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Electrostatic sensor for identifying interactions between peptides and bacterial membranes.

The use of the membrane probe fluorescein phosphatidylethanolamine (FPE) to investigate membrane binding is well established. However, until now, its use has been restricted to studies involving peptides and eukaryotic membranes. This useful tool has been developed to interrogate peptide:prokaryotic membrane interactions by introducing novel methodology to incorporate FPE into the membranes of UV killed, whole bacterial cells. The electrostatic potential of the membrane in the immediate vicinity of the probe affects the protonation state of the xanthene ring system in the fluorescein head group, which is held close to the membrane surface. When altered, e.g. by peptide binding and insertion, a change in fluorescence results, which can be measured spectrophotometrically. Applicability of this technique to bacterial surface interactions was confirmed by production of a binding curve for both a synthetic peptide and a 37kDa protein. Future investigations are anticipated to utilize this technology to characterize interactions of other toxins plus antimicrobial peptides such as lactoferricin and defensins with their target membranes.

Bacteria↗

Electrostatic interaction between NADH-cytochrome b5 reductase and cytochrome b5 studied by site-directed mutagenesis.

Electrostatic interaction between NADH-cytochrome b5 reductase and cytochrome b5 was studied by site-directed mutagenesis. The target residues for mutagenesis were selected on the basis of the previously reported chemical cross-linking study of these two proteins, which implicated possible charge-pair interactions between Lys-41, Lys-125, Lys-162, and Lys-163 of the enzyme, and Glu-47, Glu-48, Glu-52, Glu-60, Asp-64 (group A), and heme propionate of cytochrome b5. Mutant reductases that lost one of the above-listed Lys residues showed higher K(m) values for cytochrome b5 and lower kcat values than those of the wild type, suggesting that all of the examined Lys residues participate in binding with cytochrome b5 as reported previously. In contrast, a removal of one of (or even all of) the group A residues from cytochrome b5 by mutagenesis caused no significant effect on the catalytic properties of cytochrome b5. Additional elimination of another set of negative residues (Glu-41, Glu-42, Asp-57, and Glu-63 (Group B)), which are also located close to heme, elevated the K(m) value by more than five folds. These results suggest that there should be other acidic residue(s) than group A in cytochrome b5 which participate in binding with NADH-cytochrome b5 reductase.

Binding Sites↗

To fuse or not to fuse: the effects of electrostatic interactions, hydrophobic forces, and structural amphiphilicity on protein-mediated membrane destabilization.

The development of lipid-based delivery vehicles for therapeutic molecules has become a topic of intense research. Recently, much of this effort has been directed towards mimicking the characteristics of viruses that give them an advantage for the delivery of genetic medicines. One of the most desirable properties of viral-based vectors is the ability to promote the destabilization of the host cell membrane to allow the entry of the genetic medicine into the target cell. This has been found to be largely controlled by the coat proteins on the surface of enveloped viruses. Although the exact mechanism by which proteins involved in the fusion process are able to promote the destabilization of membranes has yet to be elucidated, much understanding based upon information gained from a wide variety of studies is advancing the state of knowledge in this area. Parameters such as hydrophobic and electrostatic interactions as well as structural amphiphilicity, control to a large extent, the nature of the interaction of proteins with membranes. Thus, membrane fusion is mediated primarily by these forces acting in concert with one another. Ultimately, the knowledge gained from these studies will help to develop the ideal delivery system for the next generation of therapeutics.

Journal Article↗

A Pro --> Ala substitution in melittin affects self-association, membrane binding and pore-formation kinetics due to changes in structural and electrostatic properties

Melittin, the main component of bee venom of Apis mellifera, contains a proline at position 14, which is highly conserved in related peptides of various bee venoms. To investigate the structural and functional role of Pro14 a melittin analogue was studied where proline is substituted by an alanine residue (P14A). The investigations were focussed on: (i) the secondary structure in aqueous solution and membranes; (ii) the self-association in solution; (iii) the binding to POPC membranes; and (iv) the P14A-induced leakage and pore formation in membrane vesicles. Circular dichroism and gel filtration experiments showed that P14A exists at concentrations < 12 microM in monomeric form with an alpha-helicity of 28 +/- 7%. A further increase in peptide concentration leads to the formation of large aggregates consisting of 9 +/- 1 monomers. While binding studies with POPC vesicles revealed for P14A a stronger binding affinity towards membranes than for melittin, the peptide-induced leakage of fluorescent markers from vesicles was less efficient for P14A than for melittin. Furthermore, an unexpected efflux behaviour at high values of bound P14A was observed which indicated that the pore formation kinetics for P14A is more complex than it was reported for melittin. The different features of P14A in aggregation, binding and efflux compared to melittin are mainly ascribable directly to structural changes caused by the proline --> alanine substitution. Furthermore, the results indicate an improved screening of the positively charged residues of P14A by counterions which contributes additionally to the observed differences in peptide activities. It is suggested that the presence of proline in melittin is not only of structural importance but also influences indirectly the electrostatic properties of the native peptide.

