scholarly journals Acidophilic Micrarchaeon Seems to Maintain a Slightly Alkaline Cytosolic pH

2021 ◽  
Author(s):  
Dennis Winkler ◽  
Sabrina Gfrerer ◽  
Johannes Gescher
Keyword(s):  
Reaction Rate ◽  
Ph Value ◽  
Divalent Cations ◽  
Kinetic Studies ◽  
Genetic System ◽  
Binding Pocket ◽  
Ph Optimum ◽  
Cytosolic Ph ◽  
Local Secondary Structure ◽  
Genes Encoding

AbstractDespite several discoveries in recent years, the physiology of acidophilic Micrarchaeota remains largely enigmatic. “Candidatus Micrarchaeum harzensis A_DKE”, for example, highly expresses numerous genes encoding hypothetical proteins and their function is difficult to elucidate due to a lacking genetic system. Still, not even the intracellular pH value of A_DKE is known, and heterologous production attempts are generally missing so far. Hence, A_DKE’s isocitrate dehydrogenase (MhIDH) was recombinantly produced in Escherichia coli and purified for bio-chemical characterisation. MhIDH appeared to be specific for NADP+, yet promiscuous regarding divalent cations as cofactors. Kinetic studies showed KM-values of 53.03±5.63 µM and 1.94±0.12 mM and kcat-values of 38.48±1.62 s-1 and 43.99±1.46 s-1 for DL-isocitrate and NADP+, respectively. MhIDH’s exceptionally low affinity for NADP+, potentially limiting its reaction rate, can be likely attributed to the presence of a proline residue in the NADP+ binding-pocket, which might cause a decrease in hydrogen bonding of the cofactor and a distortion of local secondary structure. Furthermore, a pH optimum of 7.89 implies, that A_DKE applies potent mechanisms of proton homoeostasis, to maintain a slightly alkaline cytosolic milieu in a highly acidic environment.

scholarly journals Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon

2021 ◽  
Vol 9 (11) ◽  
pp. 2318
Author(s):  
Dennis Winkler ◽  
Sabrina Gfrerer ◽  
Johannes Gescher
Keyword(s):  
Isocitrate Dehydrogenase ◽  
Reaction Rate ◽  
Biochemical Characterization ◽  
Divalent Cations ◽  
Kinetic Studies ◽  
Genetic System ◽  
Binding Pocket ◽  
Local Secondary Structure ◽  
Genes Encoding

Despite several discoveries in recent years, the physiology of acidophilic Micrarchaeota, such as “Candidatus Micrarchaeum harzensis A_DKE”, remains largely enigmatic, as they highly express numerous genes encoding hypothetical proteins. Due to a lacking genetic system, it is difficult to elucidate the biological function of the corresponding proteins and heterologous expression is required. In order to prove the viability of this approach, A_DKE’s isocitrate dehydrogenase (MhIDH) was recombinantly produced in Escherichia coli and purified to electrophoretic homogeneity for biochemical characterization. MhIDH showed optimal activity around pH 8 and appeared to be specific for NADP+ yet promiscuous regarding divalent cations as cofactors. Kinetic studies showed KM-values of 53.03 ± 5.63 µM and 1.94 ± 0.12 mM and kcat-values of 38.48 ± 1.62 and 43.99 ± 1.46 s−1 resulting in kcat/KM-values of 725 ± 107.62 and 22.69 ± 2.15 mM−1 s−1 for DL-isocitrate and NADP+, respectively. MhIDH’s exceptionally low affinity for NADP+, potentially limiting its reaction rate, can likely be attributed to the presence of a proline residue in the NADP+ binding pocket, which might cause a decrease in hydrogen bonding of the cofactor and a distortion of local secondary structure.

scholarly journals The acid deoxyribonuclease of neutrophils: a possible participant in apoptosis-associated genome destruction

