The presence of at least two ionizable active center groups has been detected by a study of the effect of pH upon catalysis of hydrolysis of L-alanyl-beta-naphthylamide by human liver alanine aminopeptidase and upon the inhibition of hydrolysis by inhibitors and substrate analogs. Octanoic acid, octylamine, and peptide inhibitors have been found to be competitive inhibitors and are therefore thought to bind the active center. L-Phe was previously shown to bind the active center since it was found to be a competitive inhibitor of the hydrolysis of tripeptide substrates (Garner, C. W., and Behal, F. J. (1975), Biochemistry 14, 3208). A plot of pKm vs. pH for the substrate L-Ala-beta-naphthylamide showed that binding decreased below pH 5.9 and above 7.5, the points at which the theoretical curve undergoes an integral change in slope. These points are interpreted as the pKa either of substrate ionizable groups or binding-dependent enzyme active center groups. Similar plots of pKm vs. pH for L-alanyl-p-nitroanilide (as substrate) and pKi vs. pH for L-Leu-L-Leu-L-Leu and D-Leu-L-Tyr (as inhibitors) gave pairs fo pKa values of 5.8 and 7.4, 6.0 and 7.5, and 5.7 and 7.5, respectively. All the above substrates (and D-Leu-L-Tyr) have pKa values near 7.5; therefore, the binding-dependent group with a pKa value near 7.5 is possibly this substrate group. Similar plots of pKi vs. pH for the inhibitors L-Phe, L-Met, L-Leu, octylamine, and octanoic acid had only one bending point at 7.7, 7.6, 7.4, 6.3, and 5.9, respectively. Amino acid inhibitors, octylamine, and octanoic acid have no groups with pKa values between 5 and 9. These data indicate that there are two active center ionizable groups with pKa values of approximately 6.0 and 7.5 which are involved in substrate binding or inhibitory amino acid binding but not in catalysis since Vmax was constant at all pH values tested.
1. Substrate specificity of purified king cobra (Ophiophagus hannah) venom L-amino acid oxidase was investigated. 2. The enzyme was highly specific for the L-enantiomer of amino acid. Effective oxidation of L-amino acid by the enzyme requires the presence of a free primary alpha-amino group but the alpha-carboxylate group is not as critical for the catalysis. 3. The enzyme was very active against L-Lys, L-Phe, L-Leu, L-Tyr, L-Tryp, L-Arg, L-Met, L-ornithine, L-norleucine and L-norvaline and moderately active against L-His, L-cystine and L-Ileu. Other L-amino acids were oxidized slowly or not oxidized. 4. The data suggest the presence of a side chain binding site in the enzyme, and that the binding site comprises at least five 'subsites': the hydrophobic subsites a, b and c; and the two 'amino' binding subsites d and e. Subsite b appears to be able to accommodate two methylene/methyl carbons.
Aminoacylase I (EC. 3.5.1.14) was immobilized by covalent crosslinking to alginate molecules with 1-ethyl-3-(3-dimethyl-aminopropyl)-carbodiimide HCl followed by calcium alginate bead formation for the production of L-phenylalanine from the racemic mixtures of N-acetyl-DL-phenylalanine. Different concentrations of the coupling reagent were tested and the coupling process was optimized. The immobilized and the partially purified aminoacylase were characterized in terms of the activity, operational stability, thermal stability, pH and temperature optima and kinetic constants, Km and Vmax. The activity of the enzyme covalently immobilized in calcium alginate beads was enhanced by about 75% compared to that of free enzyme. The beads showed stable activity under operational conditions, they lost about 40% of their activity after four reaction cycles. The immobilized aminoacylase was more stable over a broader pH range. Thus this simple method provides irreversible immobilization of aminoacylase to give a biocatalyst with good operational stability and enhanced activity.
Hydrolysis of palm oil has become an important process in Oleochemical industries. Therefore, an investigation was carried out for hydrolysis of palm oil to fatty acid and glycerol using immobilized lipase in packed bed reactor. The conversion vs. residence time data were used in Michaelis-Menten rate equation to evaluate the kinetic parameters. A mathematical model for the rate of palm oil hydrolysis was proposed incorporating role of external mass transfer and pore diffusion. The model was simulated for steady-state isothermal operation of immobilized lipase packed bed reactor. The experimental data were compared with the simulated results. External mass transfer was found to affect the rate of palm oil hydrolysis at higher residence time.
