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PubMed1994

Role of electrostatics in antibody-antigen association: anti-hen egg lysozyme/lysozyme complex (HyHEL-5/HEL).

A recently developed multigrid-based Newton method for solving the nonlinear Poisson-Boltzmann equation is applied in an investigation of molecular recognition in the system consisting of the monoclonal antibody HyHEL-5 and hen egg lysozyme. The electrostatic free energy of binding is calculated for the wild-type complex and various mutants in which electrostatic interactions between the two proteins are altered. Mutations which neutralize or reverse the charge of any of the residues involved in salt-links in the native system always yield decreased binding affinities. The stability of the complex can be enhanced through the formation of a new salt-bridge obtained by mutating an asparagine residue of the lysozyme to the negatively-charged aspartate. Ionic strength effects are also examined and found to be significant in some cases.

Amino Acid Sequence↗

PubMed1995

Mathematical modelling of electrostatic fluctuations in subtilisin active site.

The intensities of electrostatic fluctuations in subtilisin active site generated by conformational motion of charged side chains, polar side chains and peptide bonds of the main chain are calculated. The comparative analysis of all these fragments reveals that there are few of them which make the main contribution to the total value of the intensity, which has been found to be approximately 10(7) g.cm-1.s-2. These are Ser 125, Thr 220 and peptide bonds of aminoacids 125-126, 218-219. Our present analysis enables us to compare the relative contribution of different fragments but we do not pretend to obtain precise absolute values. The reason for this is the lack of the detailed selective information on the mean-square amplitudes and correlation times of conformational motion of the fragments and on the values of local dielectric constants in the interior of subtilisin. The possibility for electrostatic fluctuations in enzyme active site to be an efficient nonspecific source of substrate activation is discussed.

Binding Sites↗

PubMed1998

Sequence-dependent binding of metal ion to DNA oligomeres. A comparison of molecular electrostatic potentials with NMR data.

Experimentally observed sequence-selective binding of metal ion to DNA oligonucleotides have been compared with variations of electrostatic potential (EP) along the helix. Calculations of EP have been performed for three atomic models of the oligonucleotide duplex [d(CGCGAATTCGCG)2] using several variants of EP calculations, including a solution of non-linear Poisson-Boltzmann equation (NPBE). N7 atom of guanine adjacent to adenine base was identified as a region with the most negative electrostatic potential in the major groove. The EP value for the Me ion binding site surpasses the value for N7 of other guanines by 10-26% depending on particular duplex conformation. Qualitatively, the sequence dependent variations of EP near guanine N7 atoms are in agreement with the sequence-selective behavior of Mn(II) and Zn(II) ions as revealed by NMR experiments. But the difference in EP between the two most negative regions near guanine N7 atoms does not exceed 1.25 kT/e. Simple model suggests that metal ions are capable to form ion-hydrate complexes with G-Pu steps of DNA duplex. These complexes are formed via one Me...G and five Me...water coordination bonds with water molecules hydrogen bonded to two adjacent purine bases in the same chain. We suppose that such a stereospecific structural possibility is the main factor which control the sequence-selectivity in the metal ion binding. A combination of both mechanisms allows to explain sequence specific Mn(II) and Zn(II) binding to a set of oligonucleotides.

Computer Simulation↗

PubMed2006

An exemple of particle concentration reduction in Parisian subway stations by electrostatic precipitation.

The air quality in Parisian subway stations is a great concern to users and the public authorities. Particle concentration is one of the major problems; indeed concentrations observed in stations are generally superior to those collected in the street. The subway generates its own particles from wheels / rail contact, braking, the ground... One of the ways explored to lower this level of particles is a removal treatment: the principle is to treat the ambient air using a suitable system placed in stations. Following literature, the process chosen by Paris Transport Authority is the electrostatic precipitator. An electrostatic precipitator prototype from the Recycl'Air company is installed in May 2001 in a closed station on the 5th line (Italy Place -Bobigny). Results show that, by the end of approximately one year, the efficiency has fallen by 15% and it is therefore necessary to clean the precipitation cartridges. A consideration has also been made on the possibility to equip an entire subway station. According to the results obtained, about twenty filters placed in the top of a non mechanically ventilated station would permit to half an initial concentration in particles of 230 microg m(-3).

Air Pollution↗

PubMed1990

Electrostatic effects in asbestos sampling. II: Comparison of theory and experiment.

