scholarly journals Hydrolysis of p-nitrophenyl phenylphosphonate catalysed by bovine pancreatic deoxyribonuclease

1988 ◽  
Vol 255 (3) ◽  
pp. 781-787 ◽  
Author(s):  
T H Liao ◽  
J C Hsieh
Keyword(s):  
Metal Ion ◽  
Deae Cellulose ◽  
Protein Molecule ◽  
Dna Interaction ◽  
Base Pairs ◽  
Difference Absorption Spectrum ◽  
Michaelis Constants ◽  
Elution Method ◽  
Difference Absorption ◽  
The Hill

The ability of bovine pancreatic DNAase to hydrolyse the synthetic substrate p-nitrophenyl phenylphosphonate (NPPP) is intrinsic and is not due to the contamination of the DNAase preparation by nonspecific phosphodiesterases because the activities of DNA and NPPP hydrolysis are co-eluted from a DEAE-cellulose column with use of the Ca2+-affinity elution method and because the two activities are decreased simultaneously when the purified enzyme is treated with Cu2+/iodoacetate, an active-site-labelling agent for DNAase. NPPP hydrolysis is facilitated by the metal ion-DNAase. At relatively high Na+ concentrations, where the metal ion-DNA interaction is weak, DNA hydrolysis is also facilitated by the metal ion-DNAase. With NPPP as substrate the Michaelis constants are Km 3.7 mM for Mn2+ and Km 49 mM for Mg2+ in 0.2 M-Tris/HCl buffer, pH 7.2. Ca2+ competes with Mn2+, with Ki 64 mM. Free Cu2+ ions non-competitively inhibit DNAase-catalysed DNA or NPPP hydrolysis in the presence of Mn2+ or Mg2+ and the inhibition is not relieved by Ca2+. The affinity of Cu2+ for free DNAase is higher than that for Mn2+-DNAase. Mn2+ is not bound to DNAase via a simple ionic interaction, as Mn2+ remains bound in the presence of relatively high Na+ concentrations and induces a near-u.v. difference absorption spectrum. The kinetics of NPPP hydrolysis catalysed by Mn2+-DNAase are sigmoidal. From the Hill equation, h = 2.0 is obtained, suggesting that more than two NPPP molecules are bound per molecule of DNAase with a certain amount of co-operativity. Because DNAase in solution is a monomer with a single catalytic site, the multiple NPPP molecules on a single protein molecule are probably in one location, resulting in a co-operative interaction that may resemble that in the stacked base-pairs of double-helical DNA.

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.

Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

ChemBioChem ◽  
2019 ◽  
Vol 21 (4) ◽  
pp. 517-522 ◽  
Author(s):  
Tatsuya Funai ◽  
Megumi Aotani ◽  
Risa Kiriu ◽  
Junko Nakamura ◽  
Yuki Miyazaki ◽  
...  
Keyword(s):  
Metal Ion ◽  
Dna Polymerases ◽  
Base Pairs ◽  
Ion Specificity

scholarly journals Kinetic studies on the regulation of rabbit liver pyruvate kinase

1973 ◽  
Vol 131 (2) ◽  
pp. 287-301 ◽  
Author(s):  
M. G. Irving ◽  
J. F. Williams
Keyword(s):  
Pyruvate Kinase ◽  
Specific Activity ◽  
Deae Cellulose ◽  
Kinetic Studies ◽  
Rabbit Liver ◽  
Hill Coefficient ◽  
Saturation Curve ◽  
Low Concentrations ◽  
Ammonium Sulphate Fractionation ◽  
The Hill

Two kinetically distinct forms of pyruvate kinase (EC 2.7.1.40) were isolated from rabbit liver by using differential ammonium sulphate fractionation. The L or liver form, which is allosterically activated by fructose 1,6-diphosphate, was partially purified by DEAE-cellulose chromatography to give a maximum specific activity of 20 units/mg. The L form was allosterically activated by K+ and optimum activity was recorded with 30mm-K+, 4mm-MgADP-, with a MgADP-/ADP2- ratio of 50:1, but inhibition occurred with K+ concentrations in excess of 60mm. No inhibition occurred with either ATP or GTP when excess of Mg2+ was added to counteract chelation by these ligands. Alanine (2.5mm) caused 50% inhibition at low concentrations of phosphoenolpyruvate (0.15mm). The homotropic effector, phosphoenolpyruvate, exhibited a complex allosteric pattern (nH+2.5), and negative co-operative interactions were observed in the presence of low concentrations of this substrate. The degree of this co-operative interaction was pH-dependent, with the Hill coefficient increasing from 1.1 to 3.2 as the pH was raised from 6.5 to 8.0. Fructose 1,6-diphosphate interfered with the activation by univalent ions, markedly decreased the apparent Km for phosphoenolpyruvate from 1.2mm to 0.2mm, and transformed the phosphoenolpyruvate saturation curve into a hyperbola. Concentrations of fructose 1,6-diphosphate in excess of 0.5mm inhibited this stimulated reaction. The M or muscle-type form of the enzyme was not activated by fructose 1,6-diphosphate and gave a maximum specific activity of 0.3 unit/mg. A Michaelis–Menten response was obtained when phosphoenolpyruvate was the variable substrate (Km+0.125mm), and this form was inhibited by ATP, as well as alanine, even in the presence of excess of Mg2+.

