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The FEBS Journal Aug 2008The protein tyrosine phosphatase (PTP)-like phytase, PhyAsr, from Selenomonas ruminantium is a novel member of the PTP superfamily, and the only described member that...
The protein tyrosine phosphatase (PTP)-like phytase, PhyAsr, from Selenomonas ruminantium is a novel member of the PTP superfamily, and the only described member that hydrolyzes myo-inositol-1,2,3,4,5,6-hexakisphosphate. In addition to the unique substrate specificity of PhyAsr, the phosphate-binding loop (P-loop) has been reported to undergo a conformational change from an open (inactive) to a closed (active) conformation upon ligand binding at low ionic strength. At high ionic strengths, the P-loop was observed in the closed, active conformation in both the presence and absence of ligand. To test whether the P-loop movement can be induced by changes in ionic strength, we examined the effect that ionic strength has on the catalytic efficiency of PhyAsr, and determined the structure of the enzyme at several ionic strengths. The catalytic efficiency of PhyAsr is highly sensitive to ionic strength, with a seven-fold increase in k(cat)/K(m) and a ninefold decrease in K(m) when the ionic strength is increased from 100 to 500 mm. Surprisingly, the P-loop is observed in the catalytically competent conformation at all ionic strengths, despite the absence of a ligand. Here we provide structural evidence that the ionic strength dependence of PhyAsr and the conformational change in the P-loop are not linked. Furthermore, we demonstrate that the previously reported P-loop conformational change is a result of irreversible oxidation of the active site thiolate. Finally, we rationalize the observed P-loop conformational changes observed in all oxidized PTP structures.
Topics: 6-Phytase; Catalysis; Kinetics; Models, Molecular; Osmolar Concentration; Oxidation-Reduction; Protein Conformation; Protein Tyrosine Phosphatases
PubMed: 18573100
DOI: 10.1111/j.1742-4658.2008.06524.x -
The Biochemical Journal Oct 1977Ox muscle troponin was shown by equilibrium- and velocity-sedimentation studies to undergo concentration-dependent dissociation into its constituent subunits as well as...
Ox muscle troponin was shown by equilibrium- and velocity-sedimentation studies to undergo concentration-dependent dissociation into its constituent subunits as well as self-association in imidazole buffers, pH 6.9. The extent of troponin association was found to be strongly dependent on ionic strength and also to exhibit a dependence on pH and temperature; under conditions physiological in regard to pH, temperature and ionic strength the extent of polymerization of troponin is considerable in 2 mg/ml solutions. The ability of polymeric troponin to bind to tropomyosin has been inferred from studies of mixtures containing actin-tropomyosin and an excess of troponin over the amount required for the normal 7:1:1 actin-tropomyosin-troponin complex. These findings should be relevant to studies of reconstituted actin-tropomyosin-troponin preparations, since they signify possible chemical as well as physical differences between the gel, paracrystalline and filamentous states of the complex that result from adoption of different preparative procedures for analogues of the native thin filament.
Topics: Animals; Cattle; Electrophoresis, Polyacrylamide Gel; Hydrogen-Ion Concentration; Imidazoles; Macromolecular Substances; Molecular Weight; Muscle Proteins; Osmolar Concentration; Potassium Chloride; Temperature; Troponin; Ultracentrifugation
PubMed: 22325
DOI: 10.1042/bj1670131 -
ELife Dec 2017Bacteria contain large numbers of negatively-charged proteins to avoid the electrostatic interactions with ribosomes that would dramatically reduce protein diffusion.
Bacteria contain large numbers of negatively-charged proteins to avoid the electrostatic interactions with ribosomes that would dramatically reduce protein diffusion.
Topics: Diffusion; Escherichia coli; Escherichia coli Proteins; Osmolar Concentration; Ribosomes; Static Electricity
PubMed: 29231807
DOI: 10.7554/eLife.33590 -
The Journal of General Physiology Jan 1960The electrokinetic stability of washed normal human erythrocytes is discussed from the point of view of pH, ionic strength, and composition of the suspending medium....
The electrokinetic stability of washed normal human erythrocytes is discussed from the point of view of pH, ionic strength, and composition of the suspending medium. Many of the electrophoretic characteristics at low ionic strengths (sorbitol to maintain the tonicity), such as the isopotential points, are shown to arise principally from adsorption of hemolysate. The concept of electrokinetically stable, metastable, and unstable states for the red cell at various ionic strengths is introduced in preference to the general term "cell injury." In the stable state which exists around pH 7.4 for ionic strengths >0.007, no adsorption of hemolysate occurs, in the metastable state reversible adsorption of hemolysate occurs, and in the unstable state, in which ionic strengths and pH ranges are outside the metastable range, the membrane undergoes irreversible hemolysate adsorption or more general hydrolytic degradation. It is deduced from the equivalent binding of CNS, I, Cl, and F, the pH mobility relationships, and the conformation of the ionic strength data in the stable state to a Langmuir adsorption isotherm, that the membrane of the human erythrocyte behaves as a macropolyanion whose properties are modified by gegen ion association and in some instances by hemolysate adsorption. The experimental results are insufficient to establish conclusively the nature of the ionogenic groupings present in the membrane interphase.
