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PubMed2001

Electrostatic effects play a central role in cold adaptation of trypsin.

Organisms that live in constantly cold environments have to adapt their metabolism to low temperatures, but mechanisms of enzymatic adaptation to cold environments are not fully understood. Cold active trypsin catalyses reactions more efficiently and binds ligands more strongly in comparison to warm active trypsin. We have addressed this issue by means of comparative free energy calculations studying the binding of positively charged ligands to two trypsin homologues. Stronger inhibition of the cold active trypsin by benzamidine and positively charged P1-variants of BPTI is caused by rather subtle electrostatic effects. The different affinity of benzamidine originates solely from long range interactions, while the increased binding of P1-Lys and -Arg variants of BPTI is attributed to both long and short range effects that are enhanced in the cold active trypsin compared to the warm active counterpart. Electrostatic interactions thus provide an efficient strategy for cold adaptation of trypsin.

Adaptation, Physiological↗
PubMed2003

The role of electrostatics in proton-conducting membrane protein complexes.

Electrostatic interactions play a key role in the coupling of electron and proton transfer in membrane protein complexes during the conversion of the energy stored in sunlight or reduced substrates into biochemical energy via a transmembrane electrochemical proton potential. Principles of charge stabilization within membrane proteins are reviewed and discussed for photosynthetic reaction centers, cytochrome c oxidases, and diheme-containing quinol:fumarate reductases. The impact of X-ray structure-based electrostatic calculations on the functional interpretation of these structural coordinates, on providing new explanations for experimental observations, and for the design of more focused additional experiments is illustrated by a number of key examples.

Electron Transport↗
PubMed1999

Long-range electrostatic effects on peptide folding.

The reversible folding/unfolding of a short peptide in solution is studied by molecular dynamics simulations. The effects of long-range electrostatic interactions are examined and found to be important both for the equilibrium between folded and unfolded states and the dynamics of the folding process. The neglect of long-range electrostatics leads to an increased population of unfolded states and increased structural fluctuations. When such interactions are taken into account, the peptide unfolds and folds to the experimentally determined structure several times during a 25 ns trajectory, with approximately equal populations of folded and unfolded states in the neighborhood of its proposed melting temperature. The effect of using spherical boundary conditions rather than periodic ones does not appear to have any major effect on the folding dynamics.

Computer Simulation↗
PubMed1990

Thermodynamic model for electrostatic-interaction chromatography of proteins.

A thermodynamic model derived by Record et al. [M. T. Record, Jr., Biopolymers, 14 (1975) 2137 and M. T. Record, Jr., C. F. Anderson and T. M. Lohman, Q. Rev. Biophys., 11 (1978) 103] from Wyman's linkage theory [J. Wyman, Adv. Protein Chem., 19 (1964) 223] using Manning's condensation model [J. Manning, J. Chem. Phys., 51 (1969) 924] was extended to electrostatic interaction chromatography. Mixed, electrostatic and hydrophobic interactions of a model protein, ovalbumin were characterized by ion and water release.

Chromatography↗
PubMed2003

Linear chains and chain-like fractals from electrostatic heteroaggregation.

The internal structure of materials prepared by aggregation of oppositely charged polystyrene spheres (electrostatic heteroaggregation) is investigated by static light scattering, optical microscopy, and Brownian dynamics simulation. Light scattering indicates ultralow mass fractal dimensions, as low as 1.2. Such low fractal dimensions, approaching the theoretical limit of a linear object, imply a chaining mechanism. Optical micrographs reveal linear chains with the particle charge alternating down the chains. Brownian dynamics simulation gives additional support for a chaining mechanism. For the polystyrene system (120-nm primary particle diameters), the fractal dimension is found to increase from 1.2 to 1.7 as the background electrolyte is increased. In terms of electrostatic screening, the results match those reported recently for larger polystyrene spheres. The low fractal dimensions appear to represent a crossover from linear chains to a structure of diffusion-limited aggregates; however, experiments under density-neutral conditions imply that sedimentation plays an important role in the formation of ultralow fractal dimensions. The practical implication is that microcomposites with a locally uniform distribution of starting materials and almost any degree of branching can be prepared from oppositely charged particles.

Journal Article↗
PubMed2003

DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution.

