Solvent accessibility of the thrombin-thrombomodulin interface

The kinetics of solvent accessibility at the protein-protein interface between thrombin and a fragment of thrombomodulin, TMEGF45, have been monitored by amide hydrogen/deuterium (H/2H) exchange detected by MALDI-TOF mass spectrometry. The interaction is rapid and reversible, requiring development of theory and experimental methods to distinguish H/2H exchange due to solvent accessibility at the interface from H/2H exchange due to complex dissociation. Association and dissociation rate constants were measured by surface plasmon resonance and amide H/2H exchange rates were measured at different pH values and concentrations of TMEGF45. When essentially 100% of the thrombin was bound to TMEGF45, two segments of thrombin became completely solvent-inaccessible, as evidenced by the pH insensitivity of the amide H/2H exchange rates. These segments form part of anion-binding exosite I and contain the residues for which alanine substitution abolishes TM binding. Several other regions of thrombin showed slowing of amide exchange upon TMEGF45 binding, but the exchange remained pH-dependent, suggesting that these regions of thrombin were rendered only partially solvent-inaccessible by TMEGF45 binding. These partially inaccessible regions of thrombin form both surface and buried contacts into the active site of thrombin and contain residues implicated in allosteric changes in thrombin upon TM binding.     

Electrostatic interaction in atomic force microscopy

In atomic force microscopy, the stylus experiences an electrostatic force when imaging in aqueous medium above a charged surface. This force has been calculated numerically with continuum theory for a silicon nitrite or silicon oxide stylus. For comparison, the Van der Waals force was also calculated. In contrast to the Van der Waals attraction, the electrostatic force is repulsive. At a distance of 0.5 nm the electrostatic force is typically 10^-12-10^-10 N and thus comparable in strength to the Van der Waals force. The electrostatic force increases with increasing surface charge density and decreases roughly exponentially with distance. It can be reduced by imaging in high salt concentrations. Below surface potentials of ≈50 mV, a simple analytical approximation of the electrostatic force is described.     

Electrostatic interaction between ion-penetrable multi-layered membranes

A theory of the double layer interaction regulated by the Donnan potential between two ion-penetrable membranes in an electrolyte solution developed previously by Ohshima and Kondo is extended to the case in which the membranes consist of many layers having different thickness and densities of membrane-fixed charges. The interaction force is found to be determined mainly by the contributions from layers located within the depth of 1/kappa (kappa, Debye-Hückel parameter) from the membrane surface. It is also predicted that the interaction force may alter its sign with changing electrolyte concentration.     

Electrostatic interaction in the reaction between porphyrin and DNA

The association of tetrakis(4-N-methylpyridyl)porphine with salmon testes DNA in solution has been investigated in the presence of ethanol at 25 degrees C. It was found that the association constant was 1.14 x 10(6) M-1 and it increased with increasing the mole fraction of added ethanol. The behavior was very different from that in the case of usual intercalaters.     

Electrostatic interaction between two charged spherical molecules

An explicit analytic expression is obtained for the electrostatic energy of the interaction between two ion-impenetrable space-charged hard spheres as a model for spherical molecules in an electrolyte solution on the basis of the linearized Poisson-Boltzmann equation. An explicit expression for the potential distribution in a 3D-space is also found. The polarization effects due to the mutual influence between the spheres are taken into account. The analysis is done by assuming different dielectric permittivities of the respective spheres and of the solution as well. It is shown that the correction terms in the expression for the total energy of interaction arising from the polarization effects always correspond to forces of attraction between the spheres. The contribution of these terms to the total energy of interaction depends on the distance between the two spheres and the dielectric permittivities of the spheres and the solution as well as on the electrolyte concentration in the solution. A numerical simulation of the potential field topography is carried out at several values of the Debye-Hückel parameter. It is shown that the polarization effect can produce significant changes in the potential distribution in the case of strong interacting spheres.     

Identification of structural domains in protein C involved in its interaction with thrombin-thrombomodulin on the surface of endothelial cells.

