Basic pH Region Research Articles

The heavy lanthanide of Thulium(III) separation and recovery using specific ligand-based facial composite adsorbent

The organic ligand of 3–(((5–ethoxybenzenethiol)imino)methyl)–salicylic acid (EBMS) was synthesized and then immobilized onto the mesoporous silica for the fabrication of facial composite adsorbent (FCA). The FCA was successfully utilized for the heavy lanthanide of Thulium(Tm(III)) separation, adsorption, and recovery in the solid-liquid approach. The FCA characterizations and affecting experimental parameters were assessed systematically. The Tm(III) ion was selected due to the high adsorption ability of the FCA according to the intra-series separation behaviors. The solution pH played a key role based on hydroxide formation in the basic pH region and a slightly acidic pH (3.50) was selected based on the high adsorption ability. The FCA was shown high kinetic performance and diverse competing metal ions did not interfere with Tm(III) adsorption. The Tm(III) adsorption was well-fitted with the Langmuir adsorption isotherm model with monolayer coverage and the maximum adsorption capacity was determined as 168.57 mg/g. The Tm(III) ion was strongly coordinated with the EBMS and the expected bond distance between Tm-N was shorter than the other bond length of Tm-S atoms in the complexation mechanism. The adsorbed Tm(III) ion was completely desorbed from the FCA with the suitable eluent of 0.25 M HNO3 and then simultaneously regenerated the FCA into the initial form without significant deterioration in the original functionality. The highest selectivity and maximum adsorption capacity of FCA to Tm(III) ions indicated that the proposed EBMS ligand-based composite adsorbent high potentiality to separate and recover the Tm(III) ions from waste samples effectively.

Antibacterial and Hemocompatible pH-Responsive Hydrogel for Skin Wound Healing Application: In Vitro Drug Release.

The treatment of successive skin wounds necessitates meticulous medical procedures. In the care and treatment of skin wounds, hydrogels produced from natural polymers with controlled drug release play a crucial role. Arabinoxylan is a well-known and widely available biological macromolecule. We produced various formulations of blended composite hydrogels (BCHs) from arabinoxylan (ARX), carrageenan (CG), and reduced graphene oxide (rGO) using and cross-linked them with an optimal amount of tetraethyl orthosilicate (TEOS). The structural, morphological, and mechanical behavior of the BCHs samples were determined using Fourier-transform infrared spectroscopy (FT-IR), Scanning electron microscope (SEM), mechanical testing, and wetting, respectively. The swelling and degradation assays were performed in phosphate-buffered saline (PBS) solution and aqueous media. Maximum swelling was observed at pH 7 and the least swelling in basic pH regions. All composite hydrogels were found to be hemocompatible. In vitro, silver sulfadiazine release profile in PBS solution was analyzed via the Franz diffusion method, and maximum drug release (87.9%) was observed in 48 h. The drug release kinetics was studied against different mathematical models (zero-order, first-order, Higuchi, Hixson–Crowell, Korsmeyer–Peppas, and Baker–Lonsdale models) and compared their regression coefficient (R2) values. It was observed that drug release follows the Baker–Lonsdale model, as it has the highest value (0.989) of R2. Hence, the obtained results indicated that, due to optimized swelling, wetting, and degradation, the blended composite hydrogel BCH-3 could be an essential wound dressing biomaterial for sustained drug release for skin wound care and treatment.

Thermomechanical analysis and pH-triggered elastic response of charge-balanced sulfonated poly(tertiary amine-methacrylate)-based terpolymer cryogels

