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At least 703 records · Page 39Linked to original sources
PubMed1995

Electrostatic potential in aminoacylation by aspartyl-tRNAs synthetase.

Based upon the X-ray structures of complexes between tRNAAsp and aspRS including ATP or Asp-AMP, several electrostatic potentials were calculated by solving the Poisson-Boltzmann equation. The potentials indicate clearly that a Mg2+ ion is essential for binding of ATP and that aspartate is identified electrostatically. The alpha-carboxyl group is forced to contact with the alpha-phosphorus atom of ATP, suggesting its inversion to form an Asp-AMP. When the cognate tRNA is bound to the aspRS:Asp-AMP complex, the 3'-hydroxyl group is located in an electrostatically favorable position to transfer the amino acid as a class II aminoacylation.

Acylation↗
PubMed1997

An electrostatic backpack sprayer: potential for mosquito control.

A Southwest Electrostatic Sprayers, Inc., nozzle was configured to a Hudson PortaPak backpack. A test was run to compare deposition of BVA no. 13 oil by the electrostatic nozzle to a standard nonelectrostatic nozzle as collected by Teflon slides. Results indicate that 100% greater deposition occurred with the electrostatic nozzle.

Mosquito Control↗
PubMedDate not supplied

[Applicability of molecular electrostatic interaction models to describing ionic strength dependence of reaction rate between myoglobin and cytochrome c].

The nonlinear regression method was used for the evaluation of applicability of the known model equations (Wherland-Gray, Brönsted-Debay-Hukkel and "parallel disks") which describe the ionic strength dependence of the reaction rate between charged molecules to the redox reaction of cytochrome c with sperm whale myoglobin modified at His 12(A10) with the bromoacetate spin label, and pig myoglobin. Unlike the native sperm whale Mb studied earlier [1], the objects chosen have monotonous pH-dependence of the reaction rate and are more simple with regards to electrostatic interactions in the electron-transfer complex. This allowed to study the influence of the total as well as the local protein charge on the correspondence of the ion strength dependencies to the theoretical models and optimal parameters of the equations. It was shown that the models considered, as in the case of the native sperm whale Mb-Cyt c reaction, permit satisfactory description of the experimental data, but the obtained parameters cannot be applied to the whole proteins or their contact sites. In the best case (Wherland-Gray equation) it is possible to do if the distribution of electrostatic potential in the contact area is considered. The reason can be that, unlike other protein redox-systems, the contact sites of both Mb and Cyt c have the charged residues of both signs, and the His GH1 residue located in the contact Mb site is not only involved in the electrostatic interactions in electron-transfer complex, but also participates directly in the mechanism of charge transfer.

Animals↗
PubMed1996

Identification and analysis of long-range electrostatic effects in proteins by computer modeling:aspartate transcarbamylase.

While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three-dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site-site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson-Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK1/2 values. Most of the residues with pK1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site-site interaction free energies on distance is complex, with a steep dependence at distances less than 5 A and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 A require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long-range structural effects and allosteric signals.

Aspartate Carbamoyltransferase↗
PubMed1996

The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?

We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Soc. 106:765-784, 1984; J. Comput. Chem. 7:230-252, 1986) vs. Cornell et al. (J. Am. Chem. Soc. 117:5179-5197, 1995)], different treatments of the long-range electrostatic interaction (8 A cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent-accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N-H backbone vectors. With the Cornell et al. force field and a periodic box model, the simulated structures stay much closer to the experimental X-ray structure than with the older Weiner et al. force field. A further improvement of the simulation is found when the electrostatic interaction is evaluated with the particle mesh Ewald method; after 1.2 ns of simulation the backbone RMSD amounts to only 1.13 A. The analysis of the dynamic parameters shows that this good structural agreement is not due to a damping of internal motion in the protein. For a given length of simulation time, the shell models achieve an agreement between simulated and experimental structures that is comparable to the best models that employ a periodic box of solvent models. However, compared with the box models, the fluctuations of the protein atoms in the shell models are smaller, and only with simulation times as long as 2 ns do they become of comparable size to the experimental ones.

Computer Simulation↗
PubMed1997

Role of electrostatics at the catalytic metal binding site in xylose isomerase action: Ca(2+)-inhibition and metal competence in the double mutant D254E/D256E.

