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PubMed1991

Charge grouping approaches to calculation of electrostatic forces in molecular dynamics of macromolecules.

Calculation of long-range electrostatic interactions is the most time-consuming step in theoretical simulation of the structure and dynamics of macromolecules. In practice very short cutoff distances are used, which may distort the behavior of the model system. We describe two accurate approaches to calculation of electrostatic forces based on hierarchical grouping of charges into cubes. The first is similar to the O(NlogN) algorithm developed by Barnes, J. and Hut, P., Nature (London) 324, 446-449 (1986), for simulation of a gravitational motion of N bodies. The second approach we formulate for a system with periodic boundary conditions in the nearest image approximation. The calculation of electrostatic interactions and a charge grouping procedure are faster than O(N2). The average inaccuracy in the force introduced by the grouping does not exceed 1%. We describe a small modification of the same approach which makes it suitable for long strongly charged polymers as well. This accurate approach to calculation of electrostatic interactions is illustrated with an example of the dynamics of ions near DNA. Quick equilibration of the ionic distribution is observed during molecular dynamics simulation if electrostatic forces are properly calculated, while the behavior and distribution of ions are less realistic when the conventional cutoff distances are used.

Algorithms↗
PubMed1999

Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.

Distribution of electrostatic potential of DNA fragments was evaluated. A method for calculation of electrostatic potential distribution based on Coulomb's law is proposed for long DNA fragments (approximately 1000 nucleotide pairs). For short DNA sequences, this technique provides a good correlation with the results obtained using Poisson-Boltzmann equation thus justifying its application in comparative studies for long DNA fragments. Calculation was performed for several DNA fragments from E. coli and bacteriophage T7 genomes containing promoter and nonpromoter regions. The results obtained indicate that coding regions are characterized by more homogeneous distribution of electrostatic potential whereas local inhomogeneity of DNA electrostatic profile is typical for promoter regions. The possible role of electrostatic interactions in RNA polymerase-promoter recognition is discussed.

Anion Transport Proteins↗
PubMed2005

Long-range electrostatic interactions in molecular dynamics: an endothelin-1 case study.

An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods--residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used.

Endothelin-1↗
PubMed2007

The fabrication and application of Zernike electrostatic phase plate.

The Zernike electrostatic phase plate (ZEPP) consisting of three ring electrodes and two insulating rings has been fabricated using Micro Electro-Mechanical System processes. The electrostatic field produced in the phase plate was measured by electrostatic force microscopy. The electrostatic field and focal length of the phase plate is calculated using electron optics principles. The comparison of the experimental electrostatic field and the theoretical calculated is discussed. Finally, we report the application of ZEPP to enhance contrast of the SiON(x)/SiO(2) interface in an NMOS semiconductor device. The quantitative analysis of the contrast enhancement versus the applied bias is discussed in detail.

Journal Article↗
PubMed2004

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.

Continuum solvation models, such as Poisson-Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to biomolecular structures. To address this problem, we have developed the PDB2PQR web service (http://agave.wustl.edu/pdb2pqr/). This server automates many of the common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number of missing heavy atoms to biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields, and finally generating 'PQR' output compatible with several popular computational biology packages. This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.

Databases, Protein↗
PubMed2006

PHEPS: web-based pH-dependent Protein Electrostatics Server.

PHEPS (pH-dependent Protein Electrostatics Server) is a web service for fast prediction and experiment planning support, as well as for correlation and analysis of experimentally obtained results, reflecting charge-dependent phenomena in globular proteins. Its implementation is based on long-term experience (PHEI package) and the need to explain measured physicochemical characteristics at the level of protein atomic structure. The approach is semi-empirical and based on a mean field scheme for description and evaluation of global and local pH-dependent electrostatic properties: protein proton binding; ionic sites proton population; free energy electrostatic term; ionic groups proton affinities (pK(a,i)) and their Coulomb interaction with whole charge multipole; electrostatic potential of whole molecule at fixed pH and pH-dependent local electrostatic potentials at user-defined set of points. The speed of calculation is based on fast determination of distance-dependent pair charge-charge interactions as empirical three exponential function that covers charge-charge, charge-dipole and dipole-dipole contributions. After atomic coordinates input, all standard parameters are used as defaults to facilitate non-experienced users. Special attention was given to interactive addition of non-polypeptide charges, extra ionizable groups with intrinsic pK(a)s or fixed ions. The output information is given as plain-text, readable by 'RasMol', 'Origin' and the like. The PHEPS server is accessible at http://pheps.orgchm.bas.bg/home.html.

