Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.

Distribution of electrostatic potential of DNA fragments was evaluated. A method for calculation of electrostatic potential distribution based on Coulomb's law is proposed for long DNA fragments (approximately 1000 nucleotide pairs). For short DNA sequences, this technique provides a good correlation with the results obtained using Poisson-Boltzmann equation thus justifying its application in comparative studies for long DNA fragments. Calculation was performed for several DNA fragments from E. coli and bacteriophage T7 genomes containing promoter and nonpromoter regions. The results obtained indicate that coding regions are characterized by more homogeneous distribution of electrostatic potential whereas local inhomogeneity of DNA electrostatic profile is typical for promoter regions. The possible role of electrostatic interactions in RNA polymerase-promoter recognition is discussed.     

Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.

The electrostatic properties of seven alpha/beta-barrel enzymes selected from different evolutionary families were studied: triose phosphate isomerase, fructose-1,6-bisphosphate aldolase, pyruvate kinase, mandelate racemase, trimethylamine dehydrogenase, glycolate oxidase, and narbonin, a protein without any known enzymatic activity. The backbone of the alpha/beta-barrel has a distinct electrostatic field pattern, which is dipolar along the barrel axis. When the side chains are included in the calculations the general effect is to modulate the electrostatic pattern so that the electrostatic field is generally enhanced and is focused into a specific area near the active site. We use the electrostatic flux through a square surface near the active site to gauge the functionally relevant magnitude of the electrostatic field. The calculations reveal that in six out of the seven cases the backbone itself contributes greater than 45% of the total flux. The substantial electrostatic contribution of the backbone correlates with the known preference of alpha/beta-barrel enzymes for negatively charged substrates.     

The role of electrostatic forces in pollination

This paper reviews research on the role of electrostatic forces in pollination, both in natural and in agricultural systems. Researchers from various fields of biological studies have reported phenomena which they related to electrostatic forces. The theory of electrostatically mediated pollen transfer between insect pollinators and the flowers they visit is described, including recent studies which confirmed that the accumulated charges on airborne honey bees are sufficient for non-contact pollen detachment by electrostatic forces (i.e., electrostatic pollination). The most important morphological features in flower adaptiveness to electrostatic pollination were determined by means of two theoretical models of a flower exposed to an approaching charged cloud of pollen; they are style length and flower opening. Supplementary pollination by using electrostatic techniques is reported, and its possible importance in modern agriculture is discussed.     

Spatial optimization of electrostatic interactions between the ionized groups in globular proteins

A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge–charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley-Liss, Inc.     

高压静电场对过氧化氢酶的稳定作用及机理研究

用高压静电场直接处理过氧化氢酶溶液 ,结果表明 :不同强度的高压静电场能提高和降低过氧化氢酶的活力。电场强度越大 ,酶活力达到平衡所需时间越短。处理后的过氧化氢酶溶液 ,玻棒 30秒的搅拌作用能使酶活力基本上回到原来的状态。溶液极性降低 ,酶活力达到平衡所需时间减少。处于高压静电场中的过氧化氢酶溶液 ,在 2 0℃时 ,电场强度为 3× 10 3V/cm ,活力能保持 5～ 6天 ,而对照只能保持 2～ 3天。在 30℃时 ,同样电场强度下 ,活力能保持 48小时左右 ,对照能保持 2 4小时左右。经高压静电场处理的酶 ,活力保持时间也比对照长。研究表明 :高压静电场对酶活力的稳定作用很可能是高压静电场使酶及溶液发生极化作用产生的。     

Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction

The rate of association of proteins is dictated by diffusion, but can be enhanced by favorable electrostatic forces. Here the relationship between the electrostatic energy of interaction, and the kinetics of protein-complex formation was analyzed for the protein pairs of: hirudin-thrombin, acetylcholinesterase-fasciculin and barnase-barstar, and for a panel of point mutants of these proteins. Electrostatic energies of interaction were calculated as the difference between the electrostatic energy of the complex and the sum of the energies of the two individual proteins, using the computer simulation package DelPhi. Calculated electrostatic energies of interaction were compared to experimentally determined rates of association. One kcal/mol of Coulombic interaction energy increased the rate of association by a factor of 2.8, independent of the protein-complex or mutant analyzed. Electrostatic energies of interaction were also determined from the salt dependence of the association rate constant, using the same basic equation as for the theoretical calculation. A Br?nsted analysis of the electrostatic energies of interactions plotted versus experimentally determined ln(rate)s of association shows a linear relation between the two, with a beta value close to 1. This is interpreted as the energy of the transition state varies according to the electrostatic interaction energy, fitting a two state model for the association reaction. Calculating electrostatic rate enhancement from the electrostatic interaction energy can be used as a powerful tool to design protein complexes with altered rates of association and affinities.     

Electrostatic factors in DNA intercalation

The factors that determine the binding of a chromophore between the base pairs in DNA intercalation complexes are dissected. The electrostatic potential in the intercalation plane is calculated using an accurate ab initio based distributed multipole electrostatic model for a range of intercalation sites, involving different sequences of base pairs and relative twist angles. There will be a significant electrostatic contribution to the binding energy for chromophores with a predominantly positive electrostatic potential, but this varies significantly with sequence, and somewhat with twist angle. The usefulness of these potential maps for understanding the binding of intercalators is explored by calculating the electrostatic binding energy for 9-aminoacridine, ethidium, and daunomycin in a variety of model binding sites. The electrostatic forces play a major role in the positioning of an intercalating 9-aminoacridine and a significant stabilizing role in the binding of ethidium in its sterically constrained position, but the intercalation of daunomycin is determined by the side-chain binding. Sequence preferences are likely to be determined by a complex and subtle mixture of effects, with electrostatics being just one component. The electrostatic binding energy is also unlikely to be a major determinant of the twist angle, as its variation with angle is modest for most intercalation sites. Overall, the electrostatic potential maps give guidance on how positively charged chromophores can be chemically adapted by heteroatomic substitution to optimise their binding.     

Automated computational framework for the analysis of electrostatic similarities of proteins

Charge plays an important role in protein-protein interactions. In the case of excessively charged proteins, their electrostatic potentials contribute to the processes of recognition and binding with other proteins or ligands. We present an automated computational framework for determining the contribution of each charged amino acid to the electrostatic properties of proteins, at atomic resolution level. This framework involves computational alanine scans, calculation of Poisson-Boltzmann electrostatic potentials, calculation of electrostatic similarity distances (ESDs), hierarchical clustering analysis of ESDs, calculation of solvation free energies of association, and visualization of the spatial distributions of electrostatic potentials. The framework is useful to classify families of mutants with similar electrostatic properties and to compare them with the parent proteins in the complex. The alanine scan mutants introduce perturbations in the local electrostatic properties of the proteins and aim in delineating the contribution of each mutated amino acid in the spatial distribution of electrostatic potential, and in biological function when electrostatics is a dominant contributing factor in protein-protein interactions. The framework can be used to design new proteins with tailored electrostatic properties, such as immune system regulators, inhibitors, and vaccines, and in guiding experimental studies. We present an example for the interaction of the immune system protein C3d (the d-fragment of complement protein C3) with its receptor CR2, and we discuss our data in view of a binding site controversy.     

