Role of a highly conserved electrostatic interaction on the surface of cytochrome C in control of the redox function.

PubMed

Tai, Hulin; Mikami, Shin-ichi; Irie, Kiyofumi; Watanabe, Naoki; Shinohara, Naoya; Yamamoto, Yasuhiko

2010-01-12

In Hydrogenobacter thermophilus cytochrome c(552), an electrostatic interaction between Lys8 and Glu68 in the N- and C-terminal helices, respectively, stabilizes its protein structure [Travaglini-Allocatelli, C., Gianni, S., Dubey, V. K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzola, F., Bren, K. L., and Brunori, M. (2005) J. Biol. Chem. 280, 25729-25734], this electrostatic interaction being a highly conserved structural feature of the cytochrome c family. In the present study, the functional consequences of removal of the interaction through replacement of Lys8 by Ala have been investigated in order to elucidate the molecular mechanisms responsible for functional control of the protein. The mutation resulted in a decrease in protein stability, as reflected in lowering of the denaturation temperature by approximately 2-9 degrees C, and a negative shift by approximately 8 mV of the redox potential (E(m)) of the protein. The decrease in the protein stability was attributed to the enthalpic loss due to the removal of the intramolecular interaction. The negative shift of the E(m) value was shown to be due to the effect of the mutation on the entropic contribution to the E(m) value. The small, but subtle, effects of removal of the conserved electrostatic interaction, occurring at approximately 1.4 nm away from heme iron, on the thermodynamic properties of the protein demonstrated not only that the interaction is important for maintaining the functional properties of the protein but also that amino acid residues relatively remote from the heme active site play sizable roles in functional control of the protein.

Electrostatics at the membrane define MscL channel mechanosensitivity and kinetics.

PubMed

Zhong, Dalian; Blount, Paul

2014-12-01

The bacterial mechanosensitive channel of large conductance (MscL) serves as a biological emergency release valve, preventing the occurrence of cell lysis caused by acute osmotic stress. Its tractable nature allows it to serve as a paradigm for how a protein can directly sense membrane tension. Although much is known of the importance of the hydrophobicity of specific residues in channel gating, it has remained unclear whether electrostatics at the membrane plays any role. We studied MscL chimeras derived from functionally distinct orthologues: Escherichia coli and Staphylococcus aureus. Dissection of one set led to an observation that changing the charge of a single residue, K101, of E. coli (Ec)-MscL, effects a channel phenotype: when mutated to a negative residue, the channel is less mechanosensitive and has longer open dwell times. Assuming electrostatic interactions, we determined whether they are due to protein-protein or protein-lipid interactions by performing site-directed mutagenesis elsewhere in the protein and reconstituting channels into defined lipids, with and without negative head groups. We found that although both interactions appear to play some role, the primary determinant of the channel phenotype seems to be protein-lipid electrostatics. The data suggest a model for the role of electrostatic interactions in the dynamics of MscL gating. © FASEB.

Electrohydrodynamic deformation and interaction of a pair of emulsion drops

NASA Technical Reports Server (NTRS)

Baygents, James C.

1994-01-01

The response of a pair of emulsion drops to the imposition of a uniform electric field is examined. The case studied is that of equal-sized drops whose line of centers is parallel to the axis of the applied field. A new boundary integral solution to the governing equations of the leaky dielectric model is developed; the formulation accounts for the electrostatic and hydrodynamic interactions between the drops, as well as their deformations. Numerical calculations show that, after an initial transient during which the drops primarily deform, the pair drift slowly together due to their electrostatic interactions.

Preferential binding of positive nanoparticles on cell membranes is due to electrostatic interactions: A too simplistic explanation that does not take into account the nanoparticle protein corona.

PubMed

Forest, Valérie; Pourchez, Jérémie

2017-01-01

The internalization of nanoparticles by cells (and more broadly the nanoparticle/cell interaction) is a crucial issue both for biomedical applications (for the design of nanocarriers with enhanced cellular uptake to reach their intracellular therapeutic targets) and in a nanosafety context (as the internalized dose is one of the key factors in cytotoxicity). Many parameters can influence the nanoparticle/cell interaction, among them, the nanoparticle physico-chemical features, and especially the surface charge. It is generally admitted that positive nanoparticles are more uptaken by cells than neutral or negative nanoparticles. It is supposedly due to favorable electrostatic interactions with negatively charged cell membrane. However, this theory seems too simplistic as it does not consider a fundamental element: the nanoparticle protein corona. Indeed, once introduced in a biological medium nanoparticles adsorb proteins at their surface, forming a new interface defining the nanoparticle "biological identity". This adds a new level of complexity in the interactions with biological systems that cannot be any more limited to electrostatic binding. These interactions will then influence cell behavior. Based on a literature review and on an example of our own experience the parameters involved in the nanoparticle protein corona formation as well as in the nanoparticle/cell interactions are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluorescence turn-on responses of anionic and cationic conjugated polymers toward proteins: effect of electrostatic and hydrophobic interactions.

PubMed

Pu, Kan-Yi; Liu, Bin

2010-03-11

Cationic and anionic poly(fluorenyleneethynylene-alt-benzothiadiazole)s (PFEBTs) are designed and synthesized via Sonagashira coupling reaction to show light-up signatures toward proteins. Due to the charge transfer character of the excited states, the fluorescence of PFEBTs is very weak in aqueous solution, while their yellow fluorescence can be enhanced by polymer aggregation. PFEBTs show fluorescence turn-on rather than fluorescence quenching upon complexation with proteins. Both electrostatic and hydrophobic interactions between PFEBTs and proteins are found to improve the polymer fluorescence, the extent of which is dependent on the nature of the polymer and the protein. Changes in solution pH adjust the net charges of proteins, providing an effective way to manipulate electrostatic interactions and in turn the increment in the polymer fluorescence. In addition, the effect of protein digestion on the fluorescence of polymer/protein complexes is probed. The results indicate that electrostatic interaction induced polymer fluorescence increase cannot be substantially reduced through cleaving protein into peptide fragments. In contrast, hydrophobic interactions, mainly determined by the hydrophobicity of proteins, can be minimized by digestion, imparting a light-off signature for the polymer/protein complexes. This study thus not only highlights the opportunities of exerting nonspecific interactions for protein sensing but also reveals significant implications for biosensor design.

Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

PubMed Central

Shen, Jana K.

2010-01-01

The stability and folding of proteins are modulated by energetically significant interactions in the denatured state that is in equilibrium with the native state. These interactions remain largely invisible to current experimental techniques, however, due to the sparse population and conformational heterogeneity of the denatured-state ensemble under folding conditions. Molecular dynamics simulations using physics-based force fields can in principle offer atomistic details of the denatured state. However, practical applications are plagued with the lack of rigorous means to validate microscopic information and deficiencies in force fields and solvent models. This study presents a method based on coupled titration and molecular dynamics sampling of the denatured state starting from the extended sequence under native conditions. The resulting denatured-state pKas allow for the prediction of experimental observables such as pH- and mutation-induced stability changes. I show the capability and use of the method by investigating the electrostatic interactions in the denatured states of wild-type and K12M mutant of NTL9 protein. This study shows that the major errors in electrostatics can be identified by validating the titration properties of the fragment peptides derived from the sequence of the intact protein. Consistent with experimental evidence, our simulations show a significantly depressed pKa for Asp8 in the denatured state of wild-type, which is due to a nonnative interaction between Asp8 and Lys12. Interestingly, the simulation also shows a nonnative interaction between Asp8 and Glu48 in the denatured state of the mutant. I believe the presented method is general and can be applied to extract and validate microscopic electrostatics of the entire folding energy landscape. PMID:20682271

A multiscale model for charge inversion in electric double layers

NASA Astrophysics Data System (ADS)

Mashayak, S. Y.; Aluru, N. R.

2018-06-01

Charge inversion is a widely observed phenomenon. It is a result of the rich statistical mechanics of the molecular interactions between ions, solvent, and charged surfaces near electric double layers (EDLs). Electrostatic correlations between ions and hydration interactions between ions and water molecules play a dominant role in determining the distribution of ions in EDLs. Due to highly polar nature of water, near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Classical continuum theories fail to accurately describe electrostatic correlations and molecular effects of water in EDLs. In this work, we present an empirical potential based quasi-continuum theory (EQT) to accurately predict the molecular-level properties of aqueous electrolytes. In EQT, we employ rigorous statistical mechanics tools to incorporate interatomic interactions, long-range electrostatics, correlations, and orientation polarization effects at a continuum-level. Explicit consideration of atomic interactions of water molecules is both theoretically and numerically challenging. We develop a systematic coarse-graining approach to coarse-grain interactions of water molecules and electrolyte ions from a high-resolution atomistic scale to the continuum scale. To demonstrate the ability of EQT to incorporate the water orientation polarization, ion hydration, and electrostatic correlations effects, we simulate confined KCl aqueous electrolyte and show that EQT can accurately predict the distribution of ions in a thin EDL and also predict the complex phenomenon of charge inversion.

Effect of humic acid on the sorption of perfluorooctane sulfonate (PFOS) and perfluorobutane sulfonate (PFBS) on boehmite.

PubMed

Wang, Fei; Shih, Kaimin; Leckie, James O

2015-01-01

The sorption of PFOS and PFBS on boehmite was significantly retarded by the competitive sorption of humic acid (HA), implying that PFOS and PFBS are likely more mobile in water and groundwater systems enriched with HA. The sorption behavior of PFOS and PFBS on the HA-modified boehmite surface were also found to differ due to their different chain lengths. For a partially HA-modified boehmite surface, the isotherm study showed that PFOS had a much higher maximum sorption capacity than PFBS and that PFOS might possess additional surface interactions besides electrostatic interaction. For a HA-saturated boehmite, a linear sorption isotherm was found for PFOS while nearly no PFBS sorption was observed. This indicates that sorption behavior between PFOS and the sorbed HA on boehmite was dominated by hydrophobic interactions, instead of electrostatic interaction. In addition, a conceptual model combining hydrophobic and electrostatic interaction was established to explain the sorption behavior of PFOS and PFBS on HA-modified boehmite. Finally, the results revealed that the sorption of PFOS and PFBS on HA-modified boehmite is pH-dependent. The neutralization of negative sites on HA-modified boehmite reduced the electrostatic repulsion and enhanced the partitioning of PFBS on the sorbed HA. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding

PubMed Central

Khan, Hanif M.; He, Tao; Fuglebakk, Edvin; Grauffel, Cédric; Yang, Boqian; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie

2016-01-01

Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. BtPI-PLC carries a negative net charge and its interfacial binding site has no obvious cluster of basic residues. Continuum electrostatic calculations show that, as expected, nonspecific electrostatic interactions between BtPI-PLC and membranes vary as a function of the fraction of anionic lipids present in the bilayers. Yet they are strikingly weak, with a calculated ΔGel below 1 kcal/mol, largely due to a single lysine (K44). When K44 is mutated to alanine, the equilibrium dissociation constant for small unilamellar vesicles increases more than 50 times (∼2.4 kcal/mol), suggesting that interactions between K44 and lipids are not merely electrostatic. Comparisons of molecular-dynamics simulations performed using different lipid compositions reveal that the bilayer composition does not affect either hydrogen bonds or hydrophobic contacts between the protein interfacial binding site and bilayers. However, the occupancies of cation-π interactions between PC choline headgroups and protein tyrosines vary as a function of PC content. The overall contribution of basic residues to binding affinity is also context dependent and cannot be approximated by a rule-of-thumb value because these residues can contribute to both nonspecific electrostatic and short-range protein-lipid interactions. Additionally, statistics on the distribution of basic amino acids in a data set of membrane-binding domains reveal that weak electrostatics, as observed for BtPI-PLC, might be a less unusual mechanism for peripheral membrane binding than is generally thought. PMID:27028646

Grain-grain interaction in stationary dusty plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lampe, Martin; Joyce, Glenn

We present a particle-in-cell simulation study of the steady-state interaction between two stationary dust grains in uniform stationary plasma. Both the electrostatic force and the shadowing force on the grains are calculated explicitly. The electrostatic force is always repulsive. For two grains of the same size, the electrostatic force is very nearly equal to the shielded electric field due to a single isolated grain, acting on the charge of the other grain. For two grains of unequal size, the electrostatic force on the smaller grain is smaller than the isolated-grain field, and the force on the larger grain is largermore » than the isolated-grain field. In all cases, the attractive shadowing force exceeds the repulsive electrostatic force when the grain separation d is greater than an equilibrium separation d{sub 0}. d{sub 0} is found to be between 6λ{sub D} and 9λ{sub D} in all cases. The binding energy is estimated to be between 19 eV and 900 eV for various cases.« less

Electrostatic antenna space environment interaction study

NASA Technical Reports Server (NTRS)

Katz, I.

1981-01-01

The interactions of the electrostatic antenna with the space environment in both low Earth orbit and geosynchronous orbit are investigated. It is concluded that the electrostatically controlled membrane mirror is a viable concept for space applications. However, great care must be taken to enclose the high voltage electrodes in a Faraday cage structure to separate the high voltage region from the ambient plasma. For this reason, metallized cloth is not acceptable as a membrane material. Conventional spacecraft charging at geosynchronous orbit should not be a problem provided ancillary structures (such as booms) are given nonnegligible conductivity and adequate grounding. Power loss due to plasma electrons entering the high field region is a potentially serious problem. In low earth orbit any opening whatever in the Faraday cage is likely to produce an unacceptable power drain.

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

PubMed

Liu, C Tony; Layfield, Joshua P; Stewart, Robert J; French, Jarrod B; Hanoian, Philip; Asbury, John B; Hammes-Schiffer, Sharon; Benkovic, Stephen J

2014-07-23

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and (13)C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor-acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR.

Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase

PubMed Central

2015-01-01

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and 13C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor–acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR. PMID:24977791

Electrostatic effects in the collapse transition of phospholiquid monolayer

NASA Astrophysics Data System (ADS)

Nguyen, Toan T.; Gopal, Ajaykumar; Lee, Ka Yee C.; Witten, Thomas A.

2004-03-01

We study the collapse transition of fluidic phospholipid surfactant monolayers under lateral compression. DMPC, DPPC or POPG surfactants and their binary mixtures are used. Various collapsed structures (circular discs, cylinderical tubes and pearls-on-a-string) were observed during the transition. We show that electrostatics plays an important role in the formation of these structures. By changing the composition of charged surfactant (POGP) or the screening condition of the solution, one can change the dominant collapsed structure from discs to tubes to pearls in the order of increasing the strength of electrostatic interactions, in accordance with theoretical estimates. We also study a complimentary electrostatic effect due charge relaxation in the transitions between these structures. It is shown that free energy gained from relaxations of charge molecule is small and can be neglected when considering electrostatics of these systems.

Forces between Two Glass Surfaces with Adsorbed Hexadecyltrimethylammonium Salicylate.

PubMed

Imae, T; Kato, M; Rutland, M

2000-02-22

Forces have been measured for hexadecyltrimethylammonium salicylate (C(16)TASal) layers on glass beads. During the inward process, hydrophobic attraction occurred at lower adsorption of C(16)TASal and electrostatic repulsion interactions happened at higher adsorption. While the jump-in phenomenon was observed for solutions of concentrations below the critical micelle concentration (cmc = 0.15 mM), the step-in phenomenon was characteristic for solutions at the cmc and above the cmc, suggesting the push-out of adsorbed C(16)TASal layers and/or inserted micelles. The remarkable pull-off phenomenon on the outward process occurred for all solutions, indicating a strong interaction between C(16)TASal molecules. For aqueous 0.15 mM C(16)TASal solutions of various NaSal concentrations, on the inward process, the electrostatic repulsive interaction decreased with adding NaSal. This is due to the electrostatic shielding by salt excess. The height of the force wall on the inward process reached a maximum at 0.01 M NaSal, but the interlocking between molecules on two surfaces during the outward process was minimized at 0.1 M NaSal. These tendencies, which are different from that of the electrostatic repulsion interaction, imply the strong cohesion between adsorbed C(16)TASal layers.

Energy conversion in polyelectrolyte hydrogels

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica; Erbas, Aykut; Olvera de la Cruz Team

Energy conversion and storage have been an active field of research in nanotechnology parallel to recent interests towards renewable energy. Polyelectrolyte (PE) hydrogels have attracted considerable attention in this field due to their mechanical flexibility and stimuli-responsive properties. Ideally, when a hydrogel is deformed, applied mechanical work can be converted into electrostatic, elastic and steric-interaction energies. In this talk, we discuss the results of our extensive molecular dynamics simulations of PE hydrogels. We demonstrate that, on deformation, hydrogels adjust their deformed state predominantly by altering electrostatic interactions between their charged groups rather than excluded-volume and bond energies. This is due to the hydrogel's inherent tendency to preserve electro-neutrality in its interior, in combination with correlations imposed by backbone charges. Our findings are valid for a wide range of compression ratios and ionic strengths. The electrostatic-energy alterations that we observe in our MD simulations may induce pH or redox-potential changes inside the hydrogels. The resulting energetic difference can be harvested, for instance, analogously to a Carnot engine, or facilitated for sensor applications. Center for Bio-inspired Energy Science (CBES).

A Measurement and Modeling Study of Hair Partition of Neutral, Cationic, and Anionic Chemicals.

PubMed

Li, Lingyi; Yang, Senpei; Chen, Tao; Han, Lujia; Lian, Guoping

2018-04-01

Various neutral, cationic, and anionic chemicals contained in hair care products can be absorbed into hair fiber to modulate physicochemical properties such as color, strength, style, and volume. For environmental safety, there is also an interest in understanding hair absorption to wide chemical pollutants. There have been very limited studies on the absorption properties of chemicals into hair. Here, an experimental and modeling study has been carried out for the hair-water partition of a range of neutral, cationic, and anionic chemicals at different pH. The data showed that hair-water partition not only depends on the hydrophobicity of the chemical but also the pH. The partition of cationic chemicals to hair increased with pH, and this is due to their electrostatic interaction with hair increased from repulsion to attraction. For anionic chemicals, their hair-water partition coefficients decreased with increasing pH due to their electrostatic interaction with hair decreased from attraction to repulsion. Increase in pH did not change the partition of neutral chemicals significantly. Based on the new physicochemical insight of the pH effect on hair-water partition, a new quantitative structure property relationship model has been proposed, taking into account of both the hydrophobic interaction and electrostatic interaction of chemical with hair fiber. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Investigation of Singly Ionized Iodine Spectroscopy in Support of Electrostatic Propulsion Diagnostics Development

DTIC Science & Technology

2012-07-02

from complex user interactions due to the use of liquid lasing medium with finite lifetime. Solid state lasers such as titanium sapphire (Ti:Sapphire...transitions for laser -induced fluorescence of an accelerated atomic iodine singly charged ion (I+). While the second spectrum of iodine has been analyzed...diagnostics tools, such as laser -induced fluorescence (LIF), to examine the plasma acceleration within an electro-static plasma propulsion thruster. While

FY04 LDRD Final Report: Interaction of Viruses with Membranes and Soil Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaldach, C M

2005-02-08

The influence of ionic strength on the electrostatic interaction of viruses with environmentally relevant surfaces was determined for three viruses, MS2, Q{beta} and Norwalk. The environmental surface is modeled as charged Gouy-Chapman plane with and without a finite atomistic region (patch) of opposite charge. The virus is modeled as a particle comprised of ionizable amino acid residues in a shell surrounding a spherical RNA core of negative charge, these charges being compensated for by a Coulomb screening due to intercalated ions. Surface potential calculations for each of the viruses show excellent agreement with electrophoretic mobility and zeta potential measurements asmore » a function of pH. The results indicate that the electrostatic interaction between the virus and the planar surface, mitigated by the ionic strength of the solute, is dependent upon the spatial distribution of the amino acid residues in the different viruses. Specifically, the order of interaction energies with the patch (MS2 greatest at 5 mM; Norwalk greatest at 20 mM) is dependent upon the ionic strength of the fluid as a direct result of the viral coat amino acid distributions. We have developed an atomistic-scale method of calculation of the binding energy of viruses to surfaces including electrostatic, van der Waals, electron-overlap repulsion, surface charge polarization (images), and hydrophobic effects. The surface is treated as a Gouy-Chapman plane allowing inclusion of pH and ionic strength effects on the electrostatic potential at each amino acid charge. Van der Waals parameters are obtained from the DREIDING force field and from Hamaker constant measurements. We applied this method to the calculation of the Cowpea Mosaic Virus (CPMV), a negatively charged virus at a pH of 7.0, and find that the viral-gold surface interaction is very long range for both signs of surface potential, a result due to the electrostatic forces. For a negative (Au) surface potential of -0.05 volts, a nearly 4 eV barrier must be overcome to reach 1 nm from the surface.« less

Electrostatic effects on hyaluronic acid configuration

NASA Astrophysics Data System (ADS)

Berezney, John; Saleh, Omar

2015-03-01

In systems of polyelectrolytes, such as solutions of charged biopolymers, the electrostatic repulsion between charged monomers plays a dominant role in determining the molecular conformation. Altering the ionic strength of the solvent thus affects the structure of such a polymer. Capturing this electrostatically-driven structural dependence is important for understanding many biological systems. Here, we use single molecule manipulation experiments to collect force-extension behavior on hyaluronic acid (HA), a polyanion which is a major component of the extracellular matrix in all vertebrates. By measuring HA elasticity in a variety of salt conditions, we are able to directly assess the contribution of electrostatics to the chain's self-avoidance and local stiffness. Similar to recent results from our group on single-stranded nucleic acids, our data indicate that HA behaves as a swollen chain of electrostatic blobs, with blob size proportional to the solution Debye length. Our data indicate that the chain structure within the blob is not worm-like, likely due to long-range electrostatic interactions. We discuss potential models of this effect.

Electrostatic screening in classical Coulomb fluids: exponential or power-law decay or both? An investigation into the effect of dispersion interactions

NASA Astrophysics Data System (ADS)

Kjellander, Roland

2006-04-01

It is shown that the nature of the non-electrostatic part of the pair interaction potential in classical Coulomb fluids can have a profound influence on the screening behaviour. Two cases are compared: (i) when the non-electrostatic part equals an arbitrary finite-ranged interaction and (ii) when a dispersion r-6 interaction potential is included. A formal analysis is done in exact statistical mechanics, including an investigation of the bridge function. It is found that the Coulombic r-1 and the dispersion r-6 potentials are coupled in a very intricate manner as regards the screening behaviour. The classical one-component plasma (OCP) is a particularly clear example due to its simplicity and is investigated in detail. When the dispersion r-6 potential is turned on, the screened electrostatic potential from a particle goes from a monotonic exponential decay, exp(-κr)/r, to a power-law decay, r-8, for large r. The pair distribution function acquire, at the same time, an r-10 decay for large r instead of the exponential one. There still remains exponentially decaying contributions to both functions, but these contributions turn oscillatory when the r-6 interaction is switched on. When the Coulomb interaction is turned off but the dispersion r-6 pair potential is kept, the decay of the pair distribution function for large r goes over from the r-10 to an r-6 behaviour, which is the normal one for fluids of electroneutral particles with dispersion interactions. Differences and similarities compared to binary electrolytes are pointed out.

The role of electrostatic interactions in protease surface diffusion and the consequence for interfacial biocatalysis.

PubMed

Feller, Bob E; Kellis, James T; Cascão-Pereira, Luis G; Robertson, Channing R; Frank, Curtis W

2010-12-21

This study examines the influence of electrostatic interactions on enzyme surface diffusion and the contribution of diffusion to interfacial biocatalysis. Surface diffusion, adsorption, and reaction were investigated on an immobilized bovine serum albumin (BSA) multilayer substrate over a range of solution ionic strength values. Interfacial charge of the enzyme and substrate surface was maintained by performing the measurements at a fixed pH; therefore, electrostatic interactions were manipulated by changing the ionic strength. The interfacial processes were investigated using a combination of techniques: fluorescence recovery after photobleaching, surface plasmon resonance, and surface plasmon fluorescence spectroscopy. We used an enzyme charge ladder with a net charge ranging from -2 to +4 with respect to the parent to systematically probe the contribution of electrostatics in interfacial enzyme biocatalysis on a charged substrate. The correlation between reaction rate and adsorption was determined for each charge variant within the ladder, each of which displayed a maximum rate at an intermediate surface concentration. Both the maximum reaction rate and adsorption value at which this maximum rate occurs increased in magnitude for the more positive variants. In addition, the specific enzyme activity increased as the level of adsorption decreased, and for the lowest adsorption values, the specific enzyme activity was enhanced compared to the trend at higher surface concentrations. At a fixed level of adsorption, the specific enzyme activity increased with positive enzyme charge; however, this effect offers diminishing returns as the enzyme becomes more highly charged. We examined the effect of electrostatic interactions on surface diffusion. As the binding affinity was reduced by increasing the solution ionic strength, thus weakening electrostatic interaction, the rate of surface diffusion increased considerably. The enhancement in specific activity achieved at the lowest adsorption values is explained by the substantial rise in surface diffusion at high ionic strength due to decreased interactions with the surface. Overall, knowledge of the electrostatic interactions can be used to control surface parameters such as surface concentration and surface diffusion, which intimately correlate with surface biocatalysis. We propose that the maximum reaction rate results from a balance between adsorption and surface diffusion. The above finding suggests enzyme engineering and process design strategies for improving interfacial biocatalysis in industrial, pharmaceutical, and food applications.

Origin of translocation barriers for polyelectrolyte chains.

PubMed

Kumar, Rajeev; Muthukumar, M

2009-11-21

For single-file translocations of a charged macromolecule through a narrow pore, the crucial step of arrival of an end at the pore suffers from free energy barriers, arising from changes in intrachain electrostatic interaction, distribution of ionic clouds and solvent molecules, and conformational entropy of the chain. All contributing factors to the barrier in the initial stage of translocation are evaluated by using the self-consistent field theory for the polyelectrolyte and the coupled Poisson-Boltzmann description for ions without radial symmetry. The barrier is found to be essentially entropic due to conformational changes. For moderate and high salt concentrations, the barriers for the polyelectrolyte chain are quantitatively equivalent to that of uncharged self-avoiding walks. Electrostatic effects are shown to increase the free energy barriers, but only slightly. The degree of ionization, electrostatic interaction strength, decreasing salt concentration, and the solvent quality all result in increases in the barrier.

