. Finally the consequences of bi-periodic bebaviour on impedance measurements are pointed out experimentally

Structure-preserving infinite dimensional model reduction: Application to adsorption processes

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