A fast and efficient stabilization of firefly luciferase on MIL-53(Al) via surface adsorption mechanism

Research on Chemical Intermediates - Stabilization and immobilization on a proper support is essential in processing and production of enzymes. Luciferase is an unstable, thermally sensitive, and...     

Surface Arginine Saturation Effect on Unfolding Reaction of Firefly Luciferase: A Thermodynamic and Kinetic Perspective

Replacement of some hydrophobic solvent‐exposed residues in Lampyris turkestanicus luciferase with arginine increases thermostability of this enzyme. Herein, thermodynamic and kinetic of unfolding reactions of wild type (WT), E354R/356R, E354R/356R‐I232R and E354R/356R‐Q35R/L182R/I232R variants, has been investigated. Fluorescence and Far‐UV circular dichroism measurements using urea as a chemical denaturant indicated that the value of for all variants is greater than that of WT enzyme. Analysis of m‐values, as a measure of difference in the solvent accessible surface area between the native and denatured states of protein, revealed that higher stability of mutants is related to their higher degree of compactness in the folded state. Results of unfolding kinetic experiments showed that all variants have three‐exponential behavior in which they unfolded with three rate constants and corresponding amplitudes. Increasing the rate constants of fast unfolding phase in mutants relative to WT protein may be attributed to more compactness and more kinetic sensitivity of their folded state to urea. However, more population of WT protein was unfolded from fast unfolding phase. Results of this investigation highlight kinetic stability of luciferase via a slow rate of unfolding.     

A robust optimization approach to closed-loop supply chain network design under uncertainty

The concern about significant changes in the business environment (such as customer demands and transportation costs) has spurred an interest in designing scalable and robust supply chains. This paper proposes a robust optimization model for handling the inherent uncertainty of input data in a closed-loop supply chain network design problem. First, a deterministic mixed-integer linear programming model is developed for designing a closed-loop supply chain network. Then, the robust counterpart of the proposed mixed-integer linear programming model is presented by using the recent extensions in robust optimization theory. Finally, to assess the robustness of the solutions obtained by the novel robust optimization model, they are compared to those generated by the deterministic mixed-integer linear programming model in a number of realizations under different test problems.     

On optimality of two adaptive choices for the parameter of Dai–Liao method

Orthonormal matrices are a class of well-conditioned matrices with the least spectral condition number. Here, at first it is shown that a recently proposed choice for parameter of the Dai–Liao nonlinear conjugate gradient method makes the search direction matrix as close as possible to an orthonormal matrix in the Frobenius norm. Then, conducting a brief singular value analysis, it is shown that another recently proposed choice for the Dai–Liao parameter improves spectral condition number of the search direction matrix. Thus, theoretical justifications of the two choices for the Dai–Liao parameter are enhanced. Finally, some comparative numerical results are reported.     

Pore Aperture Control Toward Size-Exclusion-Based Hydrocarbon Separations

Metal–organic frameworks (MOFs) have been proposed as a promising material for non-thermal chemical separations owing to their high structural diversity and tunability. Here, we report the synthesis of a zinc-based MOF containing a three-dimensional (3D) linker, bicyclo[2.2.2]octane-1,4-dicarboxylic acid, with high thermal stability towards the separation of hexane isomers. The incorporation of the 3D linker enhances the structural stability and provides well-defined pore apertures/channels with sub-Ångstrom precision. This precision allowed for the separation of similarly sized hexane isomers based on subtle differences in their kinetic diameters. Multi-component liquid phase batch experiments confirmed the separation of hexanes mixture into linear, monobranched, and dibranched isomers. This work represents a significant milestone in the construction of stable Zn-based MOFs and the incorporation of 3D linkers as a potential solution to challenging separations.     

Free energies of carbon dioxide sequestration and methane recovery in clathrate hydrates

Classical molecular dynamics simulations are used to compare the stability of methane, carbon dioxide, nitrogen, and mixed CO(2)N(2) structure I (sI) clathrates under deep ocean seafloor temperature and pressure conditions (275 K and 30 MPa) which were considered suitable for CO(2) sequestration. Substitution of methane guests in both the small and large sI cages by CO(2) and N(2) fluids are considered separately to determine the separate contributions to the overall free energy of substitution. The structure I clathrate with methane in small cages and carbon dioxide in large cages is determined to be the most stable. Substitutions of methane in the small cages with CO(2) and N(2) have positive free energies. Substitution of methane with CO(2) in the large cages has a large negative free energy and substitution of the methane in the large cages with N(2) has a small positive free energy. The calculations show that under conditions where storage is being considered, carbon dioxide spontaneously replaces methane from sI clathrates, causing the release of methane. This process must be considered if there are methane clathrates present where CO(2) sequestration is to be attempted. The calculations also indicate that N(2) does not directly compete with CO(2) during methane substitution or clathrate formation and therefore can be used as a carrier gas or may be present as an impurity. Simulations further reveal that the replacement of methane with CO(2) in structure II (sII) cages also has a negative free energy. In cases where sII CO(2) clathrates are formed, only single occupancy of the large cages will be observed.     

