Influence Of Charge Distribution Research Articles

Nucleosome structure relaxation during DNA unwrapping: Molecular dynamics simulation study

Effects of local relaxation of the nucleosome structure after DNA unwrapping from the histone octamer are considered in this paper. The influence of charge distribution in histones on the kinetics of DNA rewrapping was studied. It was shown that ionic environment rapidly stabilizes during relaxation simulation of the system by molecular dynamics. In the case of short relaxation, a rapid irreversible restoration of the structure, which is similar to a crystal one, occurs. In the case of longer relaxation, DNA rewrapping does not occur despite the absence of apparent differences in the ionic environment of DNA. The change in the quadrupole moment of the system during relaxation was shown.

The Influence of Charge Distribution on Self-Association and Viscosity Behavior of Monoclonal Antibody Solutions

The present work investigates the influence of electrostatic surface potential distribution of monoclonal antibodies (MAbs) on intermolecular interactions and viscosity. Electrostatic models suggest MAb-1 has a less uniform surface charge distribution than MAb-2. The patches of positive and negative potential on MAb-1 are predicted to favor intermolecular attraction, even in the presence of a small net positive charge. Consistent with this expectation, MAb-1 exhibits a negative second virial coefficient (B₂₂), an increase in static structure factor, S((q→0)), and a decrease in hydrodynamic interaction parameter, H((q→0)), with increase in MAb-1 concentration. Conversely, MAb-2 did not show such heterogeneous charge distribution as MAb-1 and hence favors intermolecular repulsion (positive B₂₂), lower static structure factor, S((q→0)), and repulsion induced increase in momentum transfer, H((q→0)), to result in lower viscosity of MAb-2. Charge swap mutants of MAb-1, M-5 and M-7, showed a decrease in charge asymmetry and concomitantly a loss in self-associating behavior and lower viscosity than MAb-1. However, replacement of charge residues in the sequence of MAb-2, M-10, did not invoke charge distribution to the same extent as MAb-1 and hence exhibited a similar viscosity and self-association profile as MAb-2.

Complexation of Ferric Oxide Particles with Pectins of Ordered and Random Distribution of Charged Units

Complexation between ferric oxide particles and pectins with degree of methylation 50% but having ordered or random arrangement of free carboxyl groups is investigated by electric light scattering and electrophoresis. The influence of charge distribution in pectin chain on the electrical properties of oppositely charged oxide particles and stability of their suspensions is examined as a function of pectin concentration. Although the difference in charge density of pectin samples is ~5%, we found small but measurable difference in the behavior of both oxide/pectin complexes. This is attributed to condensation of counterions near the chains of pectin with ordered distribution of charges, leading to a decrease in the effective charge density and to a corresponding decrease in the contour length of the adsorbing pectin chains. Two parameters are sensitive to the conformation of the adsorbed chains in suspensions, stabilized by pectin adsorption (at particle charge reversal). The electro-optical effect is higher for the complex with less charged pectin, which is explained with larger amount of chains, adsorbed in more coiled conformation than the chains of pectin with random distribution of free carboxyl groups. The addition of small amounts of CaCl(2) has no significant influence on the thickness of the layer from the less charged pectin, in agreement with a more compact conformation of the chains in this adsorbed layer. In contrast, the thickness of the layer from pectin with random distribution of charged groups decreases with increasing concentration of CaCl(2), indicating a more loose structure of this layer.

The charge ratio between O and N on amide bonds: A new approach to the mobile proton model

The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N ( Q O/ Q N) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the Q O / Q N values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.

Influence of charge distribution on the discrepant MS/MS fragmentation of the native and oxidized FMRF: evidence for the mobile proton model

Using the mobile proton model as a framework, the influence of charge distribution on the discrepant fragmentation of peptides FMRF, FM(O)RF and FM(O(2))RF (with united peptide sequence) was explored by mass spectrometry experiments and quantum chemical calculations. With the added O atoms, more negative charges were prompted to deposit in the main protonation sites of the oxidation products. Consequently, the solvated proton to the oxidized peptides could flow to the amide bonds in an easier manner and made these bonds fragment easily. Oxidation also induced the discrepant fragmentation of these bonds in a predictable manner: the more negative charges deposited in an amide bond, the more daughter ions (a(n), b(n), y(n) ions and their derivatives) were produced. The combined methods proposed here refined the mobile proton model for peptide fragmentation and opened the way to probe the discrepant fragmentation of peptides in peptide/protein identification.

