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At least 1,315 records · Page 73Linked to original sources
PubMed1999

Electrostatic interaction between cytochrome P450 and NADPH-P450 reductase: comparison of mixed and fused systems consisting of rat cytochrome P450 1A1 and yeast NADPH-P450 reductase.

The electrostatic interaction between rat cytochrome P450 1A1 and yeast NADPH-P450 reductase was analyzed by using recombinant yeast microsomes containing both native enzymes or their fused enzyme. The Vmax of the 7-ethoxycoumarin O-deethylation in the recombinant microsomes containing both rat cytochrome P4501A1 and yeast NADPH-P450 reductase (the mixed system) was maximal when the ionic strength of the reaction mixture was 0.1-0.15. However, on the fused enzyme between rat cytochrome P450 1A1 and yeast NADPH-P450 reductase (the fused system), the activity was uniformly reduced with increasing ionic strength. The pH profiles of Vmax were also different between the mixed and the fused systems. Based on these results, we propose a hypothesis that cytochrome P450 and NADPH-P450 reductase have more than one binding mode. The maximal activity of the mixed system at ionic strength of 0.1-0.15 is explained by change of the binding mode. On the other hand, the fused enzyme appears to have only one binding mode due to the limited topology of cytochrome P450 and NADPH-P450 reductase domains.

Animals↗
PubMed1999

Localized structural effects of electrostatic interactions in a thermostable enzyme.

The sequence and resolved structure of thermotrophic isopropylmalate dehydrogenase (IPMDH) and a related protein, mesotrophic isocitrate dehydrogenase (IDH), were compared emphasizing clusters of charged residues identified from X-ray crystallographic studies (Wallon, G., Kryger, G., Lovett, S. T., Oshima, T., Ringe, D., and Petsko, G. A. (1997) J. Mol. Biol. 266, 1016-1031). Mesotrophic isocitrate dehydrogenase was used for comparison because crystallographic data for a mesotrophic form of IPMDH was not available in the database. The structural features in the region of these clusters were compared and localized conformational differences were found in the thermotroph compared to the mesotroph. Because the overall topology of the two proteins is similar, it was concluded that these localized structural differences induced by electrostatic interactions between charged residues in the thermotrophic enzyme were responsible for the enhanced thermal stability of proteins from thermotroph.

3-Isopropylmalate Dehydrogenase↗
PubMed2000

Effect of electrostatic interactions on the binding of charged substrate to GroEL studied by highly sensitive fluorescence correlation spectroscopy.

The binding processes of GroEL with apo cytochrome c (apo-cyt c) and disulfide-reduced apo alpha-lactalbumin (rLA) in homogeneous solution at low concentration were analyzed by fluorescence correlation spectroscopy (FCS) with extremely high sensitivity. Although apo-cyt c, a positively charged substrate, was tightly bound to GroEL in both the absence and the presence of 200 mM KCl, the strength of the binding was changed with varying salt concentration. Results from experiments when two different salts (KCl or MgCl(2)) were titrated into a sample solution containing GroEL and apo-cyt c clearly showed that the binding strength decreased with increasing salt concentration. On the other hand, the binding affinity of GroEL for rLA, a negatively charged substrate, increased by adding of 200 mM KCl. These results indicate that electrostatic interactions substantially contribute to the binding interactions by manipulating the binding affinity of charged substrates.

Animals↗
PubMed1997

Electrostatic Interaction between Two Ion-Penetrable Charged Spheroids

The electrostatic interaction between two ion-penetrable, charged spheroidal particles is examined theoretically. These particles can assume different sizes and an arbitrary spatial orientation. The electrical potential distribution is derived analytically under the Debye-Huckle condition. The results for two interaction spheres, one spheroidal particle and a planar surface, and rigid particles covered by an ion-penetrable membrane can be recovered as the special cases of the present general problem. We show that, for a fixed center-to-center distance between two particles, regardless of their relative sizes, the interaction free energy is the greatest if their major axes lie on the same line (head-to-head), and the smallest if their major axes are perpendicular to each other but not on the same plane (perpendicular).