Stability of rare gas structure H clathrate hydrates

Molecular dynamics simulations are used to study the stability of structure H (sH) clathrate hydrates with the rare gases Ne, Ar, Kr, and Xe. Simulations on a 3 x 3 x 3 sH unit cell replica are performed at ambient pressure at 40 and 100 K temperatures. The small and medium (s+m) cages of the sH unit cell are assigned rare gas guest occupancies of 1 and for large (l) cages guest occupancies of 1-6 are considered. Radial distribution functions for guest pairs with occupancies in the l-l, l-(s+m), and (s+m)-(s+m) cages are presented. The unit cell volumes and configurational energies are studied as a function of large cage occupancy for the rare gases. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at 100 K and 1 bar and 20 kbar pressures. These studies show that the most stable argon clathrate has five guests in the large cages. For krypton and xenon the most stable configurations have three and two guests in the large cages, respectively.     

Antifreezes Act as Catalysts for Methane Hydrate Formation from Ice

Contrary to the thermodynamic inhibiting effect of methanol on methane hydrate formation from aqueous phases, hydrate forms quickly at high yield by exposing frozen water–methanol mixtures with methanol concentrations ranging from 0.6–10 wt % to methane gas at pressures from 125 bars at 253 K. Formation rates are some two orders of magnitude greater than those obtained for samples without methanol and conversion of ice is essentially complete. Ammonia has a similar catalytic effect when used in concentrations of 0.3–2.7 wt %. The structure I methane hydrate formed in this manner was characterized by powder X‐ray diffraction and Raman spectroscopy. Steps in the possible mechanism of action of methanol were studied with molecular dynamics simulations of the Ih (0001) basal plane exposed to methanol and methane gas. Simulations show that methanol from a surface aqueous layer slowly migrates into the ice lattice. Methane gas is preferentially adsorbed into the aqueous methanol surface layer. Possible consequences of the catalytic methane hydrate formation on hydrate plug formation in gas pipelines, on large scale energy‐efficient gas hydrate formation, and in planetary science are discussed.     

The Effect of Surface Charge Saturation on Heat‐induced Aggregation of Firefly Luciferase

We present here the effect of firefly luciferase surface charge saturation and the presence of some additives on its thermal‐induced aggregation. Three mutants of firefly luciferase prepared by introduction of surface Arg residues named as 2R, 3R and 5R have two, three and five additional arginine residues substituted at their surface compared to native luciferase; respectively. Turbidimetric study of heat‐induced aggregation indicates that all three mutants were reproducibly aggregated at higher rates relative to wild type in spite of their higher thermostability. Among them, 2R had most evaluated propensity to heat‐induced aggregation. Therefore, the hydrophilization followed by appearing of more substituted arginine residues with positive charge on the firefly luciferase surface was not reduced its thermal aggregation. Nevertheless, at the same condition in the presence of charged amino acids, e.g. Arg, Lys and Glu, as well as a hydrophobic amino acid, e.g. Val, the heat‐induced aggregation of wild type and mutants of firefly luciferases was markedly decelerated than those in the absence of additives. On the basis of obtained results it seems, relinquishment of variety in charge of amino acid side chains, they via local interactions with proteins cause to decrease rate and extent of their thermal aggregation.     

Synthesis of 8-aryl-7H-acenaphtho[1,2-d]imidazoles by multicomponent reaction of acenaphthylene-1,2-dione and aromatic aldehydes with ammonium acetate catalyzed by ferric hydrogensulfate

We report a novel and efficient method of synthesis of 8-aryl-7H-acenaphtho[1,2-d]imidazole derivatives, catalyzed by ferric hydrogensulfate in ethanol under reflux. A series of acenaphtho[1,2-d]imidazoles was synthesized in good to excellent yields from aromatic aldehydes, acenaphthylene-1,2-dione, and ammonium acetate. The remarkable features of this novel method are high conversion and simple experimental and work-up procedures.