Blood ◽  
1995 ◽  
Vol 86 (6) ◽  
pp. 2414-2418 ◽  
Author(s):  
RA Gottlieb ◽  
HA Giesing ◽  
RL Engler ◽  
BM Babior
Keyword(s):  
Dna Cleavage ◽  
Ph Value ◽  
Divalent Cations ◽  
Ph Dependence ◽  
Human Neutrophils ◽  
Ph Optimum ◽  
Differentiated Cells ◽  
Plasmid Nicking Assay ◽  
Plasmid Nicking ◽  
Acid Deoxyribonuclease

Human neutrophils are terminally differentiated cells that spontaneously undergo apoptosis in tissue culture. Apoptosis in these cells can be delayed by culture in the presence of granulocyte colony- stimulating factor or other inflammatory mediators. Neutrophils were found to contain an acid endonuclease that appeared to be responsible for the internucleosomal DNA cleavage that accompanies apoptosis. As measured by a plasmid nicking assay, this endonuclease had a molecular weight (M(r)) of 35,000, a pH optimum of 5.5, and a threshold for activity of pH 6.6 to 6.8. It was weakly inhibited by divalent cations (Ca2+, Mg2+, and Zn2+) and more strongly inhibited by aurintricarboxylic acid and N-bromosuccinimide. DNA from neutrophils treated with nigericin in buffers of defined pH displayed nucleosomal ladders whose prominence varied with pH in a manner that paralleled the pH dependence of the plasmid cleavage assays, consistent with internucleosomal DNA cleavage by the acid endonuclease. We have previously shown that neutrophils undergo acidification to a pH value as low as 6.0 during apoptosis; we suggest that this endonuclease may be responsible for the DNA cleavage seen in apoptotic neutrophils.

Serum Cholinesterase Variants: Examination of Several Differential Inhibitors, Salts, and Buffers Used to Measure Enzyme Activity

1971 ◽  
Vol 17 (3) ◽  
pp. 183-191 ◽  
Author(s):  
Philip J Garry
Keyword(s):  
Enzyme Activity ◽  
Sodium Fluoride ◽  
Phosphate Buffer ◽  
Divalent Cations ◽  
Kinetic Studies ◽  
Competitive Inhibitor ◽  
Serum Cholinesterase ◽  
Low Concentrations

Abstract Dibucaine, used as a differential inhibitor with acetyl-, propionyl-, and butyrylthiocholine as substrate, clearly identified the "usual" and "atypical" serum cholinesterases. Succinylcholine was also used successfully as a differential inhibitor with butyrylthiocholine as substrate. Sodium fluoride, used as a differential inhibitor, gave conflicting results, depending on whether Tris or phosphate buffer was used in the assay. Mono- and divalent cations (NaCl, KCl, MgCl2, CaCl2, and BaCl2) activated the "usual" and inhibited the "atypical" enzyme at low concentrations. The "usual" enzyme had the same activity in 0.05 mol of Tris or phosphate buffer per liter, while the heterozygous and "atypical" enzymes showed 12 and 42% inhibition, respectively, when assayed in the phosphate buffer. Kinetic studies showed the phosphate acted as a competitive inhibitor of "atypical" enzyme. Km values, determined for "usual" and "atypical" enzymes, were 0.057 and 0.226 mmol/liter, respectively, with butyrylthiocholine as substrate.

Photocatalytic Degradation of Methyl Orange by TiO2/Schorl Photocatalyst: Kinetics and Thermodynamics

2015 ◽  
Vol 713-715 ◽  
pp. 2789-2792
Author(s):  
Huan Yan Xu ◽  
Xue Li ◽  
Yan Li ◽  
Ping Li ◽  
Wei Chao Liu
Keyword(s):  
Methyl Orange ◽  
Reaction Rate ◽  
Reaction Kinetic ◽  
Kinetic Studies ◽  
Reaction Rate Constant ◽  
Order Reaction ◽  
Solution Ph ◽  
Kinetics And Thermodynamics ◽  
Hoff Equation ◽  
Degradation Of Methyl Orange

