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PubMed1991

Surface electrostatic interactions contribute little of stability of barnase.

Electrostatic interactions are believed to play an important role in stabilizing the native structure of proteins. We have quantified the contribution to stability of an interaction between two oppositely charged side-chains on the surface of barnase. Using site-directed mutagenesis, glutamate 28 and lysine 32 were introduced onto the solvent-accessible side of the second alpha-helix in barnase. These two residues are separated by one turn of the helix, and so are ideally situated for their opposite charges to interact. Double mutant cycle analysis reveals that the interaction between Glu28 and Lys32 contributes only approximately 0.2 kcal/mol to stability of the protein. All other interactions between exposed charged side-chains in barnase examined so far also contribute little to stability. We explain this low value by their location on the surface, rather than in the interior, of the protein.

Amino Acid Sequence↗
PubMed1991

Regulation of filamentous bacteriophage length by modification of electrostatic interactions between coat protein and DNA.

Bacteriophage fd gene VIII, which encodes the major capsid protein, was mutated to convert the serine residue at position 47 to a lysine residue (S47K), thereby increasing the number of positively charged residues in the C-terminal region of the protein from four to five. The S47K coat protein underwent correct membrane insertion and processing but could not encapsidate the viral DNA, nor was it incorporated detectably with wild-type coat proteins into hybrid bacteriophage particles. However, hybrid virions could be constructed from the S47K coat protein and a second mutant coat protein, K48Q, the latter containing only three lysine residues in its C-terminal region. K48Q phage particles are approximately 35% longer than wild-type. Introducing the S47K protein shortened these particles, the S47K/K48Q hybrids exhibiting a range of lengths between those of K48Q and wild-type. These results indicate that filamentous bacteriophage length (and the DNA packaging underlying it) are regulated by unusually flexible electrostatic interactions between the C-terminal domain of the coat protein and the DNA. They strongly suggest that wild-type bacteriophage fd makes optimal use of the minimum number of coat protein subunits to package the DNA compactly.

Amino Acid Sequence↗
PubMed1984

Quantitative structure-activity relationships of cardiotonic steroids using empirical molecular electrostatic potentials and semiempirical molecular orbital calculations.

Empirical molecular electrostatic potentials and a rigid receptor H atom model are used to calculate differences in the interaction energy of cardiotonic steroids with the digitalis receptor. An attempt is made to map the receptor H binding sites for two different steroid conformations with respect to 17 beta side-chain orientation. The calculated interaction energies using single-crystal X-ray structure data indicate linear relationships with the Na+, K+-ATPase inhibitory activity. On the basis of these correlations, the activity of 8 so far pharmacologically not investigated steroids containing C = O in 17 beta substituents are estimated with the help of structural data determined by means of the semiempirical CNDO molecular orbital theory.

Cardiac Glycosides↗
PubMed1983

Charge distribution within cell surface coats of single and interacting surfaces--a minimum free electrostatic energy approach. Conclusions for electrophoretic mobility measurements.

The fixed charge distribution in a cell surface coat model was calculated using a variational approach based on the minimum of electrostatic free energy. The influence of ionic strength on distribution was analyzed. It is shown that interaction with other coats or smooth surfaces changes the fixed charge distribution. The special effect of a possible membrane charge was calculated in addition. In this case there is a fixed, charge-free space near the membrane, depending on coat thickness, ionic strength and membrane charge/surface coat charge ratio. For several cases energies, electric potentials and fixed charge distributions are given. The general result is that fixed charge distribution is always composed of a constant space charge density over a part of or the whole surface coat and, with some exceptions, of a surface charge density at the border of the surface coat. Conclusions for electrophoretic mobility measurement interpretations are drawn.

Cell Membrane↗
PubMed1983

Ionic interactions and anion binding in the gramicidin channel. An electrostatic calculation.

An electrostatic calculation is performed in order to examine basic features of interactions between ions (including anions) within the gramicidin channel. The calculation focuses on the effect of image forces. The substitute charge method is used for the calculation of image-force energies. Good arrangements of fictitious charges and contour points are described. Errors of calculated image-force energies are estimated not to greatly exceed 0.1%. The cases assumed are (i) the effective radius r of the channel is between 2.5 and 3.5 A, (ii) the binding site with the highest affinity is between 1 and 3.5 A from the channel end (outer site), and (iii) the dimple at the channel mouth is 0-5 A in depth. The induced energy of an ion placed at the outer site increases (and hence the affinity of the outer site decreases) with the increase in the depth of dimples, whereas the barrier height for translocation between the outer sites decreases in the presence of deeper dimples. The interactional energy between two monovalent cations placed at the outer sites is relatively small in the absence of dimples. It is large, however, in the presence of deeper dimples if the outer sites are 2.5 or 3.5 A from the ends; but, it is still relatively small even in the presence of dimples if the sites are 1 A from the ends. The interactional energy is very unfavorable for simultaneous occupancy by three cations. It is suggested that an ion pair may be formed at the channel mouth. Deeper positions of the outer site, smaller values of r, and deeper dimples favor the formation of the ion pair. In the presence of 5 A dimples, the binding constant of an anion (Cl-) for a cation (Na+) which has already been bound at an outer site (with no second cation at the opposite mouth) is estimated to be 0.4-8 molal-1 if local interactions between the bound anion and the channel wall is negligibly small. The anion binding constant increases in the presence of a cation (or an ion pair) at the opposite mouth. It decreases markedly in the absence of dimples. The interactional energy is considerably unfavorable for the binding of a third cation even if the presence of an ion pair is postulated. It is still large in the presence of an ion pair at each of the mouths.

