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1.
Environ Monit Assess ; 195(12): 1530, 2023 Nov 25.
Article in English | MEDLINE | ID: mdl-38006447

ABSTRACT

ZSM-5 zeolite was successfully synthesized from bentonite clay sourced from Lam Dong Province, Vietnam, using the hydrothermal method at 170 °C for 18 h. The synthesized ZSM-5 (SiO2/Al2O3 ratio ~ 34) exhibited a single phase with high crystallinity (91.8%), and a clear and uniform shape. In a detailed examination of the synthesized material's Pb(II) adsorptive capacity, various factors were taken into account, including pH, interaction time, ionic strength, and the amount of adsorbent. Isotherms and kinetics were examined to elucidate the uptake behavior. Study results suggested that Pb(II) ion uptake by ZSM-5 was most appropriately described by the Sips isotherm and intraparticle diffusion kinetic models. The calculated maximum monolayer adsorption capacity according to the Langmuir isotherm model was 48.36 mg/g. Furthermore, the adsorption mechanisms of Pb(II) on ZSM-5 involving electrostatic interactions, ion exchange, and diffusion into pores were demonstrated using the analytical techniques before and after Pb(II) adsorption. These findings demonstrate that ZSM-5 synthesized from bentonite clay exhibits an excellent adsorption capacity for Pb(II), resulting in promising applications for treating drinking water or aqueous industrial waste containing Pb(II) ions.


Subject(s)
Bentonite , Clay , Water Pollutants, Chemical , Adsorption , Environmental Monitoring , Hydrogen-Ion Concentration , Kinetics , Lead , Silicon Dioxide , Southeast Asian People , Vietnam , Water , Water Pollutants, Chemical/analysis
2.
Environ Monit Assess ; 195(11): 1266, 2023 Oct 03.
Article in English | MEDLINE | ID: mdl-37787870

ABSTRACT

Kinetic studies play an instrumental role in determining the most appropriate reaction rate model for industrial-scale applications. This study focuses on the kinetics of methylene blue (MB) adsorption from aqueous solutions by biochar derived from jackfruit peel. Various kinetic models, including pseudo-first-order (PFO), pseudo-second-order (PSO), intra-diffusion, and Elovich models, were applied to study MB adsorption kinetics of jackfruit peel biochar. The experiments were performed with two initial concentrations of MB (24.23 mg/L and 41.42 mg/L) over a span of 240 min. Our findings emphasized that the Elovich model provided the best fit of the experimental data for MB adsorption. When compared to other materials, biochar from jackfruit peel emerges as an eco-friendly adsorbent for dye decolorization, with potential applications in the treatment of environmental pollution.


Subject(s)
Artocarpus , Water Pollutants, Chemical , Methylene Blue , Kinetics , Hydrogen-Ion Concentration , Environmental Monitoring , Water , Adsorption
3.
Environ Monit Assess ; 195(2): 254, 2023 Jan 02.
Article in English | MEDLINE | ID: mdl-36592254

ABSTRACT

This study used red mud modified with chitosan (RM/CS) as a novel adsorbent to remove Ni(II) ions from an aqueous solution. The adsorbent was characterized by the techniques of the BET method, X-ray diffraction (XRD), and scanning electron microscopy (SEM) analysis. According to the findings, the surface area of RM/CS is nearly doubled compared to CS, from 68.6 to 105.7 m2.g-1. The Ni(II) batch adsorption of RM/CS was performed as a function of pH value, contact time, and volume of adsorbent. Three isotherm adsorption models (Langmuir, Freundlich, and Sips) and three kinetic models (the pseudo-first-order, the pseudo-second-order, and the intra-diffusion models) were fitted with the experimental data to calculate the maximum adsorption capacity and to estimate the uptake in nature. The Langmuir monolayer adsorption capacity for Nickel (II) is 31.66 mg.g-1 at a pH of 6.0, with an adsorption time of 180 min and a temperature of 323 K. The Ni(II) adsorption on RM/CS is the exothermic process and is controlled by the intra-diffusion model.


