scholarly journals Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis

2020 ◽  
Author(s):  
Shanzhong Gong ◽  
Serdal Kirmizialtin ◽  
Adrienne Chang ◽  
Joshua E. Mayfield ◽  
Yan Jessie Zhang ◽  
...  
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Kinetic Studies ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Hiv Reverse Transcriptase ◽  
Nucleotide Incorporation ◽  
Weak Binding ◽  
Kinetic And Thermodynamic Analysis ◽  
Nucleotide Specificity

AbstractWe examined the roles of Mg2+ ions in DNA polymerization by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase and by molecular dynamics simulation of Mg2+ binding. Binding of the Mg-nucleotide complex induces a conformational change of the enzyme from open to closed states in a process that is independent of free Mg2+ concentration. Subsequently, the second Mg2+ binds weakly to the closed state of the enzyme-DNA-Mg.dNTP complex with an apparent Kd = 3.7 mM and facilitates the catalytic reaction. This weak binding of the catalytic Mg2+ is important to maintain fidelity in that the Mg2+ samples the correctly aligned substrate without perturbing the equilibrium at physiological Mg2+ concentrations. The binding of the catalytic Mg2+ increases nucleotide specificity (kcat/Km) by increasing the rate of the chemistry and decreasing the rate of enzyme opening allowing nucleotide release. Changing the free Mg2+ concentration from 0.25 to 10 mM increased nucleotide specificity (kcat/Km) by 12-fold. Mg2+ binds very weakly to the open state of the enzyme in the absence of nucleotide (Kd ≈ 34 mM) and competes with Mg.dNTP. Analysis based on publish crystal structures showed that HIV RT binds only two metal ions during incorporation of a correct base-pair. MD simulations support the kinetic studies suggesting weak binding of the catalytic Mg2+ in open and closed states. They also support the two-metal ion mechanism, although the polymerase may bind a third metal ion in the presence of a mismatched nucleotide.

scholarly journals Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis

2020 ◽  
pp. jbc.RA120.016489
Author(s):  
Shanzhong Gong ◽  
Serdal Kirmizialtin ◽  
Adrienne Chang ◽  
Joshua E. Mayfield ◽  
Yan Jessie Zhang ◽  
...  
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Dna Polymerases ◽  
Critical Role ◽  
Md Simulations ◽  
Enzyme Analysis ◽  
Hiv Reverse Transcriptase ◽  
Nucleotide Incorporation ◽  
Weak Binding ◽  
Nucleotide Specificity

Magnesium ions play a critical role in catalysis by many enzymes and they contribute to the fidelity of DNA polymerases through a two-metal ion mechanism. However, specificity is a kinetic phenomenon and the roles of Mg2+ions in each step in catalysis have not been resolved. We first examined the roles of Mg2+ by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase We show that Mg.dNTP binding induces an enzyme conformational change at a rate that is independent of free Mg2+ concentration. Subsequently, the second Mg2+ binds to the closed state of the enzyme-DNA-Mg.dNTP complex (Kd = 3.7 mM) to facilitate catalysis. Weak binding of the catalytic Mg2+ contributes to fidelity by sampling the correctly aligned substrate without perturbing the equilibrium for nucleotide binding at physiological Mg2+ concentrations. Increasing Mg2+ concentration from 0.25 to 10 mM increases nucleotide specificity (kcat/Km) 12-fold by largely increasing the rate of the chemistry relative to the rate of nucleotide release. Mg2+ binds very weakly (Kd ≤ 37 mM) to the open state of the enzyme. Analysis of published crystal structures showed that HIV RT binds only two metal ions prior to incorporation of a correct base-pair. MD simulations support the two-metal ion mechanism and the kinetic data indicating weak binding of the catalytic Mg2+. MD simulations also revealed the importance of the divalent cation cloud surrounding exposed phosphates on the DNA. These results enlighten the roles of the two metal ions the specificity of DNA polymerases.

Efficient Preconcentration of Cu2+, Zn2+ and Fe3+ with an Agarose-Schiff Base Sorbent

2007 ◽  
Vol 72 (7) ◽  
pp. 908-916 ◽  
Author(s):  
Payman Hashemi ◽  
Hatam Hassanvand ◽  
Hossain Naeimi
Keyword(s):  
Schiff Base ◽  
Metal Ions ◽  
Metal Ion ◽  
Good Accuracy ◽  
Kinetic Studies ◽  
Sample Volume ◽  
Effects Of Ph ◽  
Glass Column ◽  
High Concentrations ◽  
Ph Range