Binding Sites↗
PubMed1984

Effects of DEAE-dextran on infection and hemolysis by VSV. Evidence that nonspecific electrostatic interactions mediate effective binding of VSV to cells.

The polycation DEAE-dextran increased the binding of VSV to BHK cells about fourfold over a wide range of VSV concentrations. The same proportion of bound virions was internalized by the cell in the presence or absence of DEAE-dextran. Viral primary RNA production was increased to the equivalent of a 4- to 4.5-fold increase in multiplicity of infection in the presence of DEAE-dextran, closely paralleling the increase in total VSV binding to the cell. Viral secondary RNA production was increased only to the equivalent of about twofold increase in multiplicity. The kinetics of both primary and secondary RNA production were indistinguishable in the presence or absence of DEAE-dextran. DEAE-dextran had to be present simultaneously with the input virions in order to enhance RNA production; addition even 30 min after infection was ineffective. Addition of the polycation DEAE-dextran was also required for appreciable VSV-induced hemolysis of human erythrocytes; erythrocytes of several other species were hemolyzed in the absence of DEAE-dextran, but hemolysis was enhanced by its presence. Maximal binding and hemolysis occurred at pH 5.0 and 37 degrees. Vesicles containing only G protein and viral lipid were 40% as hemolytic as intact virions at pH 5.0, but were inactive at pH 6.0; "spikeless" virions lacking G, or protein-free viral lipid vesicles were not hemolytic, showing that G protein is necessary for hemolysis. These results, together with other recent observations, suggest that multiple electrostatic interactions between VSV and the cell surface, rather than an affinity for specific surface molecules, mediated the productive (infection producing) binding of VSV to the cell surface.

Animals↗
PubMed1994

Thermodynamics of protein folding: effects of hydration and electrostatic interactions.

DNA base sequences contain a variety of information, and this information flows from DNA to a protein through the steps of transcription and translation. The one dimensional information given from DNA is the amino acid sequence of the protein. In an organism, a nascent chain synthesized in vivo from the N-terminus according to the information in DNA folds spontaneously to a native conformation under a given environmental condition, i.e., water is the solvent and concentration of salts, pH, temperature, and pressure are appropriate. The polypeptide chain synthesized chemically from the C-terminus also folds to the native conformation, and often exhibits the proper enzymic activity. X-ray crystallography reveals the three dimensional structure of a protein in crystal, indicating that the location of the constituent atoms in the space is specific for that protein, i.e., the information on how to fold is contained in the amino acid sequence. In order to understand the folding, however, other factors such as geometrical information on each amino acid should be taken into account, because a sequence is one dimensional information and a 3D structure is three dimensional. Environmental conditions are also crucial factors in the folding, since a change in conditions can destroy the native structure. The folding and unfolding phenomena are described in terms of thermodynamics when the processes occur reversibly. As experiments show, the stability of a protein conformation can be described by the free energy of folding or unfolding. Folding of a nascent chain to the native conformation, thus, is interpreted as the process towards a minimum of the folding free energy. Thermodynamic quantities of folding or unfolding are expressed as functions of temperature, pressure, and concentration of reagents such as salts, and the quantities are measured as the differences between states, e.g., the N and D states. Since the effects of surrounding media must be included, the phenomenon in aqueous solution at a given condition of pH and salt concentration is divided into the several steps shown in Fig. 12. The chain molecule has two states, N and D, in vacuo; the molecule is then transferred into water, accompanied by the hydration in both states; next, the ionization process produces electrostatic interactions in the molecule; and finally, addition of chemical reagents like denaturants has other effects on the stability.

Animals↗
PubMed1983

Electrostatic and hydrophobic effects in chromatography of rabbit IgG immunoglobulins on aminohexyl sepharose substituted with bis-(p-chlorophenyl)- acetic acid.

