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Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology
Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme’s conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme’s conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.
Development of a fully integrated analysis system for ions based on ion-selective optodes and centrifugal microfluidics
A fully integrated, miniaturized analysis system for ions based on a centrifugal microfluidics platform and ion-selective optode membranes is described. The microfluidic architecture is composed of channels, five solution reservoirs, a measuring chamber, and a waste reservoir manufactured onto a disk-shaped substrate of poly(methyl methacrylate). Ion-selective optode membranes, composed of plasticized poly(vinyl chloride) impregnated with an ionophore, a proton chromoionophore, and a lipophilic anionic additive, were cast, with a spin-on device, onto a support layer and then immobilized on the disk. Fluid propulsion is achieved by the centrifugal force that results from spinning the disk, while a system of valves is built onto the disk to control flow. These valves operate based on fluid properties and fluid/substrate interactions and are controlled by the angular frequency of rotation. With this system, we have been able to deliver calibrant solutions, washing buffers, or "test" solutions to the measuring chamber where the optode membrane is located. An analysis system based on a potassium-selective optode has been characterized. Results indicate that optodes immobilized on the platform demonstrate theoretical responses in an absorbance mode of measurement. Samples of unknown concentration can be quantified to within 3% error by fitting the response function for a given optode membrane using an acid (for measuring the signal for a fully protonated chromoionophore), a base (for fully deprotonated chromoionophore), and two standard solutions. Further, the ability to measure ion concentrations by employing one standard solution in conjunction with acid and base and with two standards alone were studied to delineate whether the current architecture could be simplified. Finally, the efficacy of incorporating washing steps into the calibration protocol was investigated.
Synergistic foam stabilization and transport improvement in simulated fractures with polyelectrolyte complex nanoparticles: Microscale observation using laser etched glass micromodels
Inaccessibility to direct pore scale observation in hydrocarbon recovery of tight shale formations poses a great challenge to water-energy nexus initiatives and necessitates the use of high throughput technologies to emulate environmentally friendly processes. Herein, we employ a precise glass micromodel fabrication and visualization method to isolate the supercritical CO 2 bubbles surrounded by CO 2 -water lamella prepared in saline produced water stabilized with molecular complexation of zwitterionic surfactants (ZS) and polyelectrolyte complex nanoparticles (PECNP). The Selective Laser Enhanced Etching (SLE) technique was selected for micromodel simulation of high-pressure flow. Two representative designs, (1) fracture/micro-crack network 28 and (2) fracture/matrix were etched on fused silica glass with a laser printing machine and scCO 2 foam was injected to study the foamability, propagation, stability, and fluid loss properties. The highly monodispersed and uniformly distributed array of scCO 2 bubbles were detected in flow of scCO 2 foam in highly saline brine containing ionic complexes of positively charged PECNPs and ZS, whereas foam flow with the lamella containing ZS in fractures offered a noticeably large and polydisperse array of scCO 2 bubbles. scCO 2 bubble motion and deformation were traced, and local description of foam flow was visually examined. The confined array of scCO 2 bubbles stabilized by ZS in microcracks was affected by bubble growth and coalescence, whereas the super-populated array of monodispersed scC O2 bubbles with lamella containing complexes of PECNP and ZS were able to fill the channels with stable configurations within the timeframe of comparative stability measurements. The ability of complex fluid to prevent the formation damage was evaluated through fluid loss visualization in micromodels. Probing scCO 2 foam transport in homogenous porous media revealed smaller volume leak-off for scCO 2 foam containing PECNP-ZS ionic complexes.
CH 3 Radical Generation in Microplasmas for Up-Conversion of Methane
The conversion of methane, CH 4 , into higher value chemicals using low temperature plasmas is challenged by both improving efficiency and selectivity. One path towards selectivity is capturing plasma produced methyl radicals, CH 3 , in a solvent for aqueous processing. Due to the rapid reactions of methyl radicals in the gas phase, the transport distance from production of the CH 3 to its solvation should be short, which then motivates the use of microplasmas. The generation of CH 3 in Ar/CH 4 /H 2 O plasmas produced in nanosecond pulsed dielectric barrier discharge microplasmas is discussed using results from a computational investigation. The microplasma is sustained in the channel of a microfluidic chip in which the solvent flows along one wall or in droplets. CH 3 is primarily produced by electron-impact of and dissociative excitation transfer to CH 4 , as well as CH 2 reacting with CH 4 . CH 3 is rapidly consumed to form C 2 H 6 which, in spite of being subject to these same dissociative processes, accumulates over time, as do other stable products including C 3 H 8 and CH 3 OH. The gas mixture and electrical properties were varied to assess their effects on CH 3 production. CH 3 production is largest with 5% CH 4 in the Ar/CH 4 /H 2 O mixture due to an optimal balance of electron-impact dissociation, which increases with CH 4 percentage, and dissociative excitation transfer and CH 2 reacting with CH 4 , which decrease with CH 4 percentage. Design parameters of the microchannels were also investigated. Increasing the permittivity of the dielectrics in contact with the plasma increased the ionization wave intensity which increased CH 3 production. Increased energy deposition per pulse generally increased CH 3 production as does lengthening pulse length up to a certain point. The arrangement of the solvent flow in the microchannel can also affect the CH 3 density and fluence to the solvent. The fluence of CH 3 to the liquid solvent is increased if the liquid is immersed in the plasma as a droplet or is a layer on the wall where the ionization wave terminates. The solvation dynamics of CH 3 with varying numbers of droplets was also examined. Here, the maximum density of solvated methyl radicals CH 3aq occurs with a large number of droplets in the plasma. However, the solvated CH 3aq density can rapidly decrease due to desolvation, emphasizing the need to quickly react the solvated species in the solvent.