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PubMed1993

MEPSIM: a computational package for analysis and comparison of molecular electrostatic potentials.

MEPSIM is a computational system which allows an integrated computation, analysis, and comparison of molecular electrostatic potential (MEP) distributions. It includes several modules. Module MEPPLA supplies MEP values for the points of a grid defined on a plane which is specified by a set of three points. The results of this program can easily be converted into MEP maps using third-parties graphical software. Module MEPMIN allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values, and all the geometrical relationships between them (distances, angles, and dihedral angles). Module MEPCOMP computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes the similarity. Module MEPCONF performs the same process as MEPCOMP, considering not only the relative position of both molecules but also a conformational degree of freedom of one of them. The most recently developed module, MEPPAR, is another modification of MEPCOMP in order to compute the MEP similarity between two molecules, but only taking into account a particular plane. The latter module is particularly useful to compare MEP distributions generated by pi systems of aromatic rings. MEPSIM can use several wavefunction computation approaches to obtain MEP distributions. MEPSIM has a menu type interface to simplify the following tasks: creation of input files from output files of external programs (GAUSSIAN and AMPAC/MOPAC), setting the parameters for the current computation, and submitting jobs to the batch queues of the computer. MEPSIM has been coded in FORTRAN and its current version runs on VMS/VAX computers.

Drug Design↗
PubMed1991

Automatic search for maximum similarity between molecular electrostatic potential distributions.

A new computer program has been developed to automatically obtain the relative position of two molecules in which the similarity between molecular electrostatic-potential distributions is greatest. These distributions are considered in a volume around the molecules, and the similarity is measured by the Spearman rank coefficient. The program has been tested using several pairs of molecules: water vs. water; phenylethylamine and phenylpropylamine vs. benzylamine; and methotrexate vs. dihydrofolic acid.

Benzylamines↗
PubMed1991

The inclusion of electrostatic hydration energies in molecular mechanics calculations.

The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.

Chemical Phenomena↗
PubMed1986

Electrostatically induced growth of spiral lipid domains in the presence of cholesterol.

The formation of crystalline domains of the phospholipid L-alpha-dimyristoyl-phosphatidic acid containing 1 mol% cholesterol, was studied as a function of head group charge by fluorescence microscopy with monolayers at the air/water interface. It is shown that the usual dendritic growth occurs at low pH (8), whereas spiral domains are formed at high pH (11), where the head group contains two negative charges. The findings are ascribed to an electrostatically induced chain tilt that, in conjunction with an in-plane dipole moment, causes a ferroelectric state. This allows for domain aggregation and orientation originating in elongated domains that, additionally, are bent because of the chirality of the molecules. The structure is stabilized and further elongated due to the anisotropic edge activity of cholesterol.

Biophysical Phenomena↗
PubMed1993

Point charge representation of multicenter multipole moments in calculation of electrostatic properties.

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

Carbon Monoxide↗
PubMed1976

Cell size and mutual cell adhesion. II. Evidence for a relation between cell size, long-range electrostatic repulsion and intercellular adhesiveness during density-regulated growth in suspension.

The strength of the long-range electrostatic repulsion forces on HeLa cells is measured by agglutinative titration using low molecular weight polylysine (M.W. 11,000). Repulsion forces, found to be present on the smaller HeLa cells from density-inhibited suspension cultures, are weakened by incubation of the cells in hypotonic NaCl solutions. Repulsion forces, found to be absent on the larger cells from fast growing cultures, can be induced on these cells by incubation in hypertonic NaCl solutions. Both effects of anisotonicity are reversible, and disappear on restoration of the medium to normal tonicity. Induction of repulsion forces on fast growing cells is prevented by previous treatment of the cells with neuraminidase. Neuraminidase also abolishes repulsion on density-inhibited cells. It is proposed that alterations of the cell size, produced by anisotonicity or occurring during growth in isotonic suspension medium, affect mutual cell adhesiveness by modifying the strength of the repulsion forces generated by cell surface sialic acids.

Agglutination Tests↗
PubMed1979

Electrostatic interaction between merocyanine 540 and liposomal and mitochondrial membranes.

The fluorescence of merocyanine 540 (MC) in liposomal and mitochondrial suspensions was measured under various conditions. Under a given condition, both the amount of dye bound to the membrane and the zeta potential were determined simultaneously. It was found that the fluorescence intensity was proportional to the amount of bound dye and correlated with the zeta potential of particles. The fluorescence intensity was represented quantiatively in terms of the Langmuir adsorption isotherm, when the electrostatic interaction acting between MC and membrane surface was properly taken into account. It was concluded that the changes in MC fluorescence in the liposomal and mitochondrial suspensions are mainly attributed to the changes in the surface potential of the membranes.

