Role Of Electrostatic Interactions Research Articles

Electrostatic Interaction of Globins with Phospholipid Membranes

For the structures of sperm whale myoglobin (swMb), horse heart myoglobin (hhMb), hemoglobin I (HbI) from botfly Gasterophilus intestinalis (giHbI), and monomeric and dimeric hemoglobins HbI and HbII from Lucina pectinata mollusk (lpHbI and lpHbII), roles of electrostatic interactions in stabilization of native conformations of the heme cavity were analyzed, as well as their possible destabilization by interaction with the negatively charged phospholipid membranes. The native conformation of the heme cavity in these globins, both its proximal and distal parts, was shown to be sustained by a system of hydrogen bonds involving the proximal and distal protein residues, the heme propionates, and the nearby polar amino acids on the protein surface (His, Arg, Lys). The hydrogen bond network in the proximal part of the heme pocket controls the position of the Fe atom either outside or within the protoporphyrin plane, which affects the efficiency of ligand binding. In the distal part, the hydrogen bond network formed with the distal protein residue involved (HisE7 in swMb, hhMb, and giHbI and GlnE7 in lpHbII), should stabilize the conformation in which the protein can donate hydrogen to the O2 ligand. The hydrogen bond between the E7 distal residue and O2 ligand prevents rapid dissociation of the latter and plays an important role in the regulation of ligand affinity. The hydrogen bond networks found in the proximal and, especially, in the distal heme environments, must be disrupted when oxyglobin binds to the membrane surface. This disruption caused by interaction of negatively charged phospholipid heads with lysine or arginine residues exposed towards the membrane, altered local pH near the membrane, and the effect of negative electrostatic field of the membrane, can decrease the affinity of the protein for the O2 ligand, thus facilitating its dissociation at the physiological pO2 values in the cell.

Role of Electrostatic Interactions for the Prediction of Function and Specificity in Redox Protein-protein Interactions

Role of Electrostatic Interactions for the Prediction of Function and Specificity in Redox Protein-protein Interactions

Adsorption kinetic of myoglobin on mica and silica – Role of electrostatic interactions

Adsorption kinetics of myoglobin molecules on mica and silica was studied using the atomic force microscopy (AFM), the colloid enhancement and the quartz microbalance (QCM) methods. Measurements were carried out for the NaCl concentration of 0.01 and 0.15 M as a function of pH comprising pH 7.4 stabilized by the PBS buffer. The electrophoretic mobility measurements enabled to derive the molecules zeta potential as a function of pH. The isoelectric point appearing at pH 5, is lower than that predicted from the theoretical calculations of the nominal dissociation charge. The AFM investigations confirmed that myoglobin molecules irreversibly adsorb at pH 3.5 yielding well-defined layers of single molecules. These layers were characterized using the colloid enhancement method involving polymer microparticles for pH range 3–9. The microparticle deposition kinetics was adequately interpreted in terms of a hybrid random sequential adsorption model. It is confirmed that the myoglobin layers exhibit a negligible zeta potential at pH equal to 5 in accordance with the electrophoretic mobility measurements. Analogous adsorption kinetic measurements were performed for the silica substrate using QCM and AFM. It is observed that myoglobin molecules irreversibly adsorb at pH 3.5 forming stable layers of single molecules. On the other hand, its adsorption kinetics at larger pHs was much slower exhibiting a poorly defined maximum coverage. This was attributed to aggregation of the myoglobin solutions due to their vanishing charge. The kinetic QCM runs were adequately interpreted in terms of a theoretical model combining the Smoluchowski aggregation theory with the convective diffusion mass transfer theory.