Journal Article↗

Modeling of electrostatic recognition processes in the mammalian mitochondrial steroid hydroxylase system.

Adrenodoxin reductase (AR) and adrenodoxin (Adx) are components of the mammalian mitochondrial steroid-hydroxylating system. Crystal structures of Adx, AR and a cross-linked Adx-AR complex have recently been determined. Based on these, we have carried out a modeling and docking study to characterize the recognition between AR, Adx and cytochrome c (Cytc). To rationalize the recognition process, electrostatic potentials were calculated by solving the Poisson-Boltzmann equations. In the Adx-AR complex modeled, a negatively charged surface of Adx recognizes a positive surface of AR, as in the crystal structure of the Adx-AR complex, proving the correct parameterization for the energy calculations. After forming salt bridges between the polar primary binding sites of Adx and AR, charge compensation causes a domain movement in AR, which closes the binding cleft by 2-4 A. Thereby, a secondary polar binding site is closed and the electron transfer pathways between the FAD of AR and the [2Fe-2S] cluster of Adx are adjusted. Next, the model structure of a complex between Adx and Cytc was derived. The lowest-energy complex between Adx and Cytc matches earlier chemical modification and cross-linking experiments, which proposed polar interactions of Lys13, Lys27, Lys72 and Lys79 of Cytc with acidic residues in Adx. Because of the short distance of 9.4 A between the redox centers, a complex, productive in electron transfer via a different outlet pathway from the inlet route in Adx, is expected. However, a ternary complex cannot be formed between the Adx-AR complex and Cytc because of steric hindrance. Therefore, a shuttle model for the role of Adx in the electron transfer process to Cytc is preferable to a relay model. In addition, no preferable docking site could be detected for a second Adx when probing the Adx-AR complex, which is required for a quaternary organized-cluster model of all redox partners of the hydroxylase system.

Adrenodoxin↗

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study.

Ewald and related methods are nowadays routinely used in explicit-solvent simulations of biomolecules, although they impose an artificial periodicity in systems which are inherently non-periodic. The consequences of this approximation should be assessed, since they may crucially affect the reliability of computer simulations under Ewald boundary conditions. In the present study we use a method based on continuum electrostatics to investigate the nature and magnitude of possible periodicity-induced artifacts on the potentials of mean force for conformational equilibria in biomolecules. Three model systems and pathways are considered: polyalanine oligopeptides (unfolding), a DNA tetranucleotide (separation of the strands), and the protein Sac7d (conformations from a molecular dynamics simulation). Artificial periodicity may significantly affect these conformational equilibria, in each case stabilizing the most compact conformation of the biomolecule. Three factors enhance periodicity-induced artifacts: (i) a solvent of low dielectric permittivity; (ii) a solute size which is non-negligible compared to the size of the unit cell; and (iii) a non-neutral solute. Neither the neutrality of the solute nor the absence of charge pairs at distances exceeding half the edge of the unit cell do guarantee the absence of artifacts.

Algorithms↗

Protein stability; optimization of electrostatic contributions by partially neutralizing surface ionic charges.

'Partial Charge-Neutralization Method' is developed to study influence of the relative amount of positive and negative charges in proteins on their structural stability. A given number of either positively or negatively charged groups are neutralized in all of their possible combinations to generate a whole set of distinct species. The Coulomb energy of each species is calculated by numerically solving the Poisson-Boltzmann equation for aqueous solutions. Partial neutralization of lysine residues of tuna cytochrome c in aqueous solution at neutral pH with the Debye-Hückel screening parameter kappa = 1 nm-1 reproduces qualitatively well the destabilization of acetylated cytochrome c observed in physicochemical measurements at pH 7. The stabilization of its molten globule state at pH 2 is also studied with the present method. It is shown that the electrostatic contribution to the structural stability of natural proteins can be optimized by changing the difference in number of their positive and negative charges.