Animals↗
PubMed1990

Facile isolation of endo-pectate lyase from Erwinia carotovora based on electrostatic interaction.

Endo-pectate lyase (PATE) from Erwinia carotovora was selectively cosedimented with extracellularly produced lipopolysaccharide-lipid complex (LPSLC) through dialysis of the cell free culture broth. The selective isolation of PATE was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The cosedimentation of the PATE with LPSLC was initiated by decreasing conductivity of the solution and terminated at approx 1 m siemens (mScm-1). As much as 62% of PATE activity in the culture broth was removed by precipitation. PATE was isolated from the precipitate by gel chromatography. The cosedimentation of PATE with LPSLC was remarkably affected by pH or ionic strength. The addition of polycationic peptide polymyxin B sulfate or a metal chloride affected the interaction. The cosedimentation was diminished by acetylation of the free amino groups of PATE. From these results, it was confirmed that the cosedimentation was induced by electrostatic interaction.

Acetylation↗
PubMed2002

Electrostatic ion chromatography using a carboxybetaine-type zwitterionic surfactant as the stationary phase.

A carboxybetaine-type zwitterionic stationary phase obtained by immobilizing Mitsubishi Reagent EF-700 (C(8)F(17)SO(2)NHC(3)H(6)N(+) (CH(3))(2)-C(2)H(4)-COO(-)) onto a reversed-phase column was used for chromatographic separation of ions. When aqueous electrolyte solutions having higher pH values (>8) were used as eluents, the model analyte ions (NO(2)(-), H(2)PO(4)(-), Cl(-), Br(-), NO(3)(-), ClO(3)(-), I(-) and SCN(-)) were co-eluted and appeared at the void volume of this HPLC system. However, when aqueous electrolyte solutions having lower pH values (<5.5) were used as eluents, these anions were well retained and separated. Furthermore, when acetate buffers (NaAc/HAc) were used as eluents, plots of log k' (k', retention factor) versus pH of eluents (at constant [NaAc+HAc]), and log k' versus log [NaAc+HAc] (at constant pH), were linear with negative slopes. Breakthrough curves for acid solutions obtained using conductivity detection showed that H(+) ions and their conjugate anions were both retained on the stationary phase and the degree of binding was found to be independent of the acid species used. The degree to which the eluent cation was bound onto the carboxylate functionality of the zwitterion was found to exert a major effect on the retention of analyte anions. A strongly bound cation, such as H(+), reduced electrostatic repulsion effects exerted by the carboxylate functionality on analyte anions, so that they could freely access the quaternary ammonium sites on the zwitterion. It is concluded based on these experimental results that both the charges on the zwitterionic stationary phase make meaningful contributions to the separation of the analyte ions.

Journal Article↗
PubMed2005

Synthesis of polyacrylamide gel beads with electrostatic functional groups for the molecular imprinting of bovine serum albumin.

Synthetic materials capable of recognizing proteins are important in separation, biosensors and biomaterials. In this study, bovine serum albumin-imprinted soft-wet polyacrylamide gel beads were prepared via inverse-phase suspension polymerization, using acrylamide and N,N'-methylene diacrylamide as polymeric matrix components and methacrylic acid as functional monomer. The adsorption study showed, through the imprinting process, that the imprinted gel beads had much higher adsorption capacity than the nonimprinted gel beads, and that the matching of the surface zeta-potential between the templates and the imprinted gel beads can enhance the imprinting effect. Adsorption kinetics indicated that the adsorption process could be described as an apparent first-order kinetic process for the gel beads. From the adsorption isotherm curve, we found that the adsorption of the imprinted gel beads was in agreement with the Langmuir adsorption model. Moreover, selectivity testing of the imprinted gel beads showed that imprinted gel beads exhibited good recognition for BSA as compared to the control protein. We speculate that the formation of complementary shapes and multiple-point electrostatic interactions between the imprinting cavities and the template proteins are the two factors that lead to the imprinting effect.

Acrylic Resins↗
PubMed2000

Analysis of inorganic anions by electrostatic ion chromatography using zwitterionic/cationic mixed micelles as the stationary phase.