The catalytic metal binding site of xylose isomerase from Arthrobacter B3728 was modified by protein engineering to diminish the inhibitory effect of Ca2+ and to study the competence of metals on catalysis. To exclude Ca2+ from Site 2 a double mutant D254E/D256E was designed with reduced space available for binding. In order to elucidate structural consequences of the mutation the binary complex of the mutant with Mg2+ as well as ternary complexes with bivalent metal ions and the open-chain inhibitor xylitol were crystallized for x-ray studies. We determined the crystal structures of the ternary complexes containing Mg2+, Mn2+, and Ca2+ at 2.2 to 2.5 A resolutions, and refined them to R factors of 16.3, 16.6, and 19.1, respectively. We found that all metals are liganded by both engineered glutamates as well as by atoms O1 and O2 of the inhibitor. The similarity of the coordination of Ca2+ to that of the cofactors as well as results with Be2+ weaken the assumption that geometry differences should account for the catalytic noncompetence of this ion. Kinetic results of the D254E/D256E mutant enzyme showed that the significant decrease in Ca2+ inhibition was accompanied by a similar reduction in the enzymatic activity. Qualitative argumentation, based on the protein electrostatic potential, indicates that the proximity of the negative side chains to the substrate significantly reduces the electrostatic stabilization of the transition state. Furthermore, due to the smaller size of the catalytic metal site, no water molecule, coordinating the metal, could be observed in ternary complexes of the double mutant. Consequently, the proton shuttle step in the overall mechanism should differ from that in the wild type. These effects can account for the observed decrease in catalytic efficiency of the D254E/D256E mutant enzyme.

Aldose-Ketose Isomerases↗
PubMed2000

Electrostatic steering of substrate to acetylcholinesterase: analysis of field fluctuations.

Based on previous molecular dynamics simulation results for acetylcholinesterase dimer, we calculate and analyse the electrostatic field fluctuations around the enzyme. The results show that dynamic features of the electrostatic field favor attraction of the positively-charged substrate. An Internet link to an animation of the results is also provided.

Acetylcholinesterase↗
PubMedDate not supplied

Membrane-perturbing activity of Viperidae myotoxins: an electrostatic surface potential approach to a puzzling problem.

Phospholipase-like myotoxins are a class of proteins present in Viperidae venom. Despite the high level of amino acid and structural homology with soluble phospholipases A(2), myotoxins are devoid of enzymatic activity and share cytolytic activity by means of a totally unknown mechanism involving the lipid bilayer perturbation. The distribution of electrostatic surface potentials of four myotoxins and seven phospholipases A(2) has been compared. The charge distribution is similar in all active non-cytolytic phospholipases with a strongly positive side corresponding to the domain interacting with the micellar substrate and with the opposite side negatively charged. In contrast, all myotoxins examined are positively charged on both sides. Myotoxin III, the only known example of a myotoxin sharing enzymatic activity, displays the same electrostatic surface potential as other related toxins. Using liposomes made with non-hydrolysable phospholipids, we demonstrate that myotoxin III perturbs the lipid bilayer like other myotoxins. Based on these results, a molecular model for myotoxin-membrane perturbing activity is proposed. In this model, potential double-face binding of myotoxic phospholipases A(2) to lipid surfaces could trigger a lipid bilayer destabilization and could generate a stable fusion pore, probably because of the presence of hydrophobic moieties that flank the cationic sites.

Cell Membrane Permeability↗
PubMedDate not supplied

Baculovirus vector requires electrostatic interactions including heparan sulfate for efficient gene transfer in mammalian cells.