The thermal properties of two forms of the Drosophila melanogaster HMG-D protein, with and without its highly basic 26 residue C-terminal tail (D100 and D74) and the thermodynamics of their non-sequence-specific interaction with linear DNA duplexes were studied using scanning and titration microcalorimetry, spectropolarimetry, fluorescence anisotropy and FRET techniques at different temperatures and salt concentrations. It was shown that the C-terminal tail of D100 is unfolded at all temperatures, whilst the state of the globular part depends on temperature in a rather complex way, being completely folded only at temperatures close to 0 degrees C and unfolding with significant heat absorption at temperatures below those of the gross denaturational changes. The association constant and thus Gibbs energy of binding for D100 is much greater than for D74 but the enthalpies of their association are similar and are large and positive, i.e. DNA binding is a completely entropy-driven process. The positive entropy of association is due to release of counterions and dehydration upon forming the protein/DNA complex. Ionic strength variation showed that electrostatic interactions play an important but not exclusive role in the DNA binding of the globular part of this non-sequence-specific protein, whilst binding of the positively charged C-terminal tail of D100 is almost completely electrostatic in origin. This interaction with the negative charges of the DNA phosphate groups significantly enhances the DNA bending. An important feature of the non-sequence-specific association of these HMG boxes with DNA is that the binding enthalpy is significantly more positive than for the sequence-specific association of the HMG box from Sox-5, despite the fact that these proteins bend the DNA duplex to a similar extent. This difference shows that the enthalpy of dehydration of apolar groups at the HMG-D/DNA interface is not fully compensated by the energy of van der Waals interactions between these groups, i.e. the packing density at the interface must be lower than for the sequence-specific Sox-5 HMG box.

Amino Acid Sequence↗
PubMed1990

Electrostatic potential maps at the quantum chemistry level of the active sites of the serine peptidases, alpha-chymotrypsin and subtilisin.

The electronic properties of the active-sites of the structurally unrelated serine peptidases, alpha-chymotrypsin and subtilisin, have been expressed in the form of three-dimensional electrostatic potential maps derived from integrals calculated at the quantum chemistry level. As a consequence of the asymmetrical distribution of the secondary structures that occur within a 7 A sphere around the serine of the catalytic triad, the active sites are highly polarized entities and exhibit large dipole moments. One part of the active sites generates a nucleophilic suction-pump. Its isocontour at -10 kcal mol-1 defines an impressive, negatively-charged volume which bears a narrow channel in the immediate vicinity of the active-site serine 195 in alpha-chymotrypsin or 221 in subtilisin. In native alpha-chymotrypsin, there is a perfect complementation between this nucleophilic suction-pump and the positively-charged electrophilic hole that is generated by the backbone NH of Ser 195 and Gly 193. In subtilisin, generation of the complementing electrophilic hole requires binding of a carbonyl donor ligand and may be achieved by rotation of the side-chain amide of Asn 155 towards the backbone NH of Ser 221. Small variations in the atomic co-ordinates of alpha-chymotrypsin used for the calculations, the presence of water molecules in its active site and the occurrence of point mutations in the amino acid sequence of subtilisin have little effects on the shape and characteristics of the electrostatic potential.

Binding Sites↗
PubMed1985

Electrostatic effect of trypsin binding on the hydrogen exchange rate of bovine pancreatic trypsin inhibitor beta-sheet NH's.

The changes of H-D exchange rates upon protein-protein interactions are generally interpreted as a result of the changes of the dynamic properties of the proteins. The effect of trypsin binding on the H-D exchange kinetics of some trypsin inhibitor amide H's was reported (Simon et al., 1984). In this paper the electrostatic potential originating from the trypsin molecule is calculated at the positions of the studied amide H's in the trypsin-trypsin inhibitor complex. We conclude that the observed decrease of the exchange rates is mainly due to the electrostatic field of the trypsin molecule.

Amino Acid Sequence↗
PubMed1986

Continuum dielectric modelling of the protein-solvent system, and calculation of the long-range electrostatic field of the enzyme phosphoglycerate mutase.

The numerical continuum electrostatic method presented previously (Warwicker, J. & Watson, H. C. (1982) J. Mol. Biol., 157, 671-679), is developed with an improved analysis of the protein-solvent system. Inclusion in the model of saturable solvent dielectric, and counterions is discussed and presented. A number of long-range electrostatic field calculations are made on bovine pancreatic trypsin inhibitor to demonstrate the differences between various solvent and counterion models. The long-range potential field, due to polar side-chain and alpha-helix dipole charge, is calculated for the glycolytic enzyme phosphoglycerate mutase. The positive potential in and around the catalytic cleft region is sufficiently large to suggest that it may play a role in long-range attraction of the enzyme's negatively charged substrates. Analogous systems with charge-charge interactions in solvent water are considered. It is suggested that a long-range enzyme-substrate attractive force-field may, in part, offset the repulsive energy arising from overlap of hydration shells between enzyme and substrate.