Improvements on modelling wettability alteration by Engineered water injection: Surface complexation at the oil/brine/rock contact

Several laboratory experiments demonstrated that different water compositions cause rocks to change from oil- to water-wet state. Although it is a consensus that wettability alteration is the main recovery process, modeling the underlying mechanism is still a major challenge. Our main goal is to improve and validate a physically based model to predict contact angles from zeta-potential measurements. We hypothesize that, if rock and oil surface are sufficiently close as consequence of thin water layer, then the charge development of one surface will be affected by the other. We propose a new mass-action formulation for surface complexation modelling that includes the energy interface of two interacting double layers. Currently, surface complexation models consider rock and oil as completely isolated surfaces. Additionally, we develop a method of determining surface complexation equilibrium constants to honor several zeta-potential measurements for different ion concentrations (Na+, Ca2+, Mg2+, SO42− and H+). Finally, we estimate contact angles using disjoining pressure calculations and compare them with experimental ones reported in the literature.For the proposed parallel surface model, the system of equations’ solution is very distinct to isolated surface approach when the interaction between surfaces are close (spacing approximately bellow 2 nm) at high salinity. Regarding zeta-potential prediction for calcite-brine system, we argue that Na+ might not be an indifferent ion as suggested previously. Our simulation results indicate that, besides the renowned potential-determining ions, sodium adsorption on calcite can play an important role in electrostatic interactions, switching surface charge polarity. Thus, we only honor zeta-potential measurements when Na+ is considered in the surface complexation reactions. Finally, contact angle estimation using proposed surface complexation modelling and disjoining pressure theory provide good predictions of seven different cases reported in the literature. We validate our method on a total of 66 and 163 contact angle and zeta-potential measurements, respectively. The present work is a novel approach to represent how electrostatic interactions among rock, brine and oil modify the rock surface charge and the rock wetting state.

Conducting Polymers: The Role of Electrostatic Interaction between Free Charge Carriers and Counterions in Thermoelectric Power Factor of Conducting Polymers: From Crystalline to Polycrystalline Domains (Adv. Theory Simul. 6/2020)

In article number 2000015, new insights into thermoelectric transport in conducting polymers based on first-principles calculations and new material design guidelines are presented by Shuo-Wang Yang and co-workers. They demonstrate that in the crystalline domains, the counterion scattering controls the power factor, and in the polycrystalline domains, the crystallite orientations and the grain sizes strongly affect the power factor.

The Role of Electrostatic Interaction between Free Charge Carriers and Counterions in Thermoelectric Power Factor of Conducting Polymers: From Crystalline to Polycrystalline Domains

AbstractOne of the most burning problems in organic thermoelectrics is the lack of deep understanding on the key limiting factors of thermoelectric efficiency at different length scales for conducting polymers. Here, by examining a prototypical π‐conjugated polymer, poly(3‐hexylthiophene) from molecular level to crystalline and polycrystalline domains, and on the basis of first‐principles calculations, new insights are presented into the thermoelectric transport in conducting polymers, and new material design guidelines are provided. It is proved that in the crystalline domains of conducting polymers, due to the strong electrostatic interactions between free charge carriers and counterions, the power factor within a wide range of doping level is governed by the counterion‐induced electronic scattering. It is corroborated that in the polycrystalline domains, although the short mean free path prevents the holes undergoing grain‐boundary scatterings, the crystallite orientations relative to the conduction path and the grain sizes strongly affect the power factor, leading to the modulation of the power factor by at least two orders of magnitude.

Zn-CysHis Protein Factor Families: Role of Electrostatic Interaction of Zn-Domains in Factor Functions

Zn-CysHis Protein Factor Families: Role of Electrostatic Interaction of Zn-Domains in Factor Functions

Temperature and electrostatics effects on charged poly(N-isopropylacrylamide) microgels at the interface