Probing lipid membrane electrostatics

NASA Astrophysics Data System (ADS)

Yang, Yi

The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by <2%. One important application of this technique is to estimate the dipole density of lipid membrane. Electrostatic analysis of DOPC lipid bilayers with the AFM reveals a repulsive force between the negatively charged probe tips and the zwitterionic lipid bilayers. This unexpected interaction has been analyzed quantitatively to reveal that the repulsion is due to a weak external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive manner will be useful in identifying the biological effects of the dipole potential. Finally, heterogeneous model membranes were studied with fluid electric force microscopy (FEFM). Electrostatic mapping was demonstrated with 50 nm resolution. The capabilities of quantitative electrostatic measurement and lateral charge density mapping make AFM a unique and powerful probe of membrane electrostatics.

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

PubMed

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules--applications in biotechnology.

PubMed

Neves-Petersen, Maria Teresa; Petersen, Steffen B

2003-01-01

The molecular understanding of the initial interaction between a protein and, e.g., its substrate, a surface or an inhibitor is essentially an understanding of the role of electrostatics in intermolecular interactions. When studying biomolecules it is becoming increasingly evident that electrostatic interactions play a role in folding, conformational stability, enzyme activity and binding energies as well as in protein-protein interactions. In this chapter we present the key basic equations of electrostatics necessary to derive the equations used to model electrostatic interactions in biomolecules. We will also address how to solve such equations. This chapter is divided into two major sections. In the first part we will review the basic Maxwell equations of electrostatics equations called the Laws of Electrostatics that combined will result in the Poisson equation. This equation is the starting point of the Poisson-Boltzmann (PB) equation used to model electrostatic interactions in biomolecules. Concepts as electric field lines, equipotential surfaces, electrostatic energy and when can electrostatics be applied to study interactions between charges will be addressed. In the second part we will arrive at the electrostatic equations for dielectric media such as a protein. We will address the theory of dielectrics and arrive at the Poisson equation for dielectric media and at the PB equation, the main equation used to model electrostatic interactions in biomolecules (e.g., proteins, DNA). It will be shown how to compute forces and potentials in a dielectric medium. In order to solve the PB equation we will present the continuum electrostatic models, namely the Tanford-Kirkwood and the modified Tandord-Kirkwood methods. Priority will be given to finding the protonation state of proteins prior to solving the PB equation. We also present some methods that can be used to map and study the electrostatic potential distribution on the molecular surface of proteins. The combination of graphical visualisation of the electrostatic fields combined with knowledge about the location of key residues on the protein surface allows us to envision atomic models for enzyme function. Finally, we exemplify the use of some of these methods on the enzymes of the lipase family.

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: numerical study.

PubMed

Nardecchia, Ilaria; Spinelli, Lionel; Preto, Jordane; Gori, Matteo; Floriani, Elena; Jaeger, Sebastien; Ferrier, Pierre; Pettini, Marco

2014-08-01

The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is shown that when the particles are uniformly distributed throughout the accessible space, the self-diffusion coefficient is always lowered by the considered interparticle interactions, irrespective of their attractive or repulsive character. This fact is also confirmed by a simple model to compute the correction to the Brownian diffusion coefficient due to the interactions among the particles. These interactions are also responsible for the onset of dynamical chaos and an associated chaotic diffusion which still follows an Einstein-Fick-like law for the mean-square displacement as a function of time. Transitional phenomena are observed for Coulomb-electrostatic (repulsive) and dipole-electrodynamic (attractive) interactions considered both separately and in competition. The outcomes reported in this paper clearly indicate a feasible experimental method to probe the activation of resonant electrodynamic interactions among biomolecules.

Long-range interaction between heterogeneously charged membranes.

PubMed

Jho, Y S; Brewster, R; Safran, S A; Pincus, P A

2011-04-19

Despite their neutrality, surfaces or membranes with equal amounts of positive and negative charge can exhibit long-range electrostatic interactions if the surface charge is heterogeneous; this can happen when the surface charges form finite-size domain structures. These domains can be formed in lipid membranes where the balance of the different ranges of strong but short-ranged hydrophobic interactions and longer-ranged electrostatic repulsion result in a finite, stable domain size. If the domain size is large enough, oppositely charged domains in two opposing surfaces or membranes can be strongly correlated by the electrostatic interactions; these correlations give rise to an attractive interaction of the two membranes or surfaces over separations on the order of the domain size. We use numerical simulations to demonstrate the existence of strong attractions at separations of tens of nanometers. Large line tensions result in larger domains but also increase the charge density within the domain. This promotes correlations and, as a result, increases the intermembrane attraction. On the other hand, increasing the salt concentration increases both the domain size and degree of domain anticorrelation, but the interactions are ultimately reduced due to increased screening. The result is a decrease in the net attraction as salt concentration is increased. © 2011 American Chemical Society

Modeling electrostatic and heterogeneity effects on proton dissociation from humic substances

USGS Publications Warehouse

Tipping, E.; Reddy, M.M.; Hurley, M.A.

1990-01-01

The apparent acid dissociation constant of humic substances increases by 2-4 pK units as ionization of the humic carboxylate groups proceeds. This change in apparent acid strength is due in part to the increase in electrical charge on the humic molecules as protons are shed. In addition, proton dissociation reactions are complicated because humic substances are heterogeneous with respect to proton dissociating groups and molecular size. In this paper, we use the Debye-Hu??ckel theory to describe the effects of electrostatic interactions on proton dissociation of humic substances. Simulations show that, for a size-heterogeneous system of molecules, the weight-average molecular weight is preferable to the number-average value for averaging the effects of electrostatic interactions. Analysis of published data on the proton dissociation of fulvic acid from the Suwannee River shows that the electrostatic interactions can be satisfactorily described by a hypothetical homogeneous compound having a molecular weight of 1000 (similar to the experimentally determined weight-average value). Titration data at three ionic strengths, for several fulvic acid concentrations, and in the pH range from 2.9 to 6.4 can be fitted with three adjustable parameters (pK??int values), given information on molecular size and carboxylate group content. ?? 1990 American Chemical Society.

Emission shaping in fluorescent proteins: role of electrostatics and π-stacking.

PubMed

Park, Jae Woo; Rhee, Young Min

2016-02-07

For many decades, simulating the excited state properties of complex systems has been an intriguing but daunting task due to its high computational cost. Here, we apply molecular dynamics based techniques with interpolated potential energy surfaces toward calculating fluorescence spectra of the green fluorescent protein (GFP) and its variants in a statistically meaningful manner. With the GFP, we show that the diverse electrostatic tuning can shape the emission features in many different ways. By computationally modulating the electrostatic interactions between the chromophore phenoxy oxygen and its nearby residues, we demonstrate that we indeed can shift the emission to the blue or to the red side in a predictable manner. We rationalize the shifting effects of individual residues in the GFP based on the responses of both the adiabatic and the diabatic electronic states of the chromophore. We next exhibit that the yellow emitting variant, the Thr203Tyr mutant, generates changes in the electrostatic interactions and an additional π-stacking interaction. These combined effects indeed induce a red shift to emit the fluorescence into the yellow region. With the series of demonstrations, we suggest that our approach can provide sound rationales and useful insights in understanding different responses of various fluorescent complexes, which may be helpful in designing new light emitting proteins and other related systems in future studies.

Substituent Effects in the Benzene Dimer are Due to Direct Interactions of the Substituents with the Unsubstituted Benzene

PubMed Central

Wheeler, Steven E.; Houk, K. N.

2009-01-01

The prevailing views of substituent effects in the sandwich configuration of the benzene dimer are flawed. For example, in the polar/π model of Cozzi and co-workers (J. Am. Chem. Soc. 1992, 114, 5729), electron-withdrawing substituents enhance binding in the benzene dimer by withdrawing electron density from the π-cloud of the substituted ring, reducing the repulsive electrostatic interaction with the non-substituted benzene. Conversely, electron-donating substituents donate excess electrons into the π-system and diminish the π-stacking interaction. We present computed interaction energies for the sandwich configuration of the benzene dimer and 24 substituted dimers, as well as sandwich complexes of substituted benzenes with perfluorobenzene. While the computed interaction energies correlate well with σm values for the substituents, interaction energies for related model systems demonstrate that this trend is independent of the substituted ring. Instead, the observed trends are consistent with direct electrostatic and dispersive interactions of the substituents with the unsubstituted ring. PMID:18652453

Surface charge-induced EDL interaction on the contact angle of surface nanobubbles.

PubMed

Jing, Dalei; Li, Dayong; Pan, Yunlu; Bhushan, Bharat

2016-11-01

The contact angle (CA) of surface nanobubbles is believed to affect the stability of nanobubbles and fluid drag in micro/nanofluidic systems. The CA of nanobubbles is dependent on size and is believed to be affected by the surface charge-induced electrical double layer (EDL). However, neither of these of attributes are well understood. In this paper, by introducing an EDL-induced electrostatic wetting tension, a theoretical model is first established to study the effect of EDLs formed near the solid-liquid interface and the liquid-nanobubble interface on the gas phase CA of nanobubbles. The size-dependence of this EDL interaction is studied as well. Next, by using atomic force microscopy (AFM), the effect of the EDL on nanobubbles' gas phase CA is studied with variable electrical potential at the solid-liquid interface, which is adjusted by an applied voltage. Both the theoretical and the experimental results show that the EDLs formed near the solid-liquid interface and the liquid-nanobubble interface lead to a reduction of gas phase CA of the surface nanobubbles because of an electrostatic wetting tension on the nanobubble due to the attractive electrostatic interaction between the liquid and nanobubble within the EDL, which is in the nanobubbles' outward direction. An EDL with a larger zeta potential magnitude leads to a larger gas phase CA reduction. Furthermore, the effect of EDL on the nanobubbles' gas phase CA shows a significant size-dependence considering the size dependence of the electrostatic wetting tension. The gas phase CA reduction due to the EDL decreases with increasing nanobubble height and increases with the nanobubble's increasing curvature radius, indicating that a surface charge-induced EDL could possibly explain the size dependence of the gas phase CA of nanobubbles.

A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design.

PubMed

Bardhan, Jaydeep P; Altman, Michael D; Tidor, B; White, Jacob K

2009-01-01

We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule's electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts-in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method.

A “Reverse-Schur” Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design

PubMed Central

Bardhan, Jaydeep P.; Altman, Michael D.

2009-01-01

We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule’s electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts–in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method. PMID:23055839

Interaction between water-soluble rhodium complex RhCl(CO)(TPPTS)₂ and surfactants probed by spectroscopic methods.

PubMed

Zhou, Li-Mei; Guo, Cai-Hong; Fu, Hai-Yan; Jiang, Xiao-Hui; Chen, Hua; Li, Rui-Xiang; Li, Xian-Jun

2012-07-01

The interactions of rhodium complex RhCl(CO)(TPPTS)(2) [TPPTS=P(m-C(6)H(4)SO(3)Na)(3)] with cationic, nonionic, and anionic surfactants have been investigated by UV-vis, fluorescence and (1)H NMR measurements. The presence of four different species of RhCl(CO)(TPPTS)(2) in cationic cetyltrimethylammonium (CTAB) solution has been demonstrated: free rhodium complex, rhodium complex bound to CTAB monomer, rhodium complex bound to CTAB premicelles, rhodium complex bound to CTAB micelles. The spectroscopy data show that RhCl(CO)(TPPTS)(2) can adsorb on the interface of cationic CTAB micelles by strong electrostatic attraction, weakly bind to the nonionic polyoxyethylene (20) sorbitan monolaurate (Tween 20) micelles by hydrophobic interaction, and does not interact with anion sodium dodecyl sulfate (SDS) micelles due to the strong electrostatic repulsion. Copyright © 2012 Elsevier B.V. All rights reserved.

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Brownian dynamics simulations of polyelectrolyte adsorption in shear flow with hydrodynamic interaction

NASA Astrophysics Data System (ADS)

Hoda, Nazish; Kumar, Satish

2007-12-01

The adsorption of single polyelectrolyte molecules in shear flow is studied using Brownian dynamics simulations with hydrodynamic interaction (HI). Simulations are performed with bead-rod and bead-spring chains, and electrostatic interactions are incorporated through a screened Coulombic potential with excluded volume accounted for by the repulsive part of a Lennard-Jones potential. A correction to the Rotne-Prager-Yamakawa tensor is derived that accounts for the presence of a planar wall. The simulations show that migration away from an uncharged wall, which is due to bead-wall HI, is enhanced by increases in the strength of flow and intrachain electrostatic repulsion, consistent with kinetic theory predictions. When the wall and polyelectrolyte are oppositely charged, chain behavior depends on the strength of electrostatic screening. For strong screening, chains get depleted from a region close to the wall and the thickness of this depletion layer scales as N1/3Wi2/3 at high Wi, where N is the chain length and Wi is the Weissenberg number. At intermediate screening, bead-wall electrostatic attraction competes with bead-wall HI, and it is found that there is a critical Weissenberg number for desorption which scales as N-1/2κ-3(lB∣σq∣)3/2, where κ is the inverse screening length, lB is the Bjerrum length, σ is the surface charge density, and q is the bead charge. When the screening is weak, adsorbed chains are observed to align in the vorticity direction at low shear rates due to the effects of repulsive intramolecular interactions. At higher shear rates, the chains align in the flow direction. The simulation method and results of this work are expected to be useful for a number of applications in biophysics and materials science in which polyelectrolyte adsorption plays a key role.

Manipulating semiconductor colloidal stability through doping.

PubMed

Fleharty, Mark E; van Swol, Frank; Petsev, Dimiter N

2014-10-10

The interface between a doped semiconductor material and electrolyte solution is of considerable fundamental interest, and is relevant to systems of practical importance. Both adjacent domains contain mobile charges, which respond to potential variations. This is exploited to design electronic and optoelectronic sensors, and other enabling semiconductor colloidal materials. We show that the charge mobility in both phases leads to a new type of interaction between semiconductor colloids suspended in aqueous electrolyte solutions. This interaction is due to the electrostatic response of the semiconductor interior to disturbances in the external field upon the approach of two particles. The electrostatic repulsion between two charged colloids is reduced from the one governed by the charged groups present at the particles surfaces. This type of interaction is unique to semiconductor particles and may have a substantial effect on the suspension dynamics and stability.

Amine-Rich Organic Thin Films for Cell Culture: Possible Electrostatic Effects in Cell-Surface Interactions

NASA Astrophysics Data System (ADS)

Wertheimer, Michael R.; St-Georges-Robillard, Amélie; Lerouge, Sophie; Mwale, Fackson; Elkin, Bentsian; Oehr, Christian; Wirges, Werner; Gerhard, Reimund

2012-11-01

In recent communications from these laboratories, we observed that amine-rich thin organic layers are very efficient surfaces for the adhesion of mammalian cells. We prepare such deposits by plasma polymerization at low pressure, atmospheric pressure, or by vacuum-ultraviolet photo-polymerization. More recently, we have also investigated a commercially available material, Parylene diX AM. In this article we first briefly introduce literature relating to electrostatic interactions between cells, proteins, and charged surfaces. We then present certain selected cell-response results that pertain to applications in orthopedic and cardiovascular medicine: we discuss the influence of surface properties on the observed behaviors of two particular cell lines, human U937 monocytes, and Chinese hamster ovary cells. Particular emphasis is placed on possible electrostatic attractive forces due to positively charged R-NH3+ groups and negatively charged proteins and cells, respectively. Experiments carried out with electrets, polymers with high positive or negative surface potentials are added for comparison.

Dirac Hamiltonian and Reissner-Nordström metric: Coulomb interaction in curved space-time

NASA Astrophysics Data System (ADS)

Noble, J. H.; Jentschura, U. D.

2016-03-01

We investigate the spin-1 /2 relativistic quantum dynamics in the curved space-time generated by a central massive charged object (black hole). This necessitates a study of the coupling of a Dirac particle to the Reissner-Nordström space-time geometry and the simultaneous covariant coupling to the central electrostatic field. The relativistic Dirac Hamiltonian for the Reissner-Nordström geometry is derived. A Foldy-Wouthuysen transformation reveals the presence of gravitational and electrogravitational spin-orbit coupling terms which generalize the Fokker precession terms found for the Dirac-Schwarzschild Hamiltonian, and other electrogravitational correction terms to the potential proportional to αnG , where α is the fine-structure constant and G is the gravitational coupling constant. The particle-antiparticle symmetry found for the Dirac-Schwarzschild geometry (and for other geometries which do not include electromagnetic interactions) is shown to be explicitly broken due to the electrostatic coupling. The resulting spectrum of radially symmetric, electrostatically bound systems (with gravitational corrections) is evaluated for example cases.

Structure and stability of charged colloid-nanoparticle mixtures

NASA Astrophysics Data System (ADS)

Weight, Braden M.; Denton, Alan R.

2018-03-01

Physical properties of colloidal materials can be modified by addition of nanoparticles. Within a model of like-charged mixtures of particles governed by effective electrostatic interactions, we explore the influence of charged nanoparticles on the structure and thermodynamic phase stability of charge-stabilized colloidal suspensions. Focusing on salt-free mixtures of particles of high size and charge asymmetry, interacting via repulsive Yukawa effective pair potentials, we perform molecular dynamics simulations and compute radial distribution functions and static structure factors. Analysis of these structural properties indicates that increasing the charge and concentration of nanoparticles progressively weakens correlations between charged colloids. We show that addition of charged nanoparticles to a suspension of like-charged colloids can induce a colloidal crystal to melt and can facilitate aggregation of a fluid suspension due to attractive van der Waals interactions. We attribute the destabilizing influence of charged nanoparticles to enhanced screening of electrostatic interactions, which weakens repulsion between charged colloids. This interpretation is consistent with recent predictions of an effective interaction theory of charged colloid-nanoparticle mixtures.

Metal-graphene heterojunction modulation via H{sub 2} interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cadore, A. R., E-mail: alissoncadore@gmail.com, E-mail: lccampos@fisica.ufmg.br; Mania, E.; Lacerda, R. G.

2016-07-18

Combining experiment and theory, we investigate how a naturally created heterojunction (pn junction) at a graphene and metallic contact interface is modulated via interaction with molecular hydrogen (H{sub 2}). Due to an electrostatic interaction, metallic electrodes induce pn junctions in graphene, leading to an asymmetrical resistance in electronic transport for electrons and holes. We report that the asymmetry in the resistance can be tuned in a reversible manner by exposing graphene devices to H{sub 2}. The interaction between the H{sub 2} and graphene occurs solely at the graphene-contact pn junction and induces a modification on the electrostatic interaction between graphenemore » and metallic contacts. We explain the experimental data with theory providing information concerning the length of the heterojunction and how it changes as a function of H{sub 2} adsorption. Our results are valuable for understanding the nature of the metal-graphene interfaces and have potential application for selective sensors of molecular hydrogen.« less

Effect of Ca2+ ion concentration on adsorption of poly(carboxylate ether)-based (PCE) superplasticizer on mica.

PubMed

Wu, Bo; Chun, Byong-Wa; Gu, Le; Kuhl, Tonya L

2018-05-09

Poly(carboxylate ether)-based (PCE) superplasticizers consist of a carboxylic acid backbone and grafted poly(ethylene glycol) (PEG) side chains. Ca 2+ ion bridging mechanism is commonly purported to control PCE's adsorption on negatively charged cement particle surfaces in cement suspension, thus PCE was expected to adsorb on negatively charged surfaces in synthetic pore solutions via Ca 2+ /COO - interactions. Adsorption behaviors of a commercial PCE on negatively charged mica were studied in aqueous electrolyte solutions by a surface forces apparatus. Direct force measurements indicated that the PCE adsorbed onto mica from 0.1 M K 2 SO 4 due to K + ion chelation by the ether oxygen units CH 2 CH 2 O on the PEG chains, but surprisingly did not adsorb from either 0.1 M K 2 SO 4 with saturated Ca(OH) 2 or 0.1 M Ca(NO 3 ) 2 . The adsorption in K 2 SO 4 was weak, enabling the adsorbed PCE layers to be squeezed out under modest compression. Upon separating the surfaces, the PCE immediately achieved an identical re-adsorption. In high-calcium conditions, the PCE was highly positively charged due to Ca 2+ ion chelation by PEG chains and backbone carboxylic groups COO - , and mica also underwent charge reversal due to electrostatic adsorption/binding of Ca 2+ ions. Consequently, the interaction between mica and PCE was electrostatically repulsive and no PCE adsorption occurred. These findings can be explained by the complex interplay of ion chelation by PEG chains, electrostatic binding and screening interactions with charged surfaces in the presence of monovalent and divalent counterions, and ultimately charge reversal of both the charged surfaces and polyelectrolyte in high divalent ion conditions. Copyright © 2018 Elsevier Inc. All rights reserved.

Ionic strength independence of charge distributions in solvation of biomolecules

NASA Astrophysics Data System (ADS)

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

2014-12-01

Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.

Computational Methods for Biomolecular Electrostatics

PubMed Central

Dong, Feng; Olsen, Brett; Baker, Nathan A.

2008-01-01

An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions. PMID:17964951

Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

PubMed Central

Chu, Wen-Ting; Clarke, Jane; Shammas, Sarah L.; Wang, Jin

2017-01-01

PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye—Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies. PMID:28369057

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

PubMed

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

PubMed Central

Wallace, Jason A.; Shen, Jana K.

2012-01-01

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future. PMID:23163362

Hydrolysis-controlled protein adsorption and antifouling behaviors of mixed charged self-assembled monolayer: A molecular simulation study.

PubMed

Liu, Jie; Zhou, Jian

2016-08-01

Understanding the mechanism of the antimicrobial and antifouling properties of mixed charged materials is of great significance. The interactions between human gamma fibrinogen (γFg) and mixed carboxylic methyl ether-terminated (COOCH3-) and trimethylamino-terminated (N(CH3)3(+)-) SAMs and the influence of hydrolysis were studied by molecular simulations. After hydrolysis, the mixed SAMs exhibit behaviors from antimicrobial to antifouling, since the COOCH3-thiols were translated into carboxylic acid (COO(-)-) terminated thiols, which carried a net charge of -1 e. Simulation results showed that the main differences between COOCH3-/N(CH3)3(+)-SAM and COO(-)-/N(CH3)3(+)-SAM are the charged property and the hydration layer above the surface. γFg could stably adsorb on the positively-charged COOCH3-/N(CH3)3(+)-SAM. The adsorption behavior is mainly induced by the strong electrostatic attraction. There is a single hydration layer bound to the surface, which is related to the N(CH3)3(+) groups. The van der Waals repulsion between γFg and the single hydration layer are not strong enough to compensate the strong electrostatic attraction. After hydrolysis, the positively-charged SAM was transferred to a neutral mixed charged surface, the electrostatic attraction between γFg and the surface disappears. Meanwhile, the SAM surface is covered by double hydration layers, which is induced by the N(CH3)3(+) and COO(-) groups; water molecules around COO(-) groups are obviously denser than that around N(CH3)3(+) groups. With the combined contribution from double hydration layers and the vanishment of electrostatic attraction, γFg is forced to desorb from the surface. After hydrolysis, the internal structure of mixed SAM appears more ordered due to the electrostatic interactions between charged groups on the top of SAMs. The antimicrobial and antifouling materials are of great importance in many biological applications. The strong hydration property of surfaces and the interactions between proteins and surfaces play a key role in resisting protein adsorption. The mixed SAMs, constructed from a 1:1 combination of COOCH3- and N(CH3)3(+)-terminated thiols, can induce protein adsorption mainly through the electrostatic interaction. When the COOCH3-terminated thiols were hydrolyzed to negatively charged COO(-)-terminated thiols, the mixed-charged SAMs switched from antimicrobial to antifouling. Due to the strong hydration property of the mixed charged SAMs, the adsorbed γFg moved away from the surface. Understanding the interactions between protein and mixed-charged SAMs in the atomistic level is important for the practical design and development of new antimicrobial and antifouling materials. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

The effect of charge mutations on the stability and aggregation of a human single chain Fv fragment.

PubMed

Austerberry, James I; Dajani, Rana; Panova, Stanislava; Roberts, Dorota; Golovanov, Alexander P; Pluen, Alain; van der Walle, Christopher F; Uddin, Shahid; Warwicker, Jim; Derrick, Jeremy P; Curtis, Robin

2017-06-01

The aggregation propensities for a series of single-chain variable fragment (scFv) mutant proteins containing supercharged sequences, salt bridges and lysine/arginine-enriched motifs were characterised as a function of pH and ionic strength to isolate the electrostatic contributions. Recent improvements in aggregation predictors rely on using knowledge of native-state protein-protein interactions. Consistent with previous findings, electrostatic contributions to native protein-protein interactions correlate with aggregate growth pathway and rates. However, strong reversible self-association observed for selected mutants under native conditions did not correlate with aggregate growth, indicating 'sticky' surfaces that are exposed in the native monomeric state are inaccessible when aggregates grow. We find that even though similar native-state protein-protein interactions occur for the arginine and lysine-enriched mutants, aggregation propensity is increased for the former and decreased for the latter, providing evidence that lysine suppresses interactions between partially folded states under these conditions. The supercharged mutants follow the behaviour observed for basic proteins under acidic conditions; where excess net charge decreases conformational stability and increases nucleation rates, but conversely reduces aggregate growth rates due to increased intermolecular electrostatic repulsion. The results highlight the limitations of using conformational stability and native-state protein-protein interactions as predictors for aggregation propensity and provide guidance on how to engineer stabilizing charged mutations. Copyright © 2017. Published by Elsevier B.V.