An active dye, Methyl Orange (MO) was employed as the target pollutant to evaluate the photocatalytic activity of TiO2/schorl composite and the kinetics and thermodynamics of this process was emphasized in this work. Langmuir–Hinshelwood kinetic model was employed for the kinetic studies and the results revealed that the process of MO photocatalytic discoloration by TiO2/schorl composite followed one order reaction kinetic equation under different conditions. The reaction rate constant (k) increased with initial MO concentration decreasing. When the catalyst dosage or solution pH increased,kvalues increased and then decreased. The possible reasons for these phenomena were discussed. Finally, the thermodynamic parameters ΔG, ΔH, ΔSwere obtained by the classical Van't Hoff equation.

STUDIES ON SOLUBILIZED ADENYLATE KINASE FROM MITOCHONDRIA

1966 ◽  
Vol 44 (11) ◽  
pp. 1469-1475 ◽  
Author(s):  
Marjorie A. Brewster ◽  
Ezzat S. Younathan
Keyword(s):  
Activation Energy ◽  
Rat Liver ◽  
Adenylate Kinase ◽  
Divalent Cations ◽  
Metabolic Function ◽  
Kcal Mole ◽  
Temperature Optimum ◽  
Ph Optimum ◽  
Sensitive Method

Adenylate kinase from mitochondria of rat liver was made soluble by sonication. The enzyme had a pH optimum of 8.0, temperature optimum of 30°, and activation energy of 12.2 kcal/mole. It was activated by several divalent cations in the following order of efficiency: Mg++ > Co++ > Mn++ > Ca++, with an optimal Mg++: ADP ratio of 1. The apparent Km value (ADP as substrate) was found to be 1.3 mM at pH 7.4 and 30°. The activity was sensitive to phloretin and mildly activated by aurovertin. Oligomycin, 2,4-dinitrophenol, p-chloromercuribenzoate, alloxan, and phlorizin had no effect on the activity. The metabolic function and a comparison of the properties of this solubilized mitochondrial adenylate kinase with those of similar preparations from other sources are discussed in the light of these findings. During this study, a sensitive method adaptable for a large number of assays of adenylate kinase was developed, and is described in detail.

scholarly journals Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease

2021 ◽  
Vol 9 ◽  
Author(s):  
Fei Wang ◽  
Deyu Zhang ◽  
Dejiu Zhang ◽  
Peifeng Li ◽  
Yanyan Gao
Keyword(s):  
Ribosomal Proteins ◽  
Large Fraction ◽  
Mitochondrial Protein ◽  
Mitochondrial Diseases ◽  
Protein Translation ◽  
Genetic System ◽  
Mitochondrial Rna ◽  
Trna Synthetases ◽  
Translation Factors ◽  
Genes Encoding

Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.

scholarly journals Mutant tryptophan aporepressors with altered specificities of corepressor recognition.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 29-35
Author(s):  
D N Arvidson ◽  
M Shapiro ◽  
P Youderian
Keyword(s):  
Dna Binding ◽  
Binding Pocket ◽  
Side Chain ◽  
Wild Type ◽  
Mutant Proteins ◽  
Naturally Occurring ◽  
Repressor Complex ◽  
Genes Encoding ◽  
Active Repressor

Abstract The Escherichia coli trpR gene encodes tryptophan aporepressor, which binds the corepressor ligand, L-tryptophan, to form an active repressor complex. The side chain of residue valine 58 of Trp aporepressor sits at the bottom of the corepressor (L-tryptophan) binding pocket. Mutant trpR genes encoding changes of Val58 to the other 19 naturally occurring amino acids were made. Each of the mutant proteins requires a higher intracellular concentration of tryptophan for activation of DNA binding than wild-type aporepressor. Whereas wild-type aporepressor is activated better by 5-methyltryptophan (5-MT) than by tryptophan, Ile58 and other mutant aporepressors prefer tryptophan to 5-MT as corepressor, and Ala58 and Gly58 prefer 5-MT much more strongly than wild-type aporepressor in vivo. These mutant aporepressors are the first examples of DNA-binding proteins with altered specificities of cofactor recognition.