Subject(s)
Chitosan , Water Pollutants, Chemical , Chitosan/chemistry , Environmental Monitoring , Nickel/chemistry , Temperature , Ions , Adsorption , Kinetics , Hydrogen-Ion Concentration , Water Pollutants, Chemical/chemistry , Thermodynamics
4.
Langmuir ; 38(50): 15604-15613, 2022 Dec 20.
Article in English | MEDLINE | ID: mdl-36507853

ABSTRACT

Manganese dioxide nanomaterials have wide applications in many areas from catalysis and Li-ion batteries to gas sensing. Understanding the crystallization pathways, morphologies, and formation of defects in their structure is particularly important but still a challenging issue. Herein, we employed an arsenal of X-ray diffraction (XRD), scanning electron microscopy (SEM), neutron diffraction, positron annihilation spectroscopies, and ab initio calculations to investigate the evolution of the morphology and structure of α-MnO2 nanomaterials prepared via reduction of KMnO4 solution with C2H5OH prior to being annealed in air at 200-600 °C. We explored a novel evolution that α-MnO2 nucleation can be formed even at room temperature and gradually developed to α-MnO2 nanorods at above 500 °C. We also found the existence of H+ or K+ ions in the [1 × 1] tunnels of α-MnO2 and observed the simultaneous presence of Mn and O vacancies in α-MnO2 crystals at low temperatures. Increasing the temperature removed these O vacancies, leaving only the Mn vacancies in the samples.

5.
Chemosphere ; 287(Pt 3): 132279, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34563768

ABSTRACT

Red mud modified by chitosan (RM/CS) was utilized as an adsorbent to effectively remove Pb(II) from aqueous solution. The surface area of RM/CS was found to significantly increase by more than 50% compared to that of original red mud. Different factors that affected the Pb(II) removal on this material, such as initial Pb(II) concentration, pH, and contact time, were investigated. The pseudo-first-order, pseudo-second-order, and intra-diffusion models were used to fit the experimental data to investigate the Pb(II)'s removal kinetics. The Pb(II) removal followed the intra-diffusion model. Additionally, the non-zero C value obtained from this model indicates that the removal was controlled by many different mechanisms. We also found that the interaction of Pb(II) and carbonate group on the material's surface played a primary role once the adsorption equilibrium was reached. Finally, the maximum adsorptive capacity was found to be about 209 mg/g. This obtained value is higher than those obtained for some other materials. Therefore, the present RM/CS should be a potential material for removing Pb(II) from aqueous solution.


Subject(s)
Chitosan , Water Pollutants, Chemical , Adsorption , Hydrogen-Ion Concentration , Kinetics , Lead
6.
Int J Biol Macromol ; 163: 1369-1374, 2020 Nov 15.
Article in English | MEDLINE | ID: mdl-32758598

ABSTRACT

Xylan and pectin are major structural components of plant cell walls. There are two independent catabolic pathways for xylan and pectin. UxaE bridges these two pathways by reversibly epimerizing D-fructuronate and D-tagaturonate. The crystal structure of UxaE from Cohnella laeviribosi (ClUxaE) shows a core scaffold of TIM-barrel with a position-changing divalent metal cofactor. ClUxaE has the flexible metal-coordination loop to allow the metal shift and the extra domains to bind a phosphate ion in the active site, which are important for catalysis and substrate specificity. Elucidation of the structure and mechanism of ClUxaE will assist in understanding the catalytic mechanism of UxaE family members, which are useful for processing both xylan and pectin-derived carbohydrates for practical and industrial purposes, including the transformation of agricultural wastes into numerous valuable products.