scholarly journals Crystal structure of d(CCGGGGTACCCCGG)2at 1.4 Å resolution

2017 ◽  
Vol 73 (5) ◽  
pp. 259-265
Author(s):  
Selvam Karthik ◽  
Arunachalam Thirugnanasambandam ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Crystal Structure ◽  
Metal Ion ◽  
Double Helix ◽  
Barium Chloride ◽  
Base Pairs ◽  
X Ray ◽  
Density Map ◽  
Solvent Molecules ◽  
Electron Density Map ◽  
Phosphate Groups

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2is reported at 1.4 Å resolution in the tetragonal space groupP41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.

Interaction of D-phenylalanine with Co(II)-substituted rabbit muscle pyruvate kinase: kinetic and optical properties

1982 ◽  
Vol 60 (9) ◽  
pp. 861-866
Author(s):  
Chiu-Yin Kwan ◽  
Robert C. Davis
Keyword(s):  
Amino Acids ◽  
Optical Properties ◽  
Pyruvate Kinase ◽  
Conformational Changes ◽  
Metal Ion ◽  
Inhibitory Effect ◽  
Rabbit Muscle ◽  
Divalent Metal Ion ◽  
Muscle Pyruvate Kinase ◽  
Difference Absorption

The kinetic and optical properties of Co(II)-substituted pyruvate kinase in the presence of D-phenylalanine (D-Phe) were investigated. The results are discussed in comparison with the effects of its optical isomer L-phenylalanine (L-Phe) on the same enzyme. The catalytic effect of D-Phe on rabbit muscle pyruvate kinase depended upon the nature of the activating divalent metal ion used. It has stimulatory effect on Mg(II)-activated enzyme, but inhibitory effect on Co(II)-activated enzyme. Unlike the inhibitory effect of L-Phe, the inhibition of Co(II)–enzyme by D-Phe was not sensitive to the changes of pH and temperature, could not be reversed by L-alanine (L-Ala), displayed hyperbolic kinetics, and was noncompetitive with respect to phosphoenolpyruvate saturation. D-Phe induced substantial visible circular dichroism (CD) spectral changes of Co(II)–enzyme similar to those induced by L-Phe. Although ultraviolet CD spectrum was not affected, D-Phe induced an ultraviolet difference absorption spectral change very similar to, but much smaller than, that induced by L-Phe. Our results support that D-Phe and other amino acids interact with the enzyme at two different sites: a common site, causing similar conformational changes which bear little direct kinetic relevance, and a kinetically relevant site, which is sterically dependent upon the side chain of the amino acids.

scholarly journals Interaction of Calf Thymus DNA with the Ni(II) Complex of Sodium 1,4-Dihydroxy-9,10-Anthraquinone-2-Sulphonate: A Novel Method of Analysis Using Cyclic Voltammetry

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Partha Sarathi Guin ◽  
Piyal Das ◽  
Saurabh Das ◽  
Parikshit Chandra Mandal
Keyword(s):  
Cyclic Voltammetry ◽  
Metal Ion ◽  
Dna Interaction ◽  
Calf Thymus Dna ◽  
Reduction Peak ◽  
Curve Fit ◽  
Diffusion Controlled ◽  
Binding Data ◽  
Calf Thymus ◽  
Electron Reduction

Hydroxy-9,10-anthraquinones are cheaper alternatives to anthracycline drugs. They closely resemble anthracycline drugs both from a structural and functional viewpoint. Electrochemical behavior of the Ni(II) complex (Na2[Ni(NaLH)2Cl2]⋅2H2O) of sodium 1,4-dihydroxy-9,10-anthraquinone-2-sulphonate (NaLH2), analogue of the core unit of anthracycline anticancer drugs, was studied at physiological pH using cyclic voltammetry. The Ni(II) complex of sodium 1,4-dihydroxy-9,10-anthraquinone-2-sulphonate undergoes diffusion-controlled one-electron reduction that enables performing an electrochemical study on the interaction of the complex with calf thymus DNA. The complex was titrated with increasing concentrations of DNA, and the reduction peak for the unbound complex helped in evaluating binding parameters. Analysis of binding data using nonlinear curve fit in a cyclic voltammetry experiment is the first such attempt. The paper evaluates site size of interaction that also serves as a means to determine stoichiometry of complex formation, between a metal ion and ligand from a DNA interaction study, probably a first of its kind.

scholarly journals The orphan receptors NGFI-B and steroidogenic factor 1 establish monomer binding as a third paradigm of nuclear receptor-DNA interaction.

