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At least 613 records · Page 34Linked to original sources
PubMed2006

Identification of precise electrostatic recognition sites between cytochrome c6 and the photosystem I subunit PsaF using mass spectrometry.

The reduction of the photo-oxidized special chlorophyll pair P700 of photosystem I (PSI) in the photosynthetic electron transport chain of eukaryotic organisms is facilitated by the soluble copper-containing protein plastocyanin (pc). In the absence of copper, pc is functionally replaced by the heme-containing protein cytochrome c6 (cyt c6) in the green alga Chlamydomonas reinhardtii. Binding and electron transfer between both donors and PSI follows a two-step mechanism that depends on electrostatic and hydrophobic recognition between the partners. Although the electrostatic and hydrophobic recognition sites on pc and PSI are well known, the precise electrostatic recognition site on cyt c6 is unknown. To specify the interaction sites on a molecular level, we cross-linked cyt c6 and PSI using a zero-length cross-linker and obtained a cross-linked complex competent in fast and efficient electron transfer. As shown previously, cyt c6 cross-links specifically with the PsaF subunit of PSI. Mass spectrometric analysis of tryptic peptides from the cross-linked product revealed specific interaction sites between residues Lys27 of PsaF and Glu69 of cyt c6 and between Lys23 of PsaF and Glu69/Glu70 of cyt c6. Using these new data, we present a molecular model of the intermolecular electron transfer complex between eukaryotic cyt c6 and PSI.

Animals↗
PubMedDate not supplied

Controlling the size of alginate gel beads by use of a high electrostatic potential.

The effect of several parameters on the size of alginate beads produced by use of an electrostatic potential bead generator was examined. Parameters studied included needle diameter, electrostatic potential, alginate solution flow rate, gelling ion concentration and alginate concentration and viscosity, as well as alginate composition. Bead size was found to decrease with increasing electrostatic potential, but only down to a certain level. Minimum bead size was reached at between 2-4 kV/cm for the needles tested. The smallest alginate beads produced (using a needle with inner diameter 0.18 mm) had a mean diameter of approximately 300 microm. Bead size was also found to be dependent upon the flow rate of the fed alginate solution. Increasing the gelling ion concentration resulted in a moderate decrease in bead size. The concentration and viscosity of the alginate solution also had an effect on bead size as demonstrated by an increased bead diameter when the concentration or viscosity was increased. This effect was primarily an effect of the viscosity properties of the solution, which led to changes in the rate of droplet formation in the bead generator. Lowering the flow rate of the alginate solution could partly compensate for the increase in bead size with increased viscosity. For a constant droplet size, alginates with a low G block content (F(GG) approximately 0.20) resulted in approximately 30% smaller beads than alginates with a high G block content (F(GG) approximately 0.60). This is explained as a result of differences in the shrinking properties of the beads.

Alginates↗
PubMed1983

Electrostatics of Polymorphic DNA.

The molecular electrostatic potential (MEP) and the molecular electrostatic field (MEF) are associated with significantly different patterns of distribution in the nucleic acids and their constituents. In particular, a) while the values of the minimal potentials at the reactive sites of the bases or at the phosphates increase manyfold when going from the subunits to the double helix, the values of the field undergo only very small changes under the same circumstances and b) while the deepest potentials are located in the grooves of the double helix, the greatest fields are concentrated on the phosphates of the backbone. They are also influenced differently by such environmental factors as counterion screening: while the absolute values of the potentials are profoundly reduced, the fields are increased with respect to those of the unscreened acids. MEP and MEF also govern the electrostatics of interaction of DNA with different types of species. The MEP being of particular significance in this respect for interaction with cations and the MEF for the association with neutral dipolar molecules. A number of examples are given to illustrate the significance of this situation for different conformers of DNA.

DNA↗
PubMed2004

Electrostatic background of chromatin fiber stretching.