Hydrogen-Ion Concentration↗
PubMed1997

A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding.

Dissecting ligand-protein binding free energies in individual contributions of protein residues (which are referred to here as 'group contributions') is of significant importance. For example, such contributions could help in estimating the corresponding mutational effects and in studies of drug resistance problems. However, the meaning of group contributions is not always uniquely defined and the approximations for rapid estimates of such contributions are not well developed. In this paper, the nature of group contributions to binding free energy is examined, focusing particularly on electrostatic contributions which are expected to be well behaved. This analysis examines different definitions of group contributions; the 'relaxed' group contributions that represent the change in binding energy upon mutation of the given residue to glycine, and the 'non-relaxed' group contributions that represent the scaled Coulomb interaction between the given residue and the ligand. Both contributions are defined and evaluated by the linear response approximation (LRA) of the PDLD/ S method. The present analysis considers the binding of pepstatin to endothiapepsin and 23 of its mutants as a test case for a neutral ligand. The 'non-relaxed' group contributions of 15 endothiapepsin residues show significant peaks in the 'electrostatic fingerprint'. The residues that contribute to the electrostatic fingerprint are located in the binding site of endothiapepsin. They include the aspartic dyad (Asp32, Asp215) with adjacent residues and the flap region. Twelve of these 15 residues have a heavy atom distance of <3.75 A to pepstatin. The contributions of 8 (10) of these 12 residues can be reconciled with the calculated 'relaxed' group contributions where one allows the protein and solvent (solvent only) to relax upon mutation of the given residue to glycine. On the other hand, it was found that residues at the second 'solvation shell' can have relaxed contributions that are not captured by the non-relaxed approach. Hence, whereas residues with significant non-relaxed electrostatic contributions are likely to contribute to binding, residues with small non-relaxed contributions may still affect the binding energy. At any rate, it is established here that even in the case of uncharged inhibitors it is possible to use the non-relaxed electrostatic fingerprint to detect 'hot' residues that are responsible for binding. This is significant since some versions of the non-relaxed approximation are faster by several orders of magnitude than more rigorous approaches. The general applicability of this approach is outlined, emphasizing its potential in studies of drug resistance where it is crucial to have a rapid way of anticipating the effect of mutation on both drug binding and catalysis.

Aspartic Acid↗
PubMed1999

Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding.

The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determinants of affinity and specificity. Here, we utilize this model system to investigate electrostatic effects in protein binding using continuum calculations. A particularly novel feature of the computations made here is that they provide an interaction-by-interaction breakdown of the electrostatic contributions to the free energy of docking that includes changes in the interaction of each functional group with solvent and changes in interactions between all pairs of functional groups on binding. The results show that (1) electrostatic effects disfavor binding by roughly 15 kcal/mol due to desolvation effects that are incompletely compensated in the bound state, (2) while no groups strongly stabilize binding, the groups that are most destabilizing are charged and polar side chains at the interface that have been implicated in determining binding specificity, and (3) attractive intramolecular interactions (e.g., backbone hydrogen bonds) that are enhanced on binding due to reduced solvent screening in the bound state contribute significantly to affinity and are likely to be a general effect in other complexes. A comparison is made between the results obtained in an electrostatic analysis carried out calculationally and simulated results corresponding to idealized data from a scanning mutagenesis experiment. It is shown that scanning experiments provide incomplete information on interactions and, if overinterpreted, tend to overestimate the energetic effect of individual side chains that make attractive interactions. Finally, a comparison is made between the results available from a continuum electrostatic model and from a simpler surface-area dependent solvation model. In this case, although the simpler model neglects certain interactions, on average it performs rather well.

DNA-Binding Proteins↗
PubMed1985

Electrostatic effects and calcium ion concentration as modulators of acid phosphatase bound to plant cell walls.

