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PubMed1997

Electrostatics of lipid bilayer bending.

The electrostatic contribution to spontaneous membrane curvature is calculated within Poisson-Boltzmann theory under a variety of assumptions and emphasizing parameters in the physiological range. Asymmetrical surface charges can be fixed with respect to bilayer midplane area or with respect to the lipid-water area, but induce curvatures of opposite signs. Unequal screening layers on the two sides of a vesicle (e.g., multivalent cationic proteins on one side and monovalent salt on the other) also induce bending. For reasonable parameters, tubules formed by electrostatically induced bending can have radii in the 50-100-nm range, often seen in many intracellular organelles. Thus membrane associated proteins may induce curvature and subsequent budding, without themselves being intrinsically curved. Furthermore, we derive the previously unexplored effects of respecting the strict conservation of charge within the interior of a vesicle. The electrostatic component of the bending modulus is small under most of our conditions and is left as an experimental parameter. The large parameter space of conditions is surveyed in an array of graphs.

Biophysical Phenomena↗
PubMed1999

NMR studies of electrostatic potential distribution around biologically important molecules.

A new experimental approach has been developed to study the distribution of local electrostatic potential around specific protons in biologically important molecules. The approach is the development of a method denoted as "spin label/spin probe," which was proposed by one of us (. Mol. Biol. 6:498-507). The proposed method is based upon the quantitative measurement of the contribution of differently charged nitroxide probes to the spin lattice relaxation rate (1/T1) of protons in the molecule of interest, followed by calculation of local electrostatic potential using the classical Debye equation. In parallel, the theoretical calculation of potential distribution with the use of the MacSpartan Plus 1.0 program has been performed. Application of the method to solutions of simple organic molecules (aliphatic and aromatic alcohols, aliphatic carboxylates (propionate anion), and protonated ethyl amine and imidazole) allowed us to estimate the effective potential around the molecules under investigation. These were found to be in good agreement with theoretically expected values. This technique was then applied to zwitterionic amino acids bearing neutral and charged side chains (glycine, lysine, histidine, and aspartic acid). The reliability of the general approach is proved by the data presented in this paper. Application of this new methodology can afford insight into the biochemical significance of electrostatic effects in biological systems.

Alcohols↗
PubMed1999

Biomolecular electrostatics with the linearized Poisson-Boltzmann equation.

Electrostatics plays a key role in many biological processes. The Poisson-Boltzmann equation (PBE) and its linearized form (LPBE) allow prediction of electrostatic effects for biomolecular systems. The discrepancies between the solutions of the PBE and those of the LPBE are well known for systems with a simple geometry, but much less for biomolecular systems. Results for high charge density systems show that there are limitations to the applicability of the LPBE at low ionic strength and, to a lesser extent, at higher ionic strength. For systems with a simple geometry, the onset of nonlinear effects has been shown to be governed by the ratio of the electric field over the Debye screening constant. This ratio is used in the present work to correct the LPBE results to reproduce fairly accurately those obtained from the PBE for systems with a simple geometry. Since the correction does not involve any geometrical parameter, it can be easily applied to real biomolecular systems. The error on the potential for the LPBE (compared to the PBE) spans few kT/q for the systems studied here and is greatly reduced by the correction. This allows for a more accurate evaluation of the electrostatic free energy of the systems.

Animals↗
PubMed1999

Electrostatic-undulatory theory of plectonemically supercoiled DNA.

We present an analytical calculation of the electrostatic interaction in a plectonemic supercoil within the Poisson-Boltzmann approximation. Undulations of the supercoil strands arising from thermal motion couple nonlinearly with the electrostatic interaction, giving rise to a strong enhancement of the bare interaction. In the limit of fairly tight winding, the free energy of a plectonemic supercoil may be split into an elastic contribution containing the bending and torsional energies and an electrostatic-undulatory free energy. The total free energy of the supercoil is minimized according to an iterative scheme, which utilizes the special symmetry inherent in the usual elastic free energy of the plectoneme. The superhelical radius, opening angle, and undulation amplitudes in the radius and pitch are obtained as a function of the specific linking difference and the concentration of monovalent salt. Our results compare favorably with the experimental values for these parameters of Boles et al. (1990. J. Mol. Biol. 213:931-951). In particular, we confirm the experimental observation that the writhe is a virtually constant fraction of the excess linking number over a wide range of superhelical densities. Another important prediction is the ionic strength dependence of the plectonemic parameters, which is in reasonable agreement with the results from computer simulations.