Sorption and preconcentration of Cu2+, Zn2+ and Fe3+ on a salen-type Schiff base, 2,2'- [ethane-1,2-diylbis(nitrilomethylidyne)]bis(2-methylphenol), chemically immobilized on a highly crosslinked agarose support, were studied. Kinetic studies showed higher sorption rates of Cu2+ and Fe3+ in comparison with Zn2+. Half-times (t1/2) of 31, 106 and 58 s were obtained for sorption of Cu2+, Zn2+ and Fe3+ by the sorbent, respectively. Effects of pH, eluent concentration and volume, ionic strength, buffer concentration, sample volume and interferences on the recovery of the metal ions were investigated. A 5-ml portion of 0.4 M HCl solution was sufficient for quantitative elution of the metal ions from 0.5 ml of the sorbent packed in a 6.5 mm i.d. glass column. Quantitative recoveries were obtained in a pH range 5.5-6.5 for all the analytes. The volumes to be concentrated exceeding 500 ml, ionic strengths as high as 0.5 mol l-1, and acetate buffer concentrations up to 0.3 mol l-1 for Zn2+ and 0.4 mol l-1 for Cu2+ and Fe3+ did not have any significant effect on the recoveries. The system tolerated relatively high concentrations of diverse ions. Preconcentration factors up to 100 and detection limits of 0.31, 0.16 and 1.73 μg l-1 were obtained for Cu2+, Zn2+ and Fe3+, respectively, for their determination by a flame AAS instrument. The method was successfully applied to the metal ion determinations in several river water samples with good accuracy.

scholarly journals A Study on the Photocatalytic Reduction of Some Metal Ions in Aqueous Solution Using UV- Titanium Dioxide System

2019 ◽  
pp. 1-7
Author(s):  
I. O. Ekwere ◽  
M. Horsfall ◽  
J. O. E. Otaigbe
Keyword(s):  
Aqueous Solution ◽  
Titanium Dioxide ◽  
Metal Ions ◽  
Metal Ion ◽  
Uv Light ◽  
Kinetic Studies ◽  
Photocatalytic Reduction ◽  
Alkaline Ph ◽  
Removal Of Metal ◽  
Removal Of Metal Ions

The photocatalytic reduction of Cu (II), Pb (II), Cd (II) and Cr (VI) ions in aqueous solution has been investigated. The photocatalyst utilized was nano titanium dioxide, composed of 80% anatase and 20% rutile; the UV light source was a 15 W UV bulb with a wavelength of 254 nm. The results obtained indicated a reduction efficiency order as follows; Cr6+ > Cu2+ > Pb2+ > Cd2+. It was observed that these results correlate with the respective reduction potentials of the metal ions. The effect of pH on the photocatalytic reduction of the metal ions was also carried out and results obtained indicated that with the exception of Cr (VI) ions, higher percentage removal of metal ions from their aqueous solution was recorded at alkaline pH than at acidic pH. This was attributed to an extensive formation of precipitate by the metal ions at alkaline pH. Kinetic studies revealed that the removal of metal ions from their solutions largely followed the pseudo- first-order kinetics. Therefore, the results of this study will be useful in metal ion removal from industrial waste water using photocatalytic process.

scholarly journals Effective removal of heavy metal ions from aqueous solutions using a new chelating resin poly [2,5-(1,3,4-thiadiazole)-benzalimine]: kinetic and thermodynamic study

2015 ◽  
Vol 6 (2) ◽  
pp. 310-324 ◽  
Author(s):  
Selvaraj Dinesh Kirupha ◽  
Selvaraj Kalaivani ◽  
Thangaraj Vidhyadevi ◽  
Periyaraman Premkumar ◽  
Palanithamy Baskaralingam ◽  
...  
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Ph Value ◽  
Thermo Gravimetric Analysis ◽  
Kinetic Studies ◽  
Ion Concentration ◽  
Chelating Resin ◽  
Gravimetric Analysis ◽  
Equilibrium Data ◽  
Experimental Values

A novel poly [2,5-(1,3,4-thiadiazole)-benzalimine] abbreviated as TDPI adsorbent was synthesized using simple polycondensation technique. The synthetic route involves the preparation of 2,5-diamino-1,3,4-thiadiazole from 2,5-dithiourea and subsequent condensation with terephthalaldehyde. The resin was chemically characterized using Fourier transform infrared (FT-IR), 1H-NMR, and 13C-NMR spectroscopic analysis. Surface morphology and thermal stability were analyzed using scanning electron microscopy (SEM) and thermo-gravimetric analysis (TGA). The effect of the pH value of solution, contact time, adsorbent dose, and initial metal ion concentration were investigated by batch equilibrium adsorption experiments. Kinetic studies show that the adsorption of metal ions onto the resin proceeds according to the pseudo-second-order model and the equilibrium data were best interpreted by the Redlich–Peterson isotherm. The experimental values of the adsorption capacities of Pb2+, Cu2+, Ni2+, and Cd2+ on to TDPI could reach up to 437.2, 491.6, 493.7, and 481.9 mg.g−1 respectively. The exothermic nature of the process, the affinity of the adsorbent towards the metal ions and the feasibility of the process are explained in the thermodynamic parameters. The resin stability and re-usability studies suggest that the resin is chemically stable (0.3 N HCl and H2SO4) and could be regenerated without any serious decline in performance.