Aprotinin↗
PubMed1987

Electrostatic repulsion of ion penetrable charged membranes: role of Donnan potential.

A model is proposed for the electrostatic repulsion between two ion-penetrable charged membranes in which fixed charges are uniformly distributed. This model assumes that the electric potential far inside the membrane is always equal to the Donnan potential, independent of the membrane separation. In this respect the present model completely differs from usual models for the electrostatic interaction of colloidal particles which assume that the surface potential or the surface charge density remains constant during interaction. It is shown that the rise in potential in the interacting membranes caused by their approach is greatly suppressed so that the potential in the membrane does not exceed the Donnan potential. Numerical results of the calculation of the repulsion by the non-linear Poisson-Boltzmann equation are displayed as a function of the membrane separation and an approximate formula is also derived.

Chemical Phenomena↗
PubMed1989

The effect of cationic electrolytes on the electrostatic behavior of cellular surfaces with ionizable groups.

Based on the assumption that the electrostatic charges on the surface of sheep leukocytes arise from the dissociation of ionogenic groups, together with the presence of divalent cation (or trivalent cation) in the suspending medium of low ionic strength (or high ionic strength), the non-linear Poisson-Boltzmann equation for cell interaction with a solid surface with constant potential (or constant charge) is numerically solved in this paper. The cellular surface potential and the repulsive (or attractive) force is expressed as the function of separation distance. Because of shrinking the thickness of the electrostatic double layer at high ionic strength, the presence of cationic electrolyte has a less influential role on both the cellular surface potential and interaction force than at low ionic strength. However, due to the continuous equilibration of the ionogenic groups on the cellular surface as separation distance decreases, the presence of cationic electrolyte will not always reduce the interaction force during the whole adhesion period. The distance at which the cationic electrolyte changes its effect from positive to negative is termed the critical separation distance in this paper.

Animals↗
PubMed1989

An electrostatic model for the interaction between growth hormone and its receptor involving chelation of Ca2+ to the human growth hormone molecule.

We previously postulated the local involvement of cations in the complex between human growth hormone and its receptors in the liver. The original electrostatic model involved convergence of unit negative charges on the hormone and receptor, towards an interposed Ca2+ ion. That model was consistent with (a) the Ca2+ dependence of human growth hormone binding, (b) the magnitude of the Ca2+ mediated increase in the affinity of human growth hormone binding, and (c) could also explain the relative affinities of human and non-primate growth hormones for growth hormone receptors. In the present report, the original electrostatic model is revised with the postulate that Ca2+ is chelated to the human growth hormone molecule. The consequences of this postulate are explored mathematically with the result that it becomes necessary to propose an additional unique hindrance determinant (positive residues in helices one and four are good candidates) to account for the lower affinity of non-primate growth hormones relative to human growth hormone. Predictions are made regarding the effect of a particular point mutation (at position 34) on the affinity of hormone binding.

Animals↗
PubMed2002

Ultrasonic measurement of gas flow using electrostatic transducers.

Ultrasonic gas flowmeters typically use narrowband piezoelectric transducer arrangements for interrogating the flow of gas in a pipe. In this work, the suitability of broadband electrostatic transducers operating at frequencies of up to 1 MHz for ultrasonic measurement of gas flow has been investigated. The transit time method of ultrasonic gas flow measurement was adopted and experiments were carried out using a laboratory test rig capable of producing a range of gas flowrates up to 17.5 m/s. The test rig also allowed easy interchange of different prototype flowmetering sections. Times of flight of ultrasonic waves interrogating the gas flow were measured using separate send/receive electrostatic transducer arrangements. Two flowmeter configurations were considered. The first interrogated the flow at 45 degrees in contra-propagating upstream and downstream directions. The second consisted of an up-stream interrogation at 45 degrees to the gas flow and an interrogation made normal to the flow direction. k factors correlating the fluid velocity along the ultrasonic path with the mean fluid velocity in the pipe were calculated using experimental ultrasonic data and anemometer measurements. All transducer configurations were numerically modelled using the computational fluid dynamics software package FLOTRAN (ANSYS Inc.). Theoretical gas flow velocities for both transducer arrangements were subsequently compared with experimental values and found to be in excellent agreement. A flow-dependent frequency shift of the received ultrasonic signals was also observed simultaneously with the transit time measurement.