A series of calculations was conducted to estimate the degree and type of electrostatic interactions that might occur with electrically charged asbestos samplers collecting charged particles. Relatively simple theoretical models were constructed assuming only charge-charge electrostatic interactions between a charged particle and a charged sampler. The results of these calculations were compared with some experimental measurements and the agreement between the two allowed some confidence in predicting behavior trends. Under conditions where both the particles and the sampler are charged, the nonconductive sampler exhibits increased particle loss, especially near the filter edge, and increased variability of the particle deposit. The variability of the deposit also tends to be greatest near the filter edge. Under similar conditions, conductive cowled samplers also can be expected to exhibit losses in particle deposit, especially near the filter edge. The variability over the filter surface, however, is less than for the nonconductive cowl. Particle collection onto the sampler filter generally is expected to be greatest for isokinetic, isoaxial sampling conditions. Particle collection on the filter decreases with lower sampling flow rates, lower air velocities near the sampler inlet, and increased turbulence near the inlet.

Air Pollutants↗

PubMed2000

Interaction between quaternary ammonium ions in the pore of potassium channels. Evidence against an electrostatic repulsion mechanism.

We have examined the interaction between internal and external ions in the pore of potassium channels. We found that external tetraethylammonium was able to antagonize block of Shaker channels by internal TEA when the external and internal solutions contained K(+) ions. This antagonism was absent in solutions with Rb(+) as the only permeant ion. An externally applied trivalent TEA analogue, gallamine, was less effective than the monovalent TEA in inhibiting block by internal TEA. In addition, block by external TEA was little affected by changes in the concentration of internal K(+) ions, but was increased by the presence of internal Na(+) ions in the pore. These results demonstrate that external and internal TEA ions, likely located at opposite ends of the pore selectivity filter, do not experience a mutual electrostatic repulsion. We found that these results can be simulated by a simple 4-barrier-3-site permeation model in which ions compete for available binding sites without long-range electrostatic interactions.

Animals↗

PubMed2001

Electrostatics and the gating pore of Shaker potassium channels.

Various experiments have suggested that the S4 segment in voltage-dependent Na(+) and K(+) channels is in contact with a solvent-accessible cavity. We explore the consequences of the existence of such a cavity through the electrostatic effects on the gating currents of Shaker K(+) channels under conditions of reduced ionic strength S. We observe that approximately 10-fold reductions of intracellular S produce reductions of the measured gating charge of approximately 10%. These effects continue at even lower values of S. The reduction of gating charge when S is reduced by 10-fold at the extracellular surface is much smaller (approximately 2%). Shifts of the Q(V) curve because of a reduced S are small (<10 mV in size), which is consistent with very little fixed surface charge. Continuum electrostatic calculations show that the S effects on gating charge can be explained by the alteration of the local potential in an intracellular conical cavity of 20-24-A depth and 12-A aperture, and a smaller extracellular cavity of 3-A depth and the same aperture. In this case, the attenuation of the membrane potential at low S leads to reduction of the apparent gating charge. We suggest that this cavity is made by a bundle of transmembrane helices, and that the gating charge movement occurs by translocation of charged residues across a thin septum of approximately 3-7 A thickness.

Animals↗

PubMed2003

Conotoxins as sensors of local pH and electrostatic potential in the outer vestibule of the sodium channel.

We examined the block of voltage-dependent rat skeletal muscle sodium channels by derivatives of mu-conotoxin GIIIA (muCTX) having either histidine, glutamate, or alanine residues substituted for arginine-13. Toxin binding and dissociation were observed as current fluctuations from single, batrachotoxin-treated sodium channels in planar lipid bilayers. R13X derivatives of muCTX only partially block the single-channel current, enabling us to directly monitor properties of both muCTX-bound and -unbound states under different conditions. The fractional residual current through the bound channel changes with pH according to a single-site titration curve for toxin derivatives R13E and R13H, reflecting the effect of changing the charge on residue 13, in the bound state. Experiments with R13A provided a control reflecting the effects of titration of all residues on toxin and channel other than toxin residue 13. The apparent pKs for the titration of residual conductance are shifted 2-3 pH units positive from the nominal pK values for histidine and glutamate, respectively, and from the values for these specific residues, determined in the toxin molecule in free solution by NMR measurements. Toxin affinity also changes dramatically as a function of pH, almost entirely due to changes in the association rate constant, kon. Interpreted electrostatically, our results suggest that, even in the presence of the bound cationic toxin, the channel vestibule strongly favors cation entry with an equivalent local electrostatic potential more negative than -100 mV at the level of the "outer charged ring" formed by channel residues E403, E758, D1241, and D1532. Association rates are apparently limited at a transition state where the pK of toxin residue 13 is closer to the solution value than in the bound state. The action of these unique peptides can thus be used to sense the local environment in the ligand--receptor complex during individual molecular transitions and defined conformational states.

