Effect Of Charged Groups Research Articles

Vibration Characteristics of Misfolded Proteins and Their Consquences

The functioning of native protein has been discussed briefly. Disruption in native protein with misfolding in its structure due to infection or otherwise has also been discussed .The physical characteristics of prion- a variety of protein responsible for number of both degenerative and non-degenerative diseases have been detailed here from the view point of protein vibration due to external stimuli. Attempts have been taken to focus on the effects of charge groups on the surface of both folded and misfolded protein. Suggestion for application of magnetic materials which may be able to create potential barrier in controlling the chain process of infectious prions and other similar proteins have also been discussed basing on the frequencies of vibration of protein and also on the vibration energy thus evaluated.

Effects of charged groups in foodstuffs on diffusion of NaCl in the foodstuff substrate

Effects of charged groups in foodstuffs on diffusion of NaCl in the foodstuff substrate

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using trajectories of at least 1 μs. The total simulation time was 37.2 μs. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. The MD simulations were done in explicit solvent with a 16-mer Nrf2 β-hairpin forming peptide using Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27, and OPLS-AA/L force fields. The effects of charge-groups, terminal capping, and phosphorylation on the peptide folding were also examined. Despite using identical starting structures and simulation parameters, we observed clear differences among the various force fields and even between replicates using the same force field. Our simulations show that the uncapped peptide folds into a native-like β-hairpin structure at 310 K when Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, or GROMOS96 53a6 were used. The CHARMM27 simulations were able to form native hairpins in some of the elevated temperature simulations, while the OPLS-AA/L simulations did not yield native hairpin structures at any temperatures tested. Simulations that used charge-groups or peptide capping groups were not largely different from their uncapped counterparts with single atom charge-groups. On the other hand, phosphorylation of the threonine residue located at the β-turn significantly affected the hairpin formation. To our knowledge, this is the first study comparing such a large set of force fields with respect to β-hairpin folding. Such a comprehensive comparison will offer useful guidance to others conducting similar types of simulations.

Combinatorial Evaluation of Cations, pH-sensitive and Hydrophobic Moieties for Polymeric Vector Design

Three combinatorial libraries of polymeric vectors were evaluated to investigate the functional roles of molecular weight (MW), cations, pH-sensitive moieties, and hydrophobic derivitization in polymer-mediated gene delivery. Four cationic and pH-sensitive moieties (imidazole, primary, secondary, and tertiary amino) and three hydrophobic residues (C4 butyl, C6 hexyl, and C8 octyl) were assessed in single and serially incremented, binary combinations. Three MWs were evaluated-10, 30, and 50 kDa. The highest levels of transfection, comparable to branched PEI (25 kDa), were achieved by 30 kDa and 50 kDa formulations containing primary amino and imidazole groups. Primary amino groups offered superior charge-neutralizing and size-condensing capacity, while imidazole groups appeared to bind with DNA via nonelectrostatically mediated interactions to produce stable polyplexes that were resistant to premature dissociation. Eight of the 10 highest-transfecting polymers possessed IC(50) values greater than the maximum concentration of free polymers exposed to cells (200 microg/ml). The results herein have identified highly efficient polymeric formulations with superb toxicity profiles and have revealed the functional roles that the investigated pendant groups play in the transfection process. The reported polymeric system offers a versatile and robust platform upon which future structure-function studies may be based to create safer and more efficient polymeric vectors.

The effect of charged groups on protein interactions with poly(HEMA) hydrogels

Proteins, lipids and other biomolecules interact strongly with the acrylic-based biomaterials used for contact lenses. Although hydrogels are nominally resistant to protein fouling, many studies have reported considerable amounts of protein bound to poly(2-hydroxyethylmethacrylate) (PHEMA) lenses. This study examined the binding of a series of biomolecules (tear protein analogues, mucin and cholesterol) to poly(methylmethacrylate) (PMMA) and three HEMA-based hydrogels (PHEMA, HEMA plus methacrylic acid (P(HEMA–MAA)), HEMA plus methacrylic acid plus N-vinylpyrrolidone (P(HEMA–MAA–NVP))) by use of a quartz crystal microbalance with dissipation (QCM-D) monitoring. The QCM-D estimates changes in the mass and viscous constant for the adsorbed layer through measurements of frequency and dissipation. Protein interaction with each of the test materials caused a net increase in mass of the material indicating protein binding except for lysozyme interacting with P(HEMA–MAA). A net decrease in mass was observed for lysozyme interacting with P(HEMA–MAA) which may be ascribed to lysozyme collapsing the hydrogel by expelling water. A net mass decrease was observed for cholesterol interacting with each of the hydrogel materials, while a mass increase was observed on PMMA.