Cytochrome c Group↗

Molecular electrostatic potentials: a new approach to the study of the metabolic and carcinogenic activities of hydrocarbons.

The electrostatic potentials of a group of aromatic hydrocarbons have been determined and have revealed that each molecule possesses several regions of negative potential, which would attract an approaching electrophile. These regions include all those portions of the molecules at which major amounts of metabolic products are found. While the K-regions of the hydrocarbons studied are invariably quite negative, the magnitudes of their potentials do not correlate with the molecules' carcinogenic potencies. The presence of other strong negative regions in addition to the K-region, especially in the more active molecules, suggests that some of these others may participate in the carcinogenic process. tof particular interest is the possibility that the significant negative potentials that have been found to be associated with many CH3 and CH2 groups may play such a role, Perhaps two or more negative regions are involved in hydrocarbon carcinogenesis.

9,10-Dimethyl-1,2-benzanthracene↗

Human acetylcholinesterase binds to mouse laminin-1 and human collagen IV by an electrostatic mechanism at the peripheral anionic site.

Acetylcholinesterase (EC 3.1.1.7; AChE) is known to induce neurite outgrowth and differentiation, but its ligands are as yet unknown. Laminin-1 and collagen IV were investigated as potential ligands for AChE. We observed specific saturable binding of biotinylated human AChE to mouse laminin and human collagen, with K(d) values of 4.9482 nM (SE 0.3145 nM) and 1.1617 nM (SE 0.1921 nM) respectively. Peripheral anionic site inhibitors (fasciculin, BW284c51, propidium and gallamine) also significantly reduced binding with fasciculin being the most effective. Significant reductions in AChE-laminin and AChE-collagen interactions were produced by a monoclonal anti-AChE antibody known to react with the peripheral anionic site, and a partial reduction with an antibody that partially recognises the site. Self-association of AChE was also observed (K(d)=16.3235 nM; SE 5.8120 nM); increasing markedly at low pH, but not significantly affected by either inhibitors or antibodies, suggesting a non-specific aggregation phenomenon. Binding to laminin and collagen was significantly reduced by increasing ionic strength and decreasing pH, indicating a dominant role for electrostatic interactions, and suggesting that the site may be different from the hydrophobic site identified for the AChE-amyloid interaction.

Acetylcholinesterase↗

Two-dimensional, electrostatic finite element study of tip-substrate interactions in electric force microscopy of high density interconnect structures.

Two-dimensional electrostatic finite element modeling is used to estimate the variation of tip force as a function of potential, dielectric film thickness, and tip-substrate spacing when imaging using electric force microscopy. Blanket dielectric films and approximately 1000 nm thick interconnect structures were studied. We conclude that sidewall damage regions can be detected but will require special processing to make an unambiguous measurement.

Journal Article↗

Accuracy of electrostatic lens computations with FOFEM.

The increased speed of personal computers enables fast computation of rotationally symmetric electrostatic lenses with the first-order finite element method in meshes with a large number of mesh points. In order to produce an estimate of accuracy of the computed potential, we propose a simple procedure based on doubling the number of mesh points in each coordinate. In this way, we can produce for the lower-density mesh at each point the information about error of the potential and visualize the sources of the computation errors.

Journal Article↗

Initial resolution measurements of miniaturized electrostatic lenses for LVSEM.

Theoretical and experimental investigations on miniaturized electrostatic lenses for high-resolution low-voltage scanning electron microscopical applications are presented. The electron optical column consists of a Schottky emitter including the extraction anode and a miniaturized three electrode lens consisting of conventional (electron microscopical) platinum apertures. The lens has been optimized with respect to resolution and a value of about 5 nm at a working distance of 1 mm and a beam energy of 1 keV is predicted by simulation. Details on the resolution measurements are presented. An initial experimental value amounts to 31 nm. Specific problems encountered during building and alignment of the lens and measuring the resolution are discussed as well.

Journal Article↗

On a class of integrals of Legendre polynomials with complicated arguments--with applications in electrostatics and biomolecular modeling.

The exact analytical result for a class of integrals involving (associated) Legendre polynomials of complicated argument is presented. The method employed can in principle be generalized to integrals involving other special functions. This class of integrals also proves useful in the electrostatic problems in which dielectric spheres are involved, which is of importance in modeling the dynamics of biological macromolecules. In fact, with this solution, a more robust foundation is laid for the Generalized Born method in modeling the dynamics of biomolecules.