We have carried out an investigation of the electrostatic forces involved in gradual removal of the DNA from the histone proteins in chromatin. Two simple models of DNA-histone core dissociation were considered. Calculations of the electrostatic free energy within the Poisson-Boltzmann theory gave similar results for the both models, which turned out to be in a qualitative agreement with recent optical tweezers stretching experiments measuring the force necessary to unwrap DNA from the histone core. Our analysis shows that the electrostatic interactions between the highly negatively charged polymeric DNA and the positively charged histones play a determining role in stabilizing the nucleosomes at physiological conditions.

Chromatin↗
PubMed2005

Combined effect of surface electrostatic charge and poly(ethyl glycol) on the association of liposomes with colon carcinoma cells.

Particulate drug formulations are considered to be a means that may improve the pharmacokinetics and biodistribution of active compounds. By using them, drug distribution is determined solely by the properties of the carrier. The surface properties of such supramolecular aggregates determine how they will interact with various biological structures. Among others, surface electrostatic charge and surface grafted polymers are considered to be among the major factors affecting its interaction with proteins and cells. In this article, we present experimental evidence that properly selected surface electrostatic charge and grafted polymers can alter the association of liposomes with colon cancer cells. The dependence of the adsorption of liposomes onto the cell surface on the quantity and length of surface grafted polymers for a certain surface charge density exhibits a distinct maximum. For example, when liposomes were formed with 20 mol% of DOTAP, PE-PEG350 increased liposome adsorption by up to 6 mol%. This adsorption maximum depends on both polymer length and charge type. Results presented in this article show that the interaction of liposomes with colon cancer cells can be tuned by a proper combination of liposome surface electrostatics and surface grafted polymers.

Cell Line, Tumor↗
PubMed1989

Molecular electrostatic potential studies on some nitroimidazolyl and nitroheterocyclic compounds.

The electronic wave functions of 11 nitroimidazolyl and nitroheterocyclic compounds were computed using the CNDO/2 quantum chemical method. The location of the greatest nucleophilic reactivity for each molecule was predicted to be mostly near or on the nitro group. As in our previous publication (Lin Liming et al. 1985) the maximum values of the superdelocalizability index for nucleophilic reactivity S(N)max and the sum of S(N)r for each of these compounds were discovered to be significantly correlated with the radiosensitivity as indicated by log(1/C1.6), where C1.6 is the concentration of the compound required to achieve an enhancement ratio of 1.6. The electrostatic potential distribution on a plane parallel to the plane of the imidazole or heterocyclic ring was computed for these compounds with the wave functions obtained from CNDO/2 calculations. In order to analyse the steric electrostatic potential maps, the overall electrostatic potential on an imaginary surface surrounding a molecule was calculated using the multicentre multipole expansion method. It was found that a wide and deep negative potential area exists in a compound which had significant radiosensitizing efficiency, while in metronidazole, which is not an efficient radiosensitizer, the corresponding area is narrow. This phenomenon may be related to the interaction between these compounds and certain biological macromolecules. These preliminary quantum chemical results support Adams' electron affinity theory, and might be helpful in searching for new radiosensitizers.

Heterocyclic Compounds↗
PubMed1990

Electrostatic effects in asbestos sampling. I: Experimental measurements.

Electrostatic charge can cause errors during sampling of airborne asbestos fibers and other particles. The change in particle trajectories caused by charge effects during sampling can result in nonuniform deposits on the collecting filter surface and net loss of sample. The degree of these electrostatic effects depends on particle charge, sampler charge, sampler conductivity, and sampling flow rate and direction. The purpose of this research was to evaluate the dependence of sampling efficiency and sample uniformity on these variables. Humidity has been postulated as a primary determinant of particle charge during aerosol generation. Measurements of particle charge and concentration were made as a function of relative humidity with chrysotile fibers generated from a fluidized bed. A strong increase in charge and a decrease in concentration of fibers was noted as the relative humidity was decreased below 15%. The effects of conductive versus nonconductive samplers and sampling flow rate were measured as a function of particle and sampler charge levels. Nonconductive samplers can carry a large and variable charge distribution on their surfaces. This can result in a biased and highly variable particle deposit on the filter when sampling charged particles. Conductive cowls spread any acquired charge over the entire surface and produce a more symmetrical and less biased charged particle deposit. Increasing the sampling flow rate will improve sampling efficiency and decrease deposit variability because the charged particle has less time to interact with the field produced by the sampler. These results suggest that sampling problems caused by electrostatic charge interactions are most likely to occur under low humidity conditions of dust generation, that sampling should be done at as high a flow rate as possible to reduce these effects, and that analysts should select fields toward the center of the filter to minimize bias and variability.