The potential of quaternized wood (QW) chips in removing hexavalent chromium from synthetic solution and chrome waste under both batch and continuous-flow conditions was investigated. Sorption was found to be dependent on pH, metal concentration, and temperature. QW chips provide higher sorption capacity and wider pH range compared with untreated wood chips. The equilibrium data could be fitted into the Langmuir isotherm model, and maximum sorption capacities were calculated to be 27.03 and 25.77 mg/g in synthetic chromate solution and chrome waste, respectively. The presence of sulfate in high concentration appeared to suppress the uptake of chromium by QW chips. Column studies showed that bed depth influenced the breakthrough time greatly whereas flow rate of influent had little effect on its sorption on the column.
The main physical properties of ferroelectric crystals are described, and the macroscopic and microscopic viewpoints are discussed along with some applications, such as in capacitors and nonlinear optics. The emphasis is on physical understanding, while the mathematical level is kept to a minimum or supplemented by graphical representations to make the article more accessible.
Protein-ligand binding free energy values of wild-type and mutant C-terminal domain of Escherichia coli arginine repressor (ArgRc) protein systems bound to L-arginine or L-citrulline molecules were calculated using the linear interaction energy (LIE) method by molecular dynamics (MD) simulation. The binding behaviour predicted by the dissociation constant (K(d)) calculations from the binding free energy values showed preferences for binding of L-arginine to the wild-type ArgRc but not to the mutant ArgRc(D128N). On the other hand, L-citrulline do not favour binding to wild-type ArgRc but prefer binding to mutant ArgRc(D128N). The dissociation constant for the wild-type ArgRc-L-arginine complex obtained in this study is in agreement with reported experimental results. Our results also support the experimental data for the binding of L-citrulline to the mutant ArgRc(D128N). These showed that LIE method for protein-ligand binding free energy calculation could be applied to the wild-type and the mutant E. coli ArgRc-L-arginine and ArgRc-L-citrulline protein-ligand complexes and possibly to other transcriptional repressor-co-repressor systems as well.
High temperature liquid chromatography using water-rich and superheated water eluent is evaluated as a new approach for the separation of selected triazole fungicides, hexaconazole, tebuconazole, propiconazole, and difenoconazole. Using a polybutadiene-coated zirconia column at temperatures of 100-150 degrees C, clear separations were achieved when 100% purified water was utilized as organic-free eluent. Excellent limits of detection down to pg level were obtained for the separation of the triazole fungicides under optimum conditions. Van't Hoff plots for the separations were linear suggesting that no changes occurred in the retention mechanism over the temperature range studied.
The adsorption of residue oil from palm oil mill effluent (POME) using chitosan powder and flake has been investigated. POME contains about 2g/l of residue oil, which has to be treated efficiently before it can be discharged. Experiments were carried out as a function of different initial concentrations of residue oil, weight dosage, contact time and pH of chitosan in powder and flake form to obtain the optimum conditions for the adsorption of residue oil from POME. The powder form of chitosan exhibited a greater rate compared to the flake type. The results obtained showed that chitosan powder, at a dosage of 0.5g/l, 15min of contact time and a pH value of 5.0, presented the most suitable conditions for the adsorption of residue oil from POME. The adsorption process performed almost 99% of residue oil removal from POME. Equilibrium studies have been carried out to determine the capacity of chitosan for the adsorption of residue oil from POME using the optimum conditions from the flocculation at different initial concentrations of residue oil. Langmuir and Freundlich adsorption models were applied to describe the experimental isotherms and isotherm constants. Equilibrium data fitted very well with the Freundlich model. The pseudo first- and second-order kinetic models and intraparticle diffusion model were used to describe the kinetic data and the rate constants were evaluated. The experimental data fitted well with the second-order kinetic model, which indicates that the chemical sorption is the rate-limiting step, i.e. chemisorption between residue oil and chitosan. The significant uptake of residue oil on chitosan was further proved by BET surface area analysis and SEM micrographs.
In the present work, a single-step purification of recombinant nucleocapsid protein (NP) of the Newcastle disease virus (NDV) directly from unclarified feedstock using an expanded bed adsorption chromatography (EBAC) was developed. Streamline 25 column (ID = 25 mm) was used as a contactor and Streamline chelating adsorbent immobilized with Ni2+ ion was used as affinity adsorbent. The dynamic binding capacity of Ni2+ -loaded Streamline chelating adsorbent for the NP protein in unclarified feedstock was found to be 2.94 mg ml(-1) adsorbent at a superficial velocity of 200 cm h(-1). The direct purification of NP protein from unclarified feedstock using expanded bed adsorption has resulted in a 31% adsorption and 9.6% recovery of NP protein. The purity of the NP protein recovered was about 70% and the volume of processing fluid was reduced by a factor of 10. The results of the present study show that the IMA-EBAC developed could be used to combine the clarification, concentration and initial purification steps into a single-step operation.