Electrostatic effects in a large enzyme complex: subunit interactions and electrostatic potential field of the icosahedral beta 60 capsid of heavy riboflavin synthase

The role of the electrostatic interactions in the stability of the icosahedral beta 60 capsid of heavy riboflavin synthase from Bacillus subtilis has been investigated using an approach based on the theory of Kirkwood and Tanford. The pH dependence of the electrostatic subunit interactions agrees well with experimental data. The electrostatic subunit interaction energy has a pronounced minimum at pH 8.2 for both the ligated and ligand-free capsid. The latter is characterized by a reduction of the magnitude and the pH range of the electrostatic attraction. It is found that only 8 charged groups, which form one cluster and two ion pairs, provide a significant contribution to the capsid stability. The analysis has shown that the aggregation/disaggregation equilibrium seems to be regulated by electrostatic interactions between beta-subunits forming dimers, which connect the relatively stable pentamers in the beta-60 capsid. The release of the ligand causes a reduction of the electrostatic attraction of the dimers, which may induce disaggregation of the capsid. The electrostatic potential field due to the titratable groups and alpha-helix macrodipoles has been calculated on the basis of the Coulomb relation. Two different values of the dielectric constant have been used for the protein and the surrounding solvent, respectively. The electrostatic potential shows a radially polar distribution with a positive pole at the inner capsid wall and a negative pole outside the capsid. An interesting feature of the electrostatic field is the formation of positive potential "channels" that coincide with the channels constituted by the pentameric and trimeric beta-subunit aggregates. It is supposed that the electrostatic potential field plays a role in enzyme-substrate recognition.     

Investigating the dielectric effects of channel pore water on the electrostatic barriers of the permeation ion by the finite difference Poisson-Boltzmann method

In this paper, the finite difference Poisson-Boltzmann (FDPB) method with four dielectric constants is developed to study the effect of dielectric saturation on the electrostatic barriers of the permeation ion. In this method, the inner shape of the channel pore is explicitly represented, and the fact that the dielectric constant inside the channel pore is different from that of bulk water is taken into account. A model channel system which is a right-handed twist bundle with four α-helical segments is provided for this study. From the FDPB calculations, it is found that the difference of the ionic electrostatic solvation energy for wider domains depends strongly on the pore radius in the vicinity of the ion when the pore dielectric constant is changed from 78 to 5. However, the electrostatic solvation energy of the permeation ion can not be significantly affected by the dielectric constant in regions with small pore radii. Our results indicate that the local electrostatic interactions inside the ion channel are of major importance for ion electrostatic solvation energies, and the effect of dielectric saturation on the electrostatic barriers is coupled to the interior channel dimensions. Received: 28 January 1997 / Accepted: 24 September 1997     

The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations

The origin of the barrier for proton transport through the aquaporin channel is a problem of general interest. It is becoming increasingly clear that this barrier is not attributable to the orientation of the water molecules across the channel but rather to the electrostatic penalty for moving the proton charge to the center of the channel. However, the reason for the high electrostatic barrier is still rather controversial. It has been argued by some workers that the barrier is due to the so-called NPA motif and/or to the helix macrodipole or to other specific elements. However, our works indicated that the main reason for the high barrier is the loss of the generalized solvation upon moving the proton charge from the bulk to the center of the channel and that this does not reflect a specific repulsive electrostatic interaction but the absence of sufficient electrostatic stabilization. At this stage it seems that the elucidation and clarification of the origin of the electrostatic barrier can serve as an instructive test case for electrostatic models. Thus, we reexamine the free-energy surface for proton transport in aquaporins using the microscopic free-energy perturbation/umbrella sampling (FEP/US) and the empirical valence bond/umbrella sampling (EVB/US) methods as well as the semimacroscopic protein dipole Langevin dipole model in its linear response approximation version (the PDLD/S-LRA). These extensive studies help to clarify the nature of the barrier and to establish the "reduced solvation effect" as the primary source of this barrier. That is, it is found that the barrier is associated with the loss of the generalized solvation energy (which includes of course all electrostatic effects) upon moving the proton charge from the bulk solvent to the center of the channel. It is also demonstrated that the residues in the NPA region and the helix dipole cannot be considered as the main reasons for the electrostatic barrier. Furthermore, our microscopic and semimacroscopic studies clarify the problems with incomplete alternative calculations, illustrating that the effects of various electrostatic elements are drastically overestimated by macroscopic calculations that use a low dielectric constant and do not consider the protein reorganization. Similarly, it is pointed out that microscopic potential of mean force calculations that do not evaluate the electrostatic barrier relative to the bulk water cannot be used to establish the origin of the electrostatic barrier. The relationship between the present study and calculations of pK(a)s in protein interiors is clarified, pointing out that approaches that are applied to study the aquaporin barrier should be validated by pK(a)s calculations. Such calculations also help to clarify the crucial role of solvation energies in establishing the barrier in aquaporins.     