Thermoresponsive microgels based on poly-N-isopropylacrylamide (PNIPAM) have many biomedical applications owing to their biocompatibility and their Volume Phase Transition Temperature (VPTT) around the physiological temperature. Understanding the surface structure of PNIPAM microgels in monolayers is important in terms of fundamental science and towards their use in thermoresponsive emulsions. However, to date there are no reported studies of PNIPAM monolayers above and below the VPTT. In addition, the role of electrostatics in surface films of charged microgels remains controversial. Hence, in the present paper, we study the surface conformation of charged PNIPAM at different swelling states. Shrunken PNIPAM microgels in bulk show higher effective charge than swollen microgels. In agreement with this, we find that monolayers of shrunken PNIPAM particles are compressed more easily than that of swollen PNIPAM particles. The role of electrostatic interactions is further addressed by modifying the concentration of electrolyte, which alters the effective charge but retains the particle size of microgels. We find that screening the effective charge of the microgel has a strong impact on the lateral packing of the monolayer displacing the compression isotherms to higher normalised areas. Moreover, the displacement correlates with the changes in the effective charge of the microgels induced by the electrolyte. Hence, we prove that beyond the different swelling ratio, electrostatics can modulate the interactions between charged microgel particles at the interface.

ЭЛЕКТРОСТАТИЧЕСКОЕ ВЗАИМОДЕЙСТВИЕ ГЛОБИНОВ С ФОСФОЛИПИДНЫМИ МЕМБРАНАМИ

The present study aimed to analyze the role of electrostatic interactions contributing to the stability of the native conformations of the heme group in the structure of sperm whale myoglobin (SWMb), horse heart myoglobin (HHMb), hemoglobin I (HbI) from the botfly Gasterophilus intestinalis (giHbI) and monomeric and dimeric hemoglobins HbI and HbII from the mollusk Lucina pectinata (lpHbI and lpHbII) as well as investigate a possible reason of destabilization due to interaction with negatively charged phospholipid membranes. It was shown that the native conformation of the heme cavity in these globins, both in its proximal and distal sides, is sustained by a system of hydrogen bonds involving the proximal and distal protein residues, both heme propionic acid groups and the nearby polar amino acids on the protein surface (His, Arg, Lys). The hydrogen bond network in the proximal part of the heme pocket controls the position of the Fe atom outside or in the protoporphyrin plane, affecting the efficiency of ligand binding, while in the distal part of the heme cavity the hydrogen bond network formed with the participation of the distal protein residue (HisE7 in swMb, hhMb and giHbI, and GlnE7 in lpHbII) should, apparently, stabilize conformation where the protein is able to donate hydrogen to O2 ligand...

Multicomponent Ionic Transport Modeling in Physically and Electrostatically Heterogeneous Porous Media With PhreeqcRM Coupling for Geochemical Reactions

AbstractLow‐permeability aquitards, such as clay layers and inclusions, are of utmost importance for contaminant transport in groundwater systems. Although most dissolved species, contaminants, and clay surfaces are charged, the role of electrostatic interactions in subsurface flow‐through systems has not been extensively investigated. This study presents a two‐dimensional multicomponent reactive transport investigation of diffusive/dispersive and electrostatic processes in homogeneous and heterogeneous clay systems. The proposed approach is based on multiple continua and is capable to accurately describe charge interactions during ionic transport in the free water, diffuse layer, and interlayer water of charged porous media. The diffuse layer composition is simulated by considering a mean electrostatic potential following Donnan approach, whereas the interlayer composition is calculated by adopting the Gaines‐Thomas convention. Diffusive/dispersive fluxes within each subcontinuum (free water, diffuse layer, and interlayer) are calculated solving the Nernst‐Planck equation while maintaining a net zero‐charge flux. Furthermore, the multidimensional flow and transport model is coupled with the geochemical code PHREEQC, by utilizing the PhreeqcRM module, thus enabling great flexibility to access all PHREEQC's reaction capabilities. The code is benchmarked in 1‐D systems against other software and previously published experimental data. Successively, reactive transport simulations are performed in 2‐D clayey‐sandy flow‐through domains with spatially variable physical and electrostatic properties at both laboratory and field scales. The results reveal that different properties of surface charge, diffuse layer, and Coulombic interactions impact the transport of charged species and lead to distinct spatial distribution of the ions in the different subcontinua and to significantly different breakthrough curves.

