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PubMed1987

Electrostatic effects of bound NADH and NAD+ on ionizing groups in liver alcohol dehydrogenase.

A simple point charge model has been used to estimate the effect of electrostatic interactions of bound NADH and NAD+ on ionizing groups in liver alcohol dehydrogenase. The results provide clear evidence that the much-discussed effects of pH on coenzyme binding in the pH range 7-10 are predominantly of electrostatic origin and attributable to ionization of the water molecule which is bound at the active-site zinc ion. Ionization of Lys-228 is proposed to account for the proton-dependent destabilization of the enzyme X NADH and enzyme X NAD+ complexes which has been reported to occur above a pKa of 10.4.

Alcohol Dehydrogenase↗

PubMed1996

Detection by physico-chemical techniques of an amphiphilic surface component on Streptococcus mitis strains involved in non-electrostatic binding to surfaces.

Indications for the presence of an amphiphilic molecule in Streptococcus mitis strains cultured on TY-agar were obtained from infrared absorption spectra, especially from the shape of the CH2/CH3 absorption bands around 2900 cm-1, which were absent when strains were grown on blood agar. It was the aim of this study to determine for S. mitis strains grown on different growth media whether the amphiphile is located intracellularly or on the cell surface by measuring zeta potentials, elemental surface compositions and adhesion to hexadecane of differently grown cells. There was no significant effect of the presence of the amphiphile on the zeta potentials of the S. mitis strains, but adhesion to hexadecane was increased by the presence of the amphiphile when the pH of the suspension was such that electrostatic interactions between the organisms and the hexadecane could be neglected. Furthermore, lower N/C surface concentration ratios were found for organisms possessing the amphiphilic molecule. Consequently, it was concluded that the amphiphilic molecule is located on the cell surface, and that it is involved in the non-electrostatic binding of S. mitis cells to surfaces.

Agar↗

PubMed2005

Mg2+-modulated KMnO4 reactivity of thymines in the open transcription complex reflects variation in the negative electrostatic potential along the separated DNA strands. Footprinting of Escherichia coli RNA polymerase complex at the lambdaP(R) promoter revisited.

There is still a controversy over the mechanism of promoter DNA strand separation upon open transcription complex (RPo) formation by Escherichia coli RNA polymerase: is it a single or a stepwise process controlled by Mg2+ ions and temperature? To resolve this question, the kinetics of pseudo-first-order oxidation of thymine residues by KMnO4 in the -11 ... +2 DNA region of RPo at the lambdaP(R) promoter was examined under single-hit conditions as a function of temperature (13-37 degrees C) in the absence or presence of 10 mm MgCl2. The reaction was also studied with respect to thymidine and its nucleotides (TMP, TTP and TpT) as a function of temperature and [MgCl2]. The kinetic parameters, (ox)k and (ox)E(a), and Mg-induced enhancement of (ox)k proved to be of the same order of magnitude for RPo-lambdaP(R) and the nucleotides. Unlike the complex, (ox)E(a) for the nucleotides was found to be Mg-independent. The isothermal increase in (ox)k with increasing [Mg2+] was thus interpreted in terms of a simple model of screening of the negative charges on phosphate groups by Mg2+ ions, lowering the electrostatic barrier to the diffusion of MnO4- anions to the reactive double bond of thymine. Similar screening isotherms were determined for the oxidation of two groups of thymines in RPo at a consensus-like Pa promoter, differing in the magnitude of the Mg effect. Together, the findings show that: (a) the two DNA strands in the -11...+2 region of RPo-lambdaP(R) are completely separated over the whole range of temperatures investigated (13-37 degrees C) in the absence of Mg2+ (b) Mg2+ ions induce an increase in the rate of the oxidation reaction by screening negatively charged phosphate and carboxylate groups; and (c) the observed thymine reactivity and the magnitude of the Mg effect reflect variation in the strength of the electrostatic potential along the separated DNA strands, in agreement with the current structural model of RPo.

Bacteriophage lambda↗

PubMed2006

The use of three-dimensional shape and electrostatic similarity searching in the identification of a melanin-concentrating hormone receptor 1 antagonist.