The inability to separate fluoride, phosphate and sulfate by electrostatic ion chromatography (EIC) was overcome by using an ODS silica column coated with mixed zwitterionic-cationic surfactants as the stationary phase. The best results were obtained using the zwitterionic surfactant, 3-(N,N-dimethylmyristylammonium)-propanesulfonate (C19H41NO3S), and the cationic surfactant, myristyltrimethylammonium, CH3(CH2)13N+(CH3)3, in a 10:1 molar ratio in the column coating solution. With a dilute solution of sodium tetraborate as the eluent the model analyte anions were completely separated in the following elution order: F, HPO42-, SO42-, Cl-, NO2-, Br-, NO3-. The very early elution of phosphate and sulfate is most unusual and is unique to this system. Detection limits better than 1.1 x 10(-4) mM and linear calibration plots up to 7.0 mM were obtained with a suppressed conductivity system.

Journal Article↗
PubMed2001

Direct determination of nitrite traces in high ionic-strength samples by electrostatic ion chromatography using diluted acid solutions as eluent.

An ion-chromatographic (IC) system with high selectivity for separation of nitrite is described. It is analogous to the EIC (electrostatic IC) previously reported and was established using 3-(N,N-dimethylstearylammonio)propanesulfonate (C23H49NO3S, a sulfobetaine type of zwitterionic surfactants) as the stationary phase and dilute aqueous HCl solutions as the mobile phase. Five inorganic anions, sulfate, chloride, bromide, nitrate, and nitrite were chosen as the model analytes and were analyzed using this EIC system. Sulfate was always eluted first, followed by chloride, bromide and nitrate. Nitrite, however, could be eluted either before or after nitrate, depending on the concentration of HCl in the eluent. An elution order nitrate< nitrite was always obtained simply by using >3 mmol L(-1) HCl as the eluent. For nitrite the detection limit was better than 2.1 x 10(-7) mol L(-1) (100 microL sample injection volume, S/N=3, UV at 210 nm). Bromide and nitrate could also be separated under these HPLC conditions. The detection limit for bromide was 7.2 x 10(-8) mol L(-1) and for nitrate 6.5 x 10(-8) mol L(-1). Both nitrite and nitrate in real seawater samples were successfully determined with direct sample injection using this EIC system.

Acids↗
PubMed2007

Pharmacology and surface electrostatics of the K channel outer pore vestibule.

In spite of a generally well-conserved outer vestibule and pore structure, there is considerable diversity in the pharmacology of K channels. We have investigated the role of specific outer vestibule charged residues in the pharmacology of K channels using tetraethylammonium (TEA) and a trivalent TEA analog, gallamine. Similar to Shaker K channels, gallamine block of Kv3.1 channels was more sensitive to solution ionic strength than was TEA block, a result consistent with a contribution from an electrostatic potential near the blocking site. In contrast, TEA block of another type of K channel (Kv2.1) was insensitive to solution ionic strength and these channels were resistant to block by gallamine. Neutralizing either of two lysine residues in the outer vestibule of these Kv2.1 channels conferred ionic strength sensitivity to TEA block. Kv2.1 channels with both lysines neutralized were sensitive to block by gallamine, and the ionic strength dependence of this block was greater than that for TEA. These results demonstrate that Kv3.1 (like Shaker) channels contain negatively charged residues in the outer vestibule of the pore that influence quaternary ammonium pharmacology. The presence of specific lysine residues in wild-type Kv2.1 channels produces an outer vestibule with little or no net charge, with important consequences for quaternary ammonium block. Neutralizing these key lysines results in a negatively charged vestibule with pharmacological properties approaching those of other types of K channels.

Action Potentials↗
PubMed2004

Adhesion and rupture of liposomes mediated by electrostatic interaction monitored by thickness shear mode resonators.

Adhesion and spreading of negatively charged unilamellar vesicles composed of POPG/POPC and DPPG/DPPC on positively charged self-assembly monolayers of 11-amino-1-undecanethiol were monitored by means of thickness shear mode (TSM) resonators with a fundamental frequency of 5 MHz. Changes of frequency and motional resistance upon vesicle adsorption were recorded as a function of surface charge density and lyotropic phase state of the lipids. From the readout of the TSM resonator, changes of the shape of the vesicles as well as the formation of supported lipid bilayers can be inferred in a quantitative manner. Increasing surface charge densities on the vesicles, which are tunable by the POPG content, led to decreasing frequency and resistance changes. At very high PG content, a lower limit of 3-12 Hz was found, indicative of the formation of planar bilayers due to vesicle rupture induced by the strong electrostatic interaction forces. Vesicles composed of DPPG/DPPC were less susceptible to deformation and rupture, a fact that can be attributed to the higher bending rigidity of DPPG/DPPC liposomes. More than 70 mol% of DPPG were needed to induce adhesion-controlled rupture of surface-attached vesicles, while only 30-50% of POPG were sufficient to form planar lipid bilayers on the quartz.