Experimental study of electrostatic discharges of spacecraft solar array protective coatings under radiation

NASA Astrophysics Data System (ADS)

Khasanshin, Rashid; Novikov, Lev

Action of charged particles on low-conductive dielectrics causes formation of areas with a high charge density inside; their fields may give rise to development of electrostatic discharge between the charged area and the surface of the dielectric. Discharge channels are growing due to breakdown of dielectric and formation of a conducting phase. Generation of the channels is a complex stochastic process accompanied by such physical and chemical processes as ionization, gas formation, heating, and so on, which cause formation of conducting phase in a glass. That is why no quantitative theory describing formation of conductive channels has been formulated yet. The study of electrostatic discharges in dielectrics under radiation is essential both from a scientific point of view and for the solution of applied problems. In particular, interaction of a spacecraft with ambient plasma causes accumulation of electric charges on its surface producing, as a consequence, electric potential between the spacecraft surface and the plasma. For example, potentials on the surface of satellites operating on a geostationary orbit reach up to 20 kV. Elec-trostatic discharges caused by such potentials can produce not only the considerable electromag-netic interference, but also lead to the destruction of hardware components and structural ele-ments. Electrostatic charging due to electrons from the Earth’s radiation belts causes degradation of solar arrays as a result of surface and internal electrostatic discharges. In the work, surface of K-208 spacecraft solar array protective coatings irradiated by 20 and 40 keV electrons and protons has studied using by AFM methods. Traces of electrostatic dis-charges at different radiation flux densities were analyzed.

Effects of conformational ordering on protein/polyelectrolyte electrostatic complexation: ionic binding and chain stiffening

PubMed Central

Cao, Yiping; Fang, Yapeng; Nishinari, Katsuyoshi; Phillips, Glyn O.

2016-01-01

Coupling of electrostatic complexation with conformational transition is rather general in protein/polyelectrolyte interaction and has important implications in many biological processes and practical applications. This work studied the electrostatic complexation between κ-carrageenan (κ-car) and type B gelatin, and analyzed the effects of the conformational ordering of κ-car induced upon cooling in the presence of potassium chloride (KCl) or tetramethylammonium iodide (Me4NI). Experimental results showed that the effects of conformational ordering on protein/polyelectrolyte electrostatic complexation can be decomposed into ionic binding and chain stiffening. At the initial stage of conformational ordering, electrostatic complexation can be either suppressed or enhanced due to the ionic bindings of K+ and I− ions, which significantly alter the charge density of κ-car or occupy the binding sites of gelatin. Beyond a certain stage of conformational ordering, i.e., helix content θ > 0.30, the effect of chain stiffening, accompanied with a rapid increase in helix length ζ, becomes dominant and tends to dissociate the electrostatic complexation. The effect of chain stiffening can be theoretically interpreted in terms of double helix association. PMID:27030165

Investigation of electrostatic behavior of a lactose carrier for dry powder inhalers.

PubMed

Chow, Keat Theng; Zhu, Kewu; Tan, Reginald B H; Heng, Paul W S

2008-12-01

This study aims to elucidate the electrostatic behavior of a model lactose carrier used in dry powder inhaler formulations by examining the effects of ambient relative humidity (RH), aerosolization air flow rate, repeated inhaler use, gelatin capsule and tapping on the specific charge (nC/g) of bulk and aerosolized lactose. Static and dynamic electrostatic charge measurements were performed using a Faraday cage connected to an electrometer. Experiments were conducted inside a walk-in environmental chamber at 25 degrees C and RHs of 20% to 80%. Aerosolization was achieved using air flow rates of 30, 45, 60 and 75 L/min. The initial charges of the bulk and capsulated lactose were a magnitude lower than the charges of tapped or aerosolized lactose. Dynamic charge increased linearly with aerosolization air flow rate and RH. Greater frictional forces at higher air flow rate induced higher electrostatic charges. Increased RH enhanced charge generation. Repeated inhaler use significantly influenced electrostatic charge due to repeated usage. This study demonstrated the significance of interacting influences by variables commonly encountered in the use DPI such as variation in patient's inspiratory flow rate, ambient RH and repeated inhaler use on the electrostatic behavior of a lactose DPI carrier.

Large heat capacity change in a protein-monovalent cation interaction.

PubMed

Guinto, E R; Di Cera, E

1996-07-09

Current views about protein-ligand interactions state that electrostatic forces drive the binding of charged species and that burial of hydrophobic and polar surfaces controls the heat capacity change associated with the reaction. For the interaction of a protein with a monovalent cation the electrostatic components are expected to be significant due to the ionic nature of the ligand, whereas the heat capacity change is expected to be small due to the size of the surface area involved in the recognition event. The physiologically important interaction of Na+ with thrombin was studied over the temperature range from 5 to 45 degrees C and the ionic strength range from 50 to 800 mM. These measurements reveal an unanticipated result that bears quite generally on studies of molecular recognition and protein folding. Binding of Na+ to thrombin is characterized by a modest dependence on ionic strength but a large and negative heat capacity change of -1.1 +/- 0.1 kcal mol-1 K-1. The small electrostatic coupling can be explained in terms of a minimal perturbation of the ionic atmosphere of the protein upon Na+ binding. The large heat capacity change, however, is difficult to reconcile with current views on the origin of this effect from surface area changes or large folding transitions coupled to binding. It is proposed that this change is linked to burial of a large cluster of water molecules in the Na+ binding pocket upon Na+ binding. Due to their reduced mobility and highly ordered structure, water molecules sequestered in the interior of a protein must have a lower heat capacity compared to those on the surface of a protein or in the bulk solvent. Hence, a binding or folding event where water molecules are buried may result in significant heat capacity changes independent of changes in exposed hydrophobic surface or coupled conformational transitions.

Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan

2012-02-07

The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated withmore » the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.« less

Interaction of lysozyme protein with different sized silica nanoparticles and their resultant structures

NASA Astrophysics Data System (ADS)

Yadav, Indresh; Aswal, V. K.; Kohlbrecher, J.

2016-05-01

The interaction of model protein-lysozyme with three different sized anionic silica nanoparticles has been studied by UV-vis spectroscopy, dynamic light scattering (DLS) and small-angle neutron scattering (SANS). The surface area and curvature of the nanoparticles change with size, which significantly influence their interaction with protein. The lysozyme adsorbs on the surface of the nanoparticles due to electrostatic attraction and leads to the phase transformation from one phase (clear) to two-phase (turbid) of the nanoparticle-protein system. The dominance of lysozyme induced short-range attraction over long-range electrostatic repulsion between nanoparticles is responsible for phase transformation and modeled by the two-Yukawa potential. The magnitude of the attractive interaction increases with the size of the nanoparticles as a result the phase transformation commences relatively at lower concentration of lysozyme. The structure of the nanoparticle-protein system in two-phase is characterized by the diffusion limited aggregate type of mass fractal morphology.

Interaction of lysozyme protein with different sized silica nanoparticles and their resultant structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Indresh, E-mail: iykumarindresh288@gmail.com; Aswal, V. K.; Kohlbrecher, J.

The interaction of model protein-lysozyme with three different sized anionic silica nanoparticles has been studied by UV-vis spectroscopy, dynamic light scattering (DLS) and small-angle neutron scattering (SANS). The surface area and curvature of the nanoparticles change with size, which significantly influence their interaction with protein. The lysozyme adsorbs on the surface of the nanoparticles due to electrostatic attraction and leads to the phase transformation from one phase (clear) to two-phase (turbid) of the nanoparticle-protein system. The dominance of lysozyme induced short-range attraction over long-range electrostatic repulsion between nanoparticles is responsible for phase transformation and modeled by the two-Yukawa potential. Themore » magnitude of the attractive interaction increases with the size of the nanoparticles as a result the phase transformation commences relatively at lower concentration of lysozyme. The structure of the nanoparticle-protein system in two-phase is characterized by the diffusion limited aggregate type of mass fractal morphology.« less

Fluorine Gauche Effect Explained by Electrostatic Polarization Instead of Hyperconjugation: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study.

PubMed

Thacker, Joseph C R; Popelier, Paul L A

2018-02-08

We present an interacting quantum atoms (IQA) study of the gauche effect by comparing 1,2-difluoroethane, 1,2-dichloroethane, and three conformers of 1,2,3,4,5,6-hexafluorocyclohexane. In the 1,2-difluoroethane, the gauche effect is observed in that the gauche conformation is more stable than the anti, whereas in 1,2-dichloroethane the opposite is true. The analysis performed here is exhaustive and unbiased thanks to using the recently introduced relative energy gradient (REG) method [ Thacker , J. C. R. ; Popelier , P. L. A. Theor. Chem. Acc . 2017 , 136 , 86 ], as implemented in the in-house program ANANKE. We challenge the common explanation that hyperconjugation is responsible for the gauche stability in 1,2-difluoroethane and instead present electrostatics as the cause of gauche stability. Our explanation of the gauche effect is also is seen in other molecules displaying local gauche conformations, such as the recently synthesized "all-cis" hexafluorocyclohexane and its conformers where all the fluorine atoms are in the equatorial positions. Using our extension of the traditional IQA methodology that allows for the partitioning of electrostatic terms into polarization and charge transfer, we propose that the cause of gauche stability is 1,3 C···F electrostatic polarization interactions. In other words, if a number of fluorine atoms are aligned, then the stability due to polarization of nearby carbon atoms is increased.

Force Field for Water Based on Neural Network.

PubMed

Wang, Hao; Yang, Weitao

2018-05-18

We developed a novel neural network based force field for water based on training with high level ab initio theory. The force field was built based on electrostatically embedded many-body expansion method truncated at binary interactions. Many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: non-polarizable and polarizable force fields. Simulation results show that the non-polarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build the next generation force fields at high accuracy and low computational costs, especially for large systems.

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

PubMed

Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

2016-01-01

While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

PubMed

Qi, Helena W; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.

The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study

PubMed Central

Qi, Helena W.; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L.

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses. PMID:24915485

Limiting assumptions in molecular modeling: electrostatics.

PubMed

Marshall, Garland R

2013-02-01

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

The electrostatic persistence length of polymers beyond the OSF limit.

PubMed

Everaers, R; Milchev, A; Yamakov, V

2002-05-01

We use large-scale Monte Carlo simulations to test scaling theories for the electrostatic persistence length l(e) of isolated, uniformly charged polymers with Debye-Hückel intrachain interactions in the limit where the screening length kappa(-1) exceeds the intrinsic persistence length of the chains. Our simulations cover a significantly larger part of the parameter space than previous studies. We observe no significant deviations from the prediction l(e) proportional to kappa(-2) by Khokhlov and Khachaturian which is based on applying the Odijk-Skolnick-Fixman theories of electrostatic bending rigidity and electrostatically excluded volume to the stretched de Gennes-Pincus-Velasco-Brochard polyelectrolyte blob chain. A linear or sublinear dependence of the persistence length on the screening length can be ruled out. We show that previous results pointing into this direction are due to a combination of excluded-volume and finite chain length effects. The paper emphasizes the role of scaling arguments in the development of useful representations for experimental and simulation data.

Wave Phenomena and Beam-Plasma Interactions at the Magnetopause Reconnection Region

NASA Astrophysics Data System (ADS)

Burch, J. L.; Webster, J. M.; Genestreti, K. J.; Torbert, R. B.; Giles, B. L.; Fuselier, S. A.; Dorelli, J. C.; Rager, A. C.; Phan, T. D.; Allen, R. C.; Chen, L.-J.; Wang, S.; Le Contel, O.; Russell, C. T.; Strangeway, R. J.; Ergun, R. E.; Jaynes, A. N.; Lindqvist, P.-A.; Graham, D. B.; Wilder, F. D.; Hwang, K.-J.; Goldstein, J.

2018-02-01

This paper reports on Magnetospheric Multiscale observations of whistler mode chorus and higher-frequency electrostatic waves near and within a reconnection diffusion region on 23 November 2016. The diffusion region is bounded by crescent-shaped electron distributions and associated dissipation just upstream of the X-line and by magnetic field-aligned currents and electric fields leading to dissipation near the electron stagnation point. Measurements were made southward of the X-line as determined by southward directed ion and electron jets. We show that electrostatic wave generation is due to magnetosheath electron beams formed by the electron jets as they interact with a cold background plasma and more energetic population of magnetospheric electrons. On the magnetosphere side of the X-line the electron beams are accompanied by a strong perpendicular electron temperature anisotropy, which is shown to be the source of an observed rising-tone whistler mode chorus event. We show that the apex of the chorus event and the onset of electrostatic waves coincide with the opening of magnetic field lines at the electron stagnation point.

Charge effects on the hindered transport of macromolecules across the endothelial surface glycocalyx layer.

PubMed

Sugihara-Seki, Masako; Akinaga, Takeshi; O-Tani, Hideyuki

2012-01-01

A fluid mechanical and electrostatic model for the transport of solute molecules across the vascular endothelial surface glycocalyx layer (EGL) was developed to study the charge effect on the diffusive and convective transport of the solutes. The solute was assumed to be a spherical particle with a constant surface charge density, and the EGL was represented as an array of periodically arranged circular cylinders of like charge, with a constant surface charge density. By combining the fluid mechanical analyses for the flow around a solute suspended in an electrolyte solution and the electrostatic analyses for the free energy of the interaction between the solute and cylinders based on a mean field theory, we estimated the transport coefficients of the solute across the EGL. Both of diffusive and convective transports are reduced compared to those for an uncharged system, due to the stronger exclusion of the solute that results from the repulsive electrostatic interaction. The model prediction for the reflection coefficient for serum albumin agreed well with experimental observations if the charge density in the EGL is ranged from approximately -10 to -30 mEq/l.

The effect of pi-stacking, h-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bravaya, Ksenia B.; Kostko, Oleg; Ahmed, Musahid

A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Adiabatic and vertical ionization energies(IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions stronglyaffect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largestchanges in vertical IEs (0.4 eV) occur in asymmetric h-bonded and symmetric pi- stacked isomers, whereas in the lowest-energy symmetric h-bonded dimer the shiftin IEs is muchmore » smaller (0.1 eV). The origin of the shift and the character of the ionized states is different in asymmetric h-bonded and symmetric stacked isomers. Inthe former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by thedipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. The shifts in AAare much smaller due to a less effcient overlap and a smaller dipole moment. The ionization of the h-bonded dimers results in barrierless (or nearly barrierless) protontransfer, whereas the pi-stacked dimers relax to structures with the hole stabilized by the delocalization or electrostatic interactions.« less

Role of electrostatic interactions in the assembly of empty spherical viral capsids

NASA Astrophysics Data System (ADS)

Šiber, Antonio; Podgornik, Rudolf

2007-12-01

We examine the role of electrostatic interactions in the assembly of empty spherical viral capsids. The charges on the protein subunits that make the viral capsid mutually interact and are expected to yield electrostatic repulsion acting against the assembly of capsids. Thus, attractive protein-protein interactions of nonelectrostatic origin must act to enable the capsid formation. We investigate whether the interplay of repulsive electrostatic and attractive interactions between the protein subunits can result in the formation of spherical viral capsids of a preferred radius. For this to be the case, we find that the attractive interactions must depend on the angle between the neighboring protein subunits (i.e., on the mean curvature of the viral capsid) so that a particular angle(s) is (are) preferred energywise. Our results for the electrostatic contributions to energetics of viral capsids nicely correlate with recent experimental determinations of the energetics of protein-protein contacts in the hepatitis B virus [P. Ceres A. Zlotnick, Biochemistry 41, 11525 (2002)].

Exploration of electrostatic interaction in the hydrophobic pocket of lysozyme: Importance of ligand-induced perturbation of the secondary structure on the mode of binding of exogenous ligand and possible consequences.

PubMed

Panja, Sudipta; Halder, Mintu

2016-08-01

Exogenous ligand binding can be adequate to alter the secondary structure of biomolecules besides other external stimuli. In such cases, structural alterations can complicate on the nature of interaction with the exogenous molecules. In order to accommodate the exogenous ligand, the biomolecule has to unfold resulting in a considerable change to its properties. If the bound ligand can be unbound, the biomolecule gets the opportunity to refold back and return to its native state. Keeping this in mind, we have purposely investigated the interaction of tartrazine (TZ), a well abundant azo food colorant, with two homologous lysozymes, namely, human lysozyme (HLZ) and chicken egg white lysozyme (CEWLZ) in physiological pH condition. The binding of TZ with lysozymes has been identified to accompany a ligand-induced secondary structure alteration as indicated by the circular dichroism spectra, and the reduction of α-helical content is more with HLZ than CEWLZ. Interestingly, the binding is identified to occur in the electronic ground state of TZ with lysozyme in its hydrophobic cavity, containing excess of positive charge, predominantly via electrostatic interaction. With increase of salinity of the medium the protein tends to refold back due to wakening of electrostatic forces and consequent reduction of strength of ligand interaction and unbinding. The entropy enthalpy compensation (EEC) has been probed to understand the binding features and it is found that CEWLZ-TZ shows better compensation than HLZ-TZ complex. This is presumably due to the fact that with CEWLZ the binding does not accompany substantial change in the protein secondary structure and hence ineffective to scramble the EEC. The present study initiates the importance of ligand-perturbed structural alteration of biomolecule in controlling the thermodynamics of binding. If there is a considerable alteration of the protein secondary structure due to binding, it is indicative that such changes should bring in the overall loss of activity of protein. Copyright © 2016 Elsevier B.V. All rights reserved.

Interplay between morphological and shielding effects in field emission via Schwarz-Christoffel transformation

NASA Astrophysics Data System (ADS)

Marcelino, Edgar; de Assis, Thiago A.; de Castilho, Caio M. C.

2018-03-01

It is well known that sufficiently strong electrostatic fields are able to change the morphology of Large Area Field Emitters (LAFEs). This phenomenon affects the electrostatic interactions between adjacent sites on a LAFE during field emission and may lead to several consequences, such as: the emitter's degradation, diffusion of absorbed particles on the emitter's surface, deflection due to electrostatic forces, and mechanical stress. These consequences are undesirable for technological applications, since they may significantly affect the macroscopic current density on the LAFE. Despite the technological importance, these processes are not completely understood yet. Moreover, the electrostatic effects due to the proximity between emitters on a LAFE may compete with the morphological ones. The balance between these effects may lead to a non trivial behavior in the apex-Field Enhancement Factor (FEF). The present work intends to study the interplay between proximity and morphological effects by studying a model amenable for an analytical treatment. In order to do that, a conducting system under an external electrostatic field, with a profile limited by two mirror-reflected triangular protrusions on an infinite line, is considered. The FEF near the apex of each emitter is obtained as a function of their shape and the distance between them via a Schwarz-Christoffel transformation. Our results suggest that a tradeoff between morphological and proximity effects on a LAFE may provide an explanation for the observed reduction of the local FEF and its variation at small distances between the emitter sites.

Molecular insight into the counteraction of trehalose on urea-induced protein denaturation using molecular dynamics simulation.

PubMed

Zhang, Na; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2012-06-21

Considerable experimental evidence indicates that trehalose can counteract the denaturing effects of urea on proteins. However, its molecular mechanism remains unknown due to the limitations of current experimental techniques. Herein, molecular dynamics simulations were performed to investigate the counteracting effects of trehalose against urea-induced denaturation of chymotrypsin inhibitor 2. The simulations indicate that the protein unfolds in 8 mol/L urea, but at the same condition the protein retains its native structure in the ternary solution of 8 mol/L urea and 1 mol/L trehalose. It is confirmed that the preferential exclusion of trehalose from the protein surface is the origin of its counteracting effects. It is found that trehalose binds urea via hydrogen bonds, so urea molecules are also expelled from the protein surface along with the preferential exclusion of trehalose. The exclusion of urea from the protein surface leads to the alleviation of the Lennard-Jones interactions between urea and the hydrophobic side chains of the protein in the ternary solution. In contrast, the electrostatic interactions between urea and the protein change little in the presence of trehalose because the decrease in the electrostatic interactions between urea and the protein backbone is canceled by the increase in the electrostatic interactions between urea and the charged side chains of the protein. The results have provided molecular explanations for the counteraction of urea-induced protein denaturation by trehalose.

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters.

PubMed

Yang, Zhong-Zhi; Wu, Yang; Zhao, Dong-Xia

2004-02-08

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.

Electro-osmosis over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions

NASA Astrophysics Data System (ADS)

Ghosh, Uddipta; Chakraborty, Suman

2016-06-01

In this study, we attempt to bring out a generalized formulation for electro-osmotic flows over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions. To this end, we start with modified electro-chemical potential of the individual species and subsequently use it to derive modified Nernst-Planck equation accounting for the ionic fluxes generated because of the presence of non-electrostatic potential. We establish what we refer to as the Poisson-Helmholtz-Nernst-Planck equations, coupled with the Navier-Stokes equations, to describe the complete transport process. Our analysis shows that the presence of non-electrostatic interactions between the ions results in an excess body force on the fluid, and modifies the osmotic pressure as well, which has hitherto remained unexplored. We further apply our analysis to a simple geometry, in an effort to work out the Smoluchowski slip velocity for thin electrical double layer limits. To this end, we employ singular perturbation and develop a general framework for the asymptotic analysis. Our calculations reveal that the final expression for slip velocity remains the same as that without accounting for non-electrostatic interactions. However, the presence of non-electrostatic interactions along with ion specificity can significantly change the quantitative behavior of Smoluchowski slip velocity. We subsequently demonstrate that the presence of non-electrostatic interactions may significantly alter the effective interfacial potential, also termed as the "Zeta potential." Our analysis can potentially act as a guide towards the prediction and possibly quantitative determination of the implications associated with the existence of non-electrostatic potential, in an electrokinetic transport process.

DEVELOPMENT OF A MODEL THAT CONTAINS BOTH MULTIPOLE MOMENTS AND GAUSSIANS FOR THE CALCULATION OF MOLECULAR ELECTROSTATIC POTENTIALS

EPA Science Inventory

The electrostatic interaction is a critical component of intermolecular interactions in biological processes. Rapid methods for the computation and characterization of the molecular electrostatic potential (MEP) that segment the molecular charge distribution and replace this cont...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Woo-Pyo; Jung, Young-Dae, E-mail: ydjung@hanyang.ac.kr; Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180–3590

The influence of electron spin-interaction on the propagation of the electrostatic space-charge quantum wave is investigated in a cylindrically bounded quantum plasma. The dispersion relation of the space-charge quantum electrostatic wave is derived including the influence of the electron spin-current in a cylindrical waveguide. It is found that the influence of electron spin-interaction enhances the wave frequency for large wave number regions. It is shown that the wave frequencies with higher-solution modes are always smaller than those with lower-solution modes in small wave number domains. In addition, it is found that the wave frequency increases with an increase of themore » radius of the plasma cylinder as well as the Fermi wave number. We discuss the effects due to the quantum and geometric on the variation of the dispersion properties of the space-charge plasma wave.« less

Fluorometric estimation of amino acids interaction with colloidal suspension of FITC functionalized graphene oxide nanoparticles

NASA Astrophysics Data System (ADS)

Dave, Kashyap; Dhayal, Marshal

2017-02-01

A hydrosol approach developed to synthesize fluorescence quenched fluorescein isothiocyanate (FITC) functionalized colloidal suspension of graphene oxide nanoparticles (GONP). UV-vis spectroscopic measurements showed characteristic peak at 236 nm and 300 nm due to pi-pi* interaction in Cdbnd C and n-pi* transition in Cdbnd O bond of GONP, respectively. Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectra showed reduced intensity of 1429 cm-1 IR band of GONP due to the electrostatic and pi-pi interactions of FITC with GONP in FITC-GONP. ATR-FTIR spectra of different amino acid co-functionalised FITC-GONP showed an increase in the FTIR band intensity at 1429 cm-1 which was significantly reduced due to electrostatic/pi-pi interactions of FITC with GONP in the absence of the amino acids. A peak at 1084 cm-1 in ATR-FTIR spectra appears which confirms the interaction between amine group of amino acids and sbnd COO- groups at GONP surface. The FITC interaction with GONP lead to fluorescence resonance energy transfers (FRET) and resulted in a liner decrease in the FITC fluorescence with an increase of GONP concentration. An increase in the reappearance of FITC fluorescence observed while the amino acid concentration was increased in co-functionalised FITC-GONP. The quantified amount of reappeared fluorescence of FITC in amino acid co-functionalised FITC-GONP depends on the concentration, polar and non-polar nature of amino acids. The reappearance of FITC from the surface of FITC-GONP with the addition of amino acid was found to be consistent with the organic substitute, size of amino acids and their functionalities. Therefore, FRET based method using FITC-GONP colloidal suspension may have potential application in determining the binding nature of biomolecules with GONP for biomedical applications.

Interaction between like-charged polyelectrolyte-colloid complexes in electrolyte solutions: a Monte Carlo simulation study in the Debye-Hückel approximation.

PubMed

Truzzolillo, D; Bordi, F; Sciortino, F; Sennato, S

2010-07-14

We study the effective interaction between differently charged polyelectrolyte-colloid complexes in electrolyte solutions via Monte Carlo simulations. These complexes are formed when short and flexible polyelectrolyte chains adsorb onto oppositely charged colloidal spheres, dispersed in an electrolyte solution. In our simulations the bending energy between adjacent monomers is small compared to the electrostatic energy, and the chains, once adsorbed, do not exchange with the solution, although they rearrange on the particles surface to accommodate further adsorbing chains or due to the electrostatic interaction with neighbor complexes. Rather unexpectedly, when two interacting particles approach each other, the rearrangement of the surface charge distribution invariably produces antiparallel dipolar doublets that invert their orientation at the isoelectric point. These findings clearly rule out a contribution of dipole-dipole interactions to the observed attractive interaction between the complexes, pointing out that such suspensions cannot be considered dipolar fluids. On varying the ionic strength of the electrolyte, we find that a screening length kappa(-1), short compared with the size of the colloidal particles, is required in order to observe the attraction between like-charged complexes due to the nonuniform distribution of the electric charge on their surface ("patch attraction"). On the other hand, by changing the polyelectrolyte/particle charge ratio xi(s), the interaction between like-charged polyelectrolyte-decorated particles, at short separations, evolves from purely repulsive to strongly attractive. Hence, the effective interaction between the complexes is characterized by a potential barrier, whose height depends on the net charge and on the nonuniformity of their surface charge distribution.