1993 ◽  
Vol 13 (9) ◽  
pp. 5794-5804 ◽  
Author(s):  
T E Wilson ◽  
T J Fahrner ◽  
J Milbrandt
Keyword(s):  
Dna Binding ◽  
Nuclear Receptors ◽  
Dna Interaction ◽  
Common Mechanism ◽  
Protein Motif ◽  
Base Pairs ◽  
Steroidogenic Factor 1 ◽  
Distinct Sequence ◽  
Carboxy Terminal ◽  
Half Site

We examined in detail the DNA interaction of the nuclear receptors NGFI-B and steroidogenic factor 1 (SF-1) by using a series of gain-of-function domain swaps. NGFI-B bound with high affinity as a monomer to a nearly linear DNA molecule. The prototypic zinc modules interacted with a half-site of the estrogen receptor class, and a distinct protein motif carboxy terminal to the zinc modules (the A box) interacted with two A/T base pairs 5' to the half-site. SF-1 bound in the same manner as NGFI-B, with an overlapping but distinct sequence requirement 5' to the half-site. The key features that distinguished the NGFI-B and SF-1 interactions were an amino group in the minor groove of the SF-1 binding sequence and an asparagine in the SF-1 A box. These results define a common mechanism of NGFI-B and SF-1 DNA binding, which may underlie a competitive mechanism of gene regulation in steroidogenic tissues that express these proteins. This monomer-DNA interaction represents a third paradigm of DNA binding by nuclear receptors in addition to direct and inverted dimerization.

scholarly journals An inducible hydrolase from Aspergillus niger, acting on carbon–carbon bonds, for phlorrhizin and other C-acylated phenols

1970 ◽  
Vol 116 (5) ◽  
pp. 889-897 ◽  
Author(s):  
T. Minamikawa ◽  
N. P. Jayasankar ◽  
B. A. Bohm ◽  
I. E. P. Taylor ◽  
G. H. N. Towers
Keyword(s):  
Aspergillus Niger ◽  
Metal Ion ◽  
Deae Cellulose ◽  
Hydrolytic Activity ◽  
Maximum Activity ◽  
Protamine Sulphate ◽  
Carbon Carbon Bonds ◽  
Alkaline Conditions ◽  
Km Value ◽  
Ammonium Sulphate Fractionation

1. An inducible enzyme catalysing the hydrolysis of phloretin to form phloroglucinol and phloretic acid has been extracted from the acetone-dried powders of the mycelial felts of an Aspergillus niger strain grown in the presence of phlorrhizin. The enzyme was partially purified by treatment with protamine sulphate, ammonium sulphate fractionation, negative adsorption on tricalcium phosphate gel, and DEAE-cellulose column chromatography. 2. The hydrolytic activity on phloretin appeared to be maximal at about pH9.6. However, the characteristics of the enzyme were studied at pH7.2, because of the lability of the product, phloroglucinol, under alkaline conditions. 3. The apparent Km value at pH7.2 was about 0.3–0.4mm for phloretin and 0.15mm for 3′-methylphloracetophenone. 4. Maximum activity of the enzyme was obtained without the addition of any cofactor or metal ion. The involvement of thiol groups in the reaction was demonstrated by the potent inhibitory action of both heavy-metal ions and p-chloromercuribenzoate. 5. The enzyme showed a rather broad substrate specificity, and some other C-acylated phenols related to phloretin were hydrolysed. It was found that 3′-methylphloracetophenone, phloracetophenone and 2′,4,4′-trihydroxydihydrochalcone were attacked more efficiently than phloretin. We propose the systematic name C-acylphenol acylhydrolase for the enzyme. This enzyme belongs to EC group 3.7.1.

Purification and properties of an extracellular proteolytic enzyme fromBacillus cereus

1973 ◽  
Vol 40 (3) ◽  
pp. 427-440 ◽  
Author(s):  
M. A. Islam ◽  
J. M. V. Blanshard
Keyword(s):  
Metal Ion ◽  
Absorption Maximum ◽  
Proteolytic Enzyme ◽  
Heavy Metal Ions ◽  
Freeze Drying ◽  
Deae Cellulose ◽  
Milk Clotting ◽  
Purification And Properties ◽  
Extracellular Proteolytic Enzyme ◽  
Metal Ion Activation

SummaryA milk-clotting proteolytic enzyme was isolated and purified from the culture filtrate ofBacillus cereusstrain x29 by fractionation with acetone or ammonium sulphate and subsequent column chromatography employing DEAE cellulose and DEAE Sephadex. The purified enzyme was found to be homogeneous by acrylamide gel electrophoresis from pH 3·5 to 8·6, with, a molecular weight of about 50000. The single absorption maximum of the native enzyme was at 277 nm and the value ofat 280 nm was 7·79. Purification resulted in a 9-fold enhancement of activity with 24 % yield. The optimum activity of the enzyme was at pH 8·0 at 40 °C with casein as the substrate. The enzyme was found to be most stable at pH 6·0 and was stable to freezing and freeze-drying. Heavy metal ions were found to inactivate the enzyme, but no metal ion activation was found. Enzyme activity was inhibited irreversibly by EDTA and reversibly by 1,10-phenanthroline. The enzyme has been identified as a Zn-containing neutral protease.

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