To aid in the identification of novel melanin-concentrating hormone receptor 1 (MCHr1) antagonists, a unique virtual library of readily synthesized molecules was designed and assembled based on 323 monomer compounds containing reactive moieties in combination with 30 core molecules having diamine functionality. The resulting library of 3,129,870 molecules was searched using three-dimensional shape similarity measures that were complimented with a novel electrostatic distribution similarity-matching algorithm. One of the top scoring hits in this library was synthesized and characterized for MCHr1 antagonism, where it exhibited at least a threefold improvement in binding affinity and cellular potency relative to the parent MCHr1 ligand. This work demonstrates that the use of shape and electrostatic similarity matching in combination with a well-designed virtual library can be used to augment standard medicinal chemistry techniques.

Algorithms↗

PubMed2002

Probing protein electrostatics with a synthetic fluorescent amino acid.

Electrostatics affect virtually all aspects of protein structure and activity and are particularly important in proteins whose primary function is to stabilize charge. Here we introduce a fluorescent amino acid, Aladan, which can probe the electrostatic character of a protein at multiple sites. Aladan is exceptionally sensitive to the polarity of its surroundings and can be incorporated site-selectively at buried and exposed sites, in both soluble and membrane proteins. Steady-state and time-resolved fluorescence measurements of Aladan residues at different buried and exposed sites in the B1 domain of protein G suggest that its interior is polar and heterogeneous.

2-Naphthylamine↗

PubMed2006

Electrostatic self-assembly of binary nanoparticle crystals with a diamond-like lattice.

Self-assembly of charged, equally sized metal nanoparticles of two types (gold and silver) leads to the formation of large, sphalerite (diamond-like) crystals, in which each nanoparticle has four oppositely charged neighbors. Formation of these non-close-packed structures is a consequence of electrostatic effects specific to the nanoscale, where the thickness of the screening layer is commensurate with the dimensions of the assembling objects. Because of electrostatic stabilization of larger crystallizing particles by smaller ones, better-quality crystals can be obtained from more polydisperse nanoparticle solutions.

Journal Article↗

PubMed1996

Evaluating electrostatic contributions to binding with the use of protein charge ladders.

Electrostatic interactions between charges on ligands and charges on proteins that are remote from the binding interface can influence the free energy of binding (delta Gb). The binding affinities between charged ligands and the members of a charge ladder of bovine carbonic anhydrase (CAII) constructed by random acetylation of the amino groups on its surface were measured by affinity capillary electrophoresis (ACE). The values of delta Gb derived from this analysis correlated approximately linearly with the charge. Opposite charges on the ligand and the members of the charge ladder of CAII were stabilizing; like charges were destabilizing. The combination of ACE and protein charge ladders provides a tool for quantitatively examining the contributions of electrostatics to free energies of molecular recognition in biology.

Acetylation↗

PubMed1978

Electrostatic effects in proteins.

Electrostatic effects dominate many aspects of protein behavior. When polypeptide chains fold up, most polar side chains seek the exterior, where they can be solvated. Water bound in the interior has been found between the domains of enzymes of the chymotrypsin family, and between the subunits of hemoglobin and tobacco mosaic virus protein. Assembly of this protein from disk to virus is triggered by electrostatic interactions between neighboring subunits. Lysozyme stabilizes the constellation of charges involved in the transition state of its substrate by both permanent and induced dipoles. All factors that lower the oxygen affinity of hemoglobin act by strengthening the salt bridges that constrain its quaternary deoxy (T) structure. Enzymes of thermophile bacteria owe their extra stability mostly to additional salt bridges. The rate of denaturation of hemoglobins by alkali is determined by the ionization of internal side chains with pK's of about 12.

Allosteric Regulation↗

PubMed1993

Hydrophobic and electrostatic cell surface properties of thermophilic dairy streptococci.

Microbial adhesion to hydrocarbons (MATH) and microelectrophoresis were done in 10 mM potassium phosphate solutions to characterize the surfaces of thermophilic dairy streptococci, isolated from pasteurizers. Regardless of whether they were grown (in M17 broth) with lactose, sucrose, or glucose added, strains were relatively hydrophilic (showing low initial removal rates by hexadecane) and slightly negatively charged. A tendency exists for cells grown with sucrose added to be more hydrophilic than cells grown with glucose or lactose added. Also, the lowest isoelectric points, i.e., the pH values for which the zeta potentials are zero, were measured for strains with glucose added to the growth medium. The isoelectric points for the strains were all rather high, between pH 3 and 5, indicative of protein-rich surfaces, although X-ray photoelectron spectroscopy did not measure excessively large amounts of nitrogen on the cell surfaces. Both MATH and microelectrophoresis were done as a function of pH. Maxima in hydrophobicity were observed at certain pH values. Usually these pH values were in the range of the isoelectric points of the cells. Thus it appears that MATH measures an interplay of hydrophobicity and electrostatic interactions. MATH measures solely hydrophobicity only when electrostatic interactions are absent, i.e., close to the isoelectric points of the cells. Considering that these thermophilic streptococci are all rather hydrophilic, a possible pathway to prevent fouling in the pasteurization process might be to render the heat exchanger plates of the pasteurizer more hydrophobic.