pH-responsive terpolymer poly(hydroxyethyl methacrylate-2-acrylamido-2-methyl-propanosulfonic acid-diethylaminoethyl methacrylate) cryogels and hydrogels (named as CGs-PHA/Dm and HGs-PHA/Dm) were synthesized in ethanol-water mixture using different monomer feed compositions. By the combination of three monomers, an interesting system was designed with tunable pH/temperature responsiveness and elasticity. ATR-FTIR spectrums obtained after swelling swelling in pH buffer solution of 2.1 indicated –R2NH+ stretching of DEAEMA moities in terpolymer matrices. By incorporation of DEAEMA units with ionizable amino groups, terpolymer CGs-PHA/Dm and HGs-PHA/Dm gels exhibited pH-responsive swelling behavior. Inclusion of DEAEMA dramatically altered pH-responsiveness of terpolymers in simulated intestinal fluid at pH 6.6. Dependence of interaction parameter χon terpolymer volume fraction in gel ν2by a linear function and its enthalpic/entropic components with swelling pH were determined. At pH < 6.6, dependence of χ parameter on the swelling was evaluated as χ=1.097-2.965ν2, while at basic pH region, pH > 6.6, χ=0.576+0.459ν2. Both pH of swelling medium and the amount of DEAEMA in terpolymer composition affected the compression moduli of terpolymer gels. Flory-Rehner theory extended to correlate the compressive modulus with swelling pH and the dependence of the effective crosslink density νeon mol% DEAEMA was expressed in both acidic and basic conditions. pH-triggered swelling/shrinking of terpolymer gels were studied as reversible cycles in buffer solutions of pH 2.1 and 9.8. DEAEMA-rich terpolymer gels showed overshooting phenomena due to dynamic conformational changes of diethylaminoethyl units. Terpolymer cryogels exhibited much faster swelling kinetics than that of terpolymer hydrogels in simulated gastric fluid at pH 2.1. The values of diffusion coefficient seemed to be strongly dependent of terpolymer composition.

Thermo-Sensitivity of poly-N-isopropylacrylamide with Statistically Introduced D,L-Allylglycine Betainic Units

Statistical copolymers of N-isopropylacrylamide containing 2.2 – 2.7 mol % D,L-allylglycine were synthesized. The sample with 2.2 mol % allylglycine and molar mass 320000 g/mol was studied using light scattering and turbidimetry while heated in water and water–salt solutions. Temperature dependencies of light scattering intensity and optical transmission as well as hydrodynamic size and composition of the scattering entities were obtained in a wide range of pH. The onset temperatures of phase separation were independent of pH; however, in the basic pH region the phase transition was widened as compared to the neutral and acid media. It was shown that a small content of allylglycine results in a different thermoresponsive behavior of the copolymer as compared with N-isopropylacrylamide homopolymer. The addition of a physiological amount of NaCl shifts the copolymer thermo-sensitivity toward lower temperatures.

Low-molecular-mass nitrophenol-based compounds suitable for the effective tracking of pH gradient in isoelectric focusing

Low-molecular-mass isoelectric point (pI) markers are a reasonable alternative to commonly used peptide and protein pI markers in the field of isoelectric focusing. We present a comparative study dealing with characterization of 44 nitrophenol-based compounds synthesized by the Mannich reaction which pI values cover a pH range from 3.2 to 10.4. The values of pIs of all the presented nitrophenol-based compounds were precisely determined by capillary isoelectric focusing technique (cIEF) when a standard deviation of measurement reached a value of a few hundredths of a pH unit (n ≥ 3). Differences have been found between in silico analysis of acid-base properties of the investigated compounds and the experimental cIEF data especially at the basic pH region. The data from the acidic pH range showed better correlation between these methods. Only three compounds were excluded from the group of pI markers because they contained impurities originating from the synthesis or long-term storage. Based on the presented results we identified 41 nitrophenol-based pI markers (NPIMs) which can fulfill requirements of the most applications in a field of isoelectric focusing analyses.