Theoretical studies of the electrostatic interactions in aspartic proteinases, intramolecular interactions in pepsin and penicillopepsin

A semi-empirical approach has been used to estimate the intramolecular electrostatic interactions in pepsin and penicillopepsin. The pH-dependence of the free energy electrostatic term was calculated, and the pH-dependence of the domain interactions has been estimated. As it was shown, the contribution of electrostatic interactions is rather small for the stabilization of the native structure. At the same time the electrostatic repulsion between domains increases with the increase of pH. The later can be the cause of the alkaline denaturation of pepsin and domain mobility.     

Local electrostatic optimization in proteins.

A simple electrostatic model has been used to investigate the extent to which the structure of protein molecules is organized to optimize the internal electrostatic interactions. We find that the model provides a favorable total intra-protein electrostatic energy for almost all polar and charged groups of atoms, suggesting a high degree of structural optimization. By contrast, a significant fraction of individual group-group interactions are found to be unfavorable. An analysis as a function of the range of interactions included shows the electrostatic organization is generally relatively short range (up to 6 or 7 A between group centers). Although the model is very simple, it is useful for assessing the overall quality of protein experimental structures, for pin-pointing some types of errors and as a guide to improving protein design.     

RNA polymerase--promoter recognition. Specific features of electrostatic potential of "early" T4 phage DNA promoters

Comparative analysis of electrostatic potential distribution for "early" T4 phage promoters was undertaken, along with calculation of topography of electrostatic potential around the native and ADP-ribosylated C-terminal domain of RNA polymerase alpha-subunit. The data obtained indicate that there is specific difference in the patterns of electrostatic potential distribution in far upstream regions of T4 promoters differing by their response to ADP-ribosylation of RNA polymerase. A specific change in profiles of electrostatic potential distribution for the native and ADP-ribosylated forms of RNA polymerase alpha-subunit was observed suggesting that this factor may be responsible for modulating T4 promoter activities in response to the enzyme modification.     

On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics

Many signaling events require the binding of cytoplasmic proteins to cell membranes by recognition of specific charged lipids, such as phosphoinositol-phosphates. As a model for a protein-membrane binding site, we consider one charged phosphoinositol phosphate (PtdIns(3)P) embedded in a phosphatidylcholine bilayer. As the protein-membrane binding is driven by electrostatic interactions, continuum solvent models require an accurate representation of the electrostatic potential of the phosphoinositol phosphate-containing membrane. We computed and analyzed the electrostatic potentials of snapshots taken at regular intervals from molecular dynamics simulations of the bilayer. We observe considerable variation in the electrostatic potential of the bilayer both along a single simulation and between simulations performed with the GAFF or CHARMM c36 force fields. However, we find that the choice of GAFF or CHARMM c36 parameters has little effect on the electrostatic potential of a given configuration of the bilayer with a PtdIns(3)P embedded in it. From our results, we propose a remedian averaging method for calculating the electrostatic potential of a membrane system that is suitable for simulations of protein-membrane binding with a continuum solvent model.     