Aerosols↗
PubMed1996

Laboratory measurements of oil mist concentrations using filters and an electrostatic precipitator.

This study investigated the potential for mineral oil mist to evaporate, during sampling, from filters and electrostatic precipitator substrates used to assess personal exposure. If sample evaporation occurs, reported mist concentrations will underestimate true exposure. Mineral oil used as a machining fluid is not normally considered volatile; however, when dispersed as mist its aggregate surface area is so high that significant evaporation can occur. National Institute for Occupational Safety and Health Method 5026 specifies that oil mist concentrations should be determined by collecting mist on filters of mixed cellulose esters (MCE) or polyvinyl chloride (PVC). Collected mist droplets remain dispersed on the filter surface and in contact with passing air while sampling continues, conditions that can lead to sample evaporation. Less evaporation should occur for samples taken with an electrostatic precipitator, where mist droplets are separated from the airflow by electrostatic force and coalesce on the precipitator wall to form a film with relatively low surface area. Collection of mineral oil mist was investigated using a precipitator designed for personal sampling and using either an MCE or a PVC filter. The amounts of oil mist collected using the precipitator were significantly higher than the amounts collected using the filters, p < 0.001. Further tests in which clean air passed through mist-loaded precipitators and filters showed that the precipitator retained substantially more collected mist than both filters, p < 0.001, and further suggested that the MCE filter retained more mist than the PVC filter, p = 0.059. Differences in sample collection and retention between the precipitator and the filters were particularly pronounced at mist loadings below 1 mg.

Aerosols↗
PubMed1998

State-dependent accessibility and electrostatic potential in the channel of the acetylcholine receptor. Inferences from rates of reaction of thiosulfonates with substituted cysteines in the M2 segment of the alpha subunit.

Ion channel function depends on the chemical and physical properties and spatial arrangement of the residues that line the channel lumen and on the electrostatic potential within the lumen. We have used small, sulfhydryl-specific thiosulfonate reagents, both positively charged and neutral, to probe the environment within the acetylcholine (ACh) receptor channel. Rate constants were determined for their reactions with cysteines substituted for nine exposed residues in the second membrane-spanning segment (M2) of the alpha subunit. The largest rate constants, both in the presence and absence of ACh, were for the reactions with the cysteine substituted for alpha Thr244, near the intracellular end of the channel. In the open state of the channel, but not in the closed state, the rate constants for the reactions of the charged reagents with several substituted cysteines depended on the transmembrane electrostatic potential, and the electrical distance of these cysteines increased from the extracellular to the intracellular end of M2. Even at zero transmembrane potential, the ratios of the rate constants for the reactions of three positively charged reagents with alpha T244C, alpha L251C, and alpha L258C to the rate constant for the reaction of an uncharged reagent were much greater in the open than in the closed state. This dependence of the rate constants on reagent charge is consistent with an intrinsic electrostatic potential in the channel that is considerably more negative in the open state than in the closed state. The effects of ACh on the rate constants for the reactions of substituted Cys along the length of alpha M2, on the dependence of the rate constants on the transmembrane potential, and on the intrinsic potential support a location of a gate more intracellular than alpha Thr244.

Algorithms↗
PubMed2005

An electrostatic engine model for autoinhibition and activation of the epidermal growth factor receptor (EGFR/ErbB) family.