Oxime-functionalized cryogel disks for catalase immobilization

Catalase is a protective enzyme against oxidative stress and converts hydrogen peroxide into water and molecular oxygen. In the current study, catalase immobilization was applied onto the oxime-functionalized cryogel disks. Cryogel disks were produced by free radical polymerization. After cutting as circular disks, oxime ligand (4-biphenylchloroglyoxime, BPCGO) was attached and oxime-functionalized cryogel disks were obtained. After optimization of several immobilization parameters such as pH, initial catalase concentration, temperature and ionic strength, maximum catalase load was detected as 261.7 ± 11.2mg/g for cryogel disk at pH5.0. Activity studies indicated that immobilization enhanced the enzyme activity in basic pH region, the temperature range of 15–35°C and at ionic strengths between 0.2 and 1.0M NaCl. Km was detected as 9.9 and 11.0mM and Vmax was 357.1 and 769.2μmol min−1 for free and immobilized catalase, respectively. kcat and Km/kcat values showed that immobilization enhanced the catalytic efficiency. Storage stability experiments demonstrated that immobilization increased the usability period. Furthermore, catalase desorption was achieved by 1.0M NaSCN at pH8.0 successfully and catalase adsorption capacity of oxime-functionalized cryogel disk was decreased by 9.9% at the end of 5 adsorption-desorption cycle.

Enhancement of sorption capacity of cocoa shell biomass modified with non-thermal plasma for removal of both cationic and anionic dyes from aqueous solution.

Removal of cationic dye, Azur II, and anionic dye, Reactive Red 2 (RR-2) from aqueous solutions, has been successfully achieved by using a modified agricultural biomaterial waste: cocoa shell husk (Theobroma cacao) treated by gliding arc plasma (CPHP). The biomass in its natural form CPHN and modified form CPHP was characterized by infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and point of zero charge (pHpzc). Experimental variables such as initial pH, contact time, and temperature were optimized for adsorptive characteristics of CPHN and CPHP. The results show that the removal of the Azur II dye was favorable in the basic pH region (pH 10) while the Reactive Red 2 dye was favorable in the acidic pH region (pH 2). The minimum equilibrium time for Azur II and RR-2 dye was obtained after 40 and 240min, respectively. The adsorption kinetics and isotherm data obtained were best described by a pseudo-second-order kinetic rate model and a combination of Langmuir-Freundlich isotherm models. This work indicates that the plasma-treated raw materials are good alternative multi-purpose sorbents for the removal of many coexisting pollutants from aqueous solutions.

Halophilic mechanism of the enzymatic function of a moderately halophilic dihydrofolate reductase from Haloarcula japonica strain TR-1.

Dihydrofolate (DHF) reductase coded by a plasmid of the extremely halophilic archaeon Haloarcula japonica strain TR-1 (HjDHFR P1) shows moderate halophilicity on enzymatic activity at pH 6.0, although there is no significant effect of NaCl on its secondary structure. To elucidate the salt-activation and -inactivation mechanisms of this enzyme, we investigated the effects of pH and salt concentration, deuterium isotope effect, steady-state kinetics, and rapid-phase ligand-binding kinetics. Enzyme activity was increased eightfold by the addition of 500mM NaCl at pH 6.0, fourfold by 250mM at pH 8.0, and became independent of salt concentration at pH 10.0. Full isotope effects observed at pH 10.0 under 0-1000mM NaCl indicated that the rate of hydride transfer, which was the rate-determining step at the basic pH region, was independent of salt concentration. Conversely, rapid-phase ligand-binding experiments showed that the amplitude of the DHF-binding reaction increased and the tetrahydrofolate (THF)-releasing rate decreased with increasing NaCl concentration. These results suggested that the salt-activation mechanism of HjDHFR P1 is via the population change of the anion-unbound and anion-bound conformers, which are binding-incompetent and -competent conformations for DHF, respectively, while that of salt inactivation is via deceleration of the THF-releasing rate, which is the rate-determining step at the neutral pH region.