At 'low' ionic strength, acid phosphatase bound to plant cell walls exhibits an apparent negative co-operativity, whereas it displays classic Michaelis-Menten kinetics in free solution. Conversely, at 'high' ionic strength, the bound enzyme and the soluble enzyme behave identically. This apparent negative co-operativity is explained by the existence of an electrostatic partition of the charged substrate by the fixed negative charges of the cell wall. Raising the ionic strength suppresses these electrostatic repulsion effects. Calcium may be removed from the cell walls by acid treatment and the acid phosphatase is apparently strongly inhibited. This inhibition occurs together with an increased apparent negative co-operativity of the enzyme. Incubating cell wall fragments previously depleted of calcium with CaCl2 restores the initial behaviour of the enzyme. Calcium, which tightly binds to cell wall pectic compounds, has by itself no effect on the enzyme in free solution. It affects the net charge of the cell wall and therefore the amplitude of electrostatic repulsion effects. Non-linear least-square fitting methods make it possible to estimate the density of fixed negative charges as well as the electrostatic partition coefficient, for both the 'native' and 'calcium-deprived' cell wall fragments. It may be shown directly that calcium loading and unloading in the cell wall controls the electrostatic effects, by monitoring proton extrusion from cell wall fragments upon raising the ionic strength. Proton outflux in the bulk phase is considerably enhanced upon removal of calcium from the cell walls. The main conclusion is that loading and unloading of calcium during cell elongation and division may regulate the activity of cell wall enzymes.

Acid Phosphatase↗
PubMed1991

Oxidation-reduction potentials of ferredoxin-NADP+ reductase and flavodoxin from Anabaena PCC 7119 and their electrostatic and covalent complexes.

The oxidation-reduction potentials of ferredoxin-NADP+ reductase and flavodoxin from the cyanobacterium Anabaena PCC 7119 were determined by potentiometry. The potentials at pH 7 for the oxidized flavodoxin/flavodoxin semiquinone couple (E2) and the flavodoxin semiquinone/hydroquinone couple (E1) were -212 mV and -436 mV, respectively. E1 was independent of pH above about pH 7, but changed by approximately -60 mV/pH below about pH 6, suggesting that the fully reduced protein has a redox-linked pKa at about 6.1, similar to those of certain other flavodoxins. E2 varied by -50 mV/pH in the range pH 5-8. The redox potential for the two-electron reduction of ferredoxin-NADP+ reductase was -344 mV at pH 7 (delta Em = -30 mV/pH). In the 1:1 electrostatic complex of the two proteins titrated at pH 7, E2 was shifted by +8 mV and E1 was shifted by -25 mV; the shift in potential for the reductase was +4 mV. The potentials again shifted following treatment of the electrostatic complex with a carbodiimide, to covalently link the two proteins. By comparison with the separate proteins at pH 7, E2 for flavodoxin shifted by -21 mV and E1 shifted by +20 mV; the reductase potential shifted by +2 mV. The potentials of the proteins in the electrostatic and covalent complexes showed similar pH dependencies to those of the individual proteins. Qualitatively similar changes occurred when ferredoxin-NADP+ reductase from Anabaena variabilis was complexed with flavodoxin from Azotobacter vinelandii. The shifts in redox potential for the complexes were used with previously determined values for the dissociation constant (Kd) of the electrostatic complex of the two oxidised proteins, in order to estimate Kd values for the interaction of the different redox forms of the proteins. The calculations showed that the electrostatic complexes, formed when the proteins differ in their redox states, are stronger than those formed when both proteins are fully oxidized or fully reduced.

Anabaena↗
PubMed1994

The contribution of electrostatic forces to the process of adherence of Candida albicans yeast cells to substrates.

The contribution of electrostatic interactions to the adherence process of Candida albicans and other Candida species was investigated by mixing cationic or anionic exchange resins possessing free -COO- or -NH+4 groups, respectively, on their surface. The adherence process of yeast cells to the anionic exchange resin is a saturable event that is essentially complete by 60 min. There is no measurable interaction of yeast cells with the cationic exchange resin. All clinical isolates of C. albicans, C. pseudotropicalis, one isolate each of C. tropicalis and Torulopsis glabrata possessed electrostatic charge as defined by this method, whereas two clinical isolates of C. parapsilosis, C. krusei and one isolate of C. tropicalis did not have measurable electrostatic surface charge. The adherence process to the exchange resin with the free -NH+4 group was dependent upon the pH of the suspending medium and varied from one isolate to another. Fixing yeast cells, or alternatively, endothelial cells, in such a manner as to change the surface charge of both and then measuring adherence of yeast cells to the target cells was an event that was not controlled by electrostatic interactions as they are defined herein. It appears that whatever contribution electrostatic charges make to the adherence process, that at best, it is a minor contribution.

Animals↗
PubMed2000

Anti-human immunodeficiency virus activities of nucleosides and nucleotides: correlation with molecular electrostatic potential data.