The structural domains of protein C involved in its interaction with thrombin-thrombomodulin on the endothelial cell surface have been investigated using isolated intact domains of bovine protein C produced from controlled proteolytic digests of the protein. The fragments investigated include the gamma-carboxyglutamic acid (Gla)-rich module, the two epidermal growth factor (EGF)-like modules, and a fragment consisting of the Gla and the two EGF-like modules. The effects of these fragments on the catalytic efficiency (Km and Vmax) of activation of protein C by the endothelial cell surface thrombin-thrombomodulin complex (IIa-TM) have been evaluated in vitro using a stirred microcarrier cell culture of bovine aortic endothelial cells and purified proteins. Neither the Gla nor the two EGF-like modules alone had any discernible effect on protein C activation. The intact Gla-EGF fragment, however, inhibited protein C activation. The results are consistent with a rapid equilibrium competitive inhibition model, in which the Gla-EGF fragment competes with protein C for binding to IIa-TM, and indicate that the Gla-EGF fragment alone accounts for most of the binding energy of intact protein C for IIa-TM. In addition, a requirement for the Gla residues of protein C for binding is implied by the observation that heat-decarboxylated Gla-EGF fragment was not an inhibitor of protein C activation. In addition, chloromethyl ketone-inactivated activated protein C was found to bind to IIa-TM with the same affinity as protein C, suggesting that the changes which occur in protein C upon activation do not affect that part of the protein responsible for binding to IIa-TM, that is the Gla-EGF region. The Gla-EGF region from factor X also weakly inhibited the IIa-TM activation of protein C.     

Electrostatic interaction of pi-acidic amides with hydrogen-bond acceptors

Interactions between N-methylacetamide (NMA) and N-methylated derivatives of uracil, isocyanurate and barbituric acid have been studied using ab initio methods at the local MP2/6-31G** level of theory. The results were compared to similar interactions between the oxygen atom of NMA and the pi-clouds of perfluorobenzene, quinone and trimethyltriazine. The pi-acidic amides of isocyanurate and barbituric acid were found to interact with a hydrogen bond acceptor primarily through electrostatic attractions. These groups may be used as alternatives of a hydrogen bond donor to complement a hydrogen bond acceptor or an anion in molecular recognition and drug design. Examples of such interactions were identified through a search of the CSD database.     

Electrostatic interaction between gating charges in nerve membranes

The electrostatic interaction between charges within a nerve membrane is considered. It is seen that the electrostatic repulsion between so called gating particles of an ionic channel cannot be neglected in the formulation of excitability models based on gating charges. Some general conclusions are drawn about different models for nerve membrane excitability.     

Electrostatic interaction between redox cofactors in photosynthetic reaction centers

Intramolecular electron transfer within proteins is an essential process in bioenergetics. Redox cofactors are embedded in proteins, and this matrix strongly influences their redox potential. Several cofactors are usually found in these complexes, and they are structurally organized in a chain with distances between the electron donor and acceptor short enough to allow rapid electron tunneling. Among the different interactions that contribute to the determination of the redox potential of these cofactors, electrostatic interactions are important but restive to direct experimental characterization. The influence of interaction between cofactors is evidenced here experimentally by means of redox titrations and time-resolved spectroscopy in a chimeric bacterial reaction center (Maki, H., Matsuura, K., Shimada, K., and Nagashima, K. V. P. (2003) J. Biol. Chem. 278, 3921-3928) composed of the core subunits of Rubrivivax gelatinosus and the tetraheme cytochrome of Blastochloris viridis. The absorption spectra and orientations of the various cofactors of this chimeric reaction center are similar to those found in their respective native protein, indicating that their local environment is conserved. However, the redox potentials of both the primary electron donor and its closest heme are changed. The redox potential of the primary electron donor is downshifted in the chimeric reaction center when compared with the wild type, whereas, conversely, that of its closet heme is upshifted. We propose a model in which these reciprocal shifts in the midpoint potentials of two electron transfer partners are explained by an electrostatic interaction between them.     