Subject(s)
Bacillales/chemistry , Catalysis/drug effects , Racemases and Epimerases/chemistry , Sugars/chemistry , Carbohydrates/chemistry , Catalytic Domain/drug effects , Metals/chemistry , Pectins/chemistry , Phosphates/chemistry , Substrate Specificity , Xylans/chemistry
7.
Chemosphere ; 257: 127147, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32473410

ABSTRACT

In this report, the adsorption of Cr(VI) onto MnO2/CS nanocomposite material from aqueous solution is investigated. All the factors, which affect the adsorption, such as pH, adsorption time, Cr(VI) initial concentration and adsorbent dosage, are also examined. The results obtained show that the Cr(VI) uptake is strongly affected by pH and ion strength. Analysis within the nonlinear isotherm models indicates that the Sips isotherm combining with the Langmuir and Freundlich models offer the best fit to the experimental data due to the obtained highest R2 and smallest RMSE and χ2 values. The calculated Langmuir monolayer adsorption capacity is 61.56 mg g-1 at pH of 2.0 and adsorption time of 120 min. Moreover, the mechanism studies by combining theoretical models with analytical spectroscopies reveal that the electrostatic attraction plays the important role to the uptake of Cr(VI) onto MnO2/CS nanocomposite. Therefore, the present nanocomposite material can be applied to remove total Cr from wastewater produced by the galvanized manufacturing factory with a relatively high efficiency.


Subject(s)
Chromium/analysis , Water Pollutants, Chemical/analysis , Water Purification/methods , Adsorption , Chitosan , Hydrogen-Ion Concentration , Kinetics , Manganese Compounds , Nanocomposites , Oxides/analysis , Wastewater/analysis , Water/analysis
8.
Chem Biol Interact ; 289: 90-97, 2018 Jun 01.
Article in English | MEDLINE | ID: mdl-29723517

ABSTRACT

Human cytochrome P450 2B6 is an important hepatic enzyme for the metabolism of xenobiotics and clinical drugs. Recently, more attention has been paid to P450 2B6 because of the increasing number of drugs it metabolizes. It has been known to interact with terpenes, the major constituents of the essential oils used for various medicinal purposes. In this study, the effect of monoterpenes on P450 2B6 catalytic activity was investigated. Recombinant P450 2B6 was expressed in Escherichia coli and purified using Ni-affinity chromatography. The purified P450 2B6 enzyme displayed bupropion hydroxylation activity in gas-mass spectrometry (GC-MS) analysis with a kcat of 0.5 min-1 and a Km of 47 µM. Many terpenes displayed the type I binding spectra to purified P450 2B6 enzyme and α-terpinyl acetate showed strong binding affinity with a Kd value of 5.4 µM. In GC-MS analysis, P450 2B6 converted α-terpinyl acetate to a putative oxidative product. The bupropion hydroxylation activity of P450 2B6 was inhibited by α-terpinyl acetate and its IC50 value was 10.4 µM α-Terpinyl acetate was determined to be a competitive inhibitor of P450 2B6 with a Ki value of 7.6 µM. The molecular docking model of the binding site of the P450 2B6 complex with α-terpinyl acetate was constructed. It showed the tight binding of α-terpinyl acetate in the active site of P450 2B6, which suggests that it could be a competitive substrate for P450 2B6.


Subject(s)
Cytochrome P-450 CYP2B6 Inhibitors/pharmacology , Cytochrome P-450 CYP2B6/metabolism , Terpenes/pharmacology , Biocatalysis , Bupropion/chemistry , Bupropion/pharmacology , Cytochrome P-450 CYP2B6/isolation & purification , Cytochrome P-450 CYP2B6 Inhibitors/chemistry , Gas Chromatography-Mass Spectrometry , Hydroxylation , Kinetics , Molecular Docking Simulation , Oxidation-Reduction , Spectrum Analysis , Terpenes/chemistry
9.
Int J Biol Macromol ; 105(Pt 1): 816-824, 2017 Dec.
Article in English | MEDLINE | ID: mdl-28732729