Topics: Erythrocyte Membrane; Erythrocytes; Humans; Osmolar Concentration
PubMed: 14400421
DOI: 10.1085/jgp.43.3.635 -
Expert Opinion on Drug Delivery Sep 2014As dissolution plays an important and vital role in the drug-delivery process of oral solid dosage forms, it is, therefore, essential to critically evaluate the... (Review)
Review
INTRODUCTION
As dissolution plays an important and vital role in the drug-delivery process of oral solid dosage forms, it is, therefore, essential to critically evaluate the parameters that can affect this process.
AREAS COVERED
The consumption of food as well as the physiological environment and properties of the gastrointestinal tract, such as its volume and composition of fluid, the fluid hydrodynamics, properties of the intestinal membrane, drug dose and solubility, pKa, diffusion coefficient, permeability and particle size, all affect drug dissolution and absorption rate. There are several dissolution approaches that have been developed to address the conditions as experienced in the in vivo environment, as the traditional dissolution being a quality control method is not biorelevant and as such do not always produce meaningful data. This review also describes the development of a systematic way that differentiates between robust and non-robust formulations by varying the effects of agitation and ionic strength through the use of the automated United States Pharmacopeia type III Bio-Dis apparatus.
EXPERT OPINION
With the improved understanding of the physiological parameters that can affect the oral bioperformance of dosage forms, strides have, therefore, been made in making dissolution testing methods more biologically based with the view of obtaining more in vitro-in vivo correlations.
Topics: Absorption; Animals; Chemistry, Pharmaceutical; Diffusion; Drug Delivery Systems; Food-Drug Interactions; Humans; Osmolar Concentration; Particle Size; Permeability; Pharmaceutical Preparations; Pharmacopoeias as Topic; Solubility; Tablets
PubMed: 24970101
DOI: 10.1517/17425247.2014.924498 -
International Journal of Molecular... Oct 2018A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial...
A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH₂, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl₂ or MgSO₄ cations. At 10 mM MgCl₂ or MgSO₄, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH₂. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH₂, MgCl₂ and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.
Topics: Aptamers, Nucleotide; Biosensing Techniques; DNA, Single-Stranded; Fluorescence Resonance Energy Transfer; Graphite; Osmolar Concentration
PubMed: 30347651
DOI: 10.3390/ijms19103230 -
Biophysical Journal Jun 2020The free-solution mobilities of small single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) have been measured by capillary electrophoresis in solutions containing...
The free-solution mobilities of small single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) have been measured by capillary electrophoresis in solutions containing 0.01-1.0 M sodium acetate. The mobility of dsDNA is greater than that of ssDNA at all ionic strengths because of the greater charge density of dsDNA. The mobilities of both ssDNA and dsDNA decrease with increasing ionic strength until approaching plateau values at ionic strengths greater than ∼0.6 M. Hence, ssDNA and dsDNA appear to interact in a similar manner with the ions in the background electrolyte. For dsDNA, the mobilities predicted by the Manning electrophoresis equation are reasonably close to the observed mobilities, using no adjustable parameters, if the average distance between phosphate residues (the b parameter) is taken to be 1.7 Å. For ssDNA, the predicted mobilities are close to the observed mobilities at ionic strengths ≤0.01 M if the b-value is taken to be 4.1 Å. The predicted and observed mobilities diverge strongly at higher ionic strengths unless the b-value is reduced significantly. The results suggest that ssDNA strands exist as an ensemble of relatively compact conformations at high ionic strengths, with b-values corresponding to the relatively short phosphate-phosphate distances through space.
Topics: DNA; DNA, Single-Stranded; Electrophoresis, Capillary; Osmolar Concentration; Solutions
PubMed: 32445623
DOI: 10.1016/j.bpj.2020.02.034 -
Viruses Oct 2023(CCMV) and (BMV) are naked plant viruses with similar characteristics; both form a T = 3 icosahedral protein capsid and are members of the family. It is well known...