scholarly journals Pre-fermentative treatment of a model wine with aim to serve as a functional food with decreased alcohol content

2017 ◽  
Vol 63 (01) ◽  
pp. 47-53
Author(s):  
Irina Mladenoska ◽  
Verica Petkova ◽  
Tatjana Kadifkova Panovska
Keyword(s):  
Enzyme Activity ◽  
Gluconic Acid ◽  
Functional Food ◽  
Ph Value ◽  
Enzymatic Reaction ◽  
Alginate Beads ◽  
High Concentration ◽  
Ph Optimum ◽  
Enzyme Preparations ◽  
Initial Ph

The effect of substrate concentration on the enzyme activity in the reaction of glucose conversion into gluconic acid was investigated by using three different enzyme preparations in media with two different glucose concentrations. The media were simulating the conditions in the must, thus named as minimal model must, and were composed form combination of several organic acids and glucose. Those media were having initial pH of 3.5 that is a very unfavorable for glucose oxidase activity having a pH optimum at the pH value of 5.5. Among the three preparations used, the bakery additive, Alphamalt Gloxy 5080, was the most active in the medium with glucose concentration of 10 g/L, showing conversion of more than 70% for the period of 24 h, while the same enzyme preparation in the medium with 100 g/L glucose converted only about 7% of glucose. The pH value of the medium at the beginning and at the end of the enzymatic reaction was a good indicator of the enzyme activity. It seems that for the conversion of glucose in higher concentration, enzymatic preparation in high concentration should also be used. The preliminary attempt of immobilization of two preparations of glucose oxidases in alginate beads was also performed and a successful immobilization procedure for utilization in food industry was preliminarily developed. Keywords: glucose oxidases, enzymatic pretreatment, glucose, gluconic acid, model wine, functional food

scholarly journals Purification and characterization of cytosolic pyruvate kinase from banana fruit

2000 ◽  
Vol 352 (3) ◽  
pp. 875-882 ◽  
Author(s):  
William L. TURNER ◽  
William C. PLAXTON
Keyword(s):  
Pyruvate Kinase ◽  
Specific Activity ◽  
Gel Filtration ◽  
Banana Fruit ◽  
Ph Optimum ◽  
Cytosolic Ph ◽  
Pep Carboxylase ◽  
Sds Page ◽  
Optimal Efficiency

Cytosolic pyruvate kinase (PKc) from ripened banana (Musa cavendishii L.) fruits has been purified 543-fold to electrophoretic homogeneity and a final specific activity of 59.7µmol of pyruvate produced/min per mg of protein. SDS/PAGE and gel-filtration FPLC of the final preparation indicated that this enzyme exists as a 240kDa homotetramer composed of subunits of 57kDa. Although the enzyme displayed a pH optimum of 6.9, optimal efficiency in substrate utilization [in terms of Vmax/Km for phosphoenolpyruvate (PEP) or ADP] was equivalent at pH6.9 and 7.5. PKc activity was absolutely dependent upon the presence of a bivalent and a univalent cation, with Mg2+ and K+ respectively fulfilling this requirement. Hyperbolic saturation kinetics were observed for the binding of PEP, ADP, Mg2+ and K+ (Km values of 0.098, 0.12, 0.27 and 0.91mM respectively). Although the enzyme utilized UDP, IDP, GDP and CDP as alternative nucleotides, ADP was the preferred substrate. L-Glutamate and MgATP were the most effective inhibitors, whereas L-aspartate functioned as an activator by reversing the inhibition of PKc by L-glutamate. The allosteric features of banana PKc are compared with those of banana PEP carboxylase [Law and Plaxton (1995) Biochem. J. 307, 807Ő816]. A model is presented which highlights the roles of cytosolic pH, MgATP, L-glutamate and L-aspartate in the co-ordinate control of the PEP branchpoint in ripening bananas.

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.

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