BACKGROUND: Recently, several reports have described the ability of recombinant baculoviruses to transduce a variety of mammalian cells. Yet, mechanisms involved in baculovirus entry in those cells remain largely unexplored, particularly at the primary binding step of the virions to the cell membrane. METHODS: This report focused on the primary virus-cell interactions that lead to in vitro transduction of human 293 cells using a polyhedrin-deleted baculovirus harboring a CMV-driven beta-galactosidase gene (BacLacZ). RESULTS: Infection rate monitored for 8 h and transduction rate with a multiplicity of infection of up to 800 were, both, non-saturable. Temperatures from 37 degrees C to 4 degrees C dramatically impaired BacLacZ but not adenovirus cell attachment. Competitive infections performed with an excess of a non LacZ-expressing baculovirus hardly competed at a 1/1 ratio. Consistent with an adsorptive binding process onto the cell surface, interactions through electrostatic charges between both viral and cell membranes appeared to be critical for BacLacZ transduction. The addition of polybrene to the cells prior to or during the infection prevented both virus binding and LacZ gene transfer, suggesting the involvement of negatively charged epitopes exposed at the cell surface. The simultaneous presence of the highly charged heparin abrogated BacLacZ binding to the cell surface and subsequent gene transfer. Lastly, direct in vitro binding of BacLacZ to heparin but not BSA columns could be demonstrated after elution of infectious BacLacZ virus in high salt molarity. CONCLUSION: Electrostatic charges play a critical role during the first step in mammalian cell transduction mediated by a recombinant baculovirus.

Animals↗
PubMed2000

On the electrostatics of cell-membrane recognition: from natural antibiotics to rigid push-pull rods.

The question why pore-forming, alpha-helical natural antibiotics are not toxic is discussed within the general context of the interaction of electrostatically asymmetric "nanorods" with neutral, anionic, and polarized bilayer membranes. We suggest that simplification of the structural complexity of natural systems will be necessary to ultimately define the involved subtle balance between constructive and destructive electrostatic interactions.

Amino Acid Sequence↗
PubMed2001

Efficient electrostatic solvation model for protein-fragment docking.

A method is presented for the fast evaluation of the binding energy of a protein-small molecule complex with electrostatic solvation. It makes use of a fast preprocessing step based on the assumption that the main contribution to electrostatic desolvation upon ligand binding originates from the displacement of the first shell of water molecules. For a rigid protein, the precomputation of the energy contributions on a set of grids allows the estimation of the energy in solution of about 300 protein-fragment binding modes per second on a personal computer. The docking procedure is applied to five rigid binding sites whose size ranges from 17 residues to a whole protein of 107 amino acids. Using a library of 70 mainly rigid molecules, known micromolar inhibitors or close analogs are docked and prioritized correctly. The docking based rank-ordering of the library requires about 5 h and is proposed as a complementary approach to structure-activity relationships by nuclear magnetic resonance. Proteins 2001;42:256-268.

Binding Sites↗
PubMed2002

Host-guest chemistry of the chromium-wheel complex [Cr8F8(tBuCO2)16]: prediction of inclusion capabilities by using an electrostatic potential distribution determined by modeling synchrotron X-ray structure factors at 16 K.

The structure and detailed electron density distribution (EDD) of the large octanuclear chromium-wheel host complex [Cr8F8(tBuCO2)16] (1) has been determined from synchrotron X-ray structure factors collected at 16(5) K. The complex has a central cavity with a minimum entry distance between carbon atoms of the pivalate methyl groups (pivalic acid = tBuCO2H) of 4.027(4) A on one side of the molecule and 7.273(4) A on the other. The screened side of the molecule can be "opened" by rotation of methyl groups to create a strained host structure, which is compensated for by improved host-guest and host-solvent interaction. The EDD of the 272-atom complex (1144 e-) was determined by multipole modeling based on the experimental structure factors. 3d orbital populations on the Cr atoms and topological analysis of the EDD show that the covalent part of the metal-ligand interactions consists mainly of sigma donation from the ligands, but that overall the interactions are predominantly electrostatic. The electrostatic potential (EP) has been calculated from the experimental EDD. Knowledge of the geometry of the naked complex 1 as well as the EP in the central cavity of this molecule allows us to deduce which characteristic properties guest molecules must have to be accepted into the void. To probe these predictions, a series of complexes of 1 with different guest inclusions were synthesized (2 = 1 + N,N'-dimethylformamide (DMF), 3 = 1 + N,N'-dimethylacetamide (DMA), 4 = 1 + DMA + DMF, 5 = 1 + 2CH3CN), and their structures were examined by using X-ray diffraction data measured at 120(1) K. Results of these studies indicate that in the crystalline state, the optimal guest molecule should be linear and possess a permanent dipole. Attempts to crystallize the host complex with cations incorporated into the cavity were fruitless, although electrospray ionization mass spectrometry showed that a [1 + potassium]+ entity pre-exists in solution and can be transferred intact into the gas phase.