Adsorptive removal of lead and cadmium ions from aqueous solutions by aluminium oxide modified onion skin wastes: Adsorbent characterization, equilibrium modelling and kinetic studies

2021 ◽  
pp. 0958305X2198988
Author(s):  
Adeyinka Sikiru Yusuff
Keyword(s):  
Metal Ions ◽  
Contact Time ◽  
Metal Ion ◽  
Aluminium Oxide ◽  
Kinetic Studies ◽  
Process Conditions ◽  
Adsorbent Dosage ◽  
Metal Ion Removal ◽  
Lead And Cadmium ◽  
Onion Skin

Aluminium oxide modified onion skin waste (Al2O3/OSW) was characterized and used for adsorption of metal ions (Pb2+ and Cd2+) in this study, and the relations between sorbent properties and metal ion sorption were investigated. The effects of adsorption process conditions on metal ion removal efficiency, including initial cation concentration, contact time, adsorbent dosage and pH, were examined. The obtained adsorption data were analyzed by various adsorption isotherm and kinetic models. It was found that the optimum values of the initial concentration, contact time, adsorbent dosage and pH were 10 mg/L, 120 min, 1.6 g/L and 6.0, respectively. At these optimum conditions, maximum removal percentages of Pb2+ and Cd2+ were 91.23 and 94.10%, respectively. The isotherm and kinetic studies showed a multilayer adsorbate-adsorbent system with the dominance of the chemisorption mechanism. The study concluded that onion skin waste is a viable, cheap and effective alternative for removing heavy metal ions from water/wastewater.

scholarly journals Nanostructured faujasite zeolite as metal ion adsorbent: kinetics, equilibrium adsorption and metal recovery studies

2020 ◽  
Author(s):  
Mariana B. Goncalves ◽  
Djanyna V. C. Schmidt ◽  
Fabiana S. dos Santos ◽  
Daniel F. Cipriano ◽  
Gustavo R. Gonçalves ◽  
...  
Keyword(s):  
Ion Exchange ◽  
Metal Ions ◽  
Metal Ion ◽  
Active Sites ◽  
Metal Removal ◽  
High Surface ◽  
High Surface Area ◽  
Kinetic Studies ◽  
Crystallization Time ◽  
X Ray

Abstract The hydrothermal synthesis of nano-faujasite has been successfully performed and the effects of some crystallization parameters were investigated, along with the use of this material as a heavy-metal ion adsorbent. X-ray diffraction patterns have shown that the structure of the nano-faujasite is strongly dependent on both the crystallization time and the alkalinity of the synthesis medium. According to N2 physisorption, X-ray fluorescence, SEM/EDS, and solid state 29Si and 27Al NMR data, the produced nano-faujasite consists of a solid with low molar Si/Al ratio (1.7), with high availability of ion exchange sites and high surface area/small particle size, allowing easy diffusion of metal ions to adsorbent active sites. As a consequence, an excellent performance on removal of Cd2+, Zn2+ and Cu2+ ions was found for this solid. The adsorption capacity followed the order Cd2+ (133 mg·g−1) > Zn2+ (115 mg·g−1) > Cu2+ (99 mg·g−1), which agrees with the order of increasing absolute values of the hydration energy of the metal ions. Kinetic studies and adsorption isotherms showed that the metal ion removal takes place by ion exchange on the monolayer surface of the nano-faujasite. The electrochemical recovery of copper in metallic form exhibited an efficiency of 80.2% after 120 min, which suggests that this process can be adequately implemented for full-scale metal removal.

scholarly journals Comparative Study on the Adsorption Kinetics and Thermodynamics of Metal Ions onto Acid Activated Low Cost Pandanus Carbon

2007 ◽  
Vol 4 (2) ◽  
pp. 238-254 ◽  
Author(s):  
R. Sudha ◽  
K. Kalpana ◽  
T. Rajachandrasekar ◽  
S. Arivoli
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Low Cost ◽  
Freundlich Isotherm ◽  
Kinetic Studies ◽  
Ion Concentration ◽  
Effect Of Temperature ◽  
Ferrous Ions ◽  
Sem Images ◽  
Operating Variables