Semiconducting carbon nanotube and covalent organic polyhedron-C60 nanohybrids for light harvesting.

PubMed

Lohrman, Jessica; Zhang, Chenxi; Zhang, Wei; Ren, Shenqiang

2012-08-28

We demonstrate noncovalent electrostatic and π-π interactions to assemble semiconducting single wall carbon nanotube (SWCNT)-C(60)@COP nanohybrids. The C(60)@COP light harvesting complexes bind strongly to SWCNTs due to significant π-π-stacking between C(60), the aromatic dicarbazolylacetylene moieties and the nanotube surfaces.

Electrostatics at the nanoscale.

PubMed

Walker, David A; Kowalczyk, Bartlomiej; de la Cruz, Monica Olvera; Grzybowski, Bartosz A

2011-04-01

Electrostatic forces are amongst the most versatile interactions to mediate the assembly of nanostructured materials. Depending on experimental conditions, these forces can be long- or short-ranged, can be either attractive or repulsive, and their directionality can be controlled by the shapes of the charged nano-objects. This Review is intended to serve as a primer for experimentalists curious about the fundamentals of nanoscale electrostatics and for theorists wishing to learn about recent experimental advances in the field. Accordingly, the first portion introduces the theoretical models of electrostatic double layers and derives electrostatic interaction potentials applicable to particles of different sizes and/or shapes and under different experimental conditions. This discussion is followed by the review of the key experimental systems in which electrostatic interactions are operative. Examples include electroactive and "switchable" nanoparticles, mixtures of charged nanoparticles, nanoparticle chains, sheets, coatings, crystals, and crystals-within-crystals. Applications of these and other structures in chemical sensing and amplification are also illustrated.

The Poisson-Helmholtz-Boltzmann model.

PubMed

Bohinc, K; Shrestha, A; May, S

2011-10-01

We present a mean-field model of a one-component electrolyte solution where the mobile ions interact not only via Coulomb interactions but also through a repulsive non-electrostatic Yukawa potential. Our choice of the Yukawa potential represents a simple model for solvent-mediated interactions between ions. We employ a local formulation of the mean-field free energy through the use of two auxiliary potentials, an electrostatic and a non-electrostatic potential. Functional minimization of the mean-field free energy leads to two coupled local differential equations, the Poisson-Boltzmann equation and the Helmholtz-Boltzmann equation. Their boundary conditions account for the sources of both the electrostatic and non-electrostatic interactions on the surface of all macroions that reside in the solution. We analyze a specific example, two like-charged planar surfaces with their mobile counterions forming the electrolyte solution. For this system we calculate the pressure between the two surfaces, and we analyze its dependence on the strength of the Yukawa potential and on the non-electrostatic interactions of the mobile ions with the planar macroion surfaces. In addition, we demonstrate that our mean-field model is consistent with the contact theorem, and we outline its generalization to arbitrary interaction potentials through the use of a Laplace transformation. © EDP Sciences / Società Italiana di Fisica / Springer-Verlag 2011

Enhanced initial protein adsorption on engineered nanostructured cubic zirconia.

PubMed

Sabirianov, R F; Rubinstein, A; Namavar, F

2011-04-14

Motivated by experimentally-observed biocompatibility enhancement of nanoengineered cubic zirconia (ZrO(2)) coatings to mesenchymal stromal cells, we have carried out computational analysis of the initial immobilization of one known structural fragment of the adhesive protein (fibronectin) on the corresponding surface. We constructed an atomistic model of the ZrO(2) nano-hillock of 3-fold symmetry based on Atom Force Microscopy and Transmission Electron Microscopy images. First principle quantum mechanical calculations show a substantial variation of electrostatic potential at the hillock due to the presence of surface features such as edges and vertexes. Using an implemented Monte Carlo simulated annealing method, we found the orientation of the immobilized protein on the ZrO(2) surface and the contribution of the amino acid residues from the protein sequence to the adsorption energy. Accounting for the variation of the dielectric permittivity at the protein-implant interface, we used a model distance-dependent dielectric function to describe the inter-atom electrostatic interactions in the adsorption potential. We found that the initial immobilization of the rigid protein fragment on the nanostructured pyramidal ZrO(2) surface is achieved with a magnitude of adsorption energy larger than that of the protein on the smooth (atomically flat) surface. The strong attractive electrostatic interactions are a major contributing factor in the enhanced adsorption at the nanostructured surface. In the case of adsorption on the flat, uncharged surface this factor is negligible. We show that the best electrostatic and steric fit of the protein to the inorganic surface corresponds to a minimum of the adsorption energy determined by the non-covalent interactions.

A new method for achieving enhanced dielectric response over a wide temperature range

DOE PAGES

Maurya, Deepam; Sun, Fu -Chang; Pamir Alpay, S.; ...

2015-10-19

We report a novel approach for achieving high dielectric response over a wide temperature range. In this approach, multilayer ceramic heterostructures with constituent compositions having strategically tuned Curie points (TC) were designed and integrated with varying electrical connectivity. Interestingly, these multilayer structures exhibited different dielectric behavior in series and parallel configuration due to variations in electrical boundary conditions resulting in the differences in the strength of the electrostatic coupling. The results are explained using nonlinear thermodynamic model taking into account electrostatic interlayer interaction. We believe that present work will have huge significance in design of high performance ceramic capacitors.

Oscillatory electrostatic potential on graphene induced by group IV element decoration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Chunyan; Yu, Liwei; Liu, Xiaojie

The structures and electronic properties of partial C, Si and Ge decorated graphene were investigated by first-principles calculations. The calculations show that the interaction between graphene and the decoration patches is weak and the semiconductor patches act as agents for weak electron doping without much disturbing graphene electronic π-bands. Redistribution of electrons due to the partial decoration causes the electrostatic potential lower in the decorated graphene areas, thus induced an electric field across the boundary between the decorated and non-decorated domains. Such an alternating electric field can change normal stochastic adatom diffusion to biased diffusion, leading to selective mass transport.

A new method for achieving enhanced dielectric response over a wide temperature range

PubMed Central

Maurya, Deepam; Sun, Fu-Chang; Pamir Alpay, S.; Priya, Shashank

2015-01-01

We report a novel approach for achieving high dielectric response over a wide temperature range. In this approach, multilayer ceramic heterostructures with constituent compositions having strategically tuned Curie points (TC) were designed and integrated with varying electrical connectivity. Interestingly, these multilayer structures exhibited different dielectric behavior in series and parallel configuration due to variations in electrical boundary conditions resulting in the differences in the strength of the electrostatic coupling. The results are explained using nonlinear thermodynamic model taking into account electrostatic interlayer interaction. We believe that present work will have huge significance in design of high performance ceramic capacitors. PMID:26477391

Oscillatory electrostatic potential on graphene induced by group IV element decoration

DOE PAGES

Du, Chunyan; Yu, Liwei; Liu, Xiaojie; ...

2017-10-13

The structures and electronic properties of partial C, Si and Ge decorated graphene were investigated by first-principles calculations. The calculations show that the interaction between graphene and the decoration patches is weak and the semiconductor patches act as agents for weak electron doping without much disturbing graphene electronic π-bands. Redistribution of electrons due to the partial decoration causes the electrostatic potential lower in the decorated graphene areas, thus induced an electric field across the boundary between the decorated and non-decorated domains. Such an alternating electric field can change normal stochastic adatom diffusion to biased diffusion, leading to selective mass transport.

The Demonstration of the Feasibility of the Tuning and Stimulation of Nuclear Radiation.

DTIC Science & Technology

1988-10-31

line, or the center of a resonance pattern, is called the isomer shift. It is due to the electrostatic interaction of the nucleus with the electron ...magnetic moment due to the presence of unpaired electrons , the material is either paramagnetic or ferromagnetic. In paramagnetic materials these moments...capture and fission.4,5,8 A very fertile interdisciplinary area of nuclear quantum electronics 7 appeared to be developing, encouraged by the

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

PubMed

Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

2004-12-01

To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software.

PubMed

Sakuraba, Shun; Fukuda, Ikuo

2018-05-04

The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter-tuned SPME implementation are performed for various-sized water systems and two protein-water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time-consuming electrostatic convolution and because the ZMM gains short neighbor-list distances due to the smooth damping feature of the pairwise potential function near the cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

A hybrid parallel architecture for electrostatic interactions in the simulation of dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping

2017-11-01

In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space, which approximately take up most of the total simulation time. Although the parallel method CU-ENUF (Yang et al., 2016) based on GPU has achieved a qualitative leap compared with previous methods in electrostatic interactions computation, the computation capability is limited to the throughput capacity of a single GPU for super-scale simulation system. Therefore, we should look for an effective method to handle the calculation of electrostatic interactions efficiently for a simulation system with super-scale size. Solution method: We constructed a hybrid parallel architecture, in which CPU and GPU are combined to accelerate the electrostatic computation effectively. Firstly, the simulation system is divided into many subtasks via domain-decomposition method. Then MPI (Message Passing Interface) is used to implement the CPU-parallel computation with each computer node corresponding to a particular subtask, and furthermore each subtask in one computer node will be executed in GPU in parallel efficiently. In this hybrid parallel method, the most critical technical problem is how to parallelize a CUNFFT (nonequispaced fast Fourier transform based on CUDA) in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Restrictions: The HP-ENUF is mainly oriented to super-scale system simulations, in which the performance superiority is shown adequately. However, for a small simulation system containing less than 106 particles, the mode of multiple computer nodes has no apparent efficiency advantage or even lower efficiency due to the serious network delay among computer nodes, than the mode of single computer node. References: (1) S.-C. Yang, H.-J. Qian, Z.-Y. Lu, Appl. Comput. Harmon. Anal. 2016, http://dx.doi.org/10.1016/j.acha.2016.04.009. (2) S.-C. Yang, Y.-L. Wang, G.-S. Jiao, H.-J. Qian, Z.-Y. Lu, J. Comput. Chem. 37 (2016) 378. (3) S.-C. Yang, Y.-L. Zhu, H.-J. Qian, Z.-Y. Lu, Appl. Chem. Res. Chin. Univ., 2017, http://dx.doi.org/10.1007/s40242-016-6354-5. (4) Y.-L. Zhu, H. Liu, Z.-W. Li, H.-J. Qian, G. Milano, Z.-Y. Lu, J. Comput. Chem. 34 (2013) 2197.

Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry*

PubMed Central

Meneses, Erick; Mittermaier, Anthony

2014-01-01

Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr–Purcell–Meiboom–Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes. PMID:25122758

Molecular simulations of the pairwise interaction of monoclonal antibodies.

PubMed

Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E

2014-11-20

Molecular simulations are employed to compute the free energy of pairwise monoclonal antibodies (mAbs) association using a conformational sampling algorithm with a scoring function. The work reported here is aimed at investigating the mAb-mAb association driven by weak interactions with a computational method capable of predicting experimental observations of low binding affinity. The simulations are able to explore the free energy landscape. A steric interaction component, electrostatic interactions, and a nonpolar component of the free energy form the energy scoring function. Electrostatic interactions are calculated by solving the Poisson-Boltzmann equation. The nonpolar component is derived from the van der Waals interactions upon close contact of the protein surfaces. Two mAbs with similar IgG1 framework but with small sequence differences, mAb1 and mAb2, are considered for their different viscosity and propensity to form a weak interacting dimer. mAb1 presents favorable free energy of association at pH 6 with 15 mM of ion concentration reproducing experimental trends of high viscosity and dimer formation at high concentration. Free energy landscape and minimum free energy configurations of the dimer, as well as the second virial coefficient (B22) values are calculated. The energy distributions for mAb1 are obtained, and the most probable configurations are seen to be consistent with experimental measurements. In contrast, mAb2 shows an unfavorable average free energy at the same buffer conditions due to poor electrostatic complementarity, and reversible dimer configurations with favorable free energy are found to be unlikely. Finally, the simulations of the mAb association dynamics provide insights on the self-association responsible for bulk solution behavior and aggregation, which are important to the processing and the quality of biopharmaceuticals.

On the importance of electrostatic interactions between cell penetrating peptides and membranes: a pathway toward tumor cell selectivity?

PubMed

Jobin, Marie-Lise; Alves, Isabel D

2014-12-01

Cell-penetrating peptides (CPPs) are small molecules of major interest due to their ability to efficiently transport cargos across cell membranes in a receptor- and energy-independent way and without being cytotoxic to cells. Since their discovery 20 years ago their potential interest in drug delivery and diagnosis became undeniable. CPPs are being used to deliver inside cells a large variety of cargos such as proteins, DNA, antibodies, imaging agents and nanoparticle drug carriers. Their cellular uptake mechanisms are still debated and may vary depending on their structure, nature and size of cargo they transport and type of cell line targeted. CPPs are generally rich in positively charged residues, thus they are prone to establish electrostatic interactions with anionic membrane components (sugars and lipids). Understanding the molecular basis of CPP membrane interaction and cellular uptake is crucial to improve their in vivo efficiency target-specificity. A great number of studies demonstrated the high potential of CPPs to translocate efficiently therapeutic cargos into cells and some peptides are even in clinical phase studies. Although these molecules seem perfect for a therapeutic or diagnosis purpose, they still possess a small but non negligible drawback: a complete lack of cell type specificity. Tumor cells have recently been shown to over-express certain glycosaminoglycans at the cell membrane surface and to possess a higher amount of anionic lipids in their outer leaflet than healthy cells. Such molecules confer the cell membrane an enhanced anionic character, property that could be used by CPPs to selectively target these cells. Moreover previous studies demonstrate the importance of electrostatic interactions between basic residues in the peptide, especially Arg, and the lipid headgroups and glycosaminoglycans in the cell membrane. Electrostatic interactions put at stake in this process might be one of the keys to resolve the puzzle of CPP cell type specificity. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Anomalous Ground State of the Electrons in Nano-confined Water

DTIC Science & Technology

2016-06-13

confined water system, Nafion, is so different from that of bulk water that the weakly electrostatically interacting molecule model of water is clearly...assume that water is made up molecules weakly interacting(on the scale of the zero point bond energy~.2eV) electrostatically with its neighbors2-3. In an...not possible for a collection of molecules interacting weakly electrostatically . These changes in the spatial distribution of valence electrons in

The electrostatics of solvent and membrane interfaces and the role of electronic polarizability

NASA Astrophysics Data System (ADS)

Vorobyov, Igor; Allen, Toby W.

2010-05-01

The electrostatics of solvent and lipid bilayer interfaces are investigated with the aim of understanding the interaction of ions and charged peptides with biological membranes. We overcome the lacking dielectric response of hydrocarbon by carrying out atomistic molecular dynamics simulations using a polarizable model. For air-solvent or solvent-solvent interfaces, the effect of polarizability itself is small, yet changes in the fixed atomic charge distribution are responsible for substantial changes in the potential. However, when electrostatics is probed by finite solutes, a cancellation of dominant quadrupolar terms from the macroscopic and microscopic (solute-solvent) interfaces eliminates this dependence and leads to small net contributions to partitioning thermodynamics. In contrast, the membrane dipole potential exhibits considerable dependence on lipid electronic polarizability, due to its dominant dipolar contribution. We report the dipole potential for a polarizable lipid hydrocarbon membrane model of 480-610 mV, in better accord with experimental measurements.

An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

NASA Astrophysics Data System (ADS)

Poursina, Mohammad; Anderson, Kurt S.

2014-08-01

This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

Adsorption of guanidinium collectors on aluminosilicate minerals - a density functional study.

PubMed

Nulakani, Naga Venkateswara Rao; Baskar, Prathab; Patra, Abhay Shankar; Subramanian, Venkatesan

2015-10-07

In this density functional theory based investigation, we have modelled and studied the adsorption behaviour of guanidinium cations and substituted (phenyl, methoxy phenyl, nitro phenyl and di-nitro phenyl) guanidinium cationic collectors on the basal surfaces of kaolinite and goethite. The adsorption behaviour is assessed in three different media, such as gas, explicit water and pH medium, to understand the affinity of GC collectors to the SiO4 tetrahedral and AlO6 octahedral surfaces of kaolinite. The tetrahedral siloxane surface possesses a larger binding affinity to GC collectors than the octahedral sites due to the presence of surface exposed oxygen atoms that are active in the intermolecular interactions. Furthermore, the inductive electronic effects of substituted guanidinium cations also play a key role in the adsorption mechanism. Highly positive cations result in a stronger electrostatic interaction and preferential adsorption with the kaolinite surfaces than low positive cations. Computed interaction energies and electron densities at the bond critical points suggest that the adsorption of guanidinium cations on the surfaces of kaolinite and goethite is due to the formation of intra/inter hydrogen bonding networks. Also, the electrostatic interaction favours the high adsorption ability of GC collectors in the pH medium than gas phase and water medium. The structures and energies of GC collectors pave an intuitive view for future experimental studies on mineral flotation.

Multi-Scale Structure of Coacervates formed by Oppositely Charged Polyelectrolytes

NASA Astrophysics Data System (ADS)

Rubinstein, Michael

We develop a scaling model of coacervates formed by oppositely charged polyelectrolytes and demonstrate that they self-organize into multi-scale structures. The intramolecular electrostatic interactions in dilute polyanion or polycation solutions are characterized by the electrostatic blobs with size D- and D+ respectively, that repel neighboring blobs on the same chains with electrostatic energy on the order of thermal energy kT . After mixing, electrostatic intramolecular repulsion of polyelectrolytes with higher charged density, say polyanions, keeps these polyanions in coacervates aligned into stretched arrays of electrostatic blobs of size D-

Turbulent particulate transportation during electrostatic precipitation

NASA Astrophysics Data System (ADS)

Choi, Bum Seog

The generation of secondary flows and turbulence by a corona discharge influences particle transport in an electrostatic precipitator (ESP), and is known to play an important role in the particle collection process. However, it is difficult to characterise theoretically and experimentally the ``turbulent'' fluctuations of the gas flow produced by negative tuft corona. Because of this difficulty, only limited studies have been undertaken previously to understand the structure of corona-induced turbulence and its influence on particle transport in ESPs. The present study is aimed at modelling electrohydrodynamic turbulent flows and particle transport, and at establishing an unproved understanding of them. For a multiply interactive coupling of electrostatics, fluid dynamics and particle dynamics, a strongly coupled system of the governing equations has been solved. The present computer model has considered the most important interaction mechanisms including an ionic wind, corona- induced turbulence and the particle space charge effect. Numerical simulations have been performed for the extensive validation of the numerical and physical models. To account for electrically excited turbulence associated with the inhomogeneous and unsteady characteristics of negative corona discharges, a new turbulence model (called the electrostatic turbulence model) has been developed. In this, an additional production or destruction term is included into the turbulent kinetic energy and dissipation rate equations. It employs a gradient type model of the current density and an electrostatic diffusivity concept. The results of the computation show that the electrostatic turbulence model gives much better agreement with the experimental data than the conventional RNG k-ɛ turbulence model when predicting turbulent gas flows and particle distributions in an ESP. Computations of turbulent particulate two-phase flows for both mono-dispersed and poly-dispersed particles have been performed. The effects of coriona-induced turbulence and the particle space charge on particle transport and the collection process have been investigated. The calculated results for the poly-dispersed particulate flow were compared with those of the mono-dispersed particulate flow, and significant differences were demonstrated. It is established that effective particle- particle interaction occurs, due to the influence of the particle space charge, even for dilute gas-particle flows that occur in ESPs.

Inter-subunit electrostatic interactions in ferritin molecule: comparison with inter-molecular interactions in crystals

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Hogyoku, Michiru; Nagayama, Kuniaki

1996-10-01

We evaluated the contribution of electrostatic interactions to the stability of macromolecular assembly in a horse L ferritin molecule composed of 24 subunits and the three-dimensional crystal of the ferritin molecules with numerical calculation of Poisson-Boltzmann equation based on dielectric model. The calculation showed that the electrostatic energy both favors the assembly of the 24 subunits and the crystalline assembly of the ferritin molecules (i.e., 24-mers). Short-range interactions less than 5 Å such as salt bridges and hydrogen bonds were important for both the subunit assembly and the crystalline assembly. To elucidate the strong stabilization by electrostatic interactions in both the ferritin 24-mer and its crystal, we analyzed the contribution of individual atoms. It revealed that the stabilization was arising from buried salt bridges or hydrogen bonds, which yielded more than 5 kcal/mol in some interactions. These large electrostatic stabilization and also the unexpected small ionic strength dependence was different from those of bovine pancreatic trypsin inhibitor (BPTI) orthorhombic and pig-insulin cubic crystals previously calculated. We also evaluated changes of the accessible surface area (ASA) and hydration free energy in accordance with the process of the subunit assembly. The change of hydration free energy, which was very large (i.e. ˜ + 100 kcal/mol/subunit) and unfavorable for the assembly, was proportional to the electrostatic hydration energy (i.e. Born energy change in hydration process). Hydrophobic groups were likely to appear more frequently than hydrophilic groups at the subunit interfaces. These results suggest that the molecular structure of the ferritin 24-mer and the crystal structure of the 24-mers were both stabilized by local electrostatic interactions, in particular. We view protein crystals as an extension of the protein oligomer to an infinite number of subunits association.

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.

PubMed

Stafford, Amy J; Ensign, Daniel L; Webb, Lauren J

2010-11-25

Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.

The electronegativity equalization method fused with molecular mechanics: a fluctuating charge and flexible body potential function for [Emim][Gly] ionic liquids.

PubMed

Wu, Yang; Li, Yao; Hu, Na; Hong, Mei

2014-02-14

Recently, experimental and theoretical studies on amino acid ionic liquid (AAIL) systems have attracted much attention. A transferable intermolecular potential approach that includes fluctuating charges and a flexible body based on a combination of the electronegativity equalization method and molecular mechanics (EEM/MM), and its application to an AAIL system containing 1-ethyl-3-methylimidazolium ([Emim](+)) and glycine ([Gly](-)) are explored and tested in this study. A consistent integration of EEM with MM requires the input of the EEM charges of all atoms into the MM intermolecular electrostatic interaction term. Compared with ionic liquid (IL) force fields, the EEM/MM model has an outstanding feature: the EEM/MM model not only presents the electrostatic interaction of atoms and their changes in response to different ambient environments but also introduces "the H-bond interaction region" in which a new parameter kHB(RHB) is used to describe the electrostatic interaction of hydrogen atoms in [Emim](+) and oxygen atoms in [Gly](-), which can form hydrogen bonds. The EEM/MM model gives quite accurate predictions for gas-phase state properties of [Emim](+), [Gly](-), and ion pairs, such as optimized geometries, dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and hydrogen bonds, the EEM/MM model also performs well for the liquid-phase properties of [Emim][Gly] under ambient conditions. The calculated properties, such as density, heat of vaporization, the self-diffusion coefficient, and ionic conductivity, are fairly consistent with available experimental results.

Electrostatic Interactions in Aminoglycoside-RNA Complexes

PubMed Central

Kulik, Marta; Goral, Anna M.; Jasiński, Maciej; Dominiak, Paulina M.; Trylska, Joanna

2015-01-01

Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity. PMID:25650932

The electrostatic interaction between interfacial colloidal particles

NASA Astrophysics Data System (ADS)

Hurd, A. J.

1985-11-01

The electrostatic interaction between charged, colloidal particles trapped at an air-water interface is considered using linearised Poisson-Boltzmann results for point particles. In addition to the expected screened-Coulomb contribution, which decays exponentially, an algebraic dipole-dipole interaction occurs that may account for long-range interactions in interfacial colloidal systems.

Electrostatic interaction based approach to thrombin detection by surface-enhanced Raman spectroscopy.

PubMed

Hu, Juan; Zheng, Peng-Cheng; Jiang, Jian-Hui; Shen, Guo-Li; Yu, Ru-Qin; Liu, Guo-Kun

2009-01-01

We have developed an electrostatic interaction based biosensor for thrombin detection using surface-enhanced Raman spectroscopy (SERS). This method utilized the electrostatic interaction between capture (thrombin aptamer) and probe (crystal violet, CV) molecules. The specific interaction between thrombin and aptamer could weaken the electrostatic barrier effect from the negative charged aptamer SAMs to the diffusion process of the positively charged CV from the bulk solution to the Au nanoparticle surface. Therefore, the more the bound thrombin, the more the CV molecules near the Au nanoparticle surface and the stronger the observed Raman signal of CV, provided the Raman detections were set at the same time point for each case. This procedure presented a highly specific selectivity and a linear detection of thrombin in the range from 0.1 nM to 10 nM with a detection limit of about 20 pM and realized the thrombin detection in human blood serum solution directly. The electrostatic interaction based technique provides an easy and fast-responding optical platform for a "signal-on" detection of proteins, which might be applicable for the real time assay of proteins.