Electrostatic and hydrophobic interactions governing the interaction and binding of beta-lactoglobulin to membranes

The role of electrostatic and hydrophobic interactions in the binding and penetration of beta-lactoglobulin (betaLG) to preformed lipid membranes was studied using various phospholipid micelles and vesicles. Zwitterionic lysophospholipid micelles are able to induce the beta-sheet to alpha-helix transition, as judged by circular dichroism (CD), but the degree of transition is dramatically below and the amount of lipid required above that for anionic phospholipids with equivalent hydrocarbon chains. Anionic phospholipids with short hydrocarbon chains induce only low alpha-helical content in betaLG as compared to phospholipids with the same head group but longer hydrocarbon chains. These results suggest that both electrostatic and hydrophobic interactions are indispensable in betaLG-lipid interaction. Furthermore, air-water interface monolayer surface pressure and fluorescence anisotropy studies reveal that the membrane insertion of betaLG strongly depends on the nature of phospholipids, given the identical headgroup, particularly lipid packing. These results are supported by urea denaturation and acrylamide fluorescence quenching tests and by the FTIR-ATR polarization results for betaLG in multilayers on a surface. Under the same experimental conditions, the membrane binding and insertion of betaLG as well as the stability of the betaLG-lipid complexes can be enhanced by lowering the pH. Collectively, electrostatic interactions play a crucial role in all the processes involved in the betaLG-lipid interaction, while the presence of hydrophobic interaction remains necessary. Finally, betaLG biological function in the transport of fatty acids was tested by demonstrating the release of 2-AS from a 2-AS-betaLG complex on binding to lipids.     

pH dependence of the interaction of hirudin with thrombin.

The kinetics of the inhibition of human alpha-thrombin by recombinant hirudin have been studied over the pH range from 6 to 10. The association rate constant for hirudin did not vary significantly over this pH range. The dissociation constant of hirudin depended on the ionization state of groups with pKa values of about 7.1, 8.4, and 9.2. Optimal binding of hirudin to thrombin occurred when the groups with pKa values of 8.4 and 9.0 were protonated and the other group with a pKa of 7.1 was deprotonated. The pH kinetics of genetically engineered forms of hirudin were examined in an attempt to assign these pKa values to particular groups. By using this approach, it was possible to show that protonation His51 and ionization of acidic residues in the C-terminal region of hirudin were not responsible for the observed pKa values. In contrast, the pKa value of 8.4 was not observed when a form of hirudin with an acetylated alpha-amino group was examined, and, thus, this pKa value was assigned to the alpha-amino group of hirudin. The requirement for this group to be protonated for optimal binding to thrombin is discussed in terms of the crystal structure of the thrombin-hirudin complex. Examination of this structure allowed the other pKa values of 7.1 and 9.2 to be tentatively attributed to His57 and the alpha-amino group of Ile16 of thrombin.     

Electrostatic interaction optimization improves catalytic rates and thermotolerance on xylanases

Understanding the aspects that contribute to improving proteins’ biochemical properties is of high relevance for protein engineering. Properties such as the catalytic rate, thermal stability, and thermal resistance are crucial for applying enzymes in the industry. Different interactions can influence those biochemical properties of an enzyme. Among them, the surface charge-charge interactions have been a target of particular attention. In this study, we employ the Tanford-Kirkwood solvent accessibility model using the Monte Carlo algorithm (TKSA-MC) to predict possible interactions that could improve stability and catalytic rate of a WT xylanase (XynA^WT) and its M6 xylanase (XynA^M6) mutant. The modeling prediction indicates that mutating from a lysine in position 99 to a glutamic acid (K99E) favors the native state stabilization in both xylanases. Our lab results showed that mutated xylanases had their thermotolerance and catalytic rate increased, which conferred higher processivity of delignified sugarcane bagasse. The TKSA-MC approach employed here is presented as an efficient computational-based design strategy that can be applied to improve the thermal resistance of enzymes with industrial and biotechnological applications.     