We propose a new mechanism to explain autoinhibition of the epidermal growth factor receptor (EGFR/ErbB) family of receptor tyrosine kinases based on a structural model that postulates both their juxtamembrane and protein tyrosine kinase domains bind electrostatically to acidic lipids in the plasma membrane, restricting access of the kinase domain to substrate tyrosines. Ligand-induced dimerization promotes partial trans autophosphorylation of ErbB1, leading to a rapid rise in intracellular [Ca(2+)] that can activate calmodulin. We postulate the Ca(2+)/calmodulin complex binds rapidly to residues 645--660 of the juxtamembrane domain, reversing its net charge from +8 to -8 and repelling it from the negatively charged inner leaflet of the membrane. The repulsion has two consequences: it releases electrostatically sequestered phosphatidylinositol 4,5-bisphosphate (PIP(2)), and it disengages the kinase domain from the membrane, allowing it to become fully active and phosphorylate an adjacent ErbB molecule or other substrate. We tested various aspects of the model by measuring ErbB juxtamembrane peptide binding to phospholipid vesicles using both a centrifugation assay and fluorescence correlation spectroscopy; analyzing the kinetics of interactions between ErbB peptides, membranes, and Ca(2+)/calmodulin using fluorescence stop flow; assessing ErbB1 activation in Cos1 cells; measuring fluorescence resonance energy transfer between ErbB peptides and PIP(2); and making theoretical electrostatic calculations on atomic models of membranes and ErbB juxtamembrane and kinase domains.

Animals↗
PubMed1993

The updated electrostatic potential for cytosine completes the qualitative explanations of base alkylation regiochemistry.

The relationship between the structures of different alkylating agents and the relative extents to which they modify the oxygen and nitrogen centers of nucleic acid bases has been discussed in the literature from several points of view, although each effectively attributes the increasing preference for oxygen alkylation to the increasing importance of electrostatic interactions between the reacting moieties. This is in direct contradiction to the published electrostatic potential data for cytosine which indicate the most attractive potential to lie in the vicinity of the 3-nitrogen. However, we have discovered the latter to be an artefact of the use of inadequate levels of theory. When the electrostatic potentials of cytosine are computed using more sophisticated ab initio Hartree-Fock/6-31G* calculations the global minimum does indeed lie in the vicinity of the O2-position as required by the various rationalizations of the alkylation data.

Alkylation↗
PubMed1988

Charge calculations in molecular mechanics 6: the calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing.

A previously described scheme for the direct calculation of the partial atomic charges in molecules (CHARGE2) is applied to the nucleic acid bases. It is shown that inclusion of the omega-technique for the calculation of HMO derived pi charges is of particular importance for these highly polar systems. The molecular dipole moments obtained for the resulting charges are in very good agreement with the observed values for a variety of substituted purine and pyrimidine bases. The partial atomic charges for cytosine, thymine, guanine and adenine (as the 1-methyl and 9-methyl forms) are given and compared with values calculated by a variety of molecular orbital and empirical schemes. All the schemes reproduce the same general trends, with the possible exception of those calculated by the Del Re method, though the charges given by Kollman are in general somewhat larger than the others. The electrostatic contribution to the Watson-Crick base pair interaction energies are calculated using these partial atomic charges. The electrostatic contributions obtained from the M.O. derived atomic charges are less than half the observed values, as are those obtained by the Gasteiger method. The electrostatic contributions calculated from the CHARGE2 atomic charges and those of Kollman are in reasonable agreement with the observed values. The influence of a distant-dependent dielectric constant is examined, but no clear pattern emerges.

Chemical Phenomena↗
PubMed2003

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set.

Binding Sites↗
PubMed2006

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.

Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a 'lure and lock' model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the 'lure' step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on 'top' of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein-RNA complexes.

Amino Acid Sequence↗
PubMed1995

Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions.