Journal Article↗
PubMed2001

Reduction of fine airborne particulates (PM3) in a small city centre office, by altering electrostatic forces.

A two stage intervention study was carried out to establish the degree to which a newly developed, electrostatic air cleaning (EAC) system can improve indoor air quality (IAQ) by reducing the number of airborne fine particles. The IAQ and how employees in a city centre office (49 m2) perceived it, was monitored from May until November 1998. The number of fine particles, PM3 (0.3-3.0 microm); number of coarse particles, PM7 (3.0-7.0 microm); number of small positive and negative air ions; relative humidity and temperature were recorded in and out of doors. To assess the employees' perception of any changes in their work environment, a questionnaire was completed. Number of particles, relative humidity and temperature were also recorded in a nearby office, equipped with an identical air processor, where no interventions were made. The results from the first intervention (Stage 1), comparing number of airborne particles outdoors to indoors, gave a 19% reduction for PM3 and a 67% reduction for PM7 (P < 0.001). The reduction in PM3 was inconsistent and not statistically significant (P = 0.3). The reduction in PM7 from outdoors and the removal of PM7 created indoors was achieved by optimizing the existing air moving equipment. The results from the second intervention (Stage 2--with EAC units installed) comparing indoor to outdoor values, gave a further reduction in PM3 of 21% (P < 0.001) and a further 3% reduction for PM7 (P > 0.05). Therefore, at the end of Stage 2, the total reductions in particles from outdoors to indoors were 40% for PM3 and 70% for PM7 (P < 0.001). The Stage 2 results strongly suggest that electrostatic forces, created by the EAC unit(s) improved the removal of PM3, with no further significant improvement in the reduction of PM7. The questionnaire indicated an improvement in the IAQ, as perceived by the employees. The results suggest that the EAC system is effective in reducing PM3 and thereby improving IAQ in an urban office.

Air Movements↗
PubMed1997

The role of the electrostatic coat in the formation of cholesteric liquid crystal spherulites from alpha-chitin.

The alpha-chitin used in the experiments came from crab shell waste. This was boiled in 3M HC1 to form a colloidal suspension of chitin crystallites. The electrostatic 'cost' surrounding the chitin was then manipulated in two ways. The first was the alteration of the pH of the chitin colloid (Chitin pKa = 6.1). This allowed the charge density on the crystalline rod of chitin to be altered. The second way was to alter the background charge in the environment by adding salt solutions to the colloid. The effect of the treatments was ascertained by measuring the diameter of the spherulites formed in vitro. These spherulites formed via self assembly through a liquid crystalline cholesteric phase. Raising the pH (within limits), resulted in larger spherulites. Raising the background charge also gave larger spherulites (within limits). As such both background charge and charge on the rod can be used to control the self assembly of the cholesteric spherulites. Manipulation of the electrostatic coat of the chitin could be a method of cellular remote control for formation of the helicoid in arthropod cuticle. This would allow the arthropods to set up conditions that aid the self assembly process.

Animals↗
PubMed2003

Electrostatic charge activates inflammatory vanilloid (VR1) receptors.

The pathophysiology of neurogenic inflammation culminates in the overt symptoms of tissue inflammation through a series of events which are initiated by the activation of vanilloid receptors (VR1). This study was designed to test the hypothesis that a sufficiently negative, electrostatic charge carried on a particulate matter (PM) particle, could acquire a cloud of protons sufficient to activate proton-sensitive VR1 receptors and acid-sensitive ionic channels (ASICs) pathways. For this, nanometer-sized, synthetic polystyrene micells (SPM) or those charged with chemical groups (e.g. diamino, carboxyl) were used. These chemical groups imparted either a net positive (i.e. diamino) or negative (i.e. carboxyl) charge on the SPM when suspended in a neutral ionic medium. The zeta potential, a measure of the SPM's electronegativity, was taken in both cell culture nutrient medium and in ultraviolet light-distilled water (UV-DW). In both vehicles, the rank order of electronegativity (most to least negative) was carboxyl > polystyrene > diamino-SPM. Individual types of SPM were exposed to human, immortalized bronchial-tracheal epithelial cells (i.e. BEAS-2B) and endpoints of biological activation (i.e. membrane depolarization, increases in intracellular calcium (i.e. [Ca(2+)](i)) levels, IL-6 release) were measured. Cells loaded with a fluorescent probe for membrane depolarization (3,3'-dihexyloxacarbocyanine iodide, DiOC-6-3) showed a positive reaction when exposed to carboxyl-SPM but not to diamino-SPM. BEAS-2B cells exposed to carboxyl-SPM responded with significant increases in [Ca(2+)](i), and IL-6 release relative to uncharged SPM or diamino-SPM. This IL-6 release could be reduced by pretreatment with antagonists to the VR1 receptor (i.e. capsazepine) or to acid-sensitive ionc channels (i.e. amiloride). Although both diamino and carboxyl-SPM groups stimulated increases in IL-6 transcript, only the more electronegatively charged carboxyl-SPM stimulated mRNA-VR1 receptor. These data suggest that measurable inflammatory changes can be stimulated in human epithelial target cells by the electrostatic charge carried on an inert particle. Further, these changes appear to be mediated through acid-sensitive VR1 receptors and ASICs.