Journal Article↗
PubMed1997

Electrostatic Potential Distribution for Spheroidal Surfaces in Symmetric Electrolyte Solutions

The electrostatic potential distribution for a charged spheroidal surface immersed in a symmetric electrolyte solution is derived. Such surfaces simulate a wide class of dispersed entities. Two types of boundary condition at the solid surface are considered, constant surface potential and constant amount of surface charges; both conductive and nonconductive surfaces are examined for the latter. The present analysis extends the conventional one-dimensional treatment on simple geometries to a two-dimensional space. A perturbation method is adopted to solve the governing Poisson-Boltzmann equation for the case of thin to moderately thick double layers. The classic results for planar and spherical surfaces can be recovered as special cases of the present analysis. The basic thermodynamic properties of the system under consideration, such as Helmholtz free energy, entropy, and surface excess, are derived. We show that using an equivalent sphere to approximate a spheroid can lead to an appreciable deviation in the prediction of the Helmholtz free energy. For a thin double layer, assuming a planar geometry will underestimate the Helmholtz free energy. Copyright 1997Academic Press

Journal Article↗
PubMed1998

Electrostatic Interactions in Adsorbed Protein Layers Probed by a Sedimentation Technique.

A simple centrifugation technique has been used to determine the thicknesses of layers of alphaS1-casein and beta-casein adsorbed onto monodisperse polystyrene latex particles. The influence of electrostatic interactions within the layers on their thickness and stabilizing ability is investigated by varying the ionic strength of the suspension or by including calcium ions, known to bind specifically to the caseins. Copyright 1998 Academic Press.

Journal Article↗
PubMed1999

Long-Range Electrostatic Attractions between Identically Charged Particles in Confined Geometries: An Unresolved Problem.

Long-range electrostatic attractions between identical colloidal particles in confined geometries have been observed experimentally by many workers. A satisfactory theoretical explanation for this behavior has proven elusive. Recent numerical calculations and reports (Nature 393, 621-623, 663-665 (1998)), however, have suggested that this problem is closed by demonstrating that this surprising effect is to be found naturally within the well-established Poisson-Boltzmann (PB) theory. We rigorously prove that these claims are false; within the framework of the PB theory, the interaction between identical colloidal particles is always repulsive, irrespective of whether the particles are isolated or confined. A satisfactory theoretical explanation of this surprising phenomenon thus remains an unresolved problem. Copyright 1999 Academic Press.

Journal Article↗
PubMed1999

The Viscosity of Electrostatically Stabilized Dispersions of Spherical Colloid Particles.

The viscosity virial coefficient characteristic of a moderately concentrated dispersion [and proportional to the Huggins coefficient] is calculated for electrostatically stabilized monodisperse suspensions of spherical colloid particles. The energy of interaction between two colloid particles is modeled as the sum of dispersion (van der Waals) and electric double-layer contributions. Comparisons of theoretical predictions and experimental data permit conclusions to be drawn about the adequacy of this model. Copyright 1999 Academic Press.

Journal Article↗
PubMed2000

Influence of Temperature on Stability of Electrostatically Stabilized Alumina Suspensions.

Pure electrostatically stabilized aqueous alumina suspensions were prepared at various solid loadings in order to study the influence of temperature on the surface charge properties and rheology. Surface charge density at various temperatures was measured through potentiometric titration, and the analysis of the potentiometric data was accomplished using the constant capacitance surface model. Calculations of the pair-wise interaction potential between charged colloidal spheres dispersed in water were then carried out using conventional DLVO theory and a software package Stabil45, taking into account the temperature dependence of surface charge density and dielectric constant. The results showed that increasing temperature leads to a gradual diminution of alumina surface ionization, dielectric constant, and a total energy barrier for coagulation. The enhancement of the coagulation rate with increasing temperature leads to a gradual increase of both relative apparent viscosity and thixotropy. Copyright 2000 Academic Press.

Journal Article↗
PubMed2001

The Electrostatic Interaction of a Charged Particle with a Surface: The Effect of Surface Charge Rearrangement.

In this paper we investigate the electric interaction between a charged particle and a surface in which the charged ions are capable of moving in response to the electric potential disturbance caused by the approach of the charged particle. Such surfaces include ionic surfactants distributed in air-water interface and charged lipids in bilayer membranes. On the basis of the mean field theory, the free energy of the system, which includes the electrostatic internal energy and the entropy of the mobile ions and surface ions, can be written down. The surface charge-potential relation is then derived by the calculus of variation. When the potential disturbance is small enough, a linear charge regulation model is obtained. The interaction energy associated with a long rod parallel to the interface is studied and an analytical expression is obtained. When a rod approaches an oppositely charged surface, the interaction can change from attraction to repulsion, depending on the ratio of the characteristic regulation length to the Debye length. At low surface charge density, the surface behaves as under the condition of constant charge density and acts as that of constant potential for high enough charge density. Copyright 2001 Academic Press.