Biophysical Phenomena↗
PubMedDate not supplied

Electrostatic repulsion among erythrocytes in tube flow, demonstrated by the thickness of marginal cell-free layer.

Electrostatic repulsion among erythrocytes in flow was evaluated through measurement of the thickness of the marginal cell-free layer in narrow glass tubes of 20-50 microns in inner diameter. To reduce the electrostatic repulsive force, due mainly to sialic acid of the membrane glycoproteins, human erythrocytes were treated with neuraminidase. The surface negative charge of the erythrocytes, as determined from the electrophoretic mobility using free-flow electrophoresis, was found to be proportional to the sialic acid content. When erythrocytes with decreased sialic acid content flowed through narrow tubes, the thickness of cell-free layer determined using an image processor increased even in the absence of erythrocyte aggregation in the suspension. The effect was more pronounced at acidic pH. The addition of Dextran T-70 (70,400 Mol. Wt.) further increased the cell-free layer thickness due to erythrocyte aggregation. Thus, reducing the negative charge density on the erythrocyte surface by itself accelerates the axial accumulation of erythrocytes in flow due to the decreased electrostatic repulsive force between the cells, even in the absence of erythrocyte aggregation.

Blood Flow Velocity↗
PubMed2003

Self-aggregation of legume seed storage proteins inside the protein storage vacuoles is electrostatic in nature, rather than lectin-mediated.

Conglutins are multisubunit, glycosylated, major storage proteins present in Lupinus seeds that self-aggregate in a calcium/magnesium-dependent manner. Two of these globulins exhibit lectin activity. The 210 kDa globulin derived from beta-conglutin that accumulates in Lupinus cotyledons during germination was used as a model protein to establish whether the self-aggregation process is electrostatic in nature or lectin-mediated. This protein binds in a very strong manner to chitin and recognizes a variety of glycoproteins including immunoglobulins G. Several compounds were tested for their inhibitory effect on the cation-dependent self-aggregation process. Sialic acid and phytin were the most effective whereas chitin and mucin were totally ineffective. The inability of the oligosaccharidic side chains of the 210 kDa protein, beta-conglutin and immunoglobulin G to interfere with the aggregation strongly supports the view that Ca/Mg are electrostatically involved in the in vitro self-aggregation of Lupinus globulins. The results suggest that calcium and magnesium ions are also electrostatically involved in vivo in the macromolecular aggregation of legume seed storage proteins, ensuring their efficient packing inside the protein storage vacuoles. This mechanism is responsible for the typical insolubility of legume globulins in water.

Amino Acids↗
PubMed2004

Kinetic analysis of operator binding by the E. coli methionine repressor highlights the role(s) of electrostatic interactions.

MetJ is a member of the ribbon-helix-helix class of DNA-binding proteins whose affinity for operators is apparently controlled by an unprecedented long-range electrostatic effect from the tertiary sulphur atom of its co-repressor, S-adenosyl methionine. We report here the results of kinetic assays of DNA binding with MetJ mutant proteins having altered net charges. The results (a) suggest that MetJ locates its operators via a sliding mechanism, (b) support the idea that electrostatic steering is important in the initial DNA binding event and (c) highlight the sensitivity of this system to electrostatic effects.

Bacterial Proteins↗
PubMed1997

A native electrostatic environment near Q(B) is not sufficient to ensure rapid proton delivery in photosynthetic reaction centers.

Flash-induced absorption spectroscopy has been used to characterize Rhodobacter capsulatus reaction centers mutated in the secondary quinone acceptor site (Q(B). We compared the wild-type, the L212Glu-L213Asp --> Ala-Ala photosynthetically incompetent double mutant (DM), and two photocompetent revertants, the DM+L217Arg --> Cys and the DM+M5Asn- --> Asp strains. The electrostatic environment for Q(B)- is different in the two revertant strains. Only the L217Arg --> Cys mutation nearly restores the native electrostatic environment of Q(B)-. However, the level of recovery of the reaction center function, measured by the rates of second electron transfer and cytochrome c turnover, is quite incomplete in both strains. This shows that a wild-type-like electrostatic environment of Q(B)- cannot ensure on its own, rapid and efficient proton transfer to Q(B)-.