Electrostatic interaction between merocyanine 540 and liposomal and mitochondrial membranes

Summary The fluorescence of merocyanine 540 (MC) in liposomal and mitochondrial suspensions was measured under various conditions. Under a given condition, both the amount of dye bound to the membrane and the zeta potential were determined simultaneously. It was found that the fluorescence intensity was proportional to the amount of bound dye and correlated with the zeta potential of particles. The fluorescence intensity was represented quantitatively in terms of the Langmuir adsorption isotherm, when the electrostatic interaction acting between MC and membrane surface was properly taken into account. It was concluded that the changes in MC fluorescence in the liposomal and mitochondrial suspensions are mainly attributed to the changes in the surface potential of the membranes.     

Electrostatic interaction of pancreatic and microbial ribonucleases with macrophages in vitro

The interaction of RNase A and RNase Bacillus intermedius with peritoneal macrophage of rats has been studied. To estimate the efficiency of this interaction the spontaneous chemiluminescence and induced by phagocytosis chemiluminescence of macrophages were investigated. It has been shown that electrostatic interaction of enzyme proteins with negatively charged cell membrane makes substantional contribution to the development of chemiluminescence reply of macrophages. The RNase A, which is more basical than the other (i. e. it has larger value of pI) is less effective with respect to macrophages. The calculation of total charge and dipole moment of pancreatic and microbial RNases showed that the efficiency of interaction between protein polycation and a cell was not connected with pI and depended on the charge and its distribution on the surface of protein molecule at the given pH value.     

pH dependence of electrostatic interaction between ion-penetrable membranes

A theory on the electrostatic repulsion between ion-penetrable membranes proposed previously by us is extended by taking into account the degree of dissociation of the membrane-fixed ionizable groups. A system of equations which determines the pH dependence of the membrane interaction is presented. The density of membrane-fixed charges is consistently determined as a function of the electric potential so that both the membrane-fixed charge density and the potential are not constant but functions of the membrane separation. The pH at the surface of interacting membranes is also calculated as a function of the membrane separation.     

The pH dependence of siliconiron interaction in rats

A 2 x 2 x 3 factorial experiment was conducted to study the pH dependence of a silicon-iron interaction in vivo. The dietary treatments used in the factorial design were the following (mg/kg of diet): silicon, 0 and 500; iron, 35 and 187; acid-base, ammonium chloride as 0.5% of total diet (acidic), sodium bicarbonate as 1.0% of total diet (basic), or no supplementation of acid or base (control). The supplementation of 500 mg silicon/kg of diet increased plasma-iron concentration in rats fed the acidic or control diets, but not in rats fed the basic diet. A high dietary-iron level suppressed copper absorption and utilization and subsequently imposed a negative effect on its own utilization. An increase in the plasma total-cholesterol concentration caused by high dietary-iron level was likely a consequence of the antagonistic effect of iron on copper absorption and utilization. The use of cupric sulfate pentahydrate as the dietary-copper source in this study resulted in plasma copper concentrations that were approximately twice those obtained in a related study using cupric carbonate. Also, a 42% coefficient of variation (C.V.) for plasma-copper concentrations of rats fed cupric sulfate in this study was greatly reduced from the C.V. = 108% previously associated with the dietary cupric carbonate.     

Lac repressor-operator interaction: DNA length dependence

The interaction of the E. coli lac operon repressor with its operator DNA has been directly examined as a function of the length of operator-containing DNA. The apparent bimolecular association rate constants were calculated as ka = (kd/KD), where the dissociation equilibrium constant, KD and the dissociation rate constant, kd, were measured by nitrocellulose filter adsorption assays. The values obtained for the overall association rate constants are compared with theoretical association rate curves for specific mechanisms. Association of the repressor with short operator containing DNA fragments (less than 70 base pairs) occurs at rates expected of three-dimensional diffusion. Our data also imply that at longer DNA lengths a combination of three-dimensional diffusion with one-dimensional sliding along with hopping and/or intersegment transfer must be involved to facilitate the repressor operator association.