The binding interactions of rabbit IgG immunoglobulins with bis-(p-chlorophenyl)-acetic acid (DDA) substituted aminohexyl Sepharose (AHS) (DDA-AHS) at low ionic strength are under the influence of pH, temp, ionic strength and their antibody specificity. The IgG molecules held on a DDA-AHS column in the presence of 0.01 M phosphate buffer (pH 6.8) at 4 degrees C could be stepwise eluted by the addition of 0.01 M acetate buffers (pH 5.5, 5.0 and 4.5) followed by 3 M NaClO4, a chaotropic reagent. The adsorbability of IgG molecules by the DDA-AHS column was reinforced at temps higher than 4 degrees C and at increasing NaCl concns ranging from 0.05 to 0.2 M. The antibody specificity and, perhaps, binding affinity greatly affected this binding system. On the basis of these results, it was evident that both the DDA ligand and charged groups (omega-amino and isourea groups) took part in the binding interactions between IgG molecules and the agarose derivative at low ionic strength. Thus the binding interactions of rabbit IgG immunoglobulins with DDA-AHS at low ionic strength are assumed to be due to hydrophobic plus electrostatic interactions. It was also observed that the binding site on the surface of IgG molecules at low ionic strength was located only in the Fab region.

Animals↗
PubMed1993

CD4-derived peptide and sulfated polysaccharides have similar mechanisms of anti-HIV activity based on electrostatic interactions with positively charged gp120 fragments.

The mechanism of antiviral activity of the CD4-derived peptide 75-99 was compared with that of sulfated polysaccharides. A set of peptides representing all the high positive charge density regions of gp120 and gp41 was used to determine whether electrostatic interactions occur between these negatively charged agents and positively charged HIV envelope fragments. Synthetic peptide AZ2, amino acids 75-99 from V1 CD4, KIEDSDTYIC(Acm)-EVEDQKEEVQLLVFG, and dextran sulfate 500,000 (DS 500) were used as inhibitory agents of antibody binding in ELISA using: (1) anti-peptide rabbit antibodies; (2) sera from HIV infected persons. Peptide AZ2 and DS were both shown to block antibody binding to peptide (301-323) from the principal neutralizing domain (PND) and peptide (495-516) from the gp120 C-terminus. The blocking concns were 1-2 micrograms/ml for DS and 125-250 micrograms/ml for AZ2. The ELISA system based on rabbit anti-peptide antibodies was less sensitive than that based on positive human sera. Chemical modification of lysine epsilon-amino groups of these peptides resulted in complete failure to bind either DS or AZ2. A correlation was found between the inhibitory activities of a number of sulfated polysaccharides in a syncytium formation assay and in peptide ELISA. The mechanism of direct interactions of specific regions of gp120 with the CDR3-like region of CD4 is proposed.

Amino Acid Sequence↗
PubMed1983

Electrostatic interactions in Cu,Zn superoxide dismutase. Effects of Ca(II) and of anions not binding to the copper.

Cu,Zn superoxide dismutase (EC 1.15.1.1) from bovine erythrocyte was found to enhance Tb(III) luminescence in a way suggestive of the presence of specific sites binding calcium. Binding of Ca(II) had no effect on the enzyme activity. However, the low-temperature EPR spectra of the enzyme-bound copper were modified into a more axial line shape by Ca(II) and Tb(III), but not by other cations. This effect was not observed by room-temperature EPR and was interpreted as being due to a long-range conformational effect on the copper-binding site occurring on freezing when specific charged amino acid side-chains are neutralized. This interpretation is supported by similar effects observed with anions that neither have inhibitory effect on the activity nor bind to the copper. These results indicate the presence of specific electrostatic interactions of the protein moiety of Cu,Zn superoxide dismutase and the occurrence of changes of the symmetry of the copper site when the protein is frozen under certain conditions.

Animals↗
PubMed1988

A kinetic study of the reactions between H2O2 and Cu,Zn superoxide dismutase; evidence for an electrostatic control of the reaction rate.

H2O2 was shown to reduce the copper ion of native bovine Cu,Zn superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) (ECu2+) and to oxidize the reduced enzyme (ECu+). The time-course of these processes was monitored by NMR measurement of the longitudinal relaxation rate of the water protons. A steady-state characterized by the same ratio [ECu2+]/[( EC2+] + [ECu+]) was obtained either by starting from the oxidized or the reduced enzyme. The kinetics of these processes appear to be quite complex, since different reactions between H2O2, or its reaction products, and the enzyme-bound copper control the reaction rate. The solution of the differential equations describing the kinetic processes showed that the oxidation and the reduction of the copper ion by H2O2 are first-order with respect to the copper ion itself only when these processes approach the steady-state. The rate constants of the reduction and oxidation reactions were calculated according to these equations and were found to have comparable values which are in the range 5-80 and 5-45 M-1.min-1, respectively, changing the pH from 5.6 to 7 at 0.21 M ionic strength. This result, together with the dependence of the reaction rates on pH and ionic strength, points to HO2- as the reactive species in both processes, and indicates that the electrostatic control of the access of the peroxide to the active site is the rate-determining step of the two redox reactions.