Long-term leaching from recycled concrete aggregates applied as sub-base material in road construction

In the present study, the metal leaching from recycled concrete aggregates (RCA) used in road sub-base is presented after >10years of exposure. The released levels of inorganic constituents, the effect of small variation of pH and the use of de-icing salt during winter season were studied. In addition, speciation modelling for the major elements has been provided. The pH varied from 7.5 to 8.5 for the sub-base constructed with RCA whereas the pH of around 8 was obtained for the test section not affected by the traffic and de-icing salts. Despite a small variation in pH, the leachability of Al, Ca and Mg was found to be strongly dependent on pH and fair agreement between the measured and predicted concentrations was obtained. The speciation modelling indicated that gibbsite, calcite and magnesite controlled the solubility of Al, Ca and Mg, respectively, which was in agreement with the expected carbonation products. Due to the larger pH fluctuations in the test sections exposed to the road traffic, increased concentrations were observed for the oxyanions. The same effect was not seen for the trace metal cations Cd, Cu, Ni, Pb and Zn. The distinct pH dependent leaching profile (solubility maximum in the mildly basic pH region) for vanadium could be seen after 10years of exposure. The simplified risk assessment showed that the released quantities did not exceed the chosen acceptance criteria for groundwater and fresh water. The results obtained for the test section not influenced by road dust and de-icing salts, complied with these criteria even without considering any dilution effects caused by the mixing of pore water with groundwater.

Phosphonic Acid Containing Superporous Hydrogels and their Adsorption Properties

In this study, poly[(1-vinyl 1,2,4-triazole)-co-(vinylphosphonic acid)] (poly(VTAz/VPA)) hydrogels were prepared by 60Co γ-irradiation of binary mixtures of 1-vinyl 1,2,4-triazole and vinylphosphonic acid in the presence of NaHCO3. In binary systems, the percentage gelation decreased with increasing phosphonic acid content. For the hydrogels with a high phosphonic acid content, gelation of 75% was reached at around 25 kGy dose at the end of irradiation. The structural changes were followed by using FTIR/ATR spectroscopy. Mercury intrusion porosimetry and SEM methods were used to analyze pore structure of poly(VTAz/VPA) hydrogels. The effects of time, pH, temperature, and ionic strength on the swelling behavior were investigated. Swelling equilibrium was attained within 2 days. Rapid increase in swelling was observed at basic pH region. An increase in swelling was observed as the temperature increases. The swelling ratios of the gels decreased with increasing ionic strength. Poly(VTAz/VPA) hydrogels were tested two different area to show usability for separation purposes: One is radioactive heavy metal ion adsorption and the other is water removal from biofuels. As a result, poly(VTAz/VPA) hydrogels showed stimuli-responsive properties depending on surrounding medium; therefore, they are being considered for adoption as some kind of carrying material for separation purposes.

“Schizophrenic” Micellization of Poly(Acrylic Acid)-B-Poly(2-Dimethylamino)Ethyl Methacrylate and Responsive Behavior of the Micelles

The well-defined block polyampholyte poly(acrylic acid)-b-poly(2-dimethylamino)ethyl methacrylate (PAA-b-PDMAEMA) was synthesized by sequential atom transfer radical polymerization (ATRP) using protected group chemisty. The block polyampholyte exhibited so-called “schizophrenic” micellization behavior at different pH values. The PAA-core micelles, PDMAEMA-core micelles, and a kind of polyeletrolyte complex were formed in acidic pH (pH < 4.5), basic pH (pH > 9.0), and neutral pH region (5.5–8.5), respectively. The temperature responsive behaviors of the micelles and the complex formed in neutral environment were studied in detail via dynamic light scattering (DLS) and UV-vis transmittance. Salt effect on the temperature responsive behavior was also discussed.[Supplementary materials are available for this article. Go to the publisher's online edition of Soft Materials or http://pubs.acs.org for the following free supplemental resource(s): Synthesis of PtBA-b-PDMAEMA, 1H NMR spectra of block copolymer and TEM image of block copolymer at aqueous solution with NaCl]”

Rapid pH-dependent phase transition and elasticity of stimuli-responsive cationic poly(N,N-dimethylaminoethyl methacrylate) hydrogels prepared with a dimethacrylate crosslinker