Cytochrome c Group↗
PubMed2002

Extended thermodynamic approach to ion interaction chromatography: a thorough comparison with the electrostatic approach, and further quantitative validation.

The most reliable literature experimental results, concerning retention behavior of charged molecules, in the presence of an ion-interaction reagent (IIR), were used to obtain a further quantitative validation of a new theory. The present work emphasizes the fact that the extent to which electrostatic interactions, ion pair formation in the adsorbed and the mobile phases, and adsorption competitions are one more important than the other depends on experimental conditions. Further insight into the meaning of the linearity of the log k vs. log [IIR] plot, which is common to many theoretical models, is given. The experimental conditions under which the linearity of this plot can be expected not only practically, but also theoretically, are elucidated. The dependence of the ratio of retention factors with and without IIR in the eluent on the analyte nature, which cannot be predicted by the electrostatic approach, was explained and tracked. The difference between the actual surface potential and that predicted by the electrostatic approach is also rationalized. The model is also theoretically shown to be able to elucidate the enantioselective retention mechanism, in the presence of chiral counter ions.

Chromatography, Liquid↗
PubMed1998

Electrostatic effects on protein partitioning in size-exclusion chromatography and membrane ultrafiltration.

Although size-exclusion chromatography and membrane ultrafiltration are generally viewed as size-based separation processes, there is considerable evidence for the importance of electrostatic interactions. Experimental studies of size-exclusion chromatography and membrane ultrafiltration were performed in parallel using both neutral dextrans and charged proteins. Data for protein retention time and membrane sieving clearly indicate that the effective protein size increases with decreasing ionic strength due to the reduction in electrostatic shielding. These results were quantified using available theoretical models for the partitioning of charged solutes. The data clearly demonstrate the similarity of the electrostatic interactions and partitioning effects in size-exclusion chromatography and membrane ultrafiltration.

Chromatography, Gel↗
PubMed2003

Electrostatic interactions in a peptide--RNA complex.

Parallel experimental measurements and theoretical calculations have been used to investigate the energetics of electrostatic interactions in the complex formed between a 22 residue, alpha-helical peptide from the N protein of phage lambda and its cognate 19 nucleotide box B RNA hairpin. Salt-dependent free energies were measured for both peptide folding from coil to helix and peptide binding to RNA, and from these the salt-dependence of binding pre-folded, helical peptide to RNA was determined ( partial differential (DeltaG degrees (dock))/ partial differential log[KCl]=5.98(+/-0.21)kcal/mol). (A folding transition taking place in the RNA hairpin loop was shown to have a negligible dependence on salt concentration.) The non-linear Poisson-Boltzmann equation was used to calculate the same salt dependence of the binding free energy as 5.87(+/-0.22)kcal/mol, in excellent agreement with the measured value. Close agreement between experimental measurements and calculations was also obtained for two variant peptides in which either a basic or acidic residue was replaced with an uncharged residue, and for an RNA variant with a deletion of a single loop nucleotide. The calculations suggest that the strength of electrostatic interactions between a peptide residue and RNA varies considerably with environment, but that all 12 positive and negative N peptide charges contribute significantly to the electrostatic free energy of RNA binding, even at distances up to 11A from backbone phosphate groups. Calculations also show that the net release of ions that accompanies complex formation originates from rearrangements of both peptide and RNA ion atmospheres, and includes accumulation of ions in some regions of the complex as well as displacement of cations and anions from the ion atmospheres of the RNA and peptide, respectively.

Amino Acid Sequence↗
PubMed1991

Electrostatic potential and Born energy of charged molecules interacting with phospholipid membranes: calculation via 3-D numerical solution of the full Poisson equation.