The Effect of Lipopolysaccharide Core Oligosaccharide Size on the Electrostatic Binding of Antimicrobial Proteins to Models of the Gram Negative Bacterial Outer Membrane

PubMed Central

2016-01-01

Understanding the electrostatic interactions between bacterial membranes and exogenous proteins is crucial to designing effective antimicrobial agents against Gram-negative bacteria. Here we study, using neutron reflecometry under multiple isotopic contrast conditions, the role of the uncharged sugar groups in the outer core region of lipopolysaccharide (LPS) in protecting the phosphate-rich inner core region from electrostatic interactions with antimicrobial proteins. Models of the asymmetric Gram negative outer membrane on silicon were prepared with phopshatidylcholine (PC) in the inner leaflet (closest to the silicon), whereas rough LPS was used to form the outer leaflet (facing the bulk solution). We show how salt concentration can be used to reversibly alter the binding affinity of a protein antibiotic colicin N (ColN) to the anionic LPS confirming that the interaction is electrostatic in nature. By examining the interaction of ColN with two rough LPS types with different-sized core oligosaccharide regions we demonstrate the role of uncharged sugars in blocking short-range electrostatic interactions between the cationic antibiotics and the vulnerable anionic phosphate groups. PMID:27003358

Electrostatic Charging and Particle Interactions in Microscopic Insulating Grains

NASA Astrophysics Data System (ADS)

Lee, Victor

In this thesis, we experimentally investigate the electrostatic charging as well as the particle interactions in microscopic insulating grains. First, by tracking individual grains accelerated in an electric field, we quantitatively demonstrate that tribocharging of same-material grains depends on particle size. Large grains tend to charge positively, and small ones tend to charge negatively. Theories based on the transfer of trapped electrons can explain this tendency but have not been validated. Here we show that the number of trapped electrons, measured independently by a thermoluminescence technique, is orders of magnitude too small to be responsible for the amount of charge transferred. This result reveals that trapped electrons are not responsible for same-material tribocharging of dielectric particles. Second, same-material tribocharging in grains can result in important long-range electrostatic interactions. However, how these electrostatic interactions contribute to particle clustering remains elusive, primarily due to the lack of direct, detailed observations. Using a high-speed camera that falls with a stream charged grains, we observe for the first time how charged grains can undergo attractive as well as repulsive Kepler-like orbits. Charged particles can be captured in their mutual electrostatic potential and form clusters via multiple bounces. Dielectric polarization effects are directly observed, which lead to additional attractive forces and stabilize "molecule-like" arrangements of charged particles. Third, we have developed a new method to study the charge transfer of microscopic particles based on acoustic levitation techniques. This method allows us to narrow the complex problem of many-particle charging down to precise charge measurements of a single sub-millimeter particle colliding with a target plate. By simply attaching nonpolar groups onto glass surfaces, we show that the contact charging of a particle is highly dependent on hydrophobicity. Charging between a hydrophilic and a hydrophobic surface is enhanced in a basic atmosphere and suppressed in an acidic one. Moreover, hydrophobicity is also found to play a key role in particle charging driven by an external electric field. These results strongly support the idea that aqueous-ion transfer is responsible for the particle contact charging phenomenon.

Inter-layer potential for hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Leven, Itai; Azuri, Ido; Kronik, Leeor; Hod, Oded

2014-03-01

A new interlayer force-field for layered hexagonal boron nitride (h-BN) based structures is presented. The force-field contains three terms representing the interlayer attraction due to dispersive interactions, repulsion due to anisotropic overlaps of electron clouds, and monopolar electrostatic interactions. With appropriate parameterization, the potential is able to simultaneously capture well the binding and lateral sliding energies of planar h-BN based dimer systems as well as the interlayer telescoping and rotation of double walled boron-nitride nanotubes of different crystallographic orientations. The new potential thus allows for the accurate and efficient modeling and simulation of large-scale h-BN based layered structures.

Electrostatic contribution to the persistence length of a semiflexible dipolar chain.

PubMed

Podgornik, Rudi

2004-09-01

We investigate the electrostatic contribution to the persistence length of a semiflexible polymer chain whose segments interact via a screened Debye-Hückel dipolar interaction potential. We derive the expressions for the renormalized persistence length on the level of a 1/D-expansion method already successfully used in other contexts of polyelectrolye physics. We investigate different limiting forms of the renormalized persistence length of the dipolar chain and show that, in, general, it depends less strongly on the screening length than in the context of a monopolar chain. We show that for a dipolar chain the electrostatic persistence length in the same regime of the parameter phase space as the original Odijk-Skolnick-Fixman (OSF) form for a monopolar chain depends logarithmically on the screening length rather than quadratically. This can be understood solely on the basis of a swifter decay of the dipolar interactions with separation compared to the monopolar electrostatic interactions. We comment also on the general contribution of higher multipoles to the electrostatic renormalization of the bending rigidity.

DNA packaging in viral capsids with peptide arms.

PubMed

Cao, Qianqian; Bachmann, Michael

2017-01-18

Strong chain rigidity and electrostatic self-repulsion of packed double-stranded DNA in viruses require a molecular motor to pull the DNA into the capsid. However, what is the role of electrostatic interactions between different charged components in the packaging process? Though various theories and computer simulation models were developed for the understanding of viral assembly and packaging dynamics of the genome, long-range electrostatic interactions and capsid structure have typically been neglected or oversimplified. By means of molecular dynamics simulations, we explore the effects of electrostatic interactions on the packaging dynamics of DNA based on a coarse-grained DNA and capsid model by explicitly including peptide arms (PAs), linked to the inner surface of the capsid, and counterions. Our results indicate that the electrostatic interactions between PAs, DNA, and counterions have a significant influence on the packaging dynamics. We also find that the packed DNA conformations are largely affected by the structure of the PA layer, but the packaging rate is insensitive to the layer structure.

Encapsulation of cisplatin as an anti-cancer drug into boron-nitride and carbon nanotubes: Molecular simulation and free energy calculation.

PubMed

Roosta, Sara; Hashemianzadeh, Seyed Majid; Ketabi, Sepideh

2016-10-01

Encapsulation of cisplatin anticancer drug into the single walled (10, 0) carbon nanotube and (10, 0) boron-nitride nanotube was investigated by quantum mechanical calculations and Monte Carlo Simulation in aqueous solution. Solvation free energies and complexation free energies of the cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube complexes was determined as well as radial distribution functions of entitled compounds. Solvation free energies of cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube were -4.128kcalmol(-1) and -2457.124kcalmol(-1) respectively. The results showed that cisplatin@ boron-nitride nanotube was more soluble species in water. In addition electrostatic contribution of the interaction of boron- nitride nanotube complex and solvent was -281.937kcalmol(-1) which really more than Van der Waals and so the electrostatic interactions play a distinctive role in the solvation free energies of boron- nitride nanotube compounds. On the other hand electrostatic part of the interaction of carbon nanotube complex and solvent were almost the same as Van der Waals contribution. Complexation free energies were also computed to study the stability of related structures and the free energies were negative (-374.082 and -245.766kcalmol(-1)) which confirmed encapsulation of drug into abovementioned nanotubes. However, boron-nitride nanotubes were more appropriate for encapsulation due to their larger solubility in aqueous solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

PubMed Central

2014-01-01

Background Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme. Results We found that the inclusion of the long-range electrostatic correction increased the accuracy of both the protein-protein interaction profiles and the protein diffusion coefficients at low ionic strength. Conclusions An advantage of this method is the low additional computational cost required to treat long-range electrostatic interactions in large biomacromolecular systems. Moreover, the implementation described here for BD simulations of protein solutions can also be applied in implicit solvent molecular dynamics simulations that make use of gridded interaction potentials. PMID:25045516

A universal approach to fabricate ordered colloidal crystals arrays based on electrostatic self-assembly.

PubMed

Zhang, Xun; Zhang, Junhu; Zhu, Difu; Li, Xiao; Zhang, Xuemin; Wang, Tieqiang; Yang, Bai

2010-12-07

We present a novel and simple method to fabricate two-dimensional (2D) poly(styrene sulfate) (PSS, negatively charged) colloidal crystals on a positively charged substrate. Our strategy contains two separate steps: one is the three-dimensional (3D) assembly of PSS particles in ethanol, and the other is electrostatic adsorption in water. First, 3D assembly in ethanol phase eliminates electrostatic attractions between colloids and the substrate. As a result, high-quality colloidal crystals are easily generated, for electrostatic attractions are unfavorable for the movement of colloidal particles during convective self-assembly. Subsequently, top layers of colloidal spheres are washed away in the water phase, whereas well-packed PSS colloids that are in contact with the substrate are tightly linked due to electrostatic interactions, resulting in the formation of ordered arrays of 2D colloidal spheres. Cycling these processes leads to the layer-by-layer assembly of 3D colloidal crystals with controllable layers. In addition, this strategy can be extended to the fabrication of patterned 2D colloidal crystals on patterned polyelectrolyte surfaces, not only on planar substrates but also on nonplanar substrates. This straightforward method may open up new possibilities for practical use of colloidal crystals of excellent quality, various patterns, and controllable fashions.

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model.

PubMed

Warwicker, J

1989-03-20

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

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

PubMed Central

lee, Lee-Peng; Tidor, Bruce

2001-01-01

Theoretical and experimental studies have shown that the large desolvation penalty required for polar and charged groups frequently precludes their involvement in electrostatic interactions that contribute strongly to net stability in the folding or binding of proteins in aqueous solution near room temperature. We have previously developed a theoretical framework for computing optimized electrostatic interactions and illustrated use of the algorithm with simplified geometries. Given a receptor and model assumptions, the method computes the ligand-charge distribution that provides the most favorable balance of desolvation and interaction effects on binding. In this paper the method has been extended to treat complexes using actual molecular shapes. The barnase-barstar protein complex was investigated with barnase treated as a target receptor. The atomic point charges of barstar were varied to optimize the electrostatic binding free energy. Barnase and natural barstar form a tight complex (Kd ∼ 10−14 M) with many charged and polar groups near the interface that make this a particularly relevant system for investigating the role of electrostatic effects on binding. The results show that sets of barstar charges (resulting from optimization with different constraints) can be found that give rise to relatively large predicted improvements in electrostatic binding free energy. Principles for enhancing the effect of electrostatic interactions in molecular binding in aqueous environments are discussed in light of the optima. Our findings suggest that, in general, the enhancements in electrostatic binding free energy resulting from modification of polar and charged groups can be substantial. Moreover, a recently proposed definition of electrostatic complementarity is shown to be a useful tool for examining binding interfaces. Finally, calculational results suggest that wild-type barstar is closer to being affinity optimized than is barnase for their mutual binding, consistent with the known roles of these proteins. PMID:11266622

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Aggrecan nanoscale solid-fluid interactions are a primary determinant of cartilage dynamic mechanical properties.

PubMed

Nia, Hadi Tavakoli; Han, Lin; Bozchalooi, Iman Soltani; Roughley, Peter; Youcef-Toumi, Kamal; Grodzinsky, Alan J; Ortiz, Christine

2015-03-24

Poroelastic interactions between interstitial fluid and the extracellular matrix of connective tissues are critical to biological and pathophysiological functions involving solute transport, energy dissipation, self-stiffening and lubrication. However, the molecular origins of poroelasticity at the nanoscale are largely unknown. Here, the broad-spectrum dynamic nanomechanical behavior of cartilage aggrecan monolayer is revealed for the first time, including the equilibrium and instantaneous moduli and the peak in the phase angle of the complex modulus. By performing a length scale study and comparing the experimental results to theoretical predictions, we confirm that the mechanism underlying the observed dynamic nanomechanics is due to solid-fluid interactions (poroelasticity) at the molecular scale. Utilizing finite element modeling, the molecular-scale hydraulic permeability of the aggrecan assembly was quantified (kaggrecan = (4.8 ± 2.8) × 10(-15) m(4)/N·s) and found to be similar to the nanoscale hydraulic permeability of intact normal cartilage tissue but much lower than that of early diseased tissue. The mechanisms underlying aggrecan poroelasticity were further investigated by altering electrostatic interactions between the molecule's constituent glycosaminoglycan chains: electrostatic interactions dominated steric interactions in governing molecular behavior. While the hydraulic permeability of aggrecan layers does not change across species and age, aggrecan from adult human cartilage is stiffer than the aggrecan from newborn human tissue.

Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

NASA Astrophysics Data System (ADS)

Sagui, Celeste; Pedersen, Lee G.; Darden, Thomas A.

2004-01-01

The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is hoped that this new formalism will facilitate the systematic implementation of higher order multipoles in classical biomolecular force fields.

Effect of electrostatic interaction between fluoxetine and lipid membranes on the partitioning of fluoxetine investigated using second derivative spectrophotometry and FTIR.

PubMed

Do, Tien T T; Dao, Uyen P N; Bui, Huong T; Nguyen, Trang T

2017-10-01

The interaction between a drug molecule and lipid bilayers is highly important regarding the pharmaceutical activity of the drug. In this study, the interaction of fluoxetine, a well-known selective serotonin reuptake inhibitor antidepressant and lipid bilayers composed of 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was studied from the aspect of electrostatics using second derivative spectrophotometry and Fourier transform infrared spectroscopy (FTIR) in order to provide insights into the drug behavior. Changing pH from 7.4 to 9.5 to increases the neutral state of fluoxetine, the partitioning of fluoxetine into the zwitterionic DPPC large unilamellar vesicles (LUVs) was increased whereas it was reduced into the negatively charged DPPG LUVs. Fluoxetine was found to exhibit a disordering effect on the acyl chains of DPPC and DPPG bilayers upon its partitioning. In addition, increasing concentration of NaCl lessened the binding of fluoxetine into DPPG bilayers due to the reduction in electrostatic attraction between positively charged fluoxetine and negatively charged DPPG LUVs. In addition, the FTIR study revealed that increasing the NaCl concentration could trigger the shift to higher frequency of the CH 2 stretching as well as the notable blue shift in the PO 2 - regions of DPPG, indicating that fluoxetine had deeper penetration into DPPG LUVs. The differences in the NaCl concentration showed a negligible effect on the incorporation of fluoxetine into the zwitterionic DPPC LUVs. In summary, the electrostatic interaction plays an important role on the partitioning of a cationic amphiphilic SSIR drug into the lipid bilayers and the drug partitioning induces the lipids' conformational change. These imply a possible influence on the drug pharmacology. Copyright © 2017 Elsevier B.V. All rights reserved.

Defining protein electrostatic recognition processes

NASA Astrophysics Data System (ADS)

Getzoff, Elizabeth D.; Roberts, Victoria A.

The objective is to elucidate the nature of electrostatic forces controlling protein recognition processes by using a tightly coupled computational and interactive computer graphics approach. The TURNIP program was developed to determine the most favorable precollision orientations for two molecules by systematic search of all orientations and evaluation of the resulting electrostatic interactions. TURNIP was applied to the transient interaction between two electron transfer metalloproteins, plastocyanin and cytochrome c. The results suggest that the productive electron-transfer complex involves interaction of the positive region of cytochrome c with the negative patch of plastocyanin, consistent with experimental data. Application of TURNIP to the formation of the stable complex between the HyHEL-5 antibody and its protein antigen lysozyme showed that long-distance electrostatic forces guide lysozyme toward the HyHEL-5 binding site, but do not fine tune its orientation. Determination of docked antigen/antibody complexes requires including steric as well as electrostatic interactions, as was done for the U10 mutant of the anti-phosphorylcholine antibody S107. The graphics program Flex, a convenient desktop workstation program for visualizing molecular dynamics and normal mode motions, was enhanced. Flex now has a user interface and was rewritten to use standard graphics libraries, so as to run on most desktop workstations.

Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations.

PubMed

Ritchie, Andrew W; Webb, Lauren J

2015-11-05

Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.

Electrostatic Rate Enhancement and Transient Complex of Protein-Protein Association

PubMed Central

Alsallaq, Ramzi; Zhou, Huan-Xiang

2012-01-01

The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to ~105 – 106 M−1s−1. Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys. J. 1997;73:2441–2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by kD = kD0 exp(−*/ kBT), where kD and kD0 are the rates in the presence and absence of electrostatic interactions, respectively, * is the average electrostatic interaction energy in a “transient-complex” ensemble, and kBT is thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007, 15:215–224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations. PMID:17932929

Linear and nonlinear interactions of an electron beam with oblique whistler and electrostatic waves in the magnetosphere

NASA Astrophysics Data System (ADS)

Zhang, Y. L.; Matsumoto, H.; Omura, Y.

1993-12-01

Both linear and nonlinear interactions between oblique whistler, electrostatic, quasi-upper hybrid mode waves and an electron beam are studied by linear analyses and electromagnetic particle simulations. In addition to a background cold plasma, we assumed a hot electron beam drifting along a static magnetic field. Growth rates of the oblique whistler, oblique electrostatic, and quasi-upper hybrid instabilities were first calculated. We found that there are four kinds of unstable mode waves for parallel and oblique propagations. They are the electromagnetic whistler mode wave (WW1), the electrostatic whistler mode wave (WW2), the electrostatic mode wave (ESW), and the quasi-upper hybrid mode wave (UHW). A possible mechanism is proposed to explain the satellite observations of whistler mode chorus and accompanied electrostatic waves, whose amplitudes are sometimes modulated at the chorus frequency.

webPIPSA: a web server for the comparison of protein interaction properties

PubMed Central

Richter, Stefan; Wenzel, Anne; Stein, Matthias; Gabdoulline, Razif R.; Wade, Rebecca C.

2008-01-01

Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org. PMID:18420653

A computational study of anion-modulated cation-π interactions.

PubMed

Carrazana-García, Jorge A; Rodríguez-Otero, Jesús; Cabaleiro-Lago, Enrique M

2012-05-24

The interaction of anions with cation-π complexes formed by the guanidinium cation and benzene was thoroughly studied by means of computational methods. Potential energy surface scans were performed in order to evaluate the effect of the anion coming closer to the cation-π pair. Several structures of guanidinium-benzene complexes and anion approaching directions were examined. Supermolecule calculations were performed on ternary complexes formed by guanidinium, benzene, and one anion and the interaction energy was decomposed into its different two- and three-body contributions. The interaction energies were further dissected into their electrostatic, exchange, repulsion, polarization and dispersion contributions by means of local molecular orbital energy decomposition analysis. The results confirm that, besides the electrostatic cation-anion attraction, the effect of the anion over the cation-π interaction is mainly due to polarization and can be rationalized following the changes in the anion-π and the nonadditive (three-body) terms of the interaction. When the cation and the anion are on the same side of the π system, the three-body interaction is anticooperative, but when the anion and the cation are on opposite sides of the π system, the three-body interaction is cooperative. As far as we know, this is the first study where this kind of analysis is carried out with a structured cation as guanidinium with a significant biological interest.

The effect of betaine on the foam stability: Molecular simulation

NASA Astrophysics Data System (ADS)

Gao, Fengfeng; Liu, Guokui; Yuan, Shiling

2017-06-01

Zwitterionic betaines are widely used as foam boosters due to these can enhance the stability of foam films. In this paper, mechanistic insights of betaine to improve the stability of alkyl-polyoxyethylene carboxylate (AEC) foam are provided by molecular simulation. In the simulation, we observe the electropositive nitrogen atoms in betaine interact with the electronegative sulfur atoms, an electrostatic structure is formed at the air/water interface. Interaction energies of the mixed surfactants are calculated by the quantum chemistry methods. The calculations show betaine-AEC and betaine-betaine possess attractive interaction, and that AEC-AEC has repulsion to each other. In the other words, the repulsion between the headgroups of anionic surfactants is relaxed by betaine. Additionally, the influence of concentration of betaine on the stability of foam films is also simulated. The RDF and coordination numbers show that the electrostatic structures become denser with the increasing concentration of betaine. Therefore, entry barrier is enhanced accordingly. The SMD simulation also demonstrates the same variation tendency of entry barrier. The simulation details provide vital supplements to experiments.

Elucidation of the mechanisms of action of Bacteriophage K/nano-emulsion formulations against S. aureus via measurement of particle size and zeta potential.

PubMed

Esteban, Patricia Perez; Jenkins, A Toby A; Arnot, Tom C

2016-03-01

In earlier work we have demonstrated the effect that nano-emulsions have on bacterial growth, and most importantly the enhanced bacteriophage infectivity against Staphylococcus aureus in planktonic culture when phage are carried in nano-emulsions. However, the mechanisms of enhancement of the bacteriophage killing effect are not specifically understood. This work focuses on the investigation of the possible interactions between emulsion droplets and bacterial cells, between emulsion droplets and bacteriophages, and finally interactions between all three components: nano-emulsion droplets, bacteria, and bacteriophages. The first approach consists of simple calculations to determine the spatial distribution of the components, based on measurements of particle size. It was found that nano-emulsion droplets are much more numerous than bacteria or bacteriophage, and due to their size and surface area they must be covering the surface of both cells and bacteriophage particles. Stabilisation of bacteriophages due to electrostatic forces and interaction with nano-emulsion droplets is suspected, since bacteriophages may be protected against inactivation due to 'charge shielding'. Zeta potential was measured for the individual components in the system, and for all of them combined. It was concluded that the presence of nano-emulsions could be reducing electrostatic repulsion between bacterial cells and bacteriophage, both of which are very negatively 'charged'. Moreover, nano-emulsions lead to more favourable interaction between bacteriophages and bacteria, enhancing the anti-microbial or killing effect. These findings are relevant since the physicochemical properties of nano-emulsions (i.e. particle size distribution and zeta potential) are key in determining the efficacy of the formulation against infection in the context of responsive burn wound dressings-which is the main target for this work. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Precise control of surface electrostatic forces on polymer brush layers with opposite charges for resistance to protein adsorption.

PubMed

Sakata, Sho; Inoue, Yuuki; Ishihara, Kazuhiko

2016-10-01

Various molecular interaction forces are generated during protein adsorption process on material surfaces. Thus, it is necessary to control them to suppress protein adsorption and the subsequent cell and tissue responses. A series of binary copolymer brush layers were prepared via surface-initiated atom transfer radical polymerization, by mixing the cationic monomer unit and anionic monomer unit randomly in various ratios. Surface characterization revealed that the constructed copolymer brush layers exhibited an uniform super-hydrophilic nature and different surface potentials. The strength of the electrostatic interaction forces operating on these mixed-charge copolymer brush surfaces was evaluated quantitatively using force-versus-distance (f-d) curve measurements by atomic force microscopy (AFM) and probes modified by negatively charged carboxyl groups or positively charged amino groups. The electrostatic interaction forces were determined based on the charge ratios of the copolymer brush layers. Notably, the surface containing equivalent cationic/anionic monomer units hardly interacted with both the charged groups. Furthermore, the protein adsorption force and the protein adsorption mass on these surfaces were examined by AFM f-d curve measurement and surface plasmon resonance measurement, respectively. To clarify the influence of the electrostatic interaction on the protein adsorption behavior on the surface, three kinds of proteins having negative, positive, and relatively neutral net charges under physiological conditions were used in this study. We quantitatively demonstrated that the amount of adsorbed proteins on the surfaces would have a strong correlation with the strength of surface-protein interaction forces, and that the strength of surface-protein interaction forces would be determined from the combination between the properties of the electrostatic interaction forces on the surfaces and the charge properties of the proteins. Especially, the copolymer brush surface composed of equivalent cationic/anionic monomer units exhibited no significant interaction forces, and dramatically suppressed the adsorption of proteins regardless of their charge properties. We conclude that the established methodology could elucidate relationship between the protein adsorption behavior and molecular interaction, especially the electrostatic interaction forces, and demonstrated that the suppression of the electrostatic interactions with the ionic functional groups would be important for the development of new polymeric biomaterials with a high repellency of protein adsorption. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

The Interactions Between Three Typical PPCPs and LDH

PubMed Central

Li, Erwei; Liao, Libing; Lv, Guocheng; Li, Zhaohui; Yang, Chengxue; Lu, Yanan

2018-01-01

With a layered structure, layered double hydroxide (LDH) has potential applications in remediation of anionic contaminants, which has been a hot topic for recent years. In this study, a Cl type Mg-Al hydrotalcite (Cl-LDH) was prepared by a co-precipitation method. The adsorption process of three pharmaceuticals and personal care products (PPCPs) [tetracycline (TC), diclofenac sodium (DF), chloramphenicol (CAP)] by Cl-LDH was investigated by X-ray diffraction (XRD), Zeta potential, dynamic light scattering (DLS), BET, Fourier transform infrared (FTIR) spectroscopy, and molecular dynamics simulation. The results showed that the adsorption equilibrium of TC and DF could be reached in 120 min, and the maximum adsorption capacity of the TC and DF were 1.85 and 0.95 mmol/g, respectively. The isothermal adsorption model of TC was fitted with the Freundlich adsorption model, and the isothermal adsorption model of DF was fitted with the Langmuir adsorption model. The adsorption dynamics of TC and DF followed the pseudo-second-order model. The adsorption mechanisms of the three PPCPs into Cl-LDH were different based on the experimental results and molecular dynamics simulation. The TC adsorption on Cl-LDH was accompanied by the electrostatic interactions between the negative charge of TC and the positive charge of Cl-LDH. The uptake of DF was attributed to anion exchange and electrostatic interaction. Cl-LDH does not adsorb CAP due to no electrostatic interaction. The molecular dynamic simulation further confirmed different configurations of three selected PPCPs, which were ultimately responsible for the uptake of PPCPs on Cl-LDH. PMID:29556493

Molecular electrostatics for probing lone pair-π interactions.

PubMed

Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

2013-11-14

An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

Interactions of the α-subunits of heterotrimeric G-proteins with GPCRs, effectors and RGS proteins: a critical review and analysis of interacting surfaces, conformational shifts, structural diversity and electrostatic potentials.

PubMed

Baltoumas, Fotis A; Theodoropoulou, Margarita C; Hamodrakas, Stavros J

2013-06-01

G-protein coupled receptors (GPCRs) are one of the largest families of membrane receptors in eukaryotes. Heterotrimeric G-proteins, composed of α, β and γ subunits, are important molecular switches in the mediation of GPCR signaling. Receptor stimulation after the binding of a suitable ligand leads to G-protein heterotrimer activation and dissociation into the Gα subunit and Gβγ heterodimer. These subunits then interact with a large number of effectors, leading to several cell responses. We studied the interactions between Gα subunits and their binding partners, using information from structural, mutagenesis and Bioinformatics studies, and conducted a series of comparisons of sequence, structure, electrostatic properties and intermolecular energies among different Gα families and subfamilies. We identified a number of Gα surfaces that may, in several occasions, participate in interactions with receptors as well as effectors. The study of Gα interacting surfaces in terms of sequence, structure and electrostatic potential reveals features that may account for the Gα subunit's behavior towards its interacting partners. The electrostatic properties of the Gα subunits, which in some cases differ greatly not only between families but also between subfamilies, as well as the G-protein interacting surfaces of effectors and regulators of G-protein signaling (RGS) suggest that electrostatic complementarity may be an important factor in G-protein interactions. Energy calculations also support this notion. This information may be useful in future studies of G-protein interactions with GPCRs and effectors. Copyright © 2013 Elsevier Inc. All rights reserved.