Journal Article↗

PubMed2001

Effects of hydrophobic and electrostatic cell surface properties of bacteria on feeding rates of heterotrophic nanoflagellates.

The influence of cell surface hydrophobicity and electrostatic charge of bacteria on grazing rates of three common species of interception-feeding nanoflagellates was examined. The hydrophobicity of bacteria isolated from freshwater plankton was assessed by using two different methods (bacterial adhesion to hydrocarbon and hydrophobic interaction chromatography). The electrostatic charge of the cell surface (measured as zeta potential) was analyzed by microelectrophoresis. Bacterial ingestion rates were determined by enumerating bacteria in food vacuoles by immunofluorescence labelling via strain-specific antibodies. Feeding rates varied about twofold for each flagellate species but showed no significant dependence on prey hydrophobicity or surface charge. Further evidence was provided by an experiment involving flagellate grazing on complex bacterial communities in a two-stage continuous culture system. The hydrophobicity values of bacteria that survived protozoan grazing were variable, but the bacteria did not tend to become more hydrophilic. We concluded that variability in bacterial cell hydrophobicity and variability in surface charge do not severely affect uptake rates of suspended bacteria or food selection by interception-feeding flagellates.

Animals↗

PubMed1966

Effect of electrostatic charge on the contamination of plastic food containers by airborne bacterial spores.

Electrostatic charge of approximately -10 kv was produced by friction on polystyrene food container samples. This charge quickly decayed to a lower, more stable, level. Exposure of samples to positively charged red and negatively charged green fluorescent particles resulted in a particle-distribution pattern on the plastic surface. The dynamic attraction of fluorescent particles was illustrated by time-lapse photography. Similar distribution patterns of airborne bacterial spores were shown to develop. In controlled bacterial aerosol exposure tests, an increase in surface contamination of the plastic samples was found to be quantitatively related to an increase in negative electrostatic charge on the plastic. Static charge was found to accumulate on plastic food containers during their manufacture, and to remain indefinitely on many of the finished products. This charge was of the intensity and polarity to attract positively charged bacterial cells if such particles were present in the air.

Journal Article↗

PubMed1987

Adhesion of Aeromonas salmonicida strains associated with net electrostatic charges of host tissue cells.

The adhesion of Aeromonas salmonicida, the pathogenic bacterium of fish furunculosis in salmon and trout, to the surface of host tissue cells was investigated with two fish tissue culture cell lines (RTG-2 cells from rainbow trout, Salmo gairdneri, and CHSE-214 cells from chinook salmon, Oncorhynchus tshawytscha) and four A. salmonicida strains. Bacterial cells of pathogenic strains were highly adhesive to RTG-2 and CHSE-214 cells and were negatively charged in the net electrostatic charges, as determined by electrophoresis on filter paper strips at pH 7, whereas bacterial cells of nonpathogenic strains were nonadhesive and positively charged. The electrophoresis of RTG-2 and CHSE-214 cells with balanced salt solution (BSS), phosphate-buffered saline, or fish serum diluted with BSS (pH 7) was carried out with an appropriate electrophoretic apparatus that was devised for this study. After electrophoresis with 20 mA of direct current for 15 min at pH 7, the electrophoretic dispositions of these tissue culture cells were determined by the mode of frequency of occurrence of these cells in the partitioned chambers of the device. RTG-2 and CHSE-214 cells with BSS and fish serum were attracted from the central chamber (to which each cell sample was added) to the cathode chambers, but no attraction was detected when these cells were used with phosphate-buffered saline. Noradrenaline- and phosphoenolpyruvate-pretreated RTG-2 cells migrated more to the cathode chambers, whereas succinate- and valine-pretreated RTG-2 cells moved to the anode chambers. These movements to the cathode and anode were alleviated by the use of RTG-2 cells preincubated with pathogenic and nonpathogenic bacterial cells, respectively. The adhesion of the pathogenic bacteria to RTG-2 cells was enhanced by the use of RTG-2 cells pretreated with noradrenaline and phosphoenolpyruvate, whereas the nonpathogenic bacteria were adherent to RTG-2 cells pretreated with succinate and valine. These findings indicate that the adhesion of A. salmonicida strains to host tissue cells is closely associated with mutually converse net electrostatic charges.