Animals↗

PubMed2003

Electrostatic control and chloride regulation of the fast gating of ClC-0 chloride channels.

The opening and closing of chloride (Cl-) channels in the ClC family are thought to tightly couple to ion permeation through the channel pore. In the prototype channel of the family, the ClC-0 channel from the Torpedo electric organ, the opening-closing of the pore in the millisecond time range known as "fast gating" is regulated by both external and internal Cl- ions. Although the external Cl- effect on the fast-gate opening has been extensively studied at a quantitative level, the internal Cl- regulation remains to be characterized. In this study, we examine the internal Cl- effects and the electrostatic controls of the fast-gating mechanism. While having little effect on the opening rate, raising [Cl-]i reduces the closing rate (or increases the open time) of the fast gate, with an apparent affinity of >1 M, a value very different from the one observed in the external Cl- regulation on the opening rate. Mutating charged residues in the pore also changes the fast-gating properties-the effects are more prominent on the closing rate than on the opening rate, a phenomenon similar to the effect of [Cl-]i on the fast gating. Thus, the alteration of fast-gate closing by charge mutations may come from a combination of two effects: a direct electrostatic interaction between the manipulated charge and the negatively charged glutamate gate and a repulsive force on the gate mediated by the permeant ion. Likewise, the regulations of internal Cl- on the fast gating may also be due to the competition of Cl- with the glutamate gate as well as the overall more negative potential brought to the pore by the binding of Cl-. In contrast, the opening rate of the fast gate is only minimally affected by manipulations of [Cl-]i and charges in the inner pore region. The very different nature of external and internal Cl- regulations on the fast gating thus may suggest that the opening and the closing of the fast gate are not microscopically reversible processes, but form a nonequilibrium cycle in the ClC-0 fast-gating mechanism.

Animals↗

PubMed1990

A nonlinear electrostatic potential change in the T-system of skeletal muscle detected under passive recording conditions using potentiometric dyes.

Voltage-sensing dyes were used to examine the electrical behavior of the T-system under passive recording conditions similar to those commonly used to detect charge movement. These conditions are designed to eliminate all ionic currents and render the T-system potential linear with respect to the command potential applied at the surface membrane. However, we found an unexpected nonlinearity in the relationship between the dye signal from the T-system and the applied clamp potential. An additional voltage- and time-dependent optical signal appears over the same depolarizing range of potentials where change movement and mechanical activation occur. This nonlinearity is not associated with unblocked ionic currents and cannot be attributed to lack of voltage clamp control of the T-system, which appears to be good under these conditions. We propose that a local electrostatic potential change occurs in the T-system upon depolarization. An electrostatic potential would not be expected to extend beyond molecular distances of the membrane and therefore would be sensed by a charged dye in the membrane but not by the voltage clamp, which responds solely to the potential of the bulk solution. Results obtained with different dyes suggest that the location of the phenomena giving rise to the extra absorbance change is either intramembrane or at the inner surface of the T-system membrane.

Animals↗

PubMed1989

The conformations and electrostatic potential maps of phorbol esters, teleocidins and ingenols.

Phorbol esters and the structurally dissimilar teleocidins and ingenols bind to and activate protein kinase C (PKC) during the course of tumour promotion. These compounds are referred to as TPA-like tumour promoters (from 12-O-tetradencanoyl phorbol-13-acetate, the most active of the class) and are amongst the most potent tumour promoters known. Despite their structural dissimilarity, all three groups of molecules have been shown to bind to the diacylglycerol site of PKC with high affinity. It is thought that this binding to and consequent activation of PKC is the crucial step in tumour promotion by these compounds. The aim of this work was to provide a description of the binding site by comparing structural features (in particular the electrostatic potential) with the activity of numerous derivatives of the three classes. Initially the description was obtained by consideration of the phorbol derivatives, and then refined using the teleocidins and ingenols. The activity data were collected from a variety of sources and the structures calculated using the semi-empirical MNDO approximation embodied in the MOPAC program. Where possible, the crystal structure was obtained from the Cambridge Crystallographic Database, and used as a starting point for the calculation. In other cases, a preliminary calculation was carried out using the molecular mechanics program AMBER. Electrostatic potentials were calculated and displayed using an in-house program 3D2, while superpositions of molecules were carried out using CHEM-X.

Diterpenes↗

PubMed1984

Relationships between the electrostatic potential, epoxide hydrase inhibition and carcinogenicity for some hydrocarbon and halogenated hydrocarbon epoxides.