Understanding the physicochemical basis of the interaction of molecules with lipid bilayers is fundamental to membrane biology. In this study, a new, three-dimensional numerical solution of the full Poisson equation including local dielectric variation is developed using finite difference techniques in order to model electrostatic interactions of charged molecules with a non-uniform dielectric. This solution is used to describe the electric field and electrostatic potential profile of a charged molecule interacting with a phospholipid bilayer in a manner consistent with the known composition and structure of the membrane. Furthermore, the Born interaction energy is then calculated by appropriate integration of the electric field over whole space. Numerical computations indicate that the electrostatic potential profile surrounding a charge molecule and its resultant Born interaction energy are a function of molecular position within the membrane and change most significantly within the polar region of the bilayer. The maximum interaction energy is observed when the charge is placed at the center of the hydrophobic core of the membrane and is strongly dependent on the size of the charge and on the thickness of the hydrocarbon core of the bilayer. The numerical results of this continuum model are compared with various analytical approximations for the Born energy including models established for discontinuous slab dielectrics. The calculated energies agree with the well-known Born analytical expression only when the charge is located near the center of a hydrocarbon core of greater than 60 A in thickness. The Born-image model shows excellent agreement with the numerical results only when modified to include an appropriate effective thickness of the low dielectric region. In addition, a newly derived approximation which considers the local mean dielectric provides a simple and continuous solution that also agrees well with the numerical results.

Cell Membrane↗
PubMed2001

Engineering the pH-optimum of a triglyceride lipase: from predictions based on electrostatic computations to experimental results.

The optimisation of enzymes for particular purposes or conditions remains an important target in virtually all protein engineering endeavours. Here, we present a successful strategy for altering the pH-optimum of the triglyceride lipase cutinase from Fusarium solani pisi. The computed electrostatic pH-dependent potentials in the active site environment are correlated with the experimentally observed enzymatic activities. At pH-optimum a distinct negative potential is present in all the lipases and esterases that we studied so far. This has prompted us to propose the "The Electrostatic Catapult Model" as a model for product release after cleavage of the ester bond. The origin of the negative potential is associated with the titration status of specific residues in the vicinity of the active site cleft. In the case of cutinase, the role of Glu44 was systematically investigated by mutations into Ala and Lys. Also, the neighbouring Thr45 was mutated into Proline, with the aim of shifting the spatial location of Glu44. All the charge mutants displayed altered titration behaviour of active site electrostatic potentials. Typically, the substitution of the residue Glu44 pushes the onset of the active site negative potential towards more alkaline conditions. We, therefore, predicted more alkaline pH optima, and this was indeed the experimentally observed. Finally, it was found that the pH-dependent computed Coulombic energy displayed a strong correlation with the observed melting temperatures of native cutinase.

Amino Acid Sequence↗
PubMed2001

Electrostatic effects on the free-energy balance in folding a ribosome-inactivating protein.

Electrostatics of globular proteins provides structural integrity as well as specificity of biological function. This dual role is particularly striking for ricin A-chain (RTA), an N-glycosidase which hydrolyzes a single adenine base from a conserved region of rRNA. The reported X-ray crystallographic structure of the RTA mutant E177A demonstrated a remarkable rescue of charge balance in the active site, achieved by the rotation of a second glutamic acid (Glu-208) into the vacated space. To understand this conformational reorganization, molecular-dynamics simulations were applied to estimate relative free energies that govern the thermodynamic stability of E177A together with mutants E177Q and E177D. The simulations anticipate that while E177A is a non-conservative substitution, the protein is more stable than the other two mutants. However, the structural plasticity of the RTA active site is not obtained penalty-free, rather E177A among the mutants shows the largest unfavorable net change in the electrostatic contribution to folding. Of the E177A folded state, reorganization of Glu-208 lowers the electrostatic cost of the free-energy change, yet interestingly, protein interactions oppose the rotational shift, while solvent effects favor the transition.

Chemical Phenomena↗
PubMed2000

Electrostatic interaction between stereocilia: I. Its role in supporting the structure of the hair bundle.

This paper provides theoretical estimates for the forces of electrostatic interaction between adjacent stereocilia in auditory and vestibular hair cells. Estimates are given for parameters within the measured physiological range using constraints appropriate for the known geometry of the hair bundle. Stereocilia are assumed to possess an extended, negatively charged surface coat, the glycocalyx. Different charge distribution profiles within the glycocalyx are analysed. It is shown that charged glycocalices on the apical surface of the hair cells can support spatial separation between adjacent stereocilia in the hair bundles through electrostatic repulsion between stereocilia. The charge density profile within the glycocalyx is a crucial parameter. In fact, attraction instead of repulsion between adjacent stereocilia will be observed if the charge of the glycocalyx is concentrated near the membrane of the stereocilia, thereby making this type of charge distribution unlikely. The forces of electrostatic interaction between stereocilia may influence the mechanical properties of the hair bundle and, being strongly non-linear, contribute to the non-linear phenomena that have been recorded from the periphery of the auditory and vestibular systems.