Stimuli-responsive hydrogels prepared from poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA) and its copolymers have attracted much interest to serve in biomedical and pharmaceutical applications. To investigate pH-dependent swelling and elasticity, a series of cationic hydrogels based on N,N-dimethylaminoethyl methacrylate were prepared by free radical crosslinking copolymerization at 60 °C in the presence of tetraethylene glycol dimethacrylate as the crosslinker. The equilibrium swelling and the mechanical properties of the PDMAEMA hydrogels were investigated as a function of the gel preparation concentration. To explain the effect of pH on the equilibrium swelling of the hydrogels, pH-dependent swelling studies were carried out in solutions of pH ranging from 2.1 to 10.7. It was found that the PDMAEMA hydrogels exhibit a rapid pH-dependent phase transition in aqueous solutions; that is, the gels first remain in the swollen state at acidic pH then collapse in a very narrow range of pH. The results showed that the volume of PDMAEMA hydrogels in acidic conditions is about 10- to 40-fold larger than that in the basic pH region. By using the Flory–Rehner theory, the characteristic network parameters of the PDMAEMA hydrogels were calculated and good agreement obtained between the swelling equilibria of hydrogels and their mechanical properties over the whole range of gel preparation concentration. © 2012 Society of Chemical Industry

Chemical Mechanical Polishing of InP

Results of a detailed study of different parameters of the polishing process and their influence on the removal rates (RRs) of InP are presented. RRs with silica-based slurries as well as generation of PH3 were much higher in the acidic pH regions compared to those in basic pH regions. RRs were also higher than those obtained with harder alumina particles. Smaller silica particles led to higher RRs than larger particles at the same wt% loading, presumably due to the higher total particle surface area. These characteristics suggest an affinity between silica particles and InP similar to that observed earlier between Ta and silica. However, unlike with Ta, replacing the surface silanol groups of the silica particles with dimethyl silane did not suppress the RRs completely. It is proposed that InP removal by silica abrasives is facilitated by the formation of –Si–O–In–, –Si–In– and –Si–P– structures due not only to the reactivity of the silanol groups but also due to the combined effect of the electronegativity of Si atoms, the presence of lone pairs of electrons on In atoms on the InP surface and the electronegativity difference between Si and P.

Effect of pH on the interaction of vitamin B12 with bovine serum albumin by spectroscopic approaches

The interaction mechanism between vitamin B12 (B12, cyanocobalamin) and bovine serum albumin (BSA) has been investigated by fluorescence, synchronous fluorescence, ultraviolet–vis (UV) absorbance, and three-dimensional fluorescence. The intrinsic fluorescence of BSA was strongly quenched by the addition of B12 in different pH buffer solutions (pH 2.5, 3.5, 5.0, 7.4, and 9.0) and spectroscopic observations are mainly rationalized in terms of a static quenching process at lower concentration of B12 ( C B12/ C BSA < 5) and a combined quenching process at higher concentration of B12 ( C B12/ C BSA > 5). The structural characteristics of B12 and BSA were probed, and their binding affinities were determined under different pH conditions. The results indicated that the binding abilities of B12 to BSA in the acidic and basic pH regions (pH 2.5, 3.5, 5.0, and 9.0) were lower than that at simulating physiological condition (pH 7.4). In addition, the efficiency of energy transfer from tryptophan fluorescence to B12 was found to depend on the binding distance r between the donor and acceptor calculated using Förster's theory. The effect of B12 on the conformation of BSA was analyzed using UV, synchronous fluorescence and three-dimensional fluorescence under different pH conditions. These results showed that the binding of B12 to BSA causes apparent change in the secondary and tertiary structures of BSA.

Chemical Mechanical Polishing of Ge Using Colloidal Silica Particles and H2O2

The effects of colloidal silica particles, oxidizer (H2O2), and pH on the removal rates (RRs) of Ge have been evaluated. High removal and dissolution rates were obtained in the basic pH regions, likely caused by *OH radicals and rapid dissolution of the dissociation products of germanium hydroxides, while at pH 2, a RR of ∼420 nm/min was obtained with minimal dissolution. The surface quality of polished wafer coupons, measured using atomic force microscopy, was very good. A probable reaction mechanism for Ge removal as a function of pH is proposed.