ABSTRACT

Aldehyde dehydrogenases (ALDHs) are NAD(P)+-dependent oxidoreductases that catalyze the oxidation of a variety of aldehydes to their acid forms. In this study, we determined the crystal structures of ALDH from Bacillus cereus (BcALDH), alone, and in complex with NAD+ and NADP+. This enzyme can oxidize all-trans-retinal to all-trans-retinoic acid using either NAD+ or NADP+ with equal efficiency, and atypically, as a minor activity, can reduce all-trans-retinal to all-trans-retinol using NADPH. BcALDH accommodated the additional 2'-phosphate of NADP+ by expanding the cofactor-binding pocket and upshifting the AMP moiety in NADP+. The nicotinamide moiety in NAD+ and NADP+ had direct interactions with the conserved catalytic residues (Cys300 and Glu266) and caused concerted conformational changes. We superimposed the structure of retinoic acid bound to human ALDH1A3 onto the BcALDH structure and speculated a model of the substrate all-trans-retinal bound to BcALDH. We also proposed a plausible mechanism for the minor reducing activity of BcALDH. These BcALDH structures will be useful in understanding cofactor specificity and the catalytic mechanism of an atypical bacterial BcALDH and should help the development of a new biocatalyst to produce retinoic acid and related high-end products.


Subject(s)
Aldehyde Dehydrogenase/chemistry , Aldehyde Dehydrogenase/metabolism , Catalytic Domain , Crystallography, X-Ray , Models, Molecular , NAD/metabolism , NADP/metabolism , Oxidation-Reduction , Prohibitins , Vitamin A/metabolism
10.
Archaea ; 2017: 5395293, 2017.
Article in English | MEDLINE | ID: mdl-28536498

ABSTRACT

Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S0) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5'-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon Thermococcus onnurineus NA1.


Subject(s)
Archaeal Proteins/chemistry , Carbon-Sulfur Lyases/chemistry , Thermococcus/enzymology , Protein Conformation
11.
Appl Microbiol Biotechnol ; 101(10): 4073-4083, 2017 May.
Article in English | MEDLINE | ID: mdl-28180917

ABSTRACT

ß-1,3-1,4-Glucanase (BGlc8H) from Paenibacillus sp. X4 was mutated by error-prone PCR or truncated using termination primers to improve its enzyme properties. The crystal structure of BGlc8H was determined at a resolution of 1.8 Å to study the possible roles of mutated residues and truncated regions of the enzyme. In mutation experiments, three clones of EP 2-6, 2-10, and 5-28 were finally selected that exhibited higher specific activities than the wild type when measured using their crude extracts. Enzyme variants of BG2-6, BG2-10, and BG5-28 were mutated at two, two, and six amino acid residues, respectively. These enzymes were purified homogeneously by Hi-Trap Q and CHT-II chromatography. Specific activity of BG5-28 was 2.11-fold higher than that of wild-type BGwt, whereas those of BG2-6 and BG2-10 were 0.93- and 1.19-fold that of the wild type, respectively. The optimum pH values and temperatures of the variants were nearly the same as those of BGwt (pH 5.0 and 40 °C, respectively). However, the half-life of the enzyme activity and catalytic efficiency (k cat/K m) of BG5-28 were 1.92- and 2.12-fold greater than those of BGwt at 40 °C, respectively. The catalytic efficiency of BG5-28 increased to 3.09-fold that of BGwt at 60 °C. These increases in the thermostability and catalytic efficiency of BG5-28 might be useful for the hydrolysis of ß-glucans to produce fermentable sugars. Of the six mutated residues of BG5-28, five residues were present in mature BGlc8H protein, and two of them were located in the core scaffold of BGlc8H and the remaining three residues were in the substrate-binding pocket forming loop regions. In truncation experiments, three forms of C-terminal truncated BGlc8H were made, which comprised 360, 286, and 215 amino acid residues instead of the 409 residues of the wild type. No enzyme activity was observed for these truncated enzymes, suggesting the complete scaffold of the α6/α6-double-barrel structure is essential for enzyme activity.