For a group of nine hydrocarbon and halogenated hydrocarbon epoxides, there is shown to be a good correlation between their abilities to inhibit epoxide hydrase and the quantity Vmin /Es, where Vmin is the most negative value of the molecule's electrostatic potential in the neighborhood of the epoxide oxygen and Es is a factor that takes account of steric effects. It is also demonstrated that carcinogenicity, for thirteen epoxides, appears to be associated with Vmin having a relatively large negative value. On this basis, several other epoxides are predicted to be carcinogenic. The electrostatic potentials used in developing these relationships have been computed by an ab initio self-consistent-field molecular orbital procedure, using optimized molecular geometries.

Animals↗

PubMed2001

Electrostatic correction of the chromatic and of the spherical aberration of charged-particle lenses (part I).

A feasible electrostatic corrector (ECO) is outlined and the principle of the electrostatic correction is elucidated by means of a light-optical analogue. The ECO compensates for the chromatic and the spherical aberration of charged-particle lenses and reduces the resolution limit of a special LVSEM (low-voltage scanning electron microscope) from 6 nm to 1.4 nm. The geometry of the electrodes of the corrector is optimized with respect to the chromatic correction, the maximum strength of the electric field, and the residual higher-order aberrations which limit the resolution. In addition the stability criteria of the electric power supplies are discussed in detail.

Journal Article↗

PubMed2002

Electrostatic correction of the chromatic and of the spherical aberration of charged-particle lenses (part II).

A doubly symmetric electrostatic corrector which compensates for the axial chromatic and the axial third-order aberration of charged-particle lenses is outlined. Due to the double symmetry the corrector does not introduce linear off-axis aberrations and yields in combination with a round objective lens an electron-optical aplanat. The principle of the electrostatic correction of the axial chromatic aberration is explained in mathematical terms. The geometry of the electrodes of a suitable corrector is optimized with respect to the chromatic correction, the maximum strength of the electric field, and the residual higher-order aberrations which limit the resolution. The resulting aplanat achieves a resolution limit of about 2 nm for an image field with a diameter of 1500 nm. The required stabilities of the electric power supplies are discussed in detail.

Journal Article↗

PubMed2003

Electrostatic mirror objective with eliminated spherical and axial chromatic aberrations.

Computational formulae for the coefficients of the third-order spherical aberration and the second-order axial chromatic aberration are presented for an axially symmetric electrostatic electron mirror. A technique for eliminating the high-order derivatives of the potential axial distribution in mirror systems from the integrands is described. Conditions for elimination of spherical and axial chromatic aberrations, either separately or simultaneously, are found for a three-electrode axially symmetric mirror composed of coaxial cylinders of the same diameter. A principal scheme of the transmission electron microscope, where an electrostatic electron mirror serves as its objective, is presented.

Journal Article↗

PubMed1982

The electrostatic field of DNA: the role of the nucleic acid conformation.

Calculations of the electrostatic field of DNA in two very different double helical conformations, A and Z, are reported and compared with the results previously obtained for B-DNA. Striking contrasts between these fields and the associated electrostatic potentials are brought into evidence. One of the major differences is that while the deepest potentials are generally located in the grooves of DNA, the strongest fields are associated with the phosphate groups. The results of screening the nucleic acids by counterions are also presented.

DNA↗

PubMed2000

Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions.

Aminoglycosides are an important class of antibiotic that selectively target RNA structural motifs. Recently we have demonstrated copper derivatives of amino-glycosides to be efficient cleavage agents for cognate RNA motifs. To fully develop their potential as pharmaceutical agents it is necessary to understand both the structural mechanisms used by aminoglycosides to target RNA, and the relative contributions of hydrogen bonding and electrostatic interactions to recognition selectivity. Herein we report results from a calorimetric analysis of a stem-loop 23mer RNA aptamer complexed to the aminoglycoside neomycin B. Key thermodynamic parameters for complex formation have been determined by isothermal titration calorimetry, and from the metal-ion dependence of these binding parameters the relative contributions of electrostatics and hydrogen bonding toward binding affinity have been assessed. The principal mechanism for recognition and binding of neomycin B to the RNA major groove is mediated by hydrogen bonding.

Base Sequence↗

PubMed1980

The electrostatic molecular potential of tRNAPhe. IV. The potentials and steric accessibilities of sites associated with the bases.

The sites of the 76 nucleic acid bases of tRNAPhe potentially reactive towards electrophiles are studied by calculations on the associated molecular electrostatic potentials and the static steric accessibilities. Each of these sites is treated in its environment within the macromolecule. The influence of various schemes of screening by countercations of the backbone phosphates on the electrostatic potentials is investigated. The possible significance of the potentials and accessibilities in connection with observed chemical reactivities is discussed.

Adenine↗