A new approach to evaluate protein structure (3D)-sequence (1D) compatibility has been developed. This approach uses four functions: side-chain packing, solvation, hydrogen-bonding, and local structure functions. The side-chain packing function takes into account not only inter-residue distance but also inter-residue contact and angle. Parameters defining the functions were statistically derived from 101 proteins with known 3D structures. The functions are combined to give a score quantifying the 3D-1D compatibility. The ability to identify the native structure of a protein among a large number of incorrect structures was tested. For 69 out of the 70 proteins examined, the native structures were successfully identified. Particularly, the side-chain packing function showed clear improvement over our previous function. The only unsuccessful case was observed for cytochrome c3 containing four haems; such prosthetic groups were ignored in the calculation. In addition to the above functions, two procedures for removing membrane-spanning regions and estimating electrostatic interactions were also adopted. A sequence for which membrane-spanning regions were predicted was considered incompatible with a structure irrespective of the compatibility score. A method to calculate the electrostatic interaction energy was developed and used for the detection of electrostatically undesirable interactions between residues of a sequence threaded onto a structure. These procedures greatly help to remove false positives in the 3D-1D compatibility search.

Amino Acid Sequence↗
PubMed1998

Electrotactins: a class of adhesion proteins with conserved electrostatic and structural motifs.

The concept of an electrostatic motif on the surface of biological macromolecules as a definite topographical pattern of electrostatic potentials in three-dimensional space, provides a powerful tool for identification of functionally important regions on the surface of structurally related macromolecules. Using this approach, we identify a functional region common to cholinesterases (ChEs) and to a set of neural cell-adhesion proteins that have been suggested to be structurally related to cholinesterases due to their high sequence similarity, but lacking the key catalytically active serine. Quantitative analysis of the electrostatic surface potential in the area surrounding the entrance to the active site of acetylcholinesterase, and in the analogous zone for the ChE-like domain of the adhesion proteins reveals very good correlation. These findings, examined in the context of previous evidence involving this same region in a possible cell-recognition function for ChEs, leads us to define a class of adhesion proteins which we have named 'electrotactins'.

Animals↗
PubMed1991

Electrostatic effects in proteins: comparison of dielectric and charge models.

Two approaches for calculating electrostatic effects in proteins are compared and ana analysis is presented of the dependence of calculated properties on the model used to define the charge distribution. Changes in electrostatic free energy have been calculated using a screened Coulomb potential (SCP) with a distance-dependent effective dielectric permittivity to model bulk solvent effects and a finite difference approach to solve the Poisson-Boltzmann (FDPB) equation. The properties calculated include shifts in dissociation constants of ionizable groups, the effect of annihilating surface charges on the binding of metals, and shifts in redox potentials due to changes in the charge of ionizable groups. In the proteins considered the charged sites are separated by 3.5-12 A. It is shown that for the systems studied in this distance range the SCP yields calculated values which are at least as accurate as those obtained from solution of the FDPB equation. In addition, in the distance range 3-5 A the SCP gives substantially better results than the FDPB equation. Possible sources of this difference between the two methods are discussed. Shifts in binding constants and redox potentials were calculated with several standard charge sets, and the resulting values show a variation of 20-40% between the 'best' and 'worst' cases. From this study it is concluded that in most applications, changes in electrostatic free energies can be calculated economically and reliably using an SCP approach with a single functional form of the screening function.

Bacterial Proteins↗
PubMed2006

Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity.

To extract the general structural features of interacting protein pairs, the non-redundant homo-oligomer interfaces (393 interfaces) in the PDB were analyzed using the fine-grained molecular surface, electrostatic potentials and the hydrophobicity calculated as the solvation free energy using empirical parameters. For each property, statistical analyses of the degree of complementarity were carried out, and we developed a method to judge whether interfaces were shape-complementary, electrostatic-complementary and/or hydrophobic-complementary or not. In order to search for the correlation between the property complementarity and structure of the interfaces, at first, we roughly classified all the interfaces into the following five groups according to the structure of the interface and surveyed the correlation between the shape classification and the complementary: cyclic-oligomer (69), twisted-dimer (27), dimer-parallel (14), dimer-perpendicular (109) and dimer-circular (174), where the number in the parenthesis is the number of interfaces in each group. As a result, we found the new characteristic trends as the possible necessary conditions in the formation of homo-oligomer interfaces, especially from the viewpoint of electrostatic complementarity. In addition, we also show that complementarity analyses can be used to discriminate the biological-interface from the crystallographic-interface in homo-oligomer proteins.

Dimerization↗