Lipid Bilayers↗
PubMed1999

Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase.

Protonation equilibria of residues important in the catalytic mechanism of a protein kinase were analyzed on the basis of the Poisson-Boltzmann electrostatic model along with a cluster-based treatment of the multiple titration state problem. Calculations were based upon crystallographic structures of the mammalian cAMP-dependent protein kinase, one representing the so called closed form of the enzyme and the other representing an open conformation. It was predicted that at pH 7 the preferred form of the phosphate group at the catalytically essential threonine 197 (P-Thr197) in the closed form is dianionic, whereas in the open form a monoanionic ionization state is preferred. This dianionic state of P-Thr197, in the closed form, is stabilized by interactions with ionizable residues His87, Arg165, and Lys189. Our calculations predict that the hydroxyl of the Ser residue in the peptide substrate is very difficult to ionize, both in the closed and open structures of the complex. Also, the supposed catalytic base, Asp166, does not seem to have a pK(a) appropriate to remove the hydroxyl group proton of the peptide substrate. However, when Ser of the peptide substrate is forced to remain ionized, the predicted pK(a) of Asp166 increases strongly, which suggests that the Asp residue is a likely candidate to attract the proton if the Ser residue becomes deprotonated, possibly during some structural change preceding formation of the transition state. Finally, in accord with suggestions made on the basis of the pH-dependence of kinase kinetics, our calculations predict that Glu230 and His87 are the residues responsible for the molecular pK(a) values of 6.2 and 8.5, observed in the experiment.

Adenosine Triphosphate↗
PubMed2001

Ionization properties of titratable groups in ribonuclease T1. II. Electrostatic analysis.

The experimental NMR data for the individual titratable groups in ribonuclease T1 presented in the preceding paper were analysed by means of a continuum dielectric model. The role of two factors, the alteration of hydrogen loci on the ionizable groups and the conformational flexibility, were analysed. It was suggested that the position of the titratable hydrogen is essential mainly for strongly interacting groups. For groups which are accessible to the solvent and whose ionization is not coupled with the ionization of neighbouring groups, this factor can be neglected. The influence of the conformational flexibility on the electrostatic interactions becomes apparent for the environment of K25. For some strongly interacting groups, non-sigmoidal ionization curves were calculated. On this basis the pH dependence of the NMR chemical shift of the 13Cepsilon2 resonance of H27, whose ionization is coupled with E82, was reproduced.

Hydrogen↗
PubMed2002

Role of electrostatic interactions in cohesion of bacterial biofilms.

Significant decreases in the apparent viscosity of a bacterial biofilm suspension were measured following addition of sodium, potassium, magnesium, or calcium salts, whereas iron salts increased the viscosity. Electrostatic interactions contribute to biofilm cohesion and iron cations are potent crosslinkers of the biofilm matrix.

Biofilms↗
PubMed2001

Structural, biochemical and electrostatic basis of serotype specificity in bovine enteroviruses.

We have performed immunostructural analyses of three closely related picornaviruses in order to gain understanding of the biochemical and structural basis of serotype specificity. We carried out sequence alignments of the capsid regions of three bovine enterovirus strains: VG-5-27 and M-4 from serotype 1 and PS-87 from serotype 2. Using our knowledge of the three dimensional and antigenic structure of strain VG-5-27 and the high levels of sequence identity between the strains, we have calculated the structures and solvent-accessible electrostatic potentials of the epitopes of all three viruses. We have demonstrated the viability of the molecular models of the epitopes of the M-4 and PS-87 strains. In each of the strains, we have explained the serotype specificities in terms of specific physical and chemical properties, and identified individual residues which are pivotal in determination of antibody recognition. These changes are in agreement with the known cross-reactivity of peptide and antiviral sera, showing that it is possible to derive structures for short variable sections of proteins of high sequence identity using molecular modelling which are significant in terms of biological function. We believe this study to be a novel approach in the analysis of virus serotype specificity.

Amino Acid Sequence↗