Batch experiments were carried out for the sorption of Copper and Ferrous ions onto acid activated carbon prepared. The operating variables studied were initial metal ion concentration, pH, and temperature and contact time. The equilibrium data were fitted to the Langmuir and Freundlich isotherm equations. From this adsorption efficiency, adsorption energy, adsorption capacity, intensity of adsorption and dimensionless separation factor were calculated. From the kinetic studies the rate constant values for the adsorption process was calculated. From the effect of temperature thermodynamic parameters like ΔG°, ΔH°, and ΔS° were calculated. The mechanism of adsorption for metal ions onto carbon was investigated by using the experimental results and confirmed by FT- IR, XRD and SEM images.

Use of agro-waste (Musa paradisiaca peels) as a sustainable biosorbent for toxic metal ions removal from contaminated water

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Heavy Metal ◽  
Metal Ions ◽  
Contact Time ◽  
Metal Ion ◽  
Equilibrium Concentration ◽  
Ion Concentration ◽  
Contaminated Water ◽  
Musa Paradisiaca ◽  
Percentage Removal ◽  
Adsorbent Dose

A study of removal of heavy metal ions from heavy metal contaminated water using agro-waste was carried out with Musa paradisiaca peels as test adsorbent. The study was carried by adding known quantities of lead (II) ions and cadmium (II) ions each and respectively into specific volume of water and adding specific dose of the test adsorbent into the heavy metal ion solution, and the mixture was agitated for a specific period of time and then the concentration of the metal ion remaining in the solution was determined with Perkin Elmer Atomic absorption spectrophotometer model 2380. The effect of contact time, initial adsorbate concentration, adsorbent dose, pH and temperature were considered. From the effect of contact time results equilibrium concentration was established at 60minutes. The percentage removal of these metal ions studied, were all above 90%. Adsorption and percentage removal of Pb2+ and Cd2+ from their aqueous solutions were affected by change in initial metal ion concentration, adsorbent dose pH and temperature. Adsorption isotherm studies confirmed the adsorption of the metal ions on the test adsorbent with good mathematical fits into Langmuir and Freundlich adsorption isotherms. Regression correlation (R2) values of the isotherm plots are all positive (>0.9), which suggests too, that the adsorption fitted into the isotherms considered.

Kinetic Behaviour of Amylase According to pH: A New Perspective for Starch Hydrolysis Process

2020 ◽  
Vol 16 (2) ◽  
pp. 135-144
Author(s):  
Ravneet K. Grewal ◽  
Baldeep Kaur ◽  
Gagandeep Kaur
Keyword(s):  
Metal Ions ◽  
Competitive Inhibition ◽  
Deae Cellulose ◽  
Kinetic Studies ◽  
Cost Effective ◽  
Starch Hydrolysis ◽  
Divalent Metal Ions ◽  
Activity Data ◽  
Time Saving ◽  
Alkaline Conditions

Background: Amylases are the most widely used biocatalysts in starch saccharification and detergent industries. However, commercially available amylases have few limitations viz. limited activity at low or high pH and Ca2+ dependency. Objective: The quest for exploiting amylase for diverse applications to improve the industrial processes in terms of efficiency and feasibility led us to investigate the kinetics of amylase in the presence of metal ions as a function of pH. Methods: The crude extract from soil fungal isolate cultures is subjected to salt precipitation, dialysis and DEAE cellulose chromatography followed by amylase extraction and is incubated with divalent metal ions (i.e., Ca2+, Fe2+, Cu2+, and Hg2+); Michaelis-Menton constant (Km), and maximum reaction velocity (Vmax) are calculated by plotting the activity data obtained in the absence and presence of ions, as a function of substrate concentration in Lineweaver-Burk Plot. Results: Kinetic studies reveal that amylase is inhibited un-competitively at 5mM Cu2+ at pH 4.5 and 7.5, but non-competitively at pH 9.5. Non-competitive inhibition of amylase catalyzed starch hydrolysis is observed with 5mM Hg2+ at pH 9.5, which changes to mixed inhibition at pH 4.5 and 7.5. At pH 4.5, Ca2+ induces K- and V-type activation of amylase catalyzed starch hydrolysis; however, the enzyme has V-type activation at 7mM Ca2+ under alkaline conditions. Also, K- and V-type of activation of amylase is observed in the presence of 7mM Fe2+ at pH 4.5 and 9.5. Conclusion: These findings suggest that divalent ions modulation of amylase is pH dependent. Furthermore, a time-saving and cost-effective solution is proposed to overcome the challenges of the existing methodology of starch hydrolysis in starch and detergent industries.

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