Osmotic Pressure of Aqueous Chondroitin Sulfate Solution: A Molecular Modeling Investigation

PubMed Central

Bathe, Mark; Rutledge, Gregory C.; Grodzinsky, Alan J.; Tidor, Bruce

2005-01-01

The osmotic pressure of chondroitin sulfate (CS) solution in contact with an aqueous 1:1 salt reservoir of fixed ionic strength is studied using a recently developed coarse-grained molecular model. The effects of sulfation type (4- vs. 6-sulfation), sulfation pattern (statistical distribution of sulfate groups along a chain), ionic strength, CS intrinsic stiffness, and steric interactions on CS osmotic pressure are investigated. At physiological ionic strength (0.15 M NaCl), the sulfation type and pattern, as measured by a standard statistical description of copolymerization, are found to have a negligible influence on CS osmotic pressure, which depends principally on the mean volumetric fixed charge density. The intrinsic backbone stiffness characteristic of polysaccharides such as CS, however, is demonstrated to contribute significantly to its osmotic pressure behavior, which is similar to that of a solution of charged rods for the 20-disaccharide chains considered. Steric excluded volume is found to play a negligible role in determining CS osmotic pressure at physiological ionic strength due to the dominance of repulsive intermolecular electrostatic interactions that maintain chains maximally spaced in that regime, whereas at high ionic-strength steric interactions become dominant due to electrostatic screening. Osmotic pressure predictions are compared to experimental data and to well-established theoretical models including the Donnan theory and the Poisson-Boltzmann cylindrical cell model. PMID:16055525

Electrostatic Steering Accelerates C3d:CR2 Association.

PubMed

Mohan, Rohith R; Huber, Gary A; Morikis, Dimitrios

2016-08-25

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts.

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities.

PubMed

Lovelock, Kevin R J

2017-12-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced , is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, ced IP , where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, ced C+A , where the ionic vapour constituents are isolated ions. A ced IP dataset is presented for 64 ILs. For the first time an experimental ced C+A , a measure of the strength of the total intermolecular interaction for an IL, is presented. ced C+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between ced IP and the inverse of the molecular volume. A good linear correlation is found between IL ced IP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to ced IP . These findings show that ced IP is very important for understanding IL intermolecular interactions, in spite of ced IP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined.

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities

PubMed Central

2017-01-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced, is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, cedIP, where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, cedC+A, where the ionic vapour constituents are isolated ions. A cedIP dataset is presented for 64 ILs. For the first time an experimental cedC+A, a measure of the strength of the total intermolecular interaction for an IL, is presented. cedC+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between cedIP and the inverse of the molecular volume. A good linear correlation is found between IL cedIP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to cedIP. These findings show that cedIP is very important for understanding IL intermolecular interactions, in spite of cedIP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined. PMID:29308254

Biosensors Fabricated through Electrostatic Assembly of Enzymes/Polyelectrolyte Hybrid Layers on Carbon Nanotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Yuehe; Liu, Guodong; Wang, Jun

2006-06-01

Carbon nanotubes (CNTs) have emerged as new class of nanomaterials that is receiving considerable interest because of their unique structure, mechanical, and electronic properties. One promising application of CNTs is to fabricate highly sensitive chemo/biosensors.1-4 For construction of these CNT-based sensors, the CNTs first have to be modified with some molecules specific to the interests. Generally, covalent binding, affinity, and electrostatic interaction have been utilized for the modification of CNTs. Among them, the electrostatic method is attractive due to its simplicity and high efficiency. In present work, we have developed highly sensitively amperometric biosensors for glucose, choline, organophosphate pesticide (OPP)more » and nerve agents (NAs) based on electrostatically assembling enzymes on the surface of CNTs. All these biosensors were fabricated by immobilization of enzymes on the negatively charged CNTs surface through alternately assembling a cationic poly(diallydimethylammonium chloride) (PDDA) layer and an enzyme layer. Using this layer-by-layer (LBL) technique, a bioactive nanocomposite film was fabricated on the electrode surface. Owing to the electrocatalytic effect of CNTs, an amplified electrochemical signal was achieved, which leads to low detections limits for glucose, choline, and OPP and NAs.« less

DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome DNA elements.

PubMed

Osypov, Alexander A; Krutinin, Gleb G; Krutinina, Eugenia A; Kamzolova, Svetlana G

2012-04-01

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.

Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA.

PubMed

Osypov, Alexander A; Krutinin, Gleb G; Kamzolova, Svetlana G

2010-06-01

The electrostatic properties of genome DNA influence its interactions with different proteins, in particular, the regulation of transcription by RNA-polymerases. DEPPDB--DNA Electrostatic Potential Properties Database--was developed to hold and provide all available information on the electrostatic properties of genome DNA combined with its sequence and annotation of biological and structural properties of genome elements and whole genomes. Genomes in DEPPDB are organized on a taxonomical basis. Currently, the database contains all the completely sequenced bacterial and viral genomes according to NCBI RefSeq. General properties of the genome DNA electrostatic potential profile and principles of its formation are revealed. This potential correlates with the GC content but does not correspond to it exactly and strongly depends on both the sequence arrangement and its context (flanking regions). Analysis of the promoter regions for bacterial and viral RNA polymerases revealed a correspondence between the scale of these proteins' physical properties and electrostatic profile patterns. We also discovered a direct correlation between the potential value and the binding frequency of RNA polymerase to DNA, supporting the idea of the role of electrostatics in these interactions. This matches a pronounced tendency of the promoter regions to possess higher values of the electrostatic potential.

SAW based micro- and acousto-fluidics in biomedicine

NASA Astrophysics Data System (ADS)

Ramasamy, Mouli; Varadan, Vijay K.

2017-04-01

Protein association starts with random collisions of individual proteins. Multiple collisions and rotational diffusion brings the molecules to a state of orientation. Majority of the protein associations are influenced by electrostatic interactions. To introduce: electrostatic rate enhancement, Brownian dynamics and transient complex theory has been traditionally used. Due to the recent advances in interdisciplinary sciences, an array of molecular assembly methods is being studied. Protein nanostructural assembly and macromolecular crowding are derived from the subsets of biochemistry to study protein-protein interactions and protein self-assembly. This paper tries to investigate the issue of enhancing the protein self-association rate, and bridging the gap between the simulations and experimental results. The methods proposed here include: electrostatic rate enhancement, macromolecular crowing, nanostructural protein assembly, microfluidics based approaches and magnetic force based approaches. Despite the suggestions of several methods, microfluidic and magnetic force based approaches seem to serve the need of protein assembly in a wider scale. Congruence of these approaches may also yield better results. Even though, these methods prove to be conceptually strong, to prevent the disagreement of theory and practice, a wide range of experiments is required. This proposal intends to study theoretical and experimental methods to successfully implement the aforementioned assembly strategies, and conclude with an extensive analysis of experimental data to address practical feasibility.

Determining the Effect of pH on the Partitioning of Neutral, Cationic and Anionic Chemicals to Artificial Sebum: New Physicochemical Insight and QSPR Model.

PubMed

Yang, Senpei; Li, Lingyi; Chen, Tao; Han, Lujia; Lian, Guoping

2018-05-14

Sebum is an important shunt pathway for transdermal permeation and targeted delivery, but there have been limited studies on its permeation properties. Here we report a measurement and modelling study of solute partition to artificial sebum. Equilibrium experiments were carried out for the sebum-water partition coefficients of 23 neutral, cationic and anionic compounds at different pH. Sebum-water partition coefficients not only depend on the hydrophobicity of the chemical but also on pH. As pH increases from 4.2 to 7.4, the partition of cationic chemicals to sebum increased rapidly. This appears to be due to increased electrostatic attraction between the cationic chemical and the fatty acids in sebum. Whereas for anionic chemicals, their sebum partition coefficients are negligibly small, which might result from their electrostatic repulsion to fatty acids. Increase in pH also resulted in a slight decrease of sebum partition of neutral chemicals. Based on the observed pH impact on the sebum-water partition of neutral, cationic and anionic compounds, a new quantitative structure-property relationship (QSPR) model has been proposed. This mathematical model considers the hydrophobic interaction and electrostatic interaction as the main mechanisms for the partition of neutral, cationic and anionic chemicals to sebum.

Electrostatic rate enhancement and transient complex of protein-protein association.

PubMed

Alsallaq, Ramzi; Zhou, Huan-Xiang

2008-04-01

The association of two proteins is bounded by the rate at which they, via diffusion, find each other while in appropriate relative orientations. Orientational constraints restrict this rate to approximately 10(5)-10(6) M(-1) s(-1). Proteins with higher association rates generally have complementary electrostatic surfaces; proteins with lower association rates generally are slowed down by conformational changes upon complex formation. Previous studies (Zhou, Biophys J 1997;73:2441-2445) have shown that electrostatic enhancement of the diffusion-limited association rate can be accurately modeled by $k_{\\bf D}$ = $k_{D}0\\ {exp} ( - \\langle U_{el} \\rangle;{\\star}/k_{B} T),$ where k(D) and k(D0) are the rates in the presence and absence of electrostatic interactions, respectively, U(el) is the average electrostatic interaction energy in a "transient-complex" ensemble, and k(B)T is the thermal energy. The transient-complex ensemble separates the bound state from the unbound state. Predictions of the transient-complex theory on four protein complexes were found to agree well with the experiment when the electrostatic interaction energy was calculated with the linearized Poisson-Boltzmann (PB) equation (Alsallaq and Zhou, Structure 2007;15:215-224). Here we show that the agreement is further improved when the nonlinear PB equation is used. These predictions are obtained with the dielectric boundary defined as the protein van der Waals surface. When the dielectric boundary is instead specified as the molecular surface, electrostatic interactions in the transient complex become repulsive and are thus predicted to retard association. Together these results demonstrate that the transient-complex theory is predictive of electrostatic rate enhancement and can help parameterize PB calculations. (c) 2007 Wiley-Liss, Inc.

Ground-Based High-Power Microwave Decoy Discrimination System.

DTIC Science & Technology

1987-12-23

understanding of plasma instabilities, self-induced magnetic effects , space - charge considerations, production of ion currents, etc. 3.3.4 Cross-Field...breakdown, due to small potential differences. Interaction volumes can therefore be large, avoiding breakdown and space - charge effects (at the price...the interference of the incident and reflected wave, and by the electrostatic forces of the surface (positive) and space charge (negative) trapped in

Laser Radiation Pressure Acceleration of Monoenergetic Protons in an Ultra-Thin Foil

NASA Astrophysics Data System (ADS)

Eliasson, Bengt; Liu, Chuan S.; Shao, Xi; Sagdeev, Roald Z.; Shukla, Padma K.

2009-11-01

We present theoretical and numerical studies of the acceleration of monoenergetic protons in a double layer formed by the laser irradiation of an ultra-thin film. The stability of the foil is investigated by direct Vlasov-Maxwell simulations for different sets of laser-plasma parameters. It is found that the foil is stable, due to the trapping of both electrons and ions in the thin laser-plasma interaction region, where the electrons are trapped in a potential well composed of the ponderomo-tive potential of the laser light and the electrostatic potential due to the ions, and the ions are trapped in a potential well composed of the inertial potential in an accelerated frame and the electrostatic potential due to the electrons. The result is a stable double layer, where the trapped ions are accelerated to monoenergetic energies up to 100 MeV and beyond, which makes them suitable for medical applications cancer treatment. The underlying physics of trapped and untapped ions in a double layer is also investigated theoretically and numerically.

Electrostatic Interactions Between Glycosaminoglycan Molecules

NASA Astrophysics Data System (ADS)

Song, Fan; Moyne, Christian; Bai, Yi-Long

2005-02-01

The electrostatic interactions between nearest-neighbouring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains are obtained on the bottle brush conformation of proteoglycan aggrecan based on an asymptotic solution of the Poisson-Boltzmann equation the CS-GAGs satisfy under the physiological conditions of articular cartilage. The present results show that the interactions are associated intimately with the minimum separation distance and mutual angle between the molecular chains themselves. Further analysis indicates that the electrostatic interactions are not only expressed to be purely exponential in separation distance and decrease with the increasing mutual angle but also dependent sensitively on the saline concentration in the electrolyte solution within the tissue, which is in agreement with the existed relevant conclusions.

Human Apolipoprotein A1 at Solid/Liquid and Liquid/Gas Interfaces.

PubMed

Dogan, Susanne; Paulus, Michael; Forov, Yury; Weis, Christopher; Kampmann, Matthias; Cewe, Christopher; Kiesel, Irena; Degen, Patrick; Salmen, Paul; Rehage, Heinz; Tolan, Metin

2018-04-12

An X-ray reflectivity study on the adsorption behavior of human apolipoprotein A1 (apoA1) at hydrophilic and hydrophobic interfaces is presented. It is shown that the protein interacts via electrostatic and hydrophobic interactions with the interfaces, resulting in the absorption of the protein. pH dependent measurements at the solid/liquid interface between silicon dioxide and aqueous protein solution show that in a small pH range between pH 4 and 6, adsorption is increased due to electrostatic attraction. Here, the native shape of the protein seems to be conserved. In contrast, the adsorption at the liquid/gas interface is mainly driven by hydrophobic effects, presumably by extending the hydrophobic regions of the amphipathic helices, and results in a conformational change of the protein during adsorption. However, the addition of differently charged membrane-forming lipids at the liquid/gas interface illustrates the ability of apoA1 to include lipids, resulting in a depletion of the lipids from the interface.

Applying electric field to charged and polar particles between metallic plates: extension of the Ewald method.

PubMed

Takae, Kyohei; Onuki, Akira

2013-09-28

We develop an efficient Ewald method of molecular dynamics simulation for calculating the electrostatic interactions among charged and polar particles between parallel metallic plates, where we may apply an electric field with an arbitrary size. We use the fact that the potential from the surface charges is equivalent to the sum of those from image charges and dipoles located outside the cell. We present simulation results on boundary effects of charged and polar fluids, formation of ionic crystals, and formation of dipole chains, where the applied field and the image interaction are crucial. For polar fluids, we find a large deviation of the classical Lorentz-field relation between the local field and the applied field due to pair correlations along the applied field. As general aspects, we clarify the difference between the potential-fixed and the charge-fixed boundary conditions and examine the relationship between the discrete particle description and the continuum electrostatics.

Internal force field in proteins seen by divergence entropy

PubMed Central

Marchewka, Damian; Banach, Mateusz; Roterman, Irena

2011-01-01

The characteristic distribution of non-binding interactions in a protein is described. It establishes that hydrophobic interactions can be characterized by suitable 3D Gauss functions while electrostatic interactions generally follow a random distribution. The implementation of this observation suggests differentiated optimization procedure for these two types of interactions. The electrostatic interaction may follow traditional energy optimization while the criteria for convergence shall measure the accordance with 3-D Gauss function. PMID:21769190

Effect of electrostatic interactions on the ultrafiltration behavior of charged bacterial capsular polysaccharides.

PubMed

Hadidi, Mahsa; Buckley, John J; Zydney, Andrew L

2016-11-01

Charged polysaccharides are used in the food industry, as cosmetics, and as vaccines. The viscosity, thermodynamics, and hydrodynamic properties of these charged polysaccharides are known to be strongly dependent on the solution ionic strength because of both inter- and intramolecular electrostatic interactions. The goal of this work was to quantitatively describe the effect of these electrostatic interactions on the ultrafiltration behavior of several charged capsular polysaccharides obtained from Streptococcus pneumoniae and used in the production of Pneumococcus vaccines. Ultrafiltration data were obtained using various Biomax™ polyethersulfone membranes with different nominal molecular weight cutoffs. Polysaccharide transmission decreased with decreasing ionic strength primarily because of the expansion of the charged polysaccharide associated with intramolecular electrostatic repulsion. Data were in good agreement with a simple theoretical model based on solute partitioning in porous membranes, with the effective size of the different polysaccharide serotypes evaluated using size exclusion chromatography at the same ionic conditions. These results provide fundamental insights and practical guidelines for exploiting the effects of electrostatic interactions during the ultrafiltration of charged polysaccharides. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1531-1538, 2016. © 2016 American Institute of Chemical Engineers.

Electrostatically confined nanoparticle interactions and dynamics.

PubMed

Eichmann, Shannon L; Anekal, Samartha G; Bevan, Michael A

2008-02-05

We report integrated evanescent wave and video microscopy measurements of three-dimensional trajectories of 50, 100, and 250 nm gold nanoparticles electrostatically confined between parallel planar glass surfaces separated by 350 and 600 nm silica colloid spacers. Equilibrium analyses of single and ensemble particle height distributions normal to the confining walls produce net electrostatic potentials in excellent agreement with theoretical predictions. Dynamic analyses indicate lateral particle diffusion coefficients approximately 30-50% smaller than expected from predictions including the effects of the equilibrium particle distribution within the gap and multibody hydrodynamic interactions with the confining walls. Consistent analyses of equilibrium and dynamic information in each measurement do not indicate any roles for particle heating or hydrodynamic slip at the particle or wall surfaces, which would both increase diffusivities. Instead, lower than expected diffusivities are speculated to arise from electroviscous effects enhanced by the relative extent (kappaa approximately 1-3) and overlap (kappah approximately 2-4) of electrostatic double layers on the particle and wall surfaces. These results demonstrate direct, quantitative measurements and a consistent interpretation of metal nanoparticle electrostatic interactions and dynamics in a confined geometry, which provides a basis for future similar measurements involving other colloidal forces and specific biomolecular interactions.

Construction and Self-Assembly of Single-Chain Polymer Nanoparticles via Coordination Association and Electrostatic Repulsion in Water.

PubMed

Zhu, Zhengguang; Xu, Na; Yu, Qiuping; Guo, Lei; Cao, Hui; Lu, Xinhua; Cai, Yuanli

2015-08-01

Simultaneous coordination-association and electrostatic-repulsion interactions play critical roles in the construction and stabilization of enzymatic function metal centers in water media. These interactions are promising for construction and self-assembly of artificial aqueous polymer single-chain nanoparticles (SCNPs). Herein, the construction and self-assembly of dative-bonded aqueous SCNPs are reported via simultaneous coordination-association and electrostatic-repulsion interactions within single chains of histamine-based hydrophilic block copolymer. The electrostatic-repulsion interactions are tunable through adjusting the imidazolium/imidazole ratio in response to pH, and in situ Cu(II)-coordination leads to the intramolecular association and single-chain collapse in acidic water. SCNPs are stabilized by the electrostatic repulsion of dative-bonded block and steric shielding of nonionic water-soluble block, and have a huge specific surface area of function metal centers accessible to substrates in acidic water. Moreover, SCNPs can assemble into micelles, networks, and large particles programmably in response to the solution pH. These unique media-sensitive phase-transformation behaviors provide a general, facile, and versatile platform for the fabrication of enzyme-inspired smart aqueous catalysts. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficiency determination of an electrostatic lunar dust collector by discrete element method

NASA Astrophysics Data System (ADS)

Afshar-Mohajer, Nima; Wu, Chang-Yu; Sorloaica-Hickman, Nicoleta

2012-07-01

Lunar grains become charged by the sun's radiation in the tenuous atmosphere of the moon. This leads to lunar dust levitation and particle deposition which often create serious problems in the costly system deployed in lunar exploration. In this study, an electrostatic lunar dust collector (ELDC) is proposed to address the issue and the discrete element method (DEM) is used to investigate the effects of electrical particle-particle interactions, non-uniformity of the electrostatic field, and characteristics of the ELDC. The simulations on 20-μm-sized lunar particles reveal the electrical particle-particle interactions of the dust particles within the ELDC plates require 29% higher electrostatic field strength than that without the interactions for 100% collection efficiency. For the given ELDC geometry, consideration of non-uniformity of the electrostatic field along with electrical interactions between particles on the same ELDC geometry leads to a higher requirement of ˜3.5 kV/m to ensure 100% particle collection. Notably, such an electrostatic field is about 103 times less than required for electrodynamic self-cleaning methods. Finally, it is shown for a "half-size" system that the DEM model predicts greater collection efficiency than the Eulerian-based model at all voltages less than required for 100% efficiency. Halving the ELDC dimensions boosts the particle concentration inside the ELDC, as well as the resulting field strength for a given voltage. Though a lunar photovoltaic system was the subject, the results of this study are useful for evaluation of any system for collecting charged particles in other high vacuum environment using an electrostatic field.

Electrostatic effects in unfolded staphylococcal nuclease

PubMed Central

Fitzkee, Nicholas C.; García-Moreno E, Bertrand

2008-01-01

Structure-based calculations of pK a values and electrostatic free energies of proteins assume that electrostatic effects in the unfolded state are negligible. In light of experimental evidence showing that this assumption is invalid for many proteins, and with increasing awareness that the unfolded state is more structured and compact than previously thought, a detailed examination of electrostatic effects in unfolded proteins is warranted. Here we address this issue with structure-based calculations of electrostatic interactions in unfolded staphylococcal nuclease. The approach involves the generation of ensembles of structures representing the unfolded state, and calculation of Coulomb energies to Boltzmann weight the unfolded state ensembles. Four different structural models of the unfolded state were tested. Experimental proton binding data measured with a variant of nuclease that is unfolded under native conditions were used to establish the validity of the calculations. These calculations suggest that weak Coulomb interactions are an unavoidable property of unfolded proteins. At neutral pH, the interactions are too weak to organize the unfolded state; however, at extreme pH values, where the protein has a significant net charge, the combined action of a large number of weak repulsive interactions can lead to the expansion of the unfolded state. The calculated pK a values of ionizable groups in the unfolded state are similar but not identical to the values in small peptides in water. These studies suggest that the accuracy of structure-based calculations of electrostatic contributions to stability cannot be improved unless electrostatic effects in the unfolded state are calculated explicitly. PMID:18227429

Interaction between Stray Electrostatic Fields and a Charged Free-Falling Test Mass

NASA Astrophysics Data System (ADS)

Antonucci, F.; Cavalleri, A.; Dolesi, R.; Hueller, M.; Nicolodi, D.; Tu, H. B.; Vitale, S.; Weber, W. J.

2012-05-01

We present an experimental analysis of force noise caused by stray electrostatic fields acting on a charged test mass inside a conducting enclosure, a key problem for precise gravitational experiments. Measurement of the average field that couples to the test mass charge, and its fluctuations, is performed with two independent torsion pendulum techniques, including direct measurement of the forces caused by a change in electrostatic charge. We analyze the problem with an improved electrostatic model that, coupled with the experimental data, also indicates how to correctly measure and null the stray field that interacts with the test mass charge. Our measurements allow a conservative upper limit on acceleration noise, of 2(fm/s2)/Hz1/2 for frequencies above 0.1 mHz, for the interaction between stray fields and charge in the LISA gravitational wave mission.

Electrostatic Steering Accelerates C3d:CR2 Association

PubMed Central

2016-01-01

Electrostatic effects are ubiquitous in protein interactions and are found to be pervasive in the complement system as well. The interaction between complement fragment C3d and complement receptor 2 (CR2) has evolved to become a link between innate and adaptive immunity. Electrostatic interactions have been suggested to be the driving factor for the association of the C3d:CR2 complex. In this study, we investigate the effects of ionic strength and mutagenesis on the association of C3d:CR2 through Brownian dynamics simulations. We demonstrate that the formation of the C3d:CR2 complex is ionic strength-dependent, suggesting the presence of long-range electrostatic steering that accelerates the complex formation. Electrostatic steering occurs through the interaction of an acidic surface patch in C3d and the positively charged CR2 and is supported by the effects of mutations within the acidic patch of C3d that slow or diminish association. Our data are in agreement with previous experimental mutagenesis and binding studies and computational studies. Although the C3d acidic patch may be locally destabilizing because of unfavorable Coulombic interactions of like charges, it contributes to the acceleration of association. Therefore, acceleration of function through electrostatic steering takes precedence to stability. The site of interaction between C3d and CR2 has been the target for delivery of CR2-bound nanoparticle, antibody, and small molecule biomarkers, as well as potential therapeutics. A detailed knowledge of the physicochemical basis of C3d:CR2 association may be necessary to accelerate biomarker and drug discovery efforts. PMID:27092816

The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity.

PubMed

Kieslich, Chris A; Morikis, Dimitrios

2012-01-01

The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of -1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic "hot-spots". Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic "hot-spots" at the two functional sites of C3d, while the surface of CR2 lacks electrostatic "hot-spots" despite its excessively positive nature. We propose that the electrostatic "hot-spots" of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2), which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3d, after the divergence of jawless fish.

The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity

PubMed Central

Kieslich, Chris A.; Morikis, Dimitrios

2012-01-01

The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of −1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic “hot-spots”. Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic “hot-spots” at the two functional sites of C3d, while the surface of CR2 lacks electrostatic “hot-spots” despite its excessively positive nature. We propose that the electrostatic “hot-spots” of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2), which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3d, after the divergence of jawless fish. PMID:23300422

Kinetics of protein unfolding at interfaces

NASA Astrophysics Data System (ADS)

Yano, Yohko F.

2012-12-01

The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces.

Modulating capacitive response of MoS2 flake by controlled nanostructuring through focused laser irradiation.