Journal Article↗
PubMed2004

Electrostatic surface potential calculation on several new halogenated benzimidazole-like dopaminergic ligands.

We examined the effects of the electron density distribution (electrostatic surface potential; ESP) of several new benzimidazole-type ligands on their binding affinity for the D(1) and D(2) dopamine receptors (DAR). Receptors were prepared from synaptosomal membranes of bovine caudate nuclei. [(3)H]SCH 23390 and [(3)H]spiperone were used as specific radiolabels for the D(1) and D(2) receptors, respectively. The ESP of these compounds was calculated using Gaussian 98 W software. Calculations performed with known dopaminergic ligands showed that the electron density charge in the aromatic ring of these compounds favors a higher binding affinity for the D(2) DAR. This was confirmed by the synthesis of halogenated analogues of several known dopaminergic ligands. Halogenation resulted in an increase in the positive charge of the aromatic part of the molecule. None of the newly synthesized compounds was efficient in displacing [(3)H]SCH 23390 from the D1 DAR. The introduction of chlorine into the molecule led to a higher binding affinity for the D(2) DAR of the new ligands in comparison to both parent compounds and brominated ligands. This difference probably originates from the difference in the sizes of chlorine and bromine atoms, which could influence the interaction of a ligand with the receptor binding site. However, among the new ligands with bromine as a substituent, two compounds (8b and 10b) expressed a higher binding affinity and two of them (9b and 11b) a lower binding affinity for the D(2) DAR, when compared to unsubstituted parent compounds. These results indicate that the electrostatic surface potential of a ligand is an important factor in its interaction with the D(2) DAR and that this should be taken into account during design and synthesis of dopaminergic compounds.

Animals↗
PubMed1992

High-intensity electrostatic-field exposure system for cultured biological cells.

We describe a new system for exposing cultured biological cells that have been plated on coverslips to strong electrostatic fields at magnitudes greater than 10(3) V/cm. Techniques are described that make use of mineral oil to render insignificant electrical conduction currents (total leakage current is less than 1.0 nA or less than 0.1 nA/coverslip), joule heating (less than 10(-6) W), or current-induced magnetic fields (less than 10(-13) T) in regions inhabited by cells. The mineral oil also eliminates a reduction in the strength of the applied field, which otherwise can occur from increased electrode-to-medium impedance at the site of application. Thus the applied field is reliably specified in the vicinity of a cell membrane. Control and electrostatic field chambers are housed in a grounded metal incubator. Cylindrical mu-metal shields can be used to reduce background magnetic fields in each chamber from 40 microT static and approximately 1 microT ac to, respectively, less than 3 microT static and approximately 100 nT ac. Contamination of cells by impurity atoms that may leach from electrodes was measured by atomic-absorption spectrophotometry and found to be negligible. Stray magnetic- and electric-field components within the incubator were measured, as were background fields around the laboratory.

Animals↗
PubMed2003

Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics.

We present a theoretical thermodynamic framework for the design of more efficient oligonucleotide microarrays. A general thermodynamic relation is derived to describe the electrostatic surface effects on the binding of the assayed biomolecule to a surface-tethered molecular probe. The relation is applied to analyze how the nucleic acid target, the oligonuleotide probe, and their DNA duplex electrostatic interactions with the surface affect the hybridization on DNA arrays. Taking advantage of a closed form exact solution of the linear Poisson-Boltzmann equation for a charged ion-penetrable sphere in electrolyte solution interacting with a plane wall, we study the effects of the surface and solution conditions. Binding free energy is found as a function of the surface material, dielectric or metal, the surface charge density, linker molecule length, temperature, and added salt content. The charge or electric potential of the dielectric or metal surface, respectively, is shown to dominate the hybridization, especially at low added salt or short linker length. We predict that substantial enhancement of sensitivity, selectivity, and reliability of microarrays can be achieved by control of the surface conditions. As examples, we discuss how to overcome two limitations of current technologies: nonequal sensitivity of the probes with different GC and AT bases content, and poor match/mismatch discrimination. In addition, we suggest the design of microarray conditions where the tested nucleic acid is unfolded, thus making possible the screening of a larger sequence with single nucleotide resolution. These promising findings are discussed and further experimental tests suggested.

Base Sequence↗
PubMed2006

Electrostatic calculations for assignment of infrared difference bands to carboxyl groups getting protonated during protein reactions.