Multimodal Interactions of Dopamine Hydrochloride with the Groove Region of DNA: A Key Factor in the Enhanced Stability of DNA

Nucleic acids (DNA) and neurotransmitters integrate together in the brain of organisms to make powerful information processing systems. Dopamine is an important neurotransmitter whose complexation with DNA in its protonated form has been implemented in several applications such as sensors, antitumor drugs, and bioengineering. However, the molecular level understanding about the binding of protonated dopamine with the different regions of DNA and its effect on the structure as well as stability of DNA is very limited. The nature of binding of protonated dopamine with DNA and its effect on the stability and structural integrity of DNA have been extensively investigated using different spectroscopic and molecular dynamics (MD) simulation techniques. Spectroscopic studies suggest that the multimodal interaction of protonated dopamine with DNA bases in its groove region enhances its stabilization without causing any perturbation in the canonical form of DNA. MD simulation study depicts that protonated dopamine intrudes into the groove region of DNA by replacing the surrounding water and interacts with the bases in the major and minor grooves of DNA in a multimodal manner. Electrostatic and dispersion interactions contribute to the stabilization of the interaction of dopamine with the minor groove bases of DNA, whereas the role of electrostatic interaction is prominent in the case of the major groove. The binding of dopamine with the groove region of DNA enhances the hydrogen bond between its Watson-Crick base pairs, which results in higher stabilization of DNA as compared to that in buffer condition. This study provides a molecular level insight about the binding of dopamine with DNA, which can be useful in diverse areas ranging from medicine to bioengineering.

Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein.

The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica-exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary structure changes due to the Val66Met mutation, when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies “blobs” of 4-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β-bridging between V66 and V94 (on either side of the linker) with specific side-chain interactions between M66 and M95. The protein backbone in the vicinity of M95 is then free to form β-bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.

The role of electrostatic interactions in IFIT proteins complexed with RNA with different 5′ end predicted by the UBDB+EPMM method

The role of electrostatic interactions in IFIT proteins complexed with RNA with different 5′ end predicted by the UBDB+EPMM method

The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses.

In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures.

Acid–Base Chemistry of Porphyrin/Graphene Oxide Complex: Role of Electrostatic Interaction

The acid–base chemistry of cationic 5,10,15,20‐tetrakis(1‐methyl‐4‐pyridinio)porphyrin (TMPyP) and graphene oxide (GO) complex was studied in aqueous solution using absorption and fluorescence spectroscopy. By varying the pH from 0 to 13, we controlled the electrostatic properties of TMPyP and/or GO. The neutrality on GO or negative charge on TMPyP induced the dissociation of the TMPyP/GO complex, indicating that the electrostatic attractive force is indispensable for both forming and preserving the complex. Furthermore, our results suggest that the molecular flattening of the TMPyP in the TMPyP/GO complex is mainly caused by the π–π interaction.

A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey

Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering.AbbreviationsMDMolecular DynamicsNSCsNeural Stem CellsPMEParticle mesh EwaldRDFRadial Distribution FunctionRGRadius of gyrationRASARelative Accessible Surface AreaRMSDRoot Mean Square DeviationsSASASolvent Accessible Surface Area.Communicated by Ramaswamy H. Sarma

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.

Role of Electrostatic Interactions in Oil-in-Water Emulsions Stabilized by Heteroaggregation: An Experimental and Simulation Study.

Oil-in-water emulsion stabilization by heteroaggregation of hydrophilic particles without a surfactant is of importance in a wide range of applications; however, the stabilization mechanism is little described. To shed light on the early stage of the stabilization mechanism, a model system composed of an oil wax phase dispersed in water with oppositely charged colloidal particles is studied experimentally and numerically. Experiments show that the colloids do not penetrate deeply in the oil phase, suggesting that adsorption of the colloidal particles on the wax droplets is mainly due to electrostatic interactions. Experiments and Brownian dynamics simulations show also that when oppositely charged colloidal particles are present in the emulsion, a multilayer coating of heteroaggregated colloidal particles is formed around the wax droplets. This protective coating is expected to prevent from the oil droplet coalescence and therefore to stabilize the emulsion.