Examination of the anti-human immunodeficiency virus (HIV) data of some normal and isomeric dideoxynucleosides (ddNs and isoddNs), their three-dimensional (3-D) electron density patterns, their electrostatic potential surfaces (EPS), and their conformational maps reveals some interesting correlations. For example, the EPS of (S,S)-isoddA shows regions of high and low electrostatic potential remarkably similar to those of beta-D-3'-azido-3'-deoxythymidine (beta-D-AZT), (-)-oxetanocin A, and (-)-carbovir. Such correlations involving EPS data and anti-HIV activity were also found with many other active nucleosides. Conversely, inactive compounds had EPS different from those of compounds in the same series that were active. For example, apio-ddNs, which are inactive against HIV, exhibit clear differences in electrostatic potential and 3-D electron density shape from isoddNs that are active against HIV. Additionally, the inactivity of (S,S)-isoddC and (S,S)-isoddT can be correlated convincingly with a combination of their EPS data and their conformational energy maps. The electrostatic potential distributions of active nucleoside triphosphates show remarkable correlations. For example, (S,S)-isoddATP, AZT triphosphate (AZTTP), and oxetanocin A TP have similar 3-D electron density surface patterns and similar high and low regions of electrostatic potential, which may suggest that these compounds proceed through related mechanisms in their interactions with, and inhibition of, HIV reverse transcriptase (RT). Docking of AZTTP, (S,S)-isoddATP, and other active triphosphates into the active site of HIV RT and calculation of the EPS of both the nucleotide and the active site show that there is excellent matching between inhibitor and enzyme binding site EPS data. The structure-activity profile discovered has contributed to the development of a first predictive quantitative structure-activity relationship analysis in the area.

Anti-HIV Agents↗
PubMed2001

Randomised controlled study of clinical efficacy of spacer therapy in asthma with regard to electrostatic charge.

BACKGROUND: Inhalation therapy using a pressured metered dose inhaler (pMDI) and a spacer is frequently used in the treatment of airway disease in children. Several laboratory studies found a clear negative influence of electrostatic charge (ESC) on plastic spacers on the delivery of aerosol. AIMS: To investigate whether ESC on plastic spacers could diminish bronchodilating responses to salbutamol. METHODS: Ninety asthmatic children (aged 4-8 years) were randomised into three groups: metal Nebuchamber, plastic Volumatic, and plastic Aerochamber. The bronchodilating response was measured by the change in peak expiratory flow rate (PEF) after 100 microgram and 400 microgram salbutamol. Within the Volumatic and Aerochamber groups, a crossover comparison was made between electrostatic and non-electrostatic spacers. RESULTS: We found no significant effect of ESC on the bronchodilating response to salbutamol with any of the doses in the Aerochamber and Volumatic groups. For the plastic spacers, the mean difference of the change in PEF after 100 microgram salbutamol between non-electrostatic and electrostatic spacers was only +1.7% (95% CI -1.3% to 4.7%). After 400 microgram salbutamol this was +1.9% (95% CI -1.4% to 5.1%). A comparable efficacy was found for the Nebuchamber, the Aerochamber, and Volumatic with respect to the change in PEF after 100 and 400 microgram salbutamol. CONCLUSION: This study showed no negative influence of ESC on plastic spacers with regard to clinical efficacy of a beta(2) agonist (salbutamol) in children with asthma. The metal Nebuchamber, plastic Aerochamber, and plastic Volumatic were equally effective.

Administration, Inhalation↗
PubMed2006

The effect of electrostatic force on the evolution of sand saltation cloud.

In a wind-blown sand layer, it has been found that wind transport of particles is always associated with separation of electric charge. This electrification in turn produces some electrostatic forces in addition to the gravitational and fluid friction forces that affect the movement of saltating sand particles, further, the wind-blown sand saltation. To evaluate this effect quantitatively, this paper presents a simulation of evolution of wind-blown sand grains after the electrostatic forces exerted on the grains are taken into account in the wind feedback mechanism of wind-blown saltation. That is, the coupling interaction between the wind flow and the saltating sand particles is employed in the simulation to the non-stationary wind and sand flows when considering fluid drag, gravitation, and a kind of electrostatic force generated from a distribution of electric field changing with time in the evolution process of the sand saltation. On the basis of the proposed simulation model, a numerical program is given to perform the simulation of this dynamic process and some characteristic quantities, e.g., duration of the system to reach the steady state, and curves of the saltating grain number, grain transport rate, mass-flux profile, and wind profile varying with time during the non-stationary evolution are displayed. The obtained numerical results exhibit that the electrostatic force is closely related to the average charge-to-mass ratio of sand particles and has obvious influence on these characteristic quantities. The obtained results also show that the duration of the system to reach the steady state, the sand transport rate and the mass flux profile coincide well with experimental results by Shao and Raupach (1992) when the average charge-to-mass ratio of sand particles is 60 microC/kg for the sand particles with average diameter of 0.25 mm. When the average charge-to-mass ratios of sand particles are taken as some other certain values, the calculation results still show that the mass flux profiles are well in agreement with the experimental data by Rasmussen and Mikkelsen (1998) for another category of sand particles, which tell us that the electrostatic force is one of main factors that have to be considered in the research of mechanism of wind-blown sand saltation.