Animals↗
PubMed1991

Electrostatic effects in the alpha-chymotrypsin-catalyzed acyl transfer. II. Efficiency of nucleophiles bearing charged groups in various locations.

We investigated the alpha-chymotrypsin-catalyzed acyl transfer to a series of glycine oligomers. It could be established that the electrostatic interactions between the carboxylate group of the nucleophiles and the S'-subsites of the enzyme fall off with the length of the nucleophile molecule. Additional negatively charged residues in the nucleophile lead to a considerable reduction of the acyl transfer efficiency. An arginine residue in P'1- or P'3-position, but not in P'2-position, makes favourable interactions with the appropriate S'-subsites of the enzyme.

Acylation↗
PubMed1986

Contribution of electrostatic and hydrophobic interactions of bitter substances with taste receptor membranes to generation of receptor potentials.

The effects of changed ionic environments on the frog taste nerve responses to the bitter substances were examined. The responses to quinine and strychnine carrying a positive charge were suppressed by an increase in ionic strength of stimulating solutions. It was concluded that electrostatic interaction of these positive bitter substances with the receptor membranes greatly contributes to the adsorption of the substances on the membranes and that this interaction was suppressed by an increase in ionic strength. The responses to neutral bitter substances (caffeine and theophylline) were unchanged by an increase in salt concentration. The zeta potential of the mouse neuroblastoma (N-18 clone), which was depolarized by various bitter substances similarly to a taste cell, was measured in the presence of the bitter substances. The zeta potential was a little changed by quinine and practically unchanged by strychnine, caffeine and theophylline. The membrane fluidity of the N-18 cell monitored with 2-(9-anthroyloxy)stearic acid was changed in response to the bitter substances, while the fluidity monitored with 12-(9-anthroyloxy)stearic acid or 1,6-diphenyl-1,3,5-hexatriene was unchanged. This suggested that the bitter substances are adsorbed on the hydrophobic region near the surface and induce a conformational change at the region. The depolarization by the bitter substances seems to stem from changes in the "boundary potential" at the region near the surface within the membrane interior.

Adsorption↗
PubMed1989

An electrostatic mechanism of muscular contraction.

The electrostatic mechanism proposed in the theory of muscular contraction propounded by Iwazumi is the force produced between an electric dipole and induced dipoles on a high dielectric rod. This force is similar to one between a short bar magnet and an iron rod. The force is always attractive and unidirectional and the rod orients itself to the direction pointing to the centre of the magnet. In muscle, the active cross-projection of myosin is analogous to the bar magnet, but an electric field is created by the dipole properties of myosin which are amplified during activation by the action of calcium ions and adenosine triphosphate. The filaments of actin are analogous to the iron rod. Detailed mathematical application of this principle to the array of filaments found in muscle, with incorporation of the troponin/tropomyosin complex, yields a complete theory of muscular contraction which provides explanations for many as yet unexplained phenomena, and provides a set of specific predictions for test.

Actins↗
PubMed1993

Reproduction of correct electrostatic field by charges and dipoles on a closed surface.

A general algorithm based on the Green function theorem has been developed to correctly reproduce electrostatic fields inside a closed space by point charges and point dipoles on the surface surrounding the space. For actual computations, limited numbers of point charges, including charge pairs replacing point dipoles, are enough to approximate the inner fields. As examples, reaction fields were reproduced by the current surface charges and dipoles for the dielectric models, where a monopole, dipole, or quadrupole was individually set at the center in a vacuum sphere surrounded by high dielectric continuum. The potentials due to those reaction fields agree well with the analytical ones. As an application of this method to the analysis of the electronic structure of the active site of a protein, a combination of the continuum dielectric model and ab initio molecular orbital calculation was carried out. Other applications to molecular dynamics and quantum mechanical calculations are also discussed.

Algorithms↗
PubMed1994

Calculated surface electrostatic potentials of molecular sieve models containing SiO4, AlO4, and PO4 units.

Surface electrostatic potentials have been computed at the ab initio HF/STO-5G* level for two model systems: a fragment of a zeolite channel wall; and a fragment composed of SiO4, AlO4 and PO4 units. The potential above the SiO4 network is negative everywhere, despite these units commonly being regarded as electrically neutral. In marked contrast, the AlO4 and PO4 units introduce strongly negative and positive regions, respectively, giving rise to a much more heterogeneous surface potential.

Aluminum Compounds↗