PubMed

Rani, Renu; Kundu, Anirban; Balal, Mohammad; Sheet, Goutam; Hazra, Kiran Shankar

2018-08-24

Unlike graphene nanostructures, various physical properties of nanostructured MoS 2 have remained unexplored due to the lack of established fabrication routes. Herein, we have reported unique electrostatic properties of MoS 2 nanostructures, fabricated in a controlled manner of different geometries on 2D flake by using focused laser irradiation technique. Electrostatic force microscopy has been carried out on MoS 2 nanostructures by varying tip bias voltage and lift height. The analysis depicts no contrast flip in phase image of the patterned nanostructure due to the absence of free surface charges. However, prominent change in phase shift at the patterned area is observed. Such contrast changes signify the capacitive interaction between tip and nanostructures at varying tip bias voltage and lift height, irrespective of their shape and size. Such unperturbed capacitive behavior of the MoS 2 nanostructures offer modulation of capacitance in periodic array on 2D MoS 2 flake for potential application in capacitive devices.

Flocculation of colloidal clay by bacterial polysaccharides: effect of macromolecule charge and structure.

PubMed

Labille, J; Thomas, F; Milas, M; Vanhaverbeke, C

2005-04-01

The molecular mechanism of montmorillonite flocculation by bacterial polysaccharides was investigated, with special emphasis on the effect of carboxylic charges in the macromolecules on the mechanisms of interaction with the clay surface. An indirect way to quantify the energy of interaction was used, by comparing the flocculation ability of variously acidic polysaccharides. Data on tensile strength of aggregates in diluted suspension were collected by timed size measurements in the domain 0.1-600 microm, using laser diffraction. The flow behavior of settled aggregates was studied by rheology measurements. Flocculation of colloidal clay suspension by polysaccharides requires cancelling of the electrostatic repulsions by salts, which allows approach of clay surfaces close enough to be bridged by adsorbing macromolecules. The amount of acidic charges of the polysaccharides, and especially their location in the molecular structure, governs the bridging mechanism and the resulting tensile strength of the aggregates. The exposure of carboxylate groups located on side chains strongly promotes flocculation. In turn, charges located on the backbone of the polysaccharide are less accessible to interaction, and the flocculation ability of such polysaccharides is lowered. Measurements at different pH indicate that adsorption of acidic polysaccharides occurs via electrostatic interactions on the amphoteric edge surface of clay platelets, whereas neutral polysaccharides rather adsorb via weak interactions. Increased tensile strength in diluted aggregates due to strong surface interactions results in proportionally increased viscosity of the concentrated aggregates.

Ferroelectric-like hysteresis loop originated from non-ferroelectric effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Bora; Seol, Daehee; Lee, Shinbuhm

Piezoresponse force microscopy (PFM) has provided advanced nanoscale understanding and analysis of ferroelectric and piezoelectric properties. In PFM-based studies, electromechanical strain induced by the converse piezoelectric effect is probed and analyzed as a PFM response. However, electromechanical strain can also arise from several non-piezoelectric origins that may lead to a misinterpretation of the observed response. Among them, electrostatic interaction can significantly affect the PFM response. Nonetheless, previous studies explored solely the influence of electrostatic interaction on the PFM response under the situation accompanied with polarization switching. Here, we show the influence of the electrostatic interaction in the absence of polarizationmore » switching by using unipolar voltage sweep. The obtained results reveal that the electromechanical neutralization between piezoresponse of polarization and electrostatic interaction plays a crucial role in the observed ferroelectric-like hysteresis loop despite the absence of polarization switching. Furthermore, our work can provide a basic guideline for the correct interpretation of the hysteresis loop in PFM-based studies.« less

Ferroelectric-like hysteresis loop originated from non-ferroelectric effects

DOE PAGES

Kim, Bora; Seol, Daehee; Lee, Shinbuhm; ...

2016-09-06

Piezoresponse force microscopy (PFM) has provided advanced nanoscale understanding and analysis of ferroelectric and piezoelectric properties. In PFM-based studies, electromechanical strain induced by the converse piezoelectric effect is probed and analyzed as a PFM response. However, electromechanical strain can also arise from several non-piezoelectric origins that may lead to a misinterpretation of the observed response. Among them, electrostatic interaction can significantly affect the PFM response. Nonetheless, previous studies explored solely the influence of electrostatic interaction on the PFM response under the situation accompanied with polarization switching. Here, we show the influence of the electrostatic interaction in the absence of polarizationmore » switching by using unipolar voltage sweep. The obtained results reveal that the electromechanical neutralization between piezoresponse of polarization and electrostatic interaction plays a crucial role in the observed ferroelectric-like hysteresis loop despite the absence of polarization switching. Furthermore, our work can provide a basic guideline for the correct interpretation of the hysteresis loop in PFM-based studies.« less

Biomolecular electrostatics and solvation: a computational perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. Thismore » review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.« less

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael J.; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water

NASA Astrophysics Data System (ADS)

Pal, Somedatta; Bandyopadhyay, Sanjoy

2013-07-01

Protein-water interactions and their influence on surrounding water is a long-standing problem. Despite its importance, the origin of differential water behavior at the protein surface is still elusive. We have performed molecular simulations of the protein barstar in aqueous medium. Efforts have been made to explore how the conformational motions of the protein segments in the native form and the heterogeneous electrostatic interactions with the polar and charged groups of the protein affect the interfacial water properties. The calculations reveal that reduced dimension of the hydration layer on freezing the protein's degrees of freedom does not modify the heterogeneous water distributions around the protein. However, turning off the protein-water electrostatic contribution leads to non-preferential near-uniform water arrangements at the surface. It is further shown that with protein-water electrostatic interactions turned on, the local structuring of water molecules around the segments are correlated with their degree of exposure to the solvent.

Electrostatic actuators for portable microfluidic systems

NASA Astrophysics Data System (ADS)

Tice, Joshua

Both developed and developing nations have an urgent need to diagnose disease cheaply, reliably, and independently of centralized facilities. Microfulidic platforms are well-positioned to address the need for portable diagnostics, mainly due to their obvious advantage in size. However, most microfluidic methods rely on equipment outside of the chip either for driving fluid flow (e.g., syringe pumps) or for taking measurements (e.g., lasers or microscopes). The energy and space requirements of the whole system inhibit portability and contribute to costs. To capitalize on the strengths of microfluidic platforms and address the serious needs of society, system components need to be miniaturized. Also, miniaturization should be accomplished as simply as possible, considering that simplicity is usually requisite for achieving truly transformative technology. Herein, I attempt to address the issue of controlling fluid flow in portable microfluidic systems. I focus on systems that are driven by elastomer-based membrane valves, since these valves are inherently simple, yet they are capable of sophisticated fluid manipulation. Others have attempted to modify pneumatic microvalves for portable applications, e.g., by transitioning to electromagnetic, thermopneumatic, or piezoelectric actuation principles. However, none of these strategies maintain the proper balance of simplicity, functionality, and ease of integration. My research centers on electrostatic actuators, due to their conceptual simplicity and the efficacy of electrostatic forces on the microscale. To ensure easy integration with polymer-based systems, and to maintain simplicity in the fabrication procedure, the actuators were constructed solely from poly(dimethylsiloxane) and multi-walled carbon nanotubes. In addition, the actuators were fabricated exclusively with soft-lithographic techniques. A mathematical model was developed to identify actuator parameters compatible with soft-lithography, and also to minimize actuation potentials while eliminating stiction. Two strategies were developed to overcome challenges with electrode screening in the presence of aqueous fluids. First, instead of using the electrostatic actuators to interact directly with aqueous solutions, the actuators were used to regulate pressurized control lines for pneumatic microvalves. Secondly, by adopting a normally-closed architecture, the actuators were converted into microvalves capable of directly interacting with aqueous solutions. The two strategies are complementary, and together should enable sophisticated microfluidic systems for applications ranging from point-of-care diagnostics to portable chemical detection. To conclude the dissertation, I demonstrate a proof-of-principle microfluidic system that contained sixteen independently-operated electrostatic valves, operated with battery-operated electrical ancillaries in a hand-held format.

Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c.

PubMed

Roberts, V A; Freeman, H C; Olson, A J; Tainer, J A; Getzoff, E D

1991-07-15

To understand the specificity and efficiency of protein-protein interactions promoting electron transfer, we evaluated the role of electrostatic forces in precollision orientation by the development of two new methods, computer graphics alignment of protein electrostatic fields and a systematic orientational search of intermolecular electrostatic energies for two proteins at present separation distances. We applied these methods to the plastocyanin/cytochrome c interaction, which is faster than random collision, but too slow for study by molecular dynamics techniques. Significant electrostatic potentials were concentrated on one-fourth (969 A2) of the plastocyanin surface, with the greatest negative potential centered on the Tyr-83 hydroxyl within the acidic patch, and on one-eighth (632 A2) of the cytochrome c surface, with the greatest positive potential centered near the exposed heme edge. Coherent electrostatic fields occurred only over these regions, suggesting that local, rather than global, charge complementarity controls productive recognition. The three energetically favored families of pre-collision orientations all directed the positive region surrounding the heme edge of cytochrome c toward the acidic patch of plastocyanin but differed in heme plane orientation. Analysis of electrostatic fields, electrostatic energies of precollision orientations with 12 and 6 A separation distances, and surface topographies suggested that the favored orientations should converge to productive complexes promoting a single electron-transfer pathway from the cytochrome c heme edge to Tyr-83 of plastocyanin. Direct interactions of the exposed Cu ligand in plastocyanin with the cytochrome c heme edge are not unfavorable sterically or electrostatically but should occur no faster than randomly, indicating that this is not the primary pathway for electron transfer.

Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR.

PubMed

Voinov, Maxim A; Smirnov, Alex I

2015-01-01

Electrostatic interactions are known to play a major role in the myriad of biochemical and biophysical processes. Here, we describe biophysical methods to probe local electrostatic potentials of proteins and lipid bilayer systems that are based on an observation of reversible protonation of nitroxides by electron paramagnetic resonance (EPR). Two types of probes are described: (1) methanethiosulfonate derivatives of protonatable nitroxides for highly specific covalent modification of the cysteine's sulfhydryl groups and (2) spin-labeled phospholipids with a protonatable nitroxide tethered to the polar head group. The probes of both types report on their ionization state through changes in magnetic parameters and degree of rotational averaging, thus, allowing the electrostatic contribution to the interfacial pKa of the nitroxide, and, therefore, the local electrostatic potential to be determined. Due to their small molecular volume, these probes cause a minimal perturbation to the protein or lipid system. Covalent attachment secures the position of the reporter nitroxides. Experimental procedures to characterize and calibrate these probes by EPR, and also the methods to analyze the EPR spectra by simulations are outlined. The ionizable nitroxide labels and the nitroxide-labeled phospholipids described so far cover an exceptionally wide range of ca. 2.5-7.0 pH units, making them suitable to study a broad range of biophysical phenomena, especially at the negatively charged lipid bilayer surfaces. The rationale for selecting proper electrostatically neutral interface for probe calibration, and examples of lipid bilayer surface potential studies, are also described. © 2015 Elsevier Inc. All rights reserved.

Electrostatic study of Alanine mutational effects on transcription: application to GATA-3:DNA interaction complex.

PubMed

El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges

2015-01-01

Protein-DNA interaction is of fundamental importance in molecular biology, playing roles in functions as diverse as DNA transcription, DNA structure formation, and DNA repair. Protein-DNA association is also important in medicine; understanding Protein-DNA binding kinetics can assist in identifying disease root causes which can contribute to drug development. In this perspective, this work focuses on the transcription process by the GATA Transcription Factor (TF). GATA TF binds to DNA promoter region represented by `G,A,T,A' nucleotides sequence, and initiates transcription of target genes. When proper regulation fails due to some mutations on the GATA TF protein sequence or on the DNA promoter sequence (weak promoter), deregulation of the target genes might lead to various disorders. In this study, we aim to understand the electrostatic mechanism behind GATA TF and DNA promoter interactions, in order to predict Protein-DNA binding in the presence of mutations, while elaborating on non-covalent binding kinetics. To generate a family of mutants for the GATA:DNA complex, we replaced every charged amino acid, one at a time, with a neutral amino acid like Alanine (Ala). We then applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations, for each mutation. These calculations delineate the contribution to binding from each Ala-replaced amino acid in the GATA:DNA interaction. After analyzing the obtained data in view of a two-step model, we are able to identify potential key amino acids in binding. Finally, we applied the model to GATA-3:DNA (crystal structure with PDB-ID: 3DFV) binding complex and validated it against experimental results from the literature.

The interactions between three typical PPCPs and LDH

NASA Astrophysics Data System (ADS)

Li, Erwei; Liao, Libing; Lv, Guocheng; Li, Zhaohui; Yang, Chengxue; Lu, Yanan

2018-03-01

With a positively charged layered structure, layered double hydroxide has potential applications in remediation of anionic contaminants, which has been a hot topic for recent years. In this study, a Cl type Mg-Al hydrotalcite (Cl-LDH) was prepared by a co-precipitation method. The adsorption process of three pharmaceuticals and personal care products (PPCPs) (tetracycline (TC), diclofenac sodium (DF), chloramphenicol (CAP)) by Cl-LDH was investigated by X-ray diffraction (XRD), Zeta potential, dynamic light scattering (DLS), BET, FT-IR spectroscopy and molecular dynamics simulation. The results showed that the adsorption equilibrium of TC and DF could be reached in 120 min, and the maximum adsorption capacity of the Cl-LDH for TC and DF were 1.85 mmol/g and 0.95 mmol/g, respectively. The adsorption isothermal of TC was fitted with the Freundlich adsorption model, and the adsorption isothermal of DF was fitted with the Langmuir adsorption model. The adsorption dynamics of TC and DF followed the pseudo-second-order model. The adsorption mechanisms of the three PPCPs onto Cl-LDH were different based on the experimental results and molecular dynamics simulation. The TC adsorption on Cl-LDH was mainly driven by the electrostatic interactions between the negative charge of TC and the positive charge of Cl-LDH. The uptake of anionic DF was attributed both to ion exchange of DF for Cl- and the electrostatic interaction between the negatively charged DF and the positively charged structure layer of Cl-LDH. Cl-LDH does not adsorb the neutral CAP due to no electrostatic interaction. The molecular dynamic simulation further confirmed different configurations of the three selected PPCPs in the interlayer of Cl-LDH, which were responsible for the different uptake process of PPCPs on Cl-LDH.

3D RISM theory with fast reciprocal-space electrostatics.

PubMed

Heil, Jochen; Kast, Stefan M

2015-03-21

The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

Limits of applicability of the quasilinear approximation to the electrostatic wave-plasma interaction

NASA Astrophysics Data System (ADS)

Zacharegkas, Georgios; Isliker, Heinz; Vlahos, Loukas

2016-11-01

The limitation of the Quasilinear Theory (QLT) to describe the diffusion of electrons and ions in velocity space when interacting with a spectrum of large amplitude electrostatic Langmuir, Upper and Lower hybrid waves, is analyzed. We analytically and numerically estimate the threshold for the amplitude of the waves above which the QLT breaks down, using a test particle code. The evolution of the velocity distribution, the velocity-space diffusion coefficients, the driven current, and the heating of the particles are investigated, for the interaction with small and large amplitude electrostatic waves, that is, in both regimes, where QLT is valid and where it clearly breaks down.

Dynamic Colloidal Molecules Maneuvered by Light-Controlled Janus Micromotors.

PubMed

Gao, Yirong; Mou, Fangzhi; Feng, Yizheng; Che, Shengping; Li, Wei; Xu, Leilei; Guan, Jianguo

2017-07-12

In this work, we propose and demonstrate a dynamic colloidal molecule that is capable of moving autonomously and performing swift, reversible, and in-place assembly dissociation in a high accuracy by manipulating a TiO 2 /Pt Janus micromotor with light irradiation. Due to the efficient motion of the TiO 2 /Pt Janus motor and the light-switchable electrostatic interactions between the micromotor and colloidal particles, the colloidal particles can be captured and assembled one by one on the fly, subsequently forming into swimming colloidal molecules by mimicking space-filling models of simple molecules with central atoms. The as-demonstrated dynamic colloidal molecules have a configuration accurately controlled and stabilized by regulating the time-dependent intensity of UV light, which controls the stop-and-go motion of the colloidal molecules. The dynamic colloidal molecules are dissociated when the light irradiation is turned off due to the disappearance of light-switchable electrostatic interaction between the motor and the colloidal particles. The strategy for the assembly of dynamic colloidal molecules is applicable to various charged colloidal particles. The simulated optical properties of a dynamic colloidal molecule imply that the results here may provide a novel approach for in-place building functional microdevices, such as microlens arrays, in a swift and reversible manner.

Turbulence of electrostatic electron cyclotron harmonic waves observed by Ogo 5.

NASA Technical Reports Server (NTRS)

Oya, H.

1972-01-01

Analysis of VLF emissions that have been observed near 3/2, 5/2, and 7/2 f sub H by Ogo 5 in the magnetosphere (f sub H is the electron cyclotron frequency) in the light of the mechanism used for the diffuse plasma resonance f sub Dn observed by Alouette 2 and Isis 1. The VLF emission is considered to be generated by nonlinear coupling mechanisms in certain portions of the observation as the f sub Dn is enhanced by its association with nonlinear wave-particle interaction of the electrostatic electron cyclotron harmonic wave, including the instability due to the nonlinear inverse Landau damping mechanism in the turbulence. The difference between the two observations is in the excitation mechanism of the turbulence; the turbulence in the plasma trough detected by Ogo 5 is due to natural origins, whereas the ionospheric topside sounder makes the plasma wave turbulence artificially by submitting strong stimulation pulses. Electron density values in the plasma trough are deduced by applying the f sub Dn-f sub N/f sub H relationship obtained from the Alouette 2 experiment as well as by applying the condition for the wave-particle nonlinear interactions. The electron density values reveal good agreement with the ion density values observed simultaneously by the highly sensitive ion mass spectrometer.

Controlling Ionic Transport for Device Design in Synthetic Nanopores

NASA Astrophysics Data System (ADS)

Kalman, Eric Boyd

Polymer nanopores present a number of behaviors not seen in microscale systems, such as ion current rectification, ionic selectivity, size exclusion and potential dependent ion concentrations in and near the pore. The existence of these effects stems from the small size of nanopores with respect to the characteristic length scales of surface interactions at the interface between the nanopore surface and the solution within it. The large surface-to-volume ratio due to the nanoscale geometry of a nanopore, as well as similarity in scale between geometry and interaction demands the solution interact with the nanopore walls. As surfaces in solution almost always carry residual charge, these surface forces are primarily the electrostatic interactions between the charge groups on the pore surface and the ions in solution. These interactions may be used by the experimentalist to control ionic transport through synthetic nanopores, and use them as a template for the construction of devices. In this research, we present our work on creating a number of ionic analogs to seminal electronic devices, specifically diodes, and transistors, by controlling ionic transport through the electrostatic interactions between a single synthetic nanopore and ions. Control is achieved by "doping" the effective charge carrier concentration in specific regions of the nanopore through manipulation of the pore's surface charge. This manipulation occurs through two mechanisms: chemical modification of the surface charge and electrostatic manipulation of the local internal nanopore potential using a gate electrode. Additionally, the innate selectivity of the charged nanopores walls allows for the separation of charges in solution. This well-known effect, which spawns measureable quantities, the streaming potential and current, has been used to create nanoscale water desalination membranes. We attempt to create a device using membranes with large nanopore densities for the desalination of water which should theoretically outperform currently available devices, as through our previous work we have developed techniques allowing for transport manipulation not current accessible in traditional membrane motifs.

Energy component analysis of π interactions.

PubMed

Sherrill, C David

2013-04-16

Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively unimportant. In general, a nitrogen heteroatom contracts the electron density, reducing the magnitude of both the London dispersion and the exchange-repulsion terms, but with an overall net increase in attraction. Finally, using recent advances in SAPT algorithms, researchers can now perform SAPT computations on systems with 200 atoms or more. We discuss a recent study of the intercalation complex of proflavine with a trinucleotide duplex of DNA. Here, London dispersion forces are the strongest contributors to binding, as is typical for π-π interactions. However, the electrostatic terms are larger than usual on a fractional basis, which likely results from the positive charge on the intercalator and its location between two electron-rich base pairs. These cation-π interactions also increase the induction term beyond those of typical noncovalent π-interactions.

AESOP: A Python Library for Investigating Electrostatics in Protein Interactions.

PubMed

Harrison, Reed E S; Mohan, Rohith R; Gorham, Ronald D; Kieslich, Chris A; Morikis, Dimitrios

2017-05-09

Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Solar Wind Strahl Broadening by Self-Generated Plasma Waves

NASA Technical Reports Server (NTRS)

Pavan, J.; Vinas, A. F.; Yoon, P. H.; Ziebell, L. F.; Gaelzer, R.

2013-01-01

This Letter reports on the results of numerical simulations which may provide a possible explanation for the strahl broadening during quiet solar conditions. The relevant processes involved in the broadening are due to kinetic quasi-linear wave-particle interaction. Making use of static analytical electron distribution in an inhomogeneous field, it is found that self-generated electrostatic waves at the plasma frequency, i.e., Langmuir waves, are capable of scattering the strahl component, resulting in energy and pitch-angle diffusion that broadens its velocity distribution significantly. The present theoretical results provide an alternative or complementary explanation to the usual whistler diffusion scenario, suggesting that self-induced electrostatic waves at the plasma frequency might play a key role in broadening the solar wind strahl during quiet solar conditions.

On the Proper Calculation of Electrostatic Interactions in Solid-Supported Bilayer Systems

DTIC Science & Technology

2011-01-01

the effects of im- plementing different electrostatic boundary conditions on the structural and electrostatic properties of a quartz/water/vacuum...interface and a similar quartz-supported hydrated lipid bilayer exposed to vacuum. Since these interfacial systems have a net polarization, implementing the...implemented electrostatic boundary condition removed these inconsistencies. This formulation is generally applicable to similar interfacial systems in bulk

On the role of electrostatics in protein-protein interactions

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-06-01

The role of electrostatics in protein-protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartments. The similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity.

On the role of electrostatics on protein-protein interactions

PubMed Central

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-01-01

The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

Interaction between stray electrostatic fields and a charged free-falling test mass.

PubMed

Antonucci, F; Cavalleri, A; Dolesi, R; Hueller, M; Nicolodi, D; Tu, H B; Vitale, S; Weber, W J

2012-05-04

We present an experimental analysis of force noise caused by stray electrostatic fields acting on a charged test mass inside a conducting enclosure, a key problem for precise gravitational experiments. Measurement of the average field that couples to the test mass charge, and its fluctuations, is performed with two independent torsion pendulum techniques, including direct measurement of the forces caused by a change in electrostatic charge. We analyze the problem with an improved electrostatic model that, coupled with the experimental data, also indicates how to correctly measure and null the stray field that interacts with the test mass charge. Our measurements allow a conservative upper limit on acceleration noise, of 2  (fm/s2)/Hz(1/2) for frequencies above 0.1 mHz, for the interaction between stray fields and charge in the LISA gravitational wave mission.

Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution.

PubMed

Buckle, A M; Schreiber, G; Fersht, A R

1994-08-02

We have solved, refined, and analyzed the 2.0-å resolution crystal structure of a 1:1 complex between the bacterial ribonuclease, barnase, and a Cys-->Ala(40,82) double mutant of its intracellular polypeptide inhibitor, barstar. Barstar inhibits barnase by sterically blocking the active site with a helix and adjacent loop segment. Almost half of the 14 hydrogen bonds between barnase and barstar involve two charged residues, and a third involve one charged partner. The electrostatic contribution to the overall binding energy is considerably greater than for other protein-protein interactions. Consequently, the very high rate constant for the barnase-barstar association (10(8) s-1 M-1) is most likely due to electrostatic steering effects. The barnase active-site residue His102 is located in a pocket on the surface of barstar, and its hydrogen bonds with Asp39 and Gly31 residues of barstar are directly responsible for the pH dependence of barnase-barstar binding. There is a high degree of complementarity both of the shape and of the charge of the interacting surfaces, but neither is perfect. The surface complementarity is slightly poorer than in protease-inhibitor complexes but a little better than in antibody-antigen interactions. However, since the burial of solvent in the barnase-barstar interface improves the fit significantly by filling in the majority of gaps, as well as stabilizing unfavorable electrostatic interactions, its role seems to be more important than in other protein-protein complexes. The electrostatic interactions between barnase and barstar are very similar to those between barnase and the tetranucleotide d(CGAC). In the barnase-barstar complex, the two phosphate-binding sites in the barnase active site are occupied by Asp39 and Gly43 of barstar. However, barstar has no equivalent for a guanine base of an RNA substrate, resulting in the occupation of the guanine recognition site in the barnase-barstar complex by nine ordered water molecules. Upon barnase-barstar binding, entropy losses resulting from the immobilization of segments of the protein chain and the energetic costs of conformational changes are minimized due to the essentially preformed active site of barnase. However, a certain degree of flexibility within the barnase active site is required to allow for the structural differences between barnase-barstar binding and barnase-RNA binding. A comparison between the bound and the free barstar structure shows that the overall structural response to barnase-binding is significant. This response can be best described as outwardly oriented, rigid-body movements of the four alpha-helices of barstar, resulting in the structure of bound barstar being somewhat expanded.

Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR

PubMed Central

Voinov, Maxim A.; Smirnov, Alex I.