The core protein (HBcAg) of hepatitis B virus (HBV) has been shown to interact with the large surface antigen during HBV morphogenesis, and these interactions can be blocked by small peptides selected from either linear or constrained phage display peptide libraries. The association of HBcAg with peptide inhibitors was quantitatively evaluated by isothermal titration calorimetry. The thermodynamic data show that the interaction between HBcAg and peptide MHRSLLGRMKGA is enthalpy-driven and occurs at a 3:1 stoichiometry and dissociation constant (Kd) value of 79.4 muM. However, peptide WSFFSNI displays a higher binding affinity for HBcAg with a Kd value of 18.5 muM when compared to peptide MHRSLLGRMKGA. A combinatorial approach using chemical cross-linking and surface-enhanced laser desorption/ionization-time-of-flight-mass spectrometry shows that the Lys of peptide MHRSLLGRMKGA interacted either with D64, E77, or D78 of HBcAg.
Molecular dynamics reaction simulation showed that the rate constant is not constant over the concentration profile of reactants and products over a fixed temperature regime, and this variation is expressed in terms of the defined reactivity coefficients. The ratio of these coefficients for the forward and backward reactions were found to equal that of the activity coefficient ratio for the product and reactant species. A theory was developed to explain kinetics in general based on these observations. Several other theorems had first to be developed, most striking of all was the inference that the excess Helmholtz free energy was the thermodynamical function which had a direct relation to these activity factors than the Gibbs free energy. The theory is applied to a class of ionic reactions which could not be rationalized using the standard Bjørn-Bjerrum theory of ionic reactions.
Adsorption isotherm and kinetics of methylene blue on activated carbon prepared from coconut husk were determined from batch tests. The effects of contact time (1-30 h), initial dye concentration (50-500 mg/l) and solution temperature (30-50 degrees C) were investigated. Equilibrium data were fitted to Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherm models. The equilibrium data were best represented by Langmuir isotherm model, showing maximum monolayer adsorption capacity of 434.78 mg/g. The kinetic data were fitted to pseudo-first-order, pseudo-second-order and intraparticle diffusion models, and was found to follow closely the pseudo-second-order kinetic model. Thermodynamic parameters such as standard enthalpy (DeltaH degrees), standard entropy (DeltaS degrees) and standard free energy (DeltaG degrees) were evaluated. The adsorption interaction was found to be exothermic in nature. Coconut husk-based activated carbon was shown to be a promising adsorbent for removal of methylene blue from aqueous solutions.
Biosorption of cadmium (II) ions from aqueous solution onto immobilized cells of Pycnoporus sanguineus (P. sanguineus) was investigated in a batch system. Equilibrium and kinetic studies were conducted by considering the effect of pH, initial cadmium (II) concentration, biomass loading and temperature. Results showed that the uptake of cadmium (II) ions increased with the increase of initial cadmium (II) concentration, pH and temperature. Langmuir, Freundlich and Redlich-Peterson isotherm models were used to analyze the equilibrium data at different temperatures. Langmuir isotherm model described the experimental data well followed by Redlich-Peterson and Freundlich isotherm models. Biosorption kinetics data were fitted using pseudo-first, pseudo-second-order and intraparticle diffusion. It was found that the kinetics data fitted well the pseudo-second-order followed by intraparticle diffusion. Thermodynamic parameters such as standard Gibbs free energy (Delta G0), standard enthalpy (Delta H0) and standard entropy (Delta S0) were evaluated. The result showed that biosorption of cadmium (II) ions onto immobilized cells of P. sanguineus was spontaneous and endothermic nature.
Macrolides are a group of diverse class of naturally occurring and synthetic antibiotics made of macrocyclic-lactone ring carrying one or more sugar moieties linked to various atoms of the lactone ring. These macrolides selectively bind to a single high affinity site on the prokaryotic 50S ribosomal subunit, making them highly effective towards a wide range of bacterial pathogens. The understanding of binding between macrolides and ribosome serves a good basis in elucidating how they work at the molecular level and these findings would be important in rational drug design. Here, we report refinement of reconstructed PDB structure of erythromycin-ribosome system using molecular dynamics (MD) simulation. Interesting findings were observed in this refinement stage that could improve the understanding of the binding of erythromycin A (ERYA) onto the 50S subunit. The results showed ERYA was highly hydrated and water molecules were found to be important in bridging hydrogen bond at the binding pocket during the simulation time. ERYA binding to ribosome was also strengthened by hydrogen bond network and hydrophobic interactions between the antibiotic and the ribosome. Our MD simulation also demonstrated direct interaction of ERYA with Domains II, V and with C1773 (U1782EC), a residue in Domain IV that has yet been described of its role in ERYA binding. It is hoped that this refinement will serve as a starting model for a further enhancement of our understanding towards the binding of ERYA to ribosome.
