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.

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 Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Metal Ion ◽  
Ternary Complex ◽  
Critical Role ◽  
Divalent Metal ◽  
Binary Complex ◽  
Divalent Metal Ions ◽  
Divalent Metal Ion ◽  
Initial Binding

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

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.

The Binding and Viscometric Studies of Ni+2, Co+2 and Mn+2 Ions with Protein by Spectrometric and pH Metric Techniques

2019 ◽  
Vol 9 (2) ◽  
pp. 151-162
Author(s):  
Shveta Acharya ◽  
Arun Kumar Sharma
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Protein Molecule ◽  
Vital Role ◽  
Sufficient Evidence ◽  
Structural Requirement ◽  
Nickel Ions ◽  
Cobalt Ions ◽  
Lower Temperature ◽  
Specific Oxidation

Background: The metal ions play a vital role in a large number of widely differing biological processes. Some of these processes are quite specific in their metal ion requirements. In that only certain metal ions, in specific oxidation states, can full fill the necessary catalytic or structural requirement, while other processes are much less specific. Objective: In this paper we report the binding of Mn (II), Ni (II) and Co (II) with albumin are reported employing spectrophotometric and pH metric method. In order to distinguish between ionic and colloidal linking, the binding of metal by using pH metric and viscometric methods and the result are discussed in terms of electrovalent and coordinate bonding. Methods: The binding of Ni+2, Co+2 and Mn+2 ions have been studied with egg protein at different pH values and temperatures by the spectrometric technique. Results: The binding data were found to be pH and temperature dependent. The intrinsic association constants (k) and the number of binding sites (n) were calculated from Scatchard plots and found to be at the maximum at lower pH and at lower temperatures. Therefore, a lower temperature and lower pH offered more sites in the protein molecule for interaction with these metal ions. Statistical effects seem to be more significant at lower Ni+2, Co+2 and Mn+2 ions concentrations, while at higher concentrations electrostatic effects and heterogeneity of sites are more significant. Conclusion: The pH metric as well as viscometric data provided sufficient evidence about the linking of cobalt, nickel and manganese ions with the nitrogen groups of albumin. From the nature and height of curves in the three cases it may be concluded that nickel ions bound strongly while the cobalt ions bound weakly.

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 Detection of metal ions in biological systems: A review

2020 ◽  
Vol 39 (1) ◽  
pp. 231-246 ◽  
Author(s):  
Xian Zheng ◽  
Wenyu Cheng ◽  
Chendong Ji ◽  
Jin Zhang ◽  
Meizhen Yin
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Metabolic Regulation ◽  
Organic Dyes ◽  
Biological Systems ◽  
High Sensitivity ◽  
Transportation Energy ◽  
Material Transportation ◽  
High Fluorescence ◽  
Metal Ion Detection

Abstract Metal ions are widely present in biological systems and participate in many critical biochemical processes such as material transportation, energy conversion, information transmission and metabolic regulation, making them indispensable substance in our body. They can cause health problems when deficiency or excess occurs. To understand various metabolic processes and facilitate diseases diagnosis, it is very important to measure the content and monitor the distribution of metal ions in individual cells, tissues and whole organisms. Among the various methods for metal ion detection, fluorescent sensors with organic dyes have attracted tremendous attention due to many advantages such as high fluorescence quantum yield, facile modification approaches and biocompatibility in addition to operation ease, high sensitivity, fast detection speed, and real-time detection. This review summarizes the recent progress on the detection and imaging of the metal ions in biological systems including Na+, K+, Ca2+, Mg2+, Fe2+/Fe3+, Zn2+, and Cu2+ provides an opinion on remaining challenges to be addressed in this field.

Solution-based chemical pre-alkaliation of metal-ion battery cathode materials for increased capacity

2021 ◽  
Author(s):  
Roman Kapaev ◽  
Keith Stevenson
Keyword(s):  
Metal Ions ◽  
Cathode Materials ◽  
Metal Ion

For metal-ion batteries, the limited amount of metal ions that can be reversibly extracted from a cathode is a major problem, which leads to decreased capacity (mA h g−1) and...

scholarly journals Snapshots of a Non-Canonical RdRP in Action

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1260
Author(s):  
Diego S. Ferrero ◽  
Michela Falqui ◽  
Nuria Verdaguer
Keyword(s):  
Metal Ion ◽  
Rna Viruses ◽  
Ion Binding ◽  
Genome Replication ◽  
Metal Ion Binding ◽  
Insect Virus ◽  
X Ray ◽  
Template Strand ◽  
Nucleotide Incorporation ◽  
Elongation Process

RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.

scholarly journals Ag-Functionalized Si Nanowire Arrays Aligned Vertically for SERS Detection of Captured Heavy Metal Ions by BSA

Coatings ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 685
Author(s):  
Ai-Huei Chiou ◽  
Jun-Luo Wei ◽  
Ssu-Han Chen
Keyword(s):  
Heavy Metal ◽  
Raman Scattering ◽  
Metal Ions ◽  
Metal Ion ◽  
Heavy Metal Ions ◽  
Great Promise ◽  
Ag Nps ◽  
Water Contact ◽  
Oh Groups ◽  
Si Nanowire

A novel surface-enhanced Raman scattering (SERS)-based probe to capture heavy metal ion (Zn2+) by bovine serum albumin (BSA) using Si-nanowire (SiNW) arrays with silver nanoparticles (AgNPs) was developed. A layer with AgNPs was deposited on the SiNW surface by RF magnetron sputtering for enhancement of SERS signals. Using a high-resolution transmission electron microscope (HRTEM), the observation reveals that the AgNP layer with depths of 30–75 nm was successfully deposited on SiNW arrays. The Ag peaks in EDS and XRD spectra of SiNW arrays confirmed the presence of Ag particles on SiNW arrays. The WCA observations showed a high affinity of the Ag–SiNW arrays immobilized with BSA (water contact angle (WCA) = 87.1°) and ZnSO4 (WCA = 8.8°). The results of FTIR analysis illustrate that the conjugate bonds exist between zinc sulfate (ZnSO4) and –OH groups/–NH groups of BSA. The resulting SiNWs/Ag NPs composite interfaces showed large Raman scattering enhancement for the capture of heavy metal ions by BSA with a detection of 0.1 μM. BSA and ZnSO4 conjugations, illustrating specific SERS spectra with high sensitivity, which suggests great promise in developing label-free biosensors.

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