Journal Article↗
PubMed2006

Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70.

A comparative analysis of electrostatic patterns for 359 sigma70-specific promoters and 359 nonpromoter regions on electrostatic map of Escherichia coli genome was carried out. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile which correlate with promoter sequences. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which differ for different promoter groups and may be involved as signal elements in differential recognition of various promoters by the enzyme. Some specific electrostatic elements which are responsible for modulating promoter activities due to ADP-ribosylation of RNA polymerase alpha-subunit were found in far upstream regions of T4 phage early promoters and E. coli ribosomal promoters.

Base Sequence↗
PubMedDate not supplied

Effect of different types of textile fabric on spermatogenesis: electrostatic potentials generated on the surface of the human scrotum by wearing different types of fabric.

This study was conducted to evaluate the effect of the electrostatic potentials generated on the surface of the scrotal area when different types of textile fabric were worn. Twenty-one healthy volunteers were divided into three equal groups. The first group was dressed in underpants made of 100% polyester, the second wore underpants of 100% cotton, and the third wore a 50/50% polyester/cotton mixture. With an electrostatic kilovoltmeter, the electrostatic potentials were measured 1 h after wearing the pants once during the day and a second time at night. The test was repeated 4 times, each on a separate day. No electrostatic potentials were detected on the cotton underpants. The polyester pants showed the highest potentials (mean 338.9 +/- 25 SD V/cm2), while the mixed polyester/cotton pants produced less than half that level (mean 148.3 +/- 16 SD V/cm2). The readings during the day were higher than those at night, probably due to the higher temperature during the day. This study could explain the cause of diminished spermatogenesis in dogs dressed in polyester pants. A new theory is put forward holding that the polyester underpants create an "electrostatic field" across the scrotal sac that disturbs the testicular and/or epididymal function.

Adult↗
PubMed2000

Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper.

In solution proteins often exhibit backbone and side-chain flexibility. Yet electrostatic interactions in proteins are sensitive to motions. Hence, here we study the contribution of ion pairs toward protein stability in a range of conformers which sample the conformational space in solution. Specifically, we focus on the electrostatic contributions of ion pairs to the stability of each of the conformers in the NMR ensemble of the c-Myc-Max leucine zipper and to their average energy minimized structure. We compute the electrostatic contributions of inter- and intra-helical ion pairs and of an ion pair network. We find that the electrostatic contributions vary considerably among the 40 NMR conformers. Each ion pair, and the network, fluctuates between being stabilizing and being destabilizing. This fluctation reflects the variability in the location of the ion pairing residues and in the geometric orientation of these residues, both with respect to each other and with respect to other charged groups in the rest of the protein. Ion pair interactions in the c-Myc-Max leucine zipper in solution depend on the protein conformer which is analyzed. Hence, the overall stabilizing (or destabilizing) contribution of an ion pair is conformer population-dependent. This study indicates that free energy calculations performed using the continuum electrostatics methodology are sensitive to protein conformational details.

Basic Helix-Loop-Helix Leucine Zipper Transcriptio↗
PubMed2006

[Study on recovery of copper from waste printed wiring boards by electrostatic separation].

Recovery of Cu from waste printed wiring boards (PWBs) was studied by crushers and electrostatic separator. The results of pulverizing experiment show that liberation degree of metal is higher in grain size -0.9 + 0.074 mm, the product of this grain size can be used as raw material in electrostatic separation. The main factors that influence electrostatic separation are found by dynamic analysis of particles in course of electrostatic separation, it conclude electrode voltage, roller rotate speed, electric coronary polar distance and granularity of particles. The -0.9 + 0.074 mm pulverizing product is separated through single stage electrostatic separation after optimizing influence factors. Result shows that the enrichment condition of Cu in fine material is good, Cu could be concentrated from 32.0% to 63.6%, and recovery ratio is 78.7%.

Copper↗