Role of Electrostatic Interactions on Supramolecular Organization in Calf-Thymus DNA Solutions under Flow.

Previous investigations were conducted on two concentrations of DNA solution: 4 mg/mL, for which it has been shown that no supramolecular organization is induced under flow at low shear rates; and 10 mg/mL, in which a liquid crystalline-type texture is formed under flow at low shear rates, attesting to an orientation of pre-organized chains. Rheological experiments are discussed and their results supported by small-angle X-ray scattering (SAXS) and flow birefringence visualization experiments. Scattering from polyelectrolytes has a characteristic signal, which is here observed in SAXS, showing a strong correlation peak between charged chains in water, for both concentrations. This peak is weaker in the presence of 0.01 M NaCl and suppressed in salt excess at 0.1 M NaCl. No plateau in the σ() plot was observed in analysis of rheological experiments on low DNA concentration (4 mg/mL). As typically observed in polyelectrolyte systems both the dynamic moduli and shear viscosity were higher in water as electrostatic forces dominate, than in the presence of salt, especially at low shear rates. The rheological results for concentrations of 0.01 M NaCl are lower than in water as expected due to partial screening of electrostatic repulsions. Rheological data for concentrations of 0.1 M NaCl are unexpected. Electrostatic forces are partially screened in the low salt concentration, leading to a drop in the rheological values. For high salt concentration there are no longer interchain repulsions and so steric interactions dominate within the entangled network leading to the subsequent increase in rheological parameters. Regardless of the solvent, at high shear rates the solutions are birefringent. In the 10 mg/mL case, under flow, textures are formed at relatively low shear rate before all the chains align going to a pseudonematic liquid crystalline phase at high shear rate. The electrostatic repulsion between semi-rigid chains induces a correlation between the chains leading to an electrostatic pseudo-gel in water and loosely in 0.01 M NaCl at low stress applied. To the best of our knowledge, this is the first time that such behavior is observed. In 0.1 M NaCl, DNA behavior resembles the corresponding neutral polymer as expected for polyelectrolyte in salt excess, exhibiting a yield stress. When texture appears in water and in 0.01 M NaCl, a critical transition is observed in rheological curves, where the viscosity decreases sharply at a given critical shear stress corresponding to a plateau in the σ() plot also observed in creep transient experiment.

Unraveling the molecular interaction mechanism between graphene oxide and aromatic organic compounds with implications on wastewater treatment

Graphene oxide (GO) has been extensively applied in environmental and chemical engineering applications, such as wastewater remediation and organic compounds sensing, in which the adsorption of aromatic organic compounds (AOCs) (e.g., dyes, drugs and pesticides) on GO is commonly involved. Understanding the fundamental interaction mechanism of AOCs-GO is critical for these applications and designing advanced functional GO-based nanocomposites. In this work, for the first time, the nanomechanical interaction mechanism between GO and a model AOC molecule is quantitatively characterized using single-molecule force spectroscopy (SMFS) and density functional theory (DFT) simulations. The contributions of major functional groups of GO to the binding affinity and configurations of AOC/GO complex have been investigated. It is found that most binding events in the formation of AOC/GO complex should be attributed to the attraction between the cationic AOC molecule and the regions on GO with epoxy groups, the role of which has been overlooked previously, with an activation Gibbs energy for bond dissociation (ΔG) of −4.61 kcal mol−1. Surprisingly limited occurrence of binding events between the cationic AOC and the regions with ionized carboxylic groups on GO suggests that the role of electrostatic interaction has been overrated traditionally. Our results provide new nanomechanical insights into the interaction mechanism of AOCs-GO with useful implications for developing novel AOC/GO nanocomposites with environmental, biomedical and engineering applications.