Computer Simulation↗

Quantifying electrostatic interactions in pharmaceutical solid systems.

Triboelectrification of pharmaceutical powders with stainless steel and polymer contact surfaces was investigated. alpha-Lactose monohydrate, from 90 to 125 up to 355-500 microm, was used to quantify electrostatic interactions with negligible powder adhesion to the contact surface. Size fractions down to 53-75 microm alone and in binary mixtures with <10 microm lactose or micronized salbutamol were used to investigate triboelectrification with powder adhered to the contact surface. Triboelectrification was performed in a cyclone charger fitted with interchangeable contact surfaces of steel and polymers, representing the surfaces of pharmaceutical processing and manufacturing equipment, packaging materials and components of dry powder inhaler devices. The results for single component powders showed charge acquisition was inversely related to particle size, where contact surface contamination was negligible. However, with particulate contamination, triboelectrification was more complex due to particle collisions with clean and contaminated contact surfaces. Analysis of adhered and non-adhered powder provided information about changes in composition of two component powders during triboelectrification. Particle size and chemical analyses showed that composition changes of mixtures may be related to powder/contact surface affinity and interparticulate forces for separation of components in a cohesive mix during triboelectrification.

Chemistry, Pharmaceutical↗

Interactions between a pore-blocking peptide and the voltage sensor of the sodium channel: an electrostatic approach to channel geometry.

Few experimental data illuminate the relationship between the molecular structures that mediate ion conduction through voltage-dependent ion channels and the structures responsible for sensing transmembrane voltage and controlling gating. To fill this void, we have used a strongly cationic, mutated mu-conotoxin peptide, which only partially blocks current through voltage-dependent sodium channels, to study voltage-dependent activation gating in both bound and unbound channels. When the peptide binds to the ion-conducting pore, it inhibit channel opening, necessitating stronger depolarization for channel activation. We show that this activation shift could result entirely from electrostatic inhibition of the movement of the voltage-sensing S4 charges and estimate the approximate physical distance through which the S4 charges move.

Animals↗

Macromolecular electrostatics: continuum models and their growing pains.

Theoretical understanding of macromolecular electrostatics has advanced substantially over the past year. Continuum models have given promising results for calculating protein-ligand binding free energy differences, as well as pK(a)s and redox properties, particularly with explicit treatment of multiple conformers. Generalized Born and other techniques have led to the first molecular dynamics simulations of proteins and RNA with continuum solvent. Continuum and microscopic descriptions of dielectric relaxation have been critically compared.

Acid-Base Equilibrium↗

Electrostatic interactions of androgens and progesterone derivatives with rainbow trout estrogen receptor.

In primary cultures of immature male rainbow trout (rt) hepatocytes, vitellogenin (Vg) gene expression is regulated by E(2) via the estrogen receptor (ER). However, steroids other than estrogens can also stimulate Vg gene expression. These steroids are hardly converted into E(2) during incubation and their stimulatory activity is completely inhibited by tamoxifen implying rtER involvement. These steroids have no or a slightly positive charge on the Connolly surface. In contrast, steroids that failed to stimulate Vg gene expression had a strong positive or negative charge around rings C and D due to polarization. The amino acid sequences of the ligand binding domains (LBD) of rtER and human ER alpha have 57.7% homology; only one amino acid differs in the presumed steroid binding site. We modeled the three-dimensional structure of the LBD of rtER using X-ray crystallographic data for hER alpha in order to investigate the fit (structural and electrostatic) between steroid and rtER. Two factors are essential for binding to rtER: (i) hydroxyl or carbonyl groups near C3 and C17 of the steroids (hydrophilic regions) that can form hydrogen bonds with His(489), Arg(359), and Glu(318), (ii) a hydrophobic steroid nucleus that interacts with a hydrophobic region of the rtER LBD through van der Waals forces. If polar functional groups are present, the hydrophobic interaction between steroid and the rtER LBD is considerably weakened.

Amino Acid Sequence↗

Electrostatic potential surfaces of 5-HT(3)R agonists suggest accessory cation-pi site adjacent to agonist binding domain.

Electrostatic potential surface mapping of various aromatic ring systems contained in 5-HT(3)R agonists indicate that some agonists contain an aromatic moiety capable of a favorable cation-pi interaction next to the e-face of pyridine (or its bioisostere). A pharmacophore model has been proposed based on superimposition of two distinct 'aryl' interactions.

Binding Sites↗