In this paper, the ability of coconut bunch waste (CBW), an agricultural waste available in large quantity in Malaysia, to remove basic dye (methylene blue) from aqueous solution by adsorption was studied. Batch mode experiments were conducted at 30 degrees C to study the effects of pH and initial concentration of methylene blue (MB). Equilibrium adsorption isotherms and kinetics were investigated. The experimental data were analyzed by the Langmuir, Freundlich and Temkin models of adsorption. The adsorption isotherm data were fitted well to Langmuir isotherm and the monolayer adsorption capacity was found to be 70.92 mg/g at 30 degrees C. The kinetic data obtained at different concentrations have been analyzed using a pseudo-first-order, pseudo-second-order equation and intraparticle diffusion equation. The experimental data fitted very well the pseudo-second-order kinetic model.
The sorption of basic dye from aqueous solutions by banana stalk waste (BSW), an abundant agricultural waste in Malaysia, was studied in a batch system with respect to pH and initial dye concentration. Sorption isotherm of methylene blue (MB) onto the BSW was determined at 30 degrees C with the initial concentrations of MB in the range of 50-500 mg/L. At pH 2.0, the sorption of dye was not favorable, while the sorption at other pHs (4.0-12.0) was remarkable. Equilibrium data were fitted to the Langmuir, Freundlich and Temkin isotherm models. The equilibrium data were best represented by the Langmuir isotherm model, with maximum monolayer adsorption capacity of 243.90 mg/g. The sorption kinetic data were analyzed using pseudo-first-order, pseudo-second-order and intraparticle diffusion models. It was found that the pseudo-second-order kinetic model was the best applicable model to describe the sorption kinetics. The results showed that BSW sorbent was a promising for the removal of MB from aqueous solutions.
In this work, the adsorption of malachite green (MG) on rattan sawdust (RSD) was studied at 30 degrees C. The results indicated that RSD can be used as a low-cost adsorbent for the removal of MG dye from aqueous solutions. Equilibrium data were analyzed by two isotherms, namely the Freundlich isotherm and the Langmuir isotherm. The best fit to the data was obtained with the Langmuir isotherm. The monolayer adsorption capacity of RSD was found to be 62.71 mg/g. The adsorption kinetics can be predicted by the pseudo-first-order model. The mechanism of adsorption was also studied. It was found that for a short time period the rate of adsorption is controlled by film diffusion. However, at longer adsorption times, pore-diffusion controls the rate of adsorption. The amount adsorbed on the outer surface was estimated from the time where film-diffusion stops controlling the adsorption rate.
Activated carbon derived from rattan sawdust (ACR) was evaluated for its ability to remove phenol from an aqueous solution in a batch process. Equilibrium studies were conducted in the range of 25-200mg/L initial phenol concentrations, 3-10 solution pH and at temperature of 30 degrees C. The experimental data were analyzed by the Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherm models. Equilibrium data fitted well to the Langmuir model with a maximum adsorption capacity of 149.25mg/g. The dimensionless separation factor RL revealed the favorable nature of the isotherm of the phenol-activated carbon system. The pseudo-second-order kinetic model best described the adsorption process. The results proved that the prepared activated carbon was an effective adsorbent for removal of phenol from aqueous solution.
The continuing rise in tuberculosis incidence and the problem of drug resistance strains have prompted the research on new drug candidates and the mechanism of drug resistance. Molecular docking and molecular dynamics simulation (MD) were performed to study the binding of isoniazid onto the active site of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) in an attempt to address the mycobacterial resistance against isoniazid. Results show that isonicotinic acyl-NADH (INADH) has an extremely high binding affinity toward the wild type InhA by forming stronger interactions compared to the parent drug (isoniazid) (INH). Due to the increase of hydrophobicity and reduction in the side chain's volume of A94 of mutant type InhA, both INADH and the mutated protein become more mobile. Due to this reason, the molecular interactions of INADH with mutant type are weaker than that observed with the wild type. However, the reduced interaction caused by the fluctuation of INADH and the mutant protein only inflected minor resistance in the mutant strain as inferred from free energy calculation. MD results also showed there exists a water-mediated hydrogen bond between INADH and InhA. However, the bridged water molecule is only present in the INADH-wild type complex, reflecting the putative role of the water molecule in the binding of INADH to the wild type protein. The results support the assumption that the conversion of prodrug isoniazid into its active form INADH is mediated by KatG as a necessary step prior to target binding on InhA. Our findings also contribute to a better understanding of INH resistance in mutant type.