(CCMV) and (BMV) are naked plant viruses with similar characteristics; both form a T = 3 icosahedral protein capsid and are members of the family. It is well known that these viruses completely disassemble and liberate their genome at a pH around 7.2 and 1 M ionic strength. However, the 1 M ionic strength condition is not present inside cells, so an important question is how these viruses deliver their genome inside cells for their viral replication. There are some studies reporting the swelling of the CCMV virus using different techniques. For example, it is reported that at a pH~7.2 and low ionic strength, the swelling observed is about 10% of the initial diameter of the virus. Furthermore, different regions within the cell are known to have different pH levels and ionic strengths. In this work, we performed several experiments at low ionic strengths of 0.1, 0.2, and 0.3 and systematically increased the pH in 0.2 increments from 4.6 to 7.4. To determine the change in virus size at the different pHs and ionic strengths, we first used dynamic light scattering (DLS). Most of the experiments agree with a 10% capsid swelling under the conditions reported in previous works, but surprisingly, we found that at some particular conditions, the virus capsid swelling could be as big as 20 to 35% of the original size. These measurements were corroborated by atomic force microscopy (AFM) and transmission electron microscopy (TEM) around the conditions where the big swelling was determined by DLS. Therefore, this big swelling could be an easier mechanism that viruses use inside the cell to deliver their genome to the cell machinery for viral replication.
Topics: Bromovirus; Plant Viruses; Capsid Proteins; Capsid; Osmolar Concentration
PubMed: 37896823
DOI: 10.3390/v15102046 -
International Journal of Environmental... Oct 2019Rice straw is a kind of low-cost biosorbent. Through mechanical crushing, pyrolysis, incineration, and citric acid (CA) modification, it could be converted to rice straw...
Rice straw is a kind of low-cost biosorbent. Through mechanical crushing, pyrolysis, incineration, and citric acid (CA) modification, it could be converted to rice straw powder (Sp), biochar (Sb), ash (Sa), and modified rice straw (Ms) accordingly. Using rice straw as an adsorbent, the influence of pH value (2, 4, and 9), initial Cd(II) concentration (0, 200, and 800 mg/L), and ionic strength (0, 0.2, to 0.6 mg/L) on the adsorption capacity for Cd(II) were examined with three replicates, and the relevant mechanisms were explored using Fourier transform infrared (FTIR) technology. Results showed that the modifications could improve the adsorption capacity of Cd(II) by changing their chemical structures. The products (Sb and Sa) of the pyrolysis and incineration of rice straw contained fewer hydroxyl and alkyl groups, but more Si-O groups. Citric acid modification removed a portion of silica in rice straw, increased its carboxylic content, and made more -OH groups exposed. Compared with Sp, Sb, Sa, and Ms were more likely to act as donors in the Cd(II) sorption process and exhibited more carboxyl binding. The bands of C = C, -O-CH, and the O-H, carboxyl, Si-O-Si or Si-O groups were involved in the Cd(II) sorption process. The adsorption amount of Cd(II) by the four adsorbents increased with the increase in the pH value of the solution and the initial Cd(II) concentration. Affected by pH in a solution, ion exchange, surface complexation, and precipitation were the major adsorption mechanisms. Further, under the influence of the initial Cd(II) concentration, electrostatic attraction played a leading role. With no interference by ionic strength, all the adsorbents had the greatest adsorption amount of Cd(II), and the intensity of O-H vibration was also the weakest; ion exchange was the most important mechanism in this process. Regardless of the influencing factors, Sa, with the greatest specific surface area, had an absolute advantage in the adsorption capacity of Cd(II) over Sp, Sb, and Ms.
Topics: Adsorption; Cadmium; Charcoal; Hydrogen-Ion Concentration; Oryza; Osmolar Concentration; Spectroscopy, Fourier Transform Infrared; Water Pollutants, Chemical; Water Purification
PubMed: 31717746
DOI: 10.3390/ijerph16214129 -
Bioresource Technology Dec 2021Current mechanistic anaerobic digestion (AD) models cannot accurately represent the underlying processes occurring during food waste (FW) AD. This work presents an...
Current mechanistic anaerobic digestion (AD) models cannot accurately represent the underlying processes occurring during food waste (FW) AD. This work presents an update of the Anaerobic Digestion Model no. 1 (ADM1) to provide accurate estimations of free ammonia concentrations and related inhibition thresholds, and model syntrophic acetate oxidation as acetate-consuming pathway. A modified Davies equation predicted NH concentrations and pH more accurately, and better estimated associated inhibitory limits. Sensitivity analysis results showed the importance of accurate disintegration kinetics and volumetric mass transfer coefficients, as well as volatile fatty acids (VFAs) and hydrogen uptake rates. In contrast to the default ADM1, the modified ADM1 could represent methane production and VFA profiles simultaneously (particularly relevant for propionate uptake). The modified ADM1 was also able to predict the predominant acetate-consuming and methane-producing microbial clades. Modelling results using data from reactors dosed with granular activated carbon showed that this additive improves hydrogen uptake.
Topics: Acetates; Anaerobiosis; Bioreactors; Food; Methane; Osmolar Concentration; Refuse Disposal
PubMed: 34438285
DOI: 10.1016/j.biortech.2021.125802