Journal Article↗
PubMed2001

Obtaining the Osmotic Pressure of Electrostatically Stabilized Colloidal Dispersions from Frontal Ultrafiltration Experiments.

A new method for determining the osmotic pressure of electrostatically stabilized colloidal particles from frontal ultrafiltration experiments has been developed. The method is based on a reverse calculation utilizing a previously developed analysis of frontal ultrafiltration (W. R. Bowen and F. Jenner, Chem. Eng. Sci. 50, 1707, 1995; W. R. Bowen and P. M. Williams, Biotechnol. Bioeng. 50, 125, 1996). The method has the following advantages over conventional membrane osmometer measurements: (i) only very simple apparatus is required, (ii) results are obtained quickly, (iii) only small sample quantities are required, and (iv) only dilute initial samples are needed, as the ultrafiltration process creates a concentrated solution at the membrane, making sample preparation a simple task. A comparison of the osmotic pressure determined by this new method with previously measured osmotic pressure data shows excellent agreement. The approach demonstrates how analysis of process data may provide quantitative information on the interactions of concentrated colloidal systems. Copyright 2001 Academic Press.

Journal Article↗
PubMed2001

Thermodynamic Analysis of Proteins Adsorbed on Silica Particles: Electrostatic Effects.

Electrostatic effects on protein adsorption were investigated using differential scanning calorimetry (DSC) and adsorption isotherms. The thermal denaturation of lysozyme, ribonuclease A (RNase), and alpha-lactalbumin in solution and adsorbed onto silica nanoparticles was examined at three concentrations of cations: 10 and 100 mM of sodium and 100 mM of sodium to which 10 mM of calcium was added. The parameters investigated were the denaturation enthalpy (DeltaH), the temperature at which the denaturation transition was half-completed (T(m)), and the temperature range of the denaturation transition. For lysozyme and RNase, adsorption isotherms depend strongly on the ionic strength. At low ionic strength both proteins have a high affinity for the silica particles and adsorption is accompanied by a 15-25% reduction in DeltaH and a 3-6 degrees C decrease in T(m), indicating that the adsorbed state of the proteins is destabilized. Also, an increase in the width of the denaturation transition is observed, signifying a larger conformational heterogeneity of the surface bound proteins. At higher ionic strengths, both with and without the addition of calcium, no significant adsorption-induced alteration in DeltaH was observed for all three proteins. The addition of calcium, however, decreases the width of the denaturation transition for lysozyme and RNase in the adsorbed state. Copyright 2001 Academic Press.

Journal Article↗
PubMed1995

Matching electrostatic charge between DNA and coat protein in filamentous bacteriophage. Fibre diffraction of charge-deletion mutants.

The virion of Ff (fd, f1, M13) filamentous bacteriophage consists of a long tube of coat protein subunits in a shingled, helical array, surrounding a genome of circular single-stranded DNA. Modified fd virions have been generated by a mutation (K48A) that removes one positive charge from each coat protein subunit in the C-terminal region of the polypeptide chain facing the DNA. The number of nucleotides in the mutant DNA is unchanged, but the K48A virions are 35% longer than wild-type. We have measured the X-ray diffraction attributable to single virions in hydrated gels of wild-type and K48A bacteriophages. Most of the diffraction pattern shows no significant difference between wild-type and K48A. Since the DNA is only about 12% by weight of the wild-type virion, the diffraction pattern is dominated by the protein contribution, and the absence of significant differences indicates that there are no significant changes in the symmetry or structure of the protein coat. But there is a change in the diffraction pattern in a region where the DNA and protein contributions are comparable. The diffraction pattern of the K48A mutant shows an increase in intensity of one of the weaker equatorial peaks, relative to wild-type, in a region where the protein contribution has negative sign but the DNA contribution has positive sign. This is consistent with a decrease in the ratio of DNA:protein per unit length of the K48A mutant. The results support the view that the protein forms a sheath lined with positive charges interacting electrostatically and non-specifically with a negatively charged DNA core of matching charge density. The lower positive charge density lining the capsid in the K48A mutant means that correspondingly fewer nucleotides can be packaged per coat protein subunit, which in turn requires an elongation of the DNA inside the virion. A longer virion is thus required to package the same amount of DNA. Within the error of measurement, the number of positive charges on the protein interacting with the DNA is the same in K48A as in the wild-type, despite the fact that the mutant is 35% longer than the wild-type.