A pH-responsive carboxylic β-1,3-glucan polysaccharide for complexation with polymeric guests

The helix-forming nature of β-1,3-glucan polysaccharides is a characteristic that has potential for producing gene carriers, bio-nanomaterials and other chiral nanowires. Herein, carboxylic curdlan (CurCOOH) bearing the β-1,3-polyglucuronic acid structure was successfully prepared from β-1,3-glucan polysaccharide curdlan (Cur) by one-step oxidation using a 4-acetamido-TEMPO/NaClO/NaClO(2) system as the oxidant. The resulting high-molecular-weight CurCOOH was proved to bear the 6-COOH group in 100% purity. The optical rotatory dispersion (ORD) spectra indicated that the obtained CurCOOH behaves as a water-soluble single-strand in various pH aqueous media. This advantage has allowed us to use CurCOOH as a polymeric host to form various macromolecular complexes. For example, complexation of CurCOOH with single-walled carbon nanotubes (SWNTs) resulted in a water-soluble one-dimensional architecture, which formed a dispersion in aqueous solution that was stable for several months, and much more stable than SWNTs complexes of the similar negatively-charged polyacrylic acid (PAA) and polymethacrylic acid (PMAA). It was shown that in the complex, SWNTs are effectively wrapped by a small amount of CurCOOH, enabling them to avoid electrostatic repulsion. This pH-responsive CurCOOH formed a very stable complex with cationic water-soluble polythiophenes (PT-1), which was stabilized not only by the hydrophobic interaction but also by the electrostatic attraction between trimethylammonium cations in PT-1 and dissociated anionic COO(-) groups in CurCOOH. The included PT-1 became CD-active only in the neutral to basic pH region, and the positive Cotton effect suggested that the conjugated main chain is twisted in the right-handed direction. We also found that CurCOOH can interact with polycytidylic acid (poly(C)) only under high NaCl concentrations, the binding and release of which could be controlled by a change in the salt concentration. We believe, therefore, that CurCOOH bearing a dissociable COOH group can act as a new potential polymeric host to construct novel polymeric complexes applicable for gene carriers, biosensors, chiral polymer assemblies, etc.

Ferrate(VI) oxidation of glycine and glycylglycine: Kinetics and products

Amino acids and peptides may form potentially harmful disinfection byproducts during the conventional treatment of water and wastewater. Removal of these parent compounds by the use of the environmental-friendly oxidant, ferrate(VI) (Fe VIO 4 2−, Fe(VI)) was assessed by studying the kinetics of the oxidation of glycine (NH 3 +CH 2COOH, Gly) and glycylglycine (NH 3 +CH 2CONHCH 2COOH, Gly–Gly) as a function of pH (4.0–12.4) at 25 °C. This study with Gly–Gly represents an initial investigation of oxidation of peptides by Fe(VI). Generally, the second-order rate constant ( k) increased with decreased pH in the basic pH region, but this trend was reversed in the acidic pH range. Consideration of the reactivity of three oxidants (H 2FeO 4, HFeO 4 −, and FeO 4 2−) with three species of Gly and Gly–Gly (positive, neutral, and negative) reasonably explained the pH dependence of the rates. At pH 9.0, the molar consumption of Fe(VI) was nearly equal to that of Gly. The reaction of Fe(VI) with Gly at molar ratios of 1.0 and 2.0 ([Fe(VI)]:[Gly]) produced ammonia, carbon dioxide, and acetate. A reaction scheme is proposed which explains the formation of these products. The values of k for oxidation of iminodiacetate and nitriloacetate at pH 7.0 were also determined in order to compare oxidation of amines by Fe(VI). The calculated half-lives at neutral pH for the oxidation of primary and secondary amines were in seconds while decomposition of tertiary amines would occur in minutes. Overall, the reactivity of Fe(VI) with Gly and Gly–Gly indicates the significant potential of Fe(VI) to remove amine- and peptide-containing pollutants in water and wastewater.