Influence of Charge Distribution at the Active Site Surface on the Substrate Specificity of Human Neutrophil Protease 3 and Elastase: A KINETIC AND MOLECULAR MODELING ANALYSIS

The biological functions of human neutrophil protease 3 (Pr3) differ from those of neutrophil elastase despite their close structural and functional resemblance. Although both proteases are strongly cationic, their sequences differ mainly in the distribution of charged residues. We have used these differences in electrostatic surface potential in the vicinity of their active site to produce fluorescence resonance energy transfer (FRET) peptide substrates for investigating individual Pr3 subsites. The specificities of subsites S5 to S3' were investigated both kinetically and by molecular dynamic simulations. Subsites S2, S1', and S2' were the main definers of Pr3 specificity. Combinations of results for each subsite were used to deduce a consensus sequence that was complementary to the extended Pr3 active site and was not recognized by elastase. Similar sequences were identified in natural protein substrates such as NFkappaB and p21 that are specifically cleaved by Pr3. FRET peptides derived from these natural sequences were specifically hydrolyzed by Pr3 with specificity constants k(cat)/K(m) in the 10(6) m(-1) s(-1) range. The consensus Pr3 sequence may also be used to predict cleavage sites within putative protein targets like the proform of interleukin-18, or to develop specific Pr3 peptide-derived inhibitors, because none is available for further studies on the physiopathological function of this protease.

Considerations on influence of charge distribution on determination of biomolecules and microorganisms and tailoring the monolithic (continuous bed) materials for bioseparations

The importance of continuous beds (monoliths) as separation materials is connected with their better chromatographic properties and easier preparation in comparison to particulate-packed columns. Moreover the tuning of porosity as well as surface chemistry can lead to obtaining of highly selective materials, especially useful in separation of biologically important compounds or even microorganisms. To obtain high selectivity for such analytes as e.g. proteins, it is often important to have a knowledge about their shape, size, charge and finally charge distribution. This article presents our considerations on the charge distribution on the monolithic stationary phase and surface of such species as proteins or microorganisms as well as its eventual influence on the separation or sample preparation processes and tuning of their selectivity.

Influence of charge distribution on the thermophysical and dynamical properties of polar linear molecules

Gibbs ensemble Monte Carlo and molecular dynamics simulations were used to study thermophysical and dynamical properties of Kihara fluids consisting of linear molecules with dipolar symmetry. Two models differing in the electrostatic part of the intermolecular potential have been considered. The first one is an ideal dipole (ID) model where electrostatic interactions are modeled as point dipoles placed on the molecular center of mass, and the second one is a discrete charge (DC) model with single positive and negative charges placed at opposite ends of the molecules. The magnitude of the charges and the distance between them were chosen to reproduce the dipole moment of the ID model. In addition, an effective ionic strength for the DC model has been defined. Simulations were performed at several densities and temperatures in a wide range of molecular lengths and at three dipole moments. For all the systems, vapor–liquid equilibrium, thermodynamic, and structural properties, autocorrelation functions, correlation times, and transport properties such as diffusion, shear viscosity, and thermal conductivity have been obtained and analyzed. The results of the present study are in agreement with those found in previous works and they confirm that, although differences between the DC model and the ID model are small for the lower molecular lengths, they become more pronounced at higher molecular lengths. Finally, the influence of the effective ionic strength on the different properties of the system is discussed.

Influence of Charge Distribution on the Properties of Keggin- and Dawson-Type Heteropolyanions

The cyclic voltammetric behavior of selected Keggin- and Dawson-type heteropolyanions has been studied as a function of electrolyte composition. The buffer capacity of the electrolyte is shown to be an important parameter that can be used to reveal the symmetry or dissymetry in charge distribution within each oxometalate. A fully symmetrical heteropolyanion like [P2W18O62]6− exhibits a uniform protonability, while its α1 and α2 lacunary derivatives present a donor set of hard oxide ions with stepwise acid-base equilibria. The behavior of these sites is revealed readily in unbuffered or poorly buffered media at pH = 3, and is ascribed to the change in symmetry of charge distribution in the molecules. It is shown that cations other than the proton, even in very high excess, fail to give rise to the classical voltammograms of lacunary heteropolyanions. The same behavior also appears in α2[Mo2P2W15O61]10−, α[PW11O39]7−, α[SiW11O39]8−, [H2P2W12O48]12−, and, to a lesser extent, in α2[Ni(H2O)P2W17O61]8− and α2[Zn(H2O)P2W17O61]8−. The analogy in the cyclic voltammograms of most dication-substituted heteropolyanions with those of the precursor lacunary species could thus be explained.

Influence of charge distribution on the conformation of neutral polyampholytes

Two polyampholyte copolymers based on sodium-2-acrylamido-2-methylsulfonate (NaAMPS) and methacryloyloxyethyltrimethylammonium chloride (MADQUAT) have been prepared either in homogeneous solution or by an inverse microemulsion polymerization technique. The copolymer microstructure was shown to depend on the method of preparation. The microemulsion polymerization yields copolymers with a monomer sequence distribution not far from random while those obtained by polymerization in solution have a strong tendency to alternation. The aqueous-solution properties of the two samples have been investigated by viscometry. The results show that the charge distribution along the copolymer chain affects considerably its conformation, in good agreement with recent theoretical studies.

The Influence of Charge Distribution on Bond Lengths in the P4O6 Framework in Compounds of the Type P4O6X

The amount of charge transferred on substitution can be used to explain the experimentally determined difference in PO bond lengths between phosphorus oxides or oxide sulfides of the type P4O6X (X  O and S, respectively; structure shown on the right) and the parent compound P4O6. With the strongly electron-repelling substituent X  N−, the observed effects should be reversed.