Capsid↗
PubMed1994

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.

Two major components are required for a successful prediction of the three-dimensional structure of peptides and proteins: an efficient global optimization procedure which is capable of finding an appropriate local minimum for the strongly anisotropic function of hundreds of variables, and a set of free energy components for a protein molecule in solution which are computationally inexpensive enough to be used in the search procedure, yet sufficiently accurate to ensure the uniqueness of the native conformation. We here found an efficient way to make a random step in a Monte Carlo procedure given knowledge of the energy or statistical properties of conformational subspaces (e.g. phi-psi zones or side-chain torsion angles). This biased probability Monte Carlo (BPMC) procedure randomly selects the subspace first, then makes a step to a new random position independent of the previous position, but according to the predefined continuous probability distribution. The random step is followed by a local minimization in torsion angle space. The positions, sizes and preferences for high-probability zones on phi-psi maps and chi-angle maps were calculated for different residue types from the representative set of 191 and 161 protein 3D-structures, respectively. A fast and precise method to evaluate the electrostatic energy of a protein in solution is developed and combined with the BPMC procedure. The method is based on the modified spherical image charge approximation, efficiently projected onto a molecule of arbitrary shape. Comparison with the finite-difference solutions of the Poisson-Boltzmann equation shows high accuracy for our approach. The BPMC procedure is applied successfully to the structure prediction of 12- and 16-residue synthetic peptides and the determination of protein structure from NMR data, with the immunoglobulin binding domain of streptococcal protein G as an example. The BPMC runs display much better convergence properties than the non-biased simulations. The advantage of a true global optimization procedure for NMR structure determination is its ability to cope with local minima originating from data errors and ambiguities in NMR data.

Algorithms↗
PubMed1995

A molecular model for the redox potential difference between thioredoxin and DsbA, based on electrostatics calculations.

The disulphide active sites of thioredoxin and DsbA are known to possess a high degree of structural homology. However, DsbA is a much stronger oxidant than thioredoxin. The redox potential difference between DsbA and thioredoxin has been measured to be 160 mV, equivalent to a shift of 15.4 kJ/mol in the reduced/oxidised equilibrium. Electrostatics calculations have been used to study the relative stabilities of the reduced forms of the two proteins. Model calculations suggest that much of the redox potential difference between DsbA and thioredoxin arises form altered stabilisation of the exposed and ionised thiolates of the reduced forms, supporting suggestions previously made on the basis of experimental studies. The calculations have been used to construct a molecular model for the difference in thiolate stabilisation. Although specific interactions, such as thiolate-NH 35 (thioredoxin)/33 (DsbA), provide substantial stabilisation in each reduced protein, the difference between thioredoxin and DsbA is predicted to reside in several side-chain and main-chain groups acting in concert. Residues H32 and Q97 in DsbA are predicted to contribute, along with substantial regions of the polypeptide backbone in the protein domain which is common to DsbA and thioredoxin. Increased thiolate stabilisation by the peptide dipoles is suggested to arise from altered main-chain disposition, and the effect of the additional protein domain of DsbA on the electric field. Peptide dipoles in a region of about 20 residues close to the active site disulphide are predicted to contribute significantly to the redox potential difference.

Binding Sites↗
PubMed2000

Electrostatic dependence of the thrombin-thrombomodulin interaction.