Aeromonas↗

PubMed2006

Amyloidogenic properties of the artificial protein albebetin and its biologically active derivatives. The role of electrostatic interactions in fibril formation.

The artificial protein albebetin (ABB) and its derivatives containing biologically active fragments of natural proteins form fibrils at physiological pH. The amyloid nature of the fibrils was confirmed by far UV circular dichroism spectra indicating for rich beta-structure, thioflavin T binding assays, and examination of the obtained polymers by atomic force microscopy. Fusing of short peptides--octapeptide of human alpha(2)-interferon (130-137) or hexapeptide HLDF-6 (41-46) of human leukemia differentiation factor--with the N-terminus of ABB led to increased amyloidogenicity of the protein: the rate of fibril formation increased and the morphology of fibrils became more complex. The presence of free hexapeptide HLDF-6 in the ABB solution had the same effect. Increasing ionic strength also activated the process of amyloid formation, but to less extent than did the peptides fused with ABB or added to the ABB solution. We suggest an important role of electrostatic interactions in formation of ABB fibrils. The foregoing ways (addition of salt or peptides) allow decrease in electrostatic repulsion between ABB molecules carrying large negative charge (-12) at neutral pH, thus promoting fibril formation.

Amyloid↗

PubMed2002

Probing electrostatic interactions in cytochrome c using site-directed chemical modification.

This communication reports the generation of an electrostatic probe using chemical modification of methionine side chains. The alkylation of methionine by iodoacetamide was achieved in a set of Saccharomyces cerevisiae iso-1-cytochrome c mutants, introducing the nontitratable, nondelocalized positive charge of a carboxyamidomethylmethionine sulfonium (CAMMS) ion at five surface and one buried site in the protein. Changes in redox potential and its variation with temperature were used to calculate microscopic effective dielectric constants operating between the probe and the heme iron. Dielectric constants (epsilon) derived from deltadeltaG values were not useful due to entropic effects, but epsilon(deltadeltaH) gave results that supported the theory. The effect on biological activity of surface derivatization was interpreted in terms of protein-protein interactions. The introduction of an electrostatic probe in cytochrome c often resulted in marked effects on activity with one of two physiological partners: cytochrome c reductase, especially if introduced at position 65, and cytochrome c oxidase, if at position 28.

Alkylation↗

PubMed2006

Screened electrostatics of charged particles on a water droplet.

We study the electrostatic properties of charged particles trapped at an interface in a water-in-oil microemulsion. The electrostatic potential and the counterion distribution in the water droplet are given in terms of the ratio of the Debye screening length kappa(-1) and the droplet radius R. In the limit R-->infinity we recover the well-known results for a flat interface. Finite-size corrections are obtained in terms of the small parameter 1/kappaR. Part of the counterions spread along the interface and form a charged layer of one Debye length thickness. In particular, there is a uniform surface charge contribution. We derive explicit expressions for the electric field, the mobile charge density, and the charge-induced pressure on the interface.

Journal Article↗

PubMed1999

Molecular dynamics simulations of biomolecules: long-range electrostatic effects.

Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.

Computer Simulation↗

PubMed1998

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

Computer Simulation↗

PubMed1986

Electrostatic lock-and-key model for the study of biological isosterism: role of structural water in the binding of basic pancreatic trypsin inhibitor to beta-trypsin.

We propose the electrostatic lock-and-key model for the analysis of the interaction between beta-trypsin and basic pancreatic trypsin inhibitor (BPTI). Prerequisite for the proper recognition of the ligand by the protein is that, beside a steric complementarity, matching of electrostatic patterns is attained. It is found that the complementarity is imperfect in the vicinity of BPTI backbone carbonyl oxygen atoms and this imperfection is diminished by the presence of structural water molecules bound to the contact surface. Some novel types of biological isosteres are proposed. It is expected that the Gibbs free energy of binding increases upon changing the moieties greater than C = O ... H-OH and greater than C = O to greater than CHCH2 CH2OH and greater than CHOH groups, respectively.

Aprotinin↗