Animals↗
PubMed1999

Electrostatic interactions during activation of coagulation factor IX via the tissue factor pathway: effect of univalent salts.

Interaction between the Gla-domain of coagulation proteins and negatively charged phospholipid membranes is essential for blood coagulation reactions. The interaction is calcium-dependent and mediated both by electrostatic and hydrophobic forces. This report focuses on the electrostatic component of factor IX activation via the extrinsic pathway. Effective charges during the reaction are measured by ionic titration of activity, according to the Debye-Huckel and Gouy-Chapman models. Rates of activation decrease with ionic strength independently of the type of monovalent salt used to control ionic strength. Moreover, the effect of ionic strength decreases at concentrations of charged phospholipid approaching saturation levels, indicating that membrane charges participate directly in the ionic interaction measured. The effective charge on calcium-bound factor IX during activation on phospholipid membranes is 0.95+/-0.1. Possible sites mediating contacts between the Gla-domain and membranes are selected by geometrical criteria in several metal-bound Gla-domain structures. A pocket with a solvent opening-pore of area 24-38 A2 is found in the Gla-domain of factors IX, VII, and prothrombin. The pocket contains atoms with negative partial charges, including carboxylate oxygens from Gla residues, and has a volume of 57-114 A3, sufficient to accommodate additional calcium atoms. These studies demonstrate that electrostatic forces modify the activity coefficient of factor IX during functional interactions and suggest a conserved pocket motif as the contact site between the calcium-bound Gla-domain and charged membranes.

Binding Sites↗
PubMed2000

Electrostatic aspects of protein-protein interactions.

Structural and mutational analyses reveal a central role for electrostatic interactions in protein-protein association. Experiment and theory both demonstrate that clusters of charged and polar residues that are located on protein-protein interfaces may enhance complex stability, although the total effect of electrostatics is generally net destabilizing. The past year also witnessed significant progress in our understanding of the effect of electrostatics on protein association kinetics, specifically in the characterization of a partially desolvated encounter complex.

Animals↗
PubMed1999

Regulation of ARNO nucleotide exchange by a PH domain electrostatic switch.

ARNO is a member of a family of guanine nucleotide exchange factors that activate small GTPases called ADP-ribosylation factors (ARFs) [1] [2] [3], which regulate vesicular trafficking and, in one case (ARF6), also regulate cortical actin structure [4]. ARNO is located at the plasma membrane, and in the presence of activated protein kinase C (PKC) can induce cortical actin rearrangements reminiscent of those produced by active ARF6 [5] [6] [7] [8]. High-affinity binding of ARNO to membranes, which is required for exchange activity, is mediated cooperatively by a pleckstrin homology (PH) domain and an adjacent carboxy-terminal polybasic domain [3] [9]. ARNO is phosphorylated in vivo by PKC on a single serine residue, S392, located within the carboxy-terminal polybasic domain. Mutation of S392 to alanine does not prevent ARNO-mediated actin rearrangements, suggesting that phosphorylation does not lead to ARNO activation [6]. Here, we report that phosphorylation negatively regulates ARNO exchange activity through a 'PH domain electrostatic switch'. Introduction of a negatively charged phosphate into the polybasic domain reduced interaction of ARNO with membranes both in vitro and in vivo, and inhibited exchange in vitro. This regulated membrane association is similar to the myristoyl electrostatic switch that controls membrane binding of the myristoylated alanine-rich C kinase substrate (MARCKS) [10], but to our knowledge is the first demonstration of an electrostatic switch regulating the membrane interaction of a protein containing a PH domain. This mechanism allows regulation of ARNO lipid binding and exchange activity at two levels, phosphoinositide-dependent recruitment and PKC-dependent displacement from the membrane.

Binding Sites↗