The rate constants for the binding interaction between thrombin and a fully active fragment of its anticoagulant cofactor, thrombomodulin, have been determined by surface plasmon resonance. At physiological ionic strength, the k(a) was 6.7x10(6) M(-1) s(-1 )and the dissociation rate constant was 0.033 s(-1). These extremely fast association and dissociation rates resulted in an overall binding equilibrium constant of 4.9 nM, which is similar to previously reported values. Changing the ionic strength from 100 mM to 250 mM NaCl caused a tenfold decrease in the association rate while the dissociation rate did not change significantly. A similar effect was observed with tetramethylammonium chloride. A Debye-Hückel plot of the data had a slope of -6 and an intercept at 0 ionic strength of 10(9) M(-1) s(-1). The same slope and intercept were obtained for data that was collected in the presence of glycerol to slow the association rates. These results show that the thrombin-TM456 interaction is extremely rapid and nearly completely electrostatically steered. An association model is presented in which TM456 approaches thrombin along the direction of the thrombin molecular dipole.

Amino Acid Chloromethyl Ketones↗
PubMed2000

Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition.

We use a combination of spectroscopic, calorimetric, viscometric and computer modeling techniques to characterize the binding of the aminoglycoside antibiotic, tobramycin, to the polymeric RNA duplex, poly(rI).poly(rC), which exhibits the characteristic A-type conformation that is conserved among natural and synthetic double-helical RNA sequences. Our results reveal the following significant features: (i) CD-detected binding of tobramycin to poly(rI).poly(rC) reveals an apparent site size of four base-pairs per bound drug molecule; (ii) tobramycin binding enhances the thermal stability of the host poly(rI).poly(rC) duplex, the extent of which decreases upon increasing in Na(+) concentration and/or pH conditions; (iii) the enthalpy of tobramycin- poly(rI).poly(rC) complexation increases with increasing pH conditions, an observation consistent with binding-induced protonation of one or more drug amino groups; (iv) the affinity of tobramycin for poly(rI).poly(rC) is sensitive to both pH and Na(+) concentration, with increases in pH and/or Na(+) concentration resulting in a concomitant reduction in binding affinity. The salt dependence of the tobramycin binding affinity reveals that the drug binds to the host RNA duplex as trication. (v) The thermodynamic driving force for tobramycin- poly(rI).poly(rC) complexation depends on pH conditions. Specifically, at pH< or =6.0, tobramycin binding is entropy driven, but is enthalpy driven at pH > 6.0. (vi) Viscometric data reveal non-intercalative binding properties when tobramycin complexes with poly(rI).poly(rC), consistent with a major groove-directed mode of binding. These data also are consistent with a binding-induced reduction in the apparent molecular length of the host RNA duplex. (vii) Computer modeling studies reveal a tobramycin-poly(rI). poly(rC) complex in which the drug fits snugly at the base of the RNA major groove and is stabilized, at least in part, by an array of hydrogen bonding interactions with both base and backbone atoms of the host RNA. These studies also demonstrate an inability of tobramycin to form a stable low-energy complex with the minor groove of the poly(rI).poly(rC) duplex. In the aggregate, our results suggest that tobramycin-RNA recognition is dictated and controlled by a broad range of factors that include electrostatic interactions, hydrogen bonding interactions, drug protonation reactions, and binding-induced alterations in the structure of the host RNA. These modulatory effects on tobramycin-RNA complexation are discussed in terms of their potential importance for the selective recognition of specific RNA structural motifs, such as asymmetric internal loops or hairpin loop-stem junctions, by aminoglycoside antibiotics and their derivatives.

Anti-Bacterial Agents↗
PubMed1991

Protein-water interactions from 2H NMR relaxation studies: influence of hydrophilic, hydrophobic, and electrostatic interactions.

The importance of water interactions with proteins in food systems is well documented. A controversy exists, however, as to the nature of these interactions and the effect of protein structural changes on them. To clarify these questions, a method has been developed for determining hydration from the protein concentration-dependence of deuteron resonance relaxation rates. Measurements were made in D2O on beta-lactoglobulin A to study effects of hydrophilic interactions, and on both casein micelles and submicelles to study hydrophobic and electrostatic effects. From the protein concentration-dependent relaxation rates, the second viral coefficients of the proteins were obtained by nonlinear regression analysis. Using either an isotropic tumbling or an intermediate asymmetry model, hydrations, upsilon, and correlation times, tau c, were calculated for the protein-associated water; from tau c, the Stokes radius, R, was obtained. Variations in upsilon and R were in accord with known structural changes in molecular states of the proteins. The NMR results are compared with hydrations and structural information derived independently from small-angle X-ray scattering.

Chemical Phenomena↗