Fourier transform infrared (FTIR) difference spectroscopy is predestined to monitor the protonation of carboxyl groups during protein reactions, making glutamic and aspartic amino acids unique to follow proton pathways. The absorption of the corresponding vibrations are clearly distinguishable from the absorption of other amino acids. However, the assignment to specific groups within the protein needs additional information, e.g., from induced spectral changes due to isotopic labeling or mutation. Here, the capability of electrostatic calculations to assign IR difference bands to specific carboxyl groups getting protonated is demonstrated by the ion pump mechanism of the sarcoplasmic reticulum Ca(2+)-ATPase. Active Ca(2+) transport is coupled to the hydrolysis of ATP. Two Ca(2+) ions are transported per ATP hydrolysed and two or three H(+) ions are countertransported. FTIR difference spectra show that during the Ca(2+) release step, carboxyl groups become protonated. Multiconformation continuum electrostatic calculations (MCCE) have been carried out to determine the equilibrium distribution of residue ionization and side chain conformation in dependence of pH. Available structural X-ray data from the calcium-bound and the calcium-free state allows us to simulate the transition between the two states monitored in the IR difference spectra. Exemplarily for Asp 800, ligand of both calcium ions, it is shown that MCCE calculations can identify this specific Asp to contribute to the IR bands and therefore to take part in the proton countertransport of the Ca(2+)-ATPase. In addition, an energy analysis can be performed to understand what interactions shift the pK(a).

Binding Sites↗
PubMed2006

Formation of stable nanoparticles via electrostatic complexation between sodium caseinate and gum arabic.

The formation of electrostatic complexes between sodium caseinate and gum arabic (GA) was studied as a function of pH (2.0-7.0), using slow acidification in situ with glucono-delta-lactone (GDL) or titration with HCl. The colloidal behavior of the complexes under specific conditions was investigated using absorbance measurements (at 515 or 810 nm) and dynamic light scattering (DLS). In contrast to the sudden increase in absorbance and subsequent precipitation of sodium caseinate solutions at pH < 5.4, the absorbance values of mixtures of sodium caseinate and GA increased to a level that was dependent on GA concentration at pH 5.4 (pH(c)). The absorbance values remained constant with further decreases in pH until a sudden increase in absorbance was observed (at pH(phi)). The pH(phi) was also dependent upon the GA concentration. Dynamic light scattering (DLS) data showed that the sizes of the particles formed by the complexation of sodium caseinate and GA between pH(c) and pH(phi) were between 100 and 150 nm and these nanoparticles were visualized using negative staining transmission electron microscopy (TEM). Below pH(phi), the nanoparticles associated to form larger particles, causing phase separation. zeta-Potential measurements of the nanoparticles and chemical analysis after phase separation showed that phase separation was a consequence of charge neutralization. The formation of complexes between sodium caseinate and GA was inhibited at high ionic strength (>50 mM NaCl). It is postulated that the structure of the nanoparticles comprises an aggregated caseinate core, protected from further aggregation by steric repulsion of one, or more, electrostatically attached GA molecules.

Caseins↗
PubMed2007

Electrostatics dominate quadruplex stability.

Stabilization of nucleic acid structures results from a balance of multiple interactions, including electrostatics, base stacking, hydrophobic interactions, hydrogen bonding, van der Waals forces, etc. Nucleic acid quadruplexes are unusual structures in that their formation is driven by specific binding of metal ions. This unique mode of metal binding, which is tightly coupled to oligonucleotide folding, can engender correspondingly unique solution behavior. In particular, we show that addition of many cosolvents, such as primary aliphatic alcohols, increases the thermal stability of quadruplexes, as determined by melting temperature, Tm, in direct contrast to the response of duplexes to the same admixture of solvents. Thermal stability is observed to increase as the dielectric constant of the composite solvent decreases. This behavior suggests a dominant role for electrostatics in quadruplex formation and stability. Additional studies done with other cosolvents and solutes suggest that, in some cases, other forces may come into play, including the possibility of direct interaction with the quadruplex structure. Nonetheless, many cosolvents and small molecules, such as ethanol, dimethylformamide, and betaine, stabilize the quadruplex conformation in sharp distinction to their destabilization of DNA duplexes.

Acetone↗