Calcium↗
PubMed2000

Investigations on human immunodeficiency virus type 1 integrase/DNA binding interactions via molecular dynamics and electrostatics calculations.

The complete three-dimensional structure of the active site region of the human immunodeficiency virus type 1 (HIV-1) integrase (IN) is not unambiguously known. This region includes a flexible loop comprising residues 141-148 and the N-terminal portion of the helix alpha-4, which contains E152, the third catalytic residue, and Y143, which plays a secondary role in catalysis. Relatively high B-factors exist for most of the residues in the aforementioned region. The HIV-1 IN belongs to the polynucleotidyl transferase superfamily, whose members have been proposed to use two divalent metal ions for catalysis. Although only the position of the first metal ion has been determined crystallographically for the HIV-1 IN, we recently have proposed a binding site for the second metal ion. Based on this information, we have performed two 500-psec molecular dynamics simulations of the catalytic domain of the HIV-1 IN containing two Mg(2)+ ions. In one of the simulations, we included a dianionic phosphate group (HPO(4)(2)-) in the active site to mimic a portion of the DNA backbone of a substrate for the integration reaction. Electrostatics calculations and ionization state predictions were carried out on representative structures taken from the molecular dynamics simulations. Different conformational behaviors of the enzyme were observed, depending upon whether two Mg(2)+ ions were bound or two Mg(2)+ ions plus phosphate. The electrostatic calculations performed on the dynamical structures provide a further refinement about which regions of the catalytic domain of the HIV-1 IN may be involved in the DNA binding.

Avian Sarcoma Viruses↗
PubMed2001

Antibody masking renders HIV-1 resistant to cationic membrane filtration through alteration of its electrostatic characteristics.

Previously, it was demonstrated that any human immunodeficiency virus type 1 (HIV-1) strain proliferating in peripheral blood mononuclear cells (PBMCs) in vitro, and resuspended in seronegative plasma, could be captured efficiently (mean > 95%) by a porous polypropylene (PP) membrane modified cationically. We investigated if this cationic membrane could capture HIV-1 obtained from seropositive plasma, and confirmed whether this membrane was effective for the preparation of safe plasma products against HIV-1 transmission. Thirty-six seropositive plasma samples derived from HIV-1 positive cohorts in New York and Lusaka (Republic of Zambia), including 18 cases of acquired immunodeficiency syndrome (AIDS) related complex, AIDS and five terminal cases of AIDS, were filtered through the cationic membrane to determine the reduction of RNA concentration, the gag p24 concentration, and infectious titer. Only a small reduction in RNA concentration (mean < 20%) and almost no decrease in gag concentration (mean < 2%) were obtained, despite the fact that the infectivity was eliminated entirely by the filtration. Due to the possibility that anti-HIV-1 antibodies in patients' plasma combine with HIV-1, laboratory-adapted HIV-1(HTLV-IIIB) was mixed with seropositive plasma to test the effect of antibodies on HIV-1 adsorption, and also to investigate the interfacial electrokinetic potential (zeta-potential) of both intact and plasma-treated HIV-1. The zeta-potential of HIV-1(HTLV-IIIB) in the presence of seropositive plasma was neutral as opposed to negative when stored in seronegative plasma or culture medium. Also the rate of HIV-1 capture by the membrane, as determined by the reduction in RNA concentration, sank from 95% to 20%, the same capture percentage observed when filtering plasma of patients. These findings suggested that in patients' plasma, the antibody-masked HIV-1 comprise most of the viral population, and was not trapped on the cationic membrane because of its electrostatic character. Conversely, the cationic membrane was thought to adsorb antibody-free HIV-1 exclusively. It was suggested that each viral swarm had its own zeta-potential, and this difference in electrostatic character determined the extent of the viral adsorption by the cationic membrane.

Cations↗