Subject(s)
Glycoside Hydrolases/genetics , Glycoside Hydrolases/metabolism , Mutagenesis, Site-Directed , Paenibacillus/enzymology , Catalysis , Cloning, Molecular , Crystallization , DNA Primers , Gene Expression , Half-Life , Hydrogen-Ion Concentration , Kinetics , Paenibacillus/genetics , Polymerase Chain Reaction/methods , Protein Conformation , Substrate Specificity , Temperature , beta-Glucans/metabolism
12.
BMB Rep ; 49(12): 681-686, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27733232

ABSTRACT

Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2+ ion. Citrate and TRIS bound EcFBA structures showed Zn2+ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2+ within EcFBA without losing it. [BMB Reports 2016; 49(12): 681-686].


Subject(s)
Fructose-Bisphosphate Aldolase/chemistry , Zinc/metabolism , Binding Sites , Catalysis , Catalytic Domain , Citric Acid/chemistry , Citric Acid/metabolism , Crystallography, X-Ray , Escherichia coli/metabolism , Fructose-Bisphosphate Aldolase/genetics , Fructose-Bisphosphate Aldolase/metabolism , Protein Structure, Quaternary , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Zinc/chemistry
13.
J Agric Food Chem ; 64(39): 7307-7314, 2016 Oct 05.
Article in English | MEDLINE | ID: mdl-27616570

ABSTRACT

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight on rice; this species is one of the most destructive pathogenic bacteria in rice cultivation worldwide. Peptide deformylase (PDF) catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized polypeptides in bacterial cells and is an important target to develop antibacterial agents. We determined crystal structures of Xoo PDF (XoPDF) at up to 1.9 Å resolution, which include apo, two substrate-bound (methionine-alanine or methionine-alanine-serine), an inhibitor-bound (actinonin), and six fragment chemical-bound structures. Six fragment chemical compounds were bound in the substrate-binding pocket. The fragment chemical-bound structures were compared to the natural PDF inhibitor actinonin-bound structure. The fragment chemical molecules will be useful to design an inhibitor specific to XoPDF and a potential pesticide against Xoo.


Subject(s)
Amidohydrolases/chemistry , Bacterial Proteins/chemistry , Xanthomonas/enzymology , Anti-Bacterial Agents , Crystallography, X-Ray , Gene Expression Regulation, Bacterial , Hydroxamic Acids/chemistry , Oryza/microbiology , Peptides/chemistry , Plant Diseases/microbiology , Structure-Activity Relationship
14.
Acta Crystallogr F Struct Biol Commun ; 70(Pt 5): 639-42, 2014 May.
Article in English | MEDLINE | ID: mdl-24817728

ABSTRACT

RNA polymerase (RNAP) plays a crucial role in gene expression in all organisms. It is a multiprotein complex that produces primary transcript RNA. Generally, the basal transcription apparatus in archaea is simpler than the eukaryotic RNA polymerase II counterpart. To understand the structure and function of archaeal RNAP, the TON-0309 gene encoding DNA-directed RNA polymerase subunit L (ToRNAP_L) from Thermococcus onnurineus NA1 was cloned and the protein was overexpressed in Escherichia coli, purified and crystallized. The purified protein was crystallized using the hanging-drop vapour-diffusion method and the crystal diffracted to 2.10 Å resolution. The crystal belonged to the hexagonal space group P6122, with unit-cell parameters a = b = 42.3, c = 211.2 Å. One molecule was present in the asymmetric unit, with a corresponding VM of 2.5 Å(3) Da(-1) and a solvent content of 50.0%.


Subject(s)
DNA-Directed RNA Polymerases/biosynthesis , DNA/biosynthesis , Gene Expression Regulation, Enzymologic , Thermococcus/enzymology , Crystallization , Crystallography, X-Ray , DNA/chemistry , DNA-Directed RNA Polymerases/chemistry , DNA-Directed RNA Polymerases/isolation & purification
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