Effect of charged groups on the adsorption and penetration of proteins onto and into carboxymethylated poly(HEMA) hydrogels

A range of carboxymethylated poly(hydroxyethyl methacrylate) (CM-PHEMA) hydrogels with varying degrees of carboxymethylation was synthesized for a systematic study of the effects of ionized groups (‘charge’) on the uptake by hydrogel matrices of the proteins, lysozyme and human serum albumin (HSA). Using a radiolabel-tracer technique, X-ray photoelectron spectroscopy, and laser scanning confocal microscopy, we attempted to differentiate between protein molecules that were irreversibly adsorbed onto the hydrogel surface and those that penetrated into the hydrogel matrix. The effective pore size of the CM-PHEMA hydrogels was modelled and compared with the known molecular dimensions of the two proteins. The effects of the presence of varying amounts of ionized groups in the hydrogel matrix differed for the two proteins. For lysozyme, increased uptake was observed at higher carboxymethylation; this is interpreted as resulting from a combination of electrostatic attraction and increasing ease of penetration of the protein into the more porous hydrogel matrix. For HSA, on the other hand, the uptake was primarily by surface adsorption, with little diffusive penetration into the matrix.

Electrostatic screening in molecular dynamics simulations.

The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pK shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative simulations have been carried out on a protein system which explicitly included water molecules and a system in vacuo. For the system without solvent the results of using (i) the standard potential form were compared with results of (ii) the potential where the Coulomb term was modified by the inclusion of a distance dependent dielectric, epsilon (r), to model the screening effect of bulk water, and (iii) standard potential modified by reducing the charge on ionized residue side chains. All molecular dynamics simulations have been carried out on bovine pancreatic trypsin inhibitor. Comparisons between the resulting trajectories, averaged structures, hydrogen bonding patterns and properties such as solvent accessible surface area and radius of gyration are described. The results show that the dynamical behaviour of the protein calculated with a screened electrostatic term compares more favourably with the time-dependent structural changes of the full system with explicitly included water than the standard vacuum simulation.

Effect of charge groups in polyurethane and polystyrene interpenetrating polymer networks

AbstractOpposite charges, namely tertiary amine and carboxyl groups, were introduced into polyurethane (PU) and polystyrene (PS), respectively, to prepare PU/PS interpenetrating polymer networks (IPNs) by means of simultaneous bulk polymerization. Four IPNs were synthesized: a full‐IPN, two semi‐IPNs and a linear blend. The effect of charge groups on the mechanical properties and morphology of the four polymer alloys was investigated.It is found that the PU/PS IPN which was incorporated with charge groups is free of any phase‐separation, and sufficiently uniformly distributed, as can be seen from the corresponding scanning electron microscopy (SEM) photographs. Dynamic mechanical analysis indicates that the transition peak of the loss modulus E″ will move towards the centre between the two transition peaks of both components in the absence of charge groups, as a function of an increase in the contents of the opposite charge groups. Meanwhile the storage modulus E′ will decrease in a single‐stage way from the previous two‐stage mode.The tensile strength in all the four polymer alloys increased markedly along with an increase in the contents of acrylic acid (AA) in the poly(styrene‐acrylic acid) (PSAA), which clearly can be seen for the PU/PSAA full‐IPN.

Effects of charged groups in haptens on adsorption equilibrium of hapten antibody

Antisera against charged (p-azobenzoate and p-azoben zenesulfonate) and uncharged (dinitrophenyl) haptenic groups were produced in rabbits, and the equilibrium characteristics of hapten-antibody were measured by use of immunoadsorbents. The antibody to the uncharged hapten formed a stable binding with the hapten to the changes in ionic strength and pH. On the other hand, the antibodies to the charged haptens showed affinities sensitive to the changes in pH and ionic strength. Therefore, the effect of the pK(a) of ionizable haptens on the pH dependence of the hapten-antibody binding was studied by comparing the interactions between a series of para-substituted benzoic acids and the anti-p-azobenzoate antibody. The pH dependence of the interactions was strongly affected by the pK(a) of ionizable groups in haptens. Furthermore, the equilibrium characteristics of anti-p-aminobenzoyl dipeptides were compared. The characteristics of interactions were affected by the features of amino acid residues.

The preparation and kinetics of lactate dehydrogenase attached to water-insoluble particles and sheets.

1. The preparation of lactate dehydrogenase covalently attached to anion-exchange cellulose particles and sheets by use of a dichloro-sym-triazinyl dyestuff, Procion brilliant orange MGS, is described. 2. The stability and kinetic properties of these preparations were investigated. 3. An equation is derived to describe the change in concentration of a substrate when passed through a uniform bed of a substrate-inhibited enzyme. A number of theoretical curves are shown to illustrate the system. 4. A titrimetric assay for lactate dehydrogenase is described, and shown to be stoicheiometric over the range pH5.0-9.2. 5. The results are discussed in relation to previous work, and the effects of charged groups on the support, and of the diffusion film surrounding any particle in suspension, are treated qualitatively.