Particle deposition onto a human head: Influence of electrostatic and wind fields

This study investigates electrostatic fields surrounding the human head and particle deposition onto facial skin and eyes caused by the combined effect of electrostatic and wind fields. The electrostatic fields are calculated by a three-dimensional numerical model calculating the field strength between a field source and a human head. The deposition velocity can be viewed as determined by the sum of two contributions: that of an electrostatic field and that of a wind field. Deposition velocities are calculated by a semiempirical particle deposition model that considers particle transport from the free stream to the human face. The particle deposition model uses the electrostatic field model results as input parameters and is applied to the forehead and eyes of two facial shapes for two different turbulence conditions and aerosol charge distributions. The results of different practical working conditions, under which the potential difference between head (person) and source ranges from 5.6 to 15.0 kV, indicates that the presence of electrostatic fields always increases particle deposition for industrial aerosols. For aged aerosols an effect is only present for submicron particles. Bioelectromagnetics 19:246–258, 1998. © 1998 Wiley-Liss, Inc.     

Kinetics of intracomplex electron transfer and of reduction of the components of covalent and noncovalent complexes of cytochrome c and cytochrome c peroxidase by free flavin semiquinones

The kinetics of reduction of free flavin semiquinones of the individual components of 1:1 covalent and electrostatic complexes of yeast ferric and ferryl cytochrome c peroxidase and ferric horse cytochrome c have been studied. Covalent cross-linking between the peroxidase and cytochrome c at low ionic strength results in a complex that has kinetic properties both similar to and different from those of the electrostatic complex. Whereas the cytochrome c heme exposure to exogenous reductants is similar in both complexes, the apparent electrostatic environment near the cytochrome c heme edge is markedly different. In the electrostatic complex, a net positive charge is present, whereas in the covalent complex, an essentially neutral electrostatic charge is found. Intracomplex electron transfer within the two complexes is also different. For the covalent complex, electron transfer from ferrous cytochrome c to the ferryl peroxidase has a rate constant of 1560 s-1, which is invariant with respect to changes in the ionic strength. The rate constant for intracomplex electron transfer within the electrostatic complex is highly ionic strength dependent. At mu = 8 mM a value of 750 s-1 has been obtained [Hazzard, J. T., Poulos, T. L., & Tollin, G. (1987) Biochemistry 26, 2836-2848], whereas at mu = 30 mM the value is 3300 s-1. This ionic strength dependency for the electrostatic complex has been interpreted in terms of the rearrangement of the two proteins comprising the complex to a more favorable orientation for electron transfer. In the case of the covalent complex, such reorientation is apparently impeded.(ABSTRACT TRUNCATED AT 250 WORDS)     

Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex

Theoretical and experimental studies have shown that the large desolvation penalty required for polar and charged groups frequently precludes their involvement in electrostatic interactions that contribute strongly to net stability in the folding or binding of proteins in aqueous solution near room temperature. We have previously developed a theoretical framework for computing optimized electrostatic interactions and illustrated use of the algorithm with simplified geometries. Given a receptor and model assumptions, the method computes the ligand-charge distribution that provides the most favorable balance of desolvation and interaction effects on binding. In this paper the method has been extended to treat complexes using actual molecular shapes. The barnase-barstar protein complex was investigated with barnase treated as a target receptor. The atomic point charges of barstar were varied to optimize the electrostatic binding free energy. Barnase and natural barstar form a tight complex (K(d) approximately 10(-14) M) with many charged and polar groups near the interface that make this a particularly relevant system for investigating the role of electrostatic effects on binding. The results show that sets of barstar charges (resulting from optimization with different constraints) can be found that give rise to relatively large predicted improvements in electrostatic binding free energy. Principles for enhancing the effect of electrostatic interactions in molecular binding in aqueous environments are discussed in light of the optima. Our findings suggest that, in general, the enhancements in electrostatic binding free energy resulting from modification of polar and charged groups can be substantial. Moreover, a recently proposed definition of electrostatic complementarity is shown to be a useful tool for examining binding interfaces. Finally, calculational results suggest that wild-type barstar is closer to being affinity optimized than is barnase for their mutual binding, consistent with the known roles of these proteins.