Molecular Structures of Citrate and Tricarballylate Adsorbed on α-FeOOH Particles in Aqueous Suspensions

In this work, the adsorption of citric (2-hydroxypropane-1,2,3-tricarboxylic acid) and tricarballylic (propane-1,2,3-tricarboxylic acid) acids onto alpha-FeOOH (goethite) in aqueous suspensions was studied as a function of pH and total ligand concentration in 0.1 M NaCl at 25.0 degrees C, and the molecular structures of the surface complexes formed were analyzed by means of ATR-FTIR spectroscopy. The adsorption experiments were carried out as a series of batch experiments, and a newly developed simultaneous infrared and potentiometric titration technique was used to collect in situ infrared spectra with high signal-to-noise ratios. The high quality of the infrared spectra allowed analysis by means of two-dimensional correlation spectroscopy formalism that aided the resolution of pH-dependent spectral features. This has enabled the detection of two previously unidentified citrate-goethite surface complexes: one protonated species at low pH, and one inner sphere complex prevailing at high pH and coordinated via a combination of hydroxyl and carboxylate groups. In addition, an inner sphere complex involving only carboxylate coordination predominating at low pH and an outer sphere complex existing in the circumneutral pH region were identified. The behavior of tricarballylate parallels that of citrate, except no inner sphere surface complex is formed at high pH values, which is in accordance with the lack of an alpha-hydroxyl group. The comparison between citrate and tricarballylate reinforces previous observations showing that inner sphere surface complexes of pure carboxylates at water-iron oxide interfaces are suppressed at high pH values, where outer sphere species are relatively more predominant. It also shows that significant amounts of inner sphere surface complexes of carboxylates only seem to form in the basic pH region when the ligands contain complementary functional groups, such as the hydroxyl or amine groups.

Dynamic properties of pH-dependent structural organization of the amyloidogenic β-protein (1-40)

The structural organization of the amyloidogenic β-proteins containing 40 amino acid residues (Aβ40) was studied by the high temperature molecular dynamics simulations in the acidic (pH~3) and basic (pH~8) pH regions. The obtained data suggest that the central Ala21-Gly29 segment of Aβ40, can adopt folded and partially unfolded structures. At the basic pH, this segment forms folded structures, stabilized by electrostatic interactions and hydrogen bonds. At the acidic pH, it forms partially unfolded structures. Two other segments flanking to the central segment exhibit the propensity to adopt unstable inter-converting α-helical, 310-helical and turn-like structures. One of these segments is comprised of the Ala30-Val36 residues at both of the considered pHs. The second segment is comprised of the Glu11-Phe20 at the basic pH and of the Glu11-Val24 residues at the acidic pHs. The revealed pH-dependent structuration of the Aβ40 allowed us to suggest a possible scenario for initial Aβ aggregation. According to this scenario, the occurrence of the partially unfolded states of the Ala21-Gly29 segment plays main role in the Aβ oligomerization process.

Peptide separation with immobilized pI strips is an attractive alternative to in‐gel protein digestion for proteome analysis

Complex protein mixtures have traditionally been separated by 2-DE. Görg introduced IPGs as the first dimension of protein separation. In recent years, MS-based proteomics has increasingly become the method of choice for identifying and quantifying large number of proteins. In that technology, to decrease analyte complexity, proteins are often separated by 1-D SDS-gel electrophoresis before online MS analysis. Here, we investigate a recently introduced device for peptide separation with IPGs (Agilent OFFGEL). Loading capacity for optimal peptide focusing is below 100 microg and--similar to 2-D gels--IEF is more efficient in the acidic than the basic pH region. The 24-well fractionation format resulted in about 40% additional peptide identifications but less than 20% additional protein identifications than the 12-well format. Compared to in-gel digestion, peptide IEF consistently identified a third more proteins with equal number of fractions. Low protein starting amounts (10 microg) still resulted in deep proteome coverage. Advantages of the in-gel format include better reliability and robustness. Considering its superior performance, diminished sample and work-up requirements, peptide IEF will become a method of choice for sample preparation in proteomics.