2016-01-01

Electrostatic interactions are known to play one of the major roles in the myriad of biochemical and biophysical processes. In this Chapter we describe biophysical methods to probe local electrostatic potentials of proteins and lipid bilayer systems that is based on an observation of reversible protonation of nitroxides by EPR. Two types of the electrostatic probes are discussed. The first one includes methanethiosulfonate derivatives of protonatable nitroxides that could be used for highly specific covalent modification of the cysteine’s sulfhydryl groups. Such spin labels are very similar in magnetic parameters and chemical properties to conventional MTSL making them suitable for studying local electrostatic properties of protein-lipid interfaces. The second type of EPR probes is designed as spin-labeled phospholipids having a protonatable nitroxide tethered to the polar head group. The probes of both types report on their ionization state through changes in magnetic parameters and a degree of rotational averaging, thus, allowing one to determine the electrostatic contribution to the interfacial pKa of the nitroxide, and, therefore, determining the local electrostatic potential. Due to their small molecular volume these probes cause a minimal perturbation to the protein or lipid system while covalent attachment secure the position of the reporter nitroxides. Experimental procedures to characterize and calibrate these probes by EPR and also the methods to analyze the EPR spectra by least-squares simulations are also outlined. The ionizable nitroxide labels and the nitroxide-labeled phospholipids described so far cover an exceptionally wide pH range from ca. 2.5 to 7.0 pH units making them suitable to study a broad range of biophysical phenomena especially at the negatively charged lipid bilayer surfaces. The rationale for selecting proper electrostatically neutral interface for calibrating such probes and example of studying surface potential of lipid bilayer is also described. PMID:26477252

Emphasizing the Significance of Electrostatic Interactions in Chemical Bonding

ERIC Educational Resources Information Center

Venkataraman, Bhawani

2017-01-01

This paper describes a pedagogical approach to help students understand chemical bonding by emphasizing the importance of electrostatic interactions between atoms. The approach draws on prior studies that have indicated many misconceptions among students in understanding the nature of the chemical bond and energetics associated with bond formation…

PBEQ-Solver for online visualization of electrostatic potential of biomolecules.

PubMed

Jo, Sunhwan; Vargyas, Miklos; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil

2008-07-01

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 A before and 1 A after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.

Electrodynamics of Lipid Membrane Interactions in the Presence of Zwitterionic Buffers

PubMed Central

Koerner, Megan M.; Palacio, Luis A.; Wright, Johnnie W.; Schweitzer, Kelly S.; Ray, Bruce D.; Petrache, Horia I.

2011-01-01

Due to thermal motion and molecular polarizability, electrical interactions in biological systems have a dynamic character. Zwitterions are dipolar molecules that typically are highly polarizable and exhibit both a positive and a negative charge depending on the pH of the solution. We use multilamellar structures of common lipids to identify and quantify the effects of zwitterionic buffers that go beyond the control of pH. We use the fact that the repeat spacing of multilamellar lipid bilayers is a sensitive and accurate indicator of the force balance between membranes. We show that common buffers can in fact charge up neutral membranes. However, this electrostatic effect is not immediately recognized because of the concomitant modification of dispersion (van der Waals) forces. We show that although surface charging can be weak, electrostatic forces are significant even at large distances because of reduced ionic screening and reduced van der Waals attraction. The zwitterionic interactions that we identify are expected to be relevant for interfacial biological processes involving lipid bilayers, and for a wide range of biomaterials, including amino acids, detergents, and pharmaceutical drugs. An appreciation of zwitterionic electrodynamic character can lead to a better understanding of molecular interactions in biological systems and in soft materials in general. PMID:21767488

Free energy calculations of glycosaminoglycan-protein interactions.

PubMed

Gandhi, Neha S; Mancera, Ricardo L

2009-10-01

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Effective cytoplasmic release of siRNA from liposomal carriers by controlling the electrostatic interaction of siRNA with a charge-invertible peptide, in response to cytoplasmic pH

NASA Astrophysics Data System (ADS)

Itakura, Shoko; Hama, Susumu; Matsui, Ryo; Kogure, Kentaro

2016-05-01

Condensing siRNA with cationic polymers is a major strategy used in the development of siRNA carriers that can avoid degradation by nucleases and achieve effective delivery of siRNA into the cytoplasm. However, ineffective release of siRNA from such condensed forms into the cytoplasm is a limiting step for induction of RNAi effects, and can be attributed to tight condensation of siRNA with the cationic polymers, due to potent electrostatic interactions. Here, we report that siRNA condensed with a slightly acidic pH-sensitive peptide (SAPSP), whose total charge is inverted from positive to negative in response to cytoplasmic pH, is effectively released via electrostatic repulsion of siRNA with negatively charged SAPSP at cytoplasmic pH (7.4). The condensed complex of siRNA and positively-charged SAPSP at acidic pH (siRNA/SAPSP) was found to result in almost complete release of siRNA upon charge inversion of SAPSP at pH 7.4, with the resultant negatively-charged SAPSP having no undesirable interactions with endogenous mRNA. Moreover, liposomes encapsulating siRNA/SAPSP demonstrated knockdown efficiencies comparable to those of commercially available siRNA carriers. Taken together, SAPSP may be very useful as a siRNA condenser, as it facilitates effective cytoplasmic release of siRNA, and subsequent induction of specific RNAi effects.Condensing siRNA with cationic polymers is a major strategy used in the development of siRNA carriers that can avoid degradation by nucleases and achieve effective delivery of siRNA into the cytoplasm. However, ineffective release of siRNA from such condensed forms into the cytoplasm is a limiting step for induction of RNAi effects, and can be attributed to tight condensation of siRNA with the cationic polymers, due to potent electrostatic interactions. Here, we report that siRNA condensed with a slightly acidic pH-sensitive peptide (SAPSP), whose total charge is inverted from positive to negative in response to cytoplasmic pH, is effectively released via electrostatic repulsion of siRNA with negatively charged SAPSP at cytoplasmic pH (7.4). The condensed complex of siRNA and positively-charged SAPSP at acidic pH (siRNA/SAPSP) was found to result in almost complete release of siRNA upon charge inversion of SAPSP at pH 7.4, with the resultant negatively-charged SAPSP having no undesirable interactions with endogenous mRNA. Moreover, liposomes encapsulating siRNA/SAPSP demonstrated knockdown efficiencies comparable to those of commercially available siRNA carriers. Taken together, SAPSP may be very useful as a siRNA condenser, as it facilitates effective cytoplasmic release of siRNA, and subsequent induction of specific RNAi effects. Electronic supplementary information (ESI) available: De-condensation of siRNA cores by addition of heparin; time-lapse moving image of the siRNA release. See DOI: 10.1039/c5nr08365f

Surface decoration through electrostatic interaction leading to enhanced reactivity: Low temperature synthesis of nanostructured chromium borides (CrB and CrB{sub 2})

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menaka,; Kumar, Bharat; Kumar, Sandeep

The present study describes a novel low temperature route at ambient pressure for the synthesis of nanocrystalline chromium borides (CrB and CrB{sub 2}) without using any flux or additives. The favorable and intimate mixing of nanoparticles of chromium acetate (Cr source) and boron forms an active chromium–boron precursor which decomposes at much lower temperature (400 °C) to form CrB (which is ∼1000 °C less than the known ambient pressure synthesis). The chromium acetate nanoparticles (∼5 nm) decorate the larger boron particles (150–200 nm) due to electrostatic interactions resulting from opposing surface charges of boron (zeta potential:+48.101 mV) and chromium acetatemore » (zeta potential:−4.021 mV) in ethanolic medium and is evident in the TEM micrographs. The above method leads to the formation of pure CrB film like structure at 400 °C and nanospheres (40–60 nm) at 600 °C. Also, chromium diboride (CrB{sub 2}) nanoparticles (25 nm) could be obtained at 1000 °C. - Graphical abstract: Variation of surface charge of reactants, precursor and the products, chromium borides (CrB and CrB{sub 2}). Highlights: ► Novel borothermal reduction process for synthesis of chromium boride. ► Significant lowering of reaction temperature to obtain nanocrystalline chromium boride. ► Enhanced reactivity due to appropriate surface interactions.« less

Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

PubMed

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

2009-06-02

Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

Controlling adsorption of albumin with hyaluronan on silica surfaces and sulfonated latex particles.

PubMed

Berts, Ida; Fragneto, Giovanna; Porcar, Lionel; Hellsing, Maja S; Rennie, Adrian R

2017-10-15

Polysaccharides are known to modify binding of proteins at interfaces and this paper describes studies of these interactions and how they are modified by pH. Specifically, the adsorption of human serum albumin on to polystyrene latex and to silica is described, focusing on how this is affected by hyaluronan. Experiments were designed to test how such binding might be modified under relevant physiological conditions. Changes in adsorption of albumin alone and the co-adsorption of albumin and hyaluronan are driven by electrostatic interactions. Multilayer binding is found to be regulated by the pH of the solution and the molecular mass and concentration of hyaluronan. Highest adsorption was observed at pH below 4.8 and for low molecular mass hyaluronan (≤150kDa) at concentrations above 2mgml -1 . On silica with grafted hyaluronan, albumin absorption is reversed by changes in solvent pH due to their strong electrostatic attraction. Albumin physisorbed on silica surfaces is also rinsed away with dilute hyaluronan solution at pH 4.8. The results demonstrate that the protein adsorption can be controlled both by changes of pH and by interaction with other biological macromolecules. Copyright © 2017 Elsevier Inc. All rights reserved.

SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles.

PubMed

Bueno, Marta; Camacho, Carlos J; Sancho, Javier

2007-09-01

The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5-to-40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. 2007 Wiley-Liss, Inc.

Prospective Teachers' Difficulties in Interpreting Elementary Phenomena of Electrostatic Interactions: Indicators of the Status of Their Intuitive Ideas

ERIC Educational Resources Information Center

Criado, Ana Maria; Garcia-Carmona, Antonio

2010-01-01

Student teachers were tested before and after a teaching unit on electrostatic interactions in an attempt to consider their intuitive ideas and concept development. A study was made of students' explanations of basic interactions: those between two charged bodies, and those between a charged body and a neutral body. Two indicators of the cognitive…

Course 1: Physics of Protein-DNA Interaction

NASA Astrophysics Data System (ADS)

Bruinsma, R. F.

1 Introduction 1.1 The central dogma and bacterial gene expression 1.2 Molecular structure 2 Thermodynamics and kinetics of repressor-DNA interaction 2.1 Thermodynamics and the lac repressor 2.2 Kinetics of repressor-DNA interaction 3 DNA deformability and protein-DNA interaction 3.1 Introduction 3.2 The worm-like chain 3.3 The RST model 4 Electrostatics in water and protein-DNA interaction 4.1 Macro-ions and aqueous electrostatics 4.2 The primitive model 4.3 Manning condensation 4.4 Counter-ion release and non-specific protein-DNA interaction

Effect of surface chemical composition on the surface potential and iso-electric point of silicon substrates modified with self-assembled monolayers.

PubMed

Kuo, Che-Hung; Chang, Hsun-Yun; Liu, Chi-Ping; Lee, Szu-Hsian; You, Yun-Wen; Shyue, Jing-Jong

2011-03-07

Self-assembled monolayer (SAM)-modified nano-materials are a new technology to deliver drug molecules. While the majority of these depend on covalently immobilizing molecules on the surface, it is proposed that electrostatic interactions may be used to deliver drugs. By tuning the surface potential of solid substrates with SAMs, drug molecules could be either absorbed on or desorbed from substrates through the difference in electrostatic interactions around the selected iso-electric point (IEP). In this work, the surface of silicon substrates was tailored with various ratios of 3-aminopropyltrimethoxysilane (APTMS) and 3-mercaptopropyltrimethoxysilane (MPTMS), which form amine- and thiol-bearing SAMs, respectively. The ratio of the functional groups on the silicon surface was quantified by X-ray photoelectron spectrometry (XPS); in general, the deposition kinetics of APTMS were found to be faster than those of MPTMS. Furthermore, for solutions with high MPTMS concentrations, the relative deposition rate of APTMS increased dramatically due to the acid-base reaction in the solution and subsequent electrostatic interactions between the molecules and the substrate. The zeta potential in aqueous electrolytes was determined with an electro-kinetic analyzer. By depositing SAMs of binary functional groups in varied ratios, the surface potential and IEP of silicon substrates could be fine-tuned. For <50% amine concentration in SAMs, the IEP changed linearly with the chemical composition from <2 to 7.18. For higher amine concentrations, the IEP slowly increased with concentration to 7.94 because the formation of hydrogen-bonding suppressed the subsequent protonation of amines.

Improving the affinity of an antibody for its antigen via long-range electrostatic interactions.

PubMed

Fukunaga, Atsushi; Tsumoto, Kouhei

2013-12-01

To address how long-range electrostatic force can affect antibody-antigen binding, we focused on the interactions between human cardiac troponin I and its specific single-chain antibodies (scFvs). We first isolated two scFvs against two linear epitopes with distinct isoelectric points. For the scFv against the acidic epitope (A1scFv), we mutated five residues of framework region 3 of the light chain to Lys or Arg, designated as the K- or R-mutant, respectively. For the scFv against the basic epitope (A2scFv), we mutated four or three residues in framework region 3 of the light or heavy chain to Asp, to generate the VL- and VH-mutant, respectively. Surface plasmon resonance analyses showed that the kon values of all of the mutants were greater than that of wild type, even though framework region 3 does not make direct contact with the epitope. The affinity of the K-mutant was pM range, and that of the R-mutant improved further by more than two orders of magnitude due to a decrease in the dissociation rate constant. For the A2scFv mutants, the affinity of the VL-mutant for its target improved through an increase in the kon value without a decrease in the koff value. The stability slightly decreased in all mutants. These results suggest that introducing electrostatic interaction can improve the affinity of an antibody for its target, even if the mutation reduces stability of the antibody.

Long Range Debye-Hückel Correction for Computation of Grid-based Electrostatic Forces Between Biomacromolecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mereghetti, Paolo; Martinez, M.; Wade, Rebecca C.

Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulatemore » solutions of bovine serum albumin and of hen egg white lysozyme.« less

Protein-lipid interactions at the air/water interface.

PubMed

Lad, Mitaben D; Birembaut, Fabrice; Frazier, Richard A; Green, Rebecca J

2005-10-07

Surface pressure measurements and external reflection FTIR spectroscopy have been used to probe protein-lipid interactions at the air/water interface. Spread monomolecular layers of stearic acid and phosphocholine were prepared and held at different compressed phase states prior to the introduction of protein to the buffered subphase. Contrasting interfacial behaviour of the proteins, albumin and lysozyme, was observed and revealed the role of both electrostatic and hydrophobic interactions in protein adsorption. The rate of adsorption of lysozyme to the air/water interface increased dramatically in the presence of stearic acid, due to strong electrostatic interactions between the negatively charged stearic acid head group and lysozyme, whose net charge at pH 7 is positive. Introduction of albumin to the subphase resulted in solubilisation of the stearic acid via the formation of an albumin-stearic acid complex and subsequent adsorption of albumin. This observation held for both human and bovine serum albumin. Protein adsorption to a PC layer held at low surface pressure revealed adsorption rates similar to adsorption to the bare air/water interface and suggested very little interaction between the protein and the lipid. For PC layers in their compressed phase state some adsorption of protein occurred after long adsorption times. Structural changes of both lysozyme and albumin were observed during adsorption, but these were dramatically reduced in the presence of a lipid layer compared to that of adsorption to the pure air/water interface.

Electrostatic Forces as Dominant Interactions Between Proteins and Polyanions: an ESI MS Study of Fibroblast Growth Factor Binding to Heparin Oligomers

NASA Astrophysics Data System (ADS)

Minsky, Burcu Baykal; Dubin, Paul L.; Kaltashov, Igor A.

2017-04-01

The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1). This growth factor forms 1:1, 2:1, and 3:1 protein/heparinoid complexes with both dp8 and dp10, and the fraction of bound protein is highly dependent on protein/heparinoid molar ratio. Multimeric complexes are preferentially formed on the highly sulfated Hp oligomers. Although a variety of oligomers appear to be binding-competent, there is a strong correlation between the affinity and the overall level of sulfation (the highest charge density polyanions binding FGF most strongly via multivalent interactions). These results show that the interactions between FGF-1 and Hp oligomers are primarily directed by electrostatics, and also demonstrate the power of ESI MS as a tool to study multiple binding equilibria between proteins and structurally heterogeneous polyanions.

Role of electrostatic interactions during protein ultrafiltration.

PubMed

Rohani, Mahsa M; Zydney, Andrew L

2010-10-15

A number of studies over the last decade have clearly demonstrated the importance of electrostatic interactions on the transport of charged proteins through semipermeable ultrafiltration membranes. This paper provides a review of recent developments in this field with a focus on the role of both protein and membrane charge on the rate of protein transport. Experimental results are analyzed using available theoretical models developed from the solution of the Poisson-Boltzmann equation for the partitioning of a charged particle into a charged pore. The potential of exploiting these electrostatic interactions for selective protein separations and for the development of ultrafiltration membranes with enhanced performance characteristics is also examined. Copyright © 2010 Elsevier B.V. All rights reserved.

Photoionization of N,N,N',N'-tetramethylbenzidine in anionic-cationic mixed micelles of sodium dodecyl sulfate-dodecyltrimethylammonium chloride: electron spin resonance and electron spin echo modulation studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivara-Minten, E.; Baglioni, P.; Kevan, L.

1988-05-05

Electron spin echo modulation (ESEM) and electron spin resonance (ESR) spectra of the photogenerated N,N,N',N'-tetramethylbenzidine cation radical (TMB/sup +/) in frozen mixed micelles of dodecyltrimethylammonium chloride (DTAC) and sodium dodecyl sulfate (SDS) have been studied as a function of the mixed micelle composition. ESEM effects due to TMB/sup +/ interactions with deuterium in D/sub 2/O show a decrease of the TMB/sup +/-water interaction that depends on the SDS-DTAC mixed micelle composition and reaches a minimum for the equimolar mixed micelle. The efficiency of charge separation upon photoionization of TMB to produce TMB/sup +/ measured by ESR correlates with the degreemore » of water penetration into the micelle. ESEM effects due to interaction of x-doxylstearic acid nitroxide probes with deuterium in D/sub 2/O show that the decrease of water penetration is due to higher surface packing due to electrostatic attraction among the polar headgroups of the two surfactants.« less

Photonic-plasmonic hybrid single-molecule nanosensor measures the effect of fluorescent labels on DNA-protein dynamics

PubMed Central

Liang, Feng; Guo, Yuzheng; Hou, Shaocong; Quan, Qimin

2017-01-01

Current methods to study molecular interactions require labeling the subject molecules with fluorescent reporters. However, the effect of the fluorescent reporters on molecular dynamics has not been quantified because of a lack of alternative methods. We develop a hybrid photonic-plasmonic antenna-in-a-nanocavity single-molecule biosensor to study DNA-protein dynamics without using fluorescent labels. Our results indicate that the fluorescein and fluorescent protein labels decrease the interaction between a single DNA and a protein due to weakened electrostatic interaction. Although the study is performed on the DNA-XPA system, the conclusion has a general implication that the traditional fluorescent labeling methods might be misestimating the molecular interactions. PMID:28560341

Swelling of biological and semiflexible polyelectrolytes.

PubMed

Dobrynin, Andrey V; Carrillo, Jan-Michael Y

2009-10-21

We have developed a theoretical model of swelling of semiflexible (biological) polyelectrolytes in salt solutions. Our approach is based on separation of length scales which allowed us to split a chain's electrostatic energy into two parts that describe local and remote electrostatic interactions along the polymer backbone. The local part takes into account interactions between charged monomers that are separated by distances along the polymer backbone shorter than the chain's persistence length. These electrostatic interactions renormalize chain persistence length. The second part includes electrostatic interactions between remote charged pairs along the polymer backbone located at distances larger than the chain persistence length. These interactions are responsible for chain swelling. In the framework of this approach we calculated effective chain persistence length and chain size as a function of the Debye screening length, chain degree of ionization, bare persistence length and chain degree of polymerization. Our crossover expression for the effective chain's persistence length is in good quantitative agreement with the experimental data on DNA. We have been able to fit experimental datasets by using two adjustable parameters: DNA ionization degree (α = 0.15-0.17) and a bare persistence length (l(p) = 40-44 nm).

Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects

NASA Astrophysics Data System (ADS)

Chau, P.-L.; Dean, P. M.

1994-10-01

Electrostatic interactions have always been considered an important factor governing ligand-receptor interactions. Previous work in this field has established the existence of electrostatic complementarity between the ligand and its receptor site. However, this property has not been treated rigorously, and the description remains largely qualitative. In this work, 34 data sets of high quality were chosen from the Brookhaven Protein Databank. The electrostatic complementarity has been calculated between the surface potentials; complementarity is absent between adjacent or neighbouring atoms of the ligand and the receptor. There is little difference between complementarities on the total ligand surface and the interfacial region. Altering the homogeneous dielectric to distance-dependent dielectrics reduces the complementarity slightly, but does not affect the pattern of complementarity.

Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects.

PubMed

Chau, P L; Dean, P M

1994-10-01

Electrostatic interactions have always been considered an important factor governing ligand-receptor interactions. Previous work in this field has established the existence of electrostatic complementarity between the ligand and its receptor site. However, this property has not been treated rigorously, and the description remains largely qualitative. In this work, 34 data sets of high quality were chosen from the Brookhaven Protein Databank. The electrostatic complementary has been calculated between the surface potentials; complementarity is absent between adjacent or neighbouring atoms of the ligand and the receptor. There is little difference between complementarities on the total ligand surface and the interfacial region. Altering the homogeneous dielectric to distance-dependent dielectrics reduces the complementarity slightly, but does not affect the pattern of complementarity.

Additional application of the NASCAP code. Volume 2: SEPS, ion thruster neutralization and electrostatic antenna model

NASA Technical Reports Server (NTRS)

Katz, I.; Cassidy, J. J.; Mandell, M. J.; Parks, D. E.; Schnuelle, G. W.; Stannard, P. R.; Steen, P. G.

1981-01-01

The interactions of spacecraft systems with the surrounding plasma environment were studied analytically for three cases of current interest: calculating the impact of spacecraft generated plasmas on the main power system of a baseline solar electric propulsion stage (SEPS), modeling the physics of the neutralization of an ion thruster beam by a plasma bridge, and examining the physical and electrical effects of orbital ambient plasmas on the operation of an electrostatically controlled membrane mirror. In order to perform these studies, the NASA charging analyzer program (NASCAP) was used as well as several other computer models and analytical estimates. The main result of the SEPS study was to show how charge exchange ion expansion can create a conducting channel between the thrusters and the solar arrays. A fluid-like model was able to predict plasma potentials and temperatures measured near the main beam of an ion thruster and in the vicinity of a hollow cathode neutralizer. Power losses due to plasma currents were shown to be substantial for several proposed electrostatic antenna designs.

Anomalous momentum and energy transfer rates for electrostatic ion-cyclotron turbulence in downward auroral-current regions of the Earth's magnetosphere. III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jasperse, John R.; Basu, Bamandas; Lund, Eric J.

2010-06-15

Recently, a new multimoment fluid theory was developed for inhomogeneous, nonuniformly magnetized plasma in the guiding-center and gyrotropic approximation that includes the effect of electrostatic, turbulent, wave-particle interactions (see Jasperse et al. [Phys. Plasmas 13, 072903 (2006); ibid.13, 112902 (2006)]). In the present paper, which is intended as a sequel, it is concluded from FAST satellite data that the electrostatic ion-cyclotron turbulence that appears is due to the operation of an electron, bump-on-tail-driven ion-cyclotron instability for downward currents in the long-range potential region of the Earth's magnetosphere. Approximate closed-form expressions for the anomalous momentum and energy transfer rates for themore » ion-cyclotron turbulence are obtained. The turbulent, inhomogeneous, nonuniformly magnetized, multimoment fluid theory given above, in the limit of a turbulent, homogeneous, uniformly magnetized, quasisteady plasma, yields the well-known formula for the anomalous resistivity given by Gary and Paul [Phys. Rev. Lett. 26, 1097 (1971)] and Tange and Ichimaru [J. Phys. Soc. Jpn. 36, 1437 (1974)].« less

Tight ceramic UF membrane as RO pre-treatment: the role of electrostatic interactions on phosphate rejection.

PubMed

Shang, Ran; Verliefde, Arne R D; Hu, Jingyi; Zeng, Zheyi; Lu, Jie; Kemperman, Antoine J B; Deng, Huiping; Nijmeijer, Kitty; Heijman, Sebastiaan G J; Rietveld, Luuk C

2014-01-01

Phosphate limitation has been reported as an effective approach to inhibit biofouling in reverse osmosis (RO) systems for water purification. The rejection of dissolved phosphate by negatively charged TiO2 tight ultrafiltration (UF) membranes (1 kDa and 3 kDa) was observed. These membranes can potentially be adopted as an effective process for RO pre-treatment in order to constrain biofouling by phosphate limitation. This paper focuses on electrostatic interactions during tight UF filtration. Despite the larger pore size, the 3 kDa ceramic membrane exhibited greater phosphate rejection than the 1 kDa membrane, because the 3 kDa membrane has a greater negative surface charge and thus greater electrostatic repulsion against phosphate. The increase of pH from 6 to 8.5 led to a substantial increase in phosphate rejection by both membranes due to increased electrostatic repulsion. At pH 8.5, the maximum phosphate rejections achieved by the 1 kDa and 3 kDa membrane were 75% and 86%, respectively. A Debye ratio (ratio of the Debye length to the pore radius) is introduced in order to evaluate double layer overlapping in tight UF membranes. Threshold Debye ratios were determined as 2 and 1 for the 1 kDa and 3 kDa membranes, respectively. A Debye ratio below the threshold Debye ratio leads to dramatically decreased phosphate rejection by tight UF membranes. The phosphate rejection by the tight UF, in combination with chemical phosphate removal by coagulation, might accomplish phosphate-limited conditions for biological growth and thus prevent biofouling in the RO systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Protonmotive force: development of electrostatic drivers for synthetic molecular motors.

PubMed

Crowley, James D; Steele, Ian M; Bosnich, Brice

2006-12-04

Ferrocene has been investigated as a platform for developing protonmotive electrostatic drivers for molecular motors. When two 3-pyridine groups are substituted to the (rapidly rotating) cyclopentadienyl (Cp) rings of ferrocene, one on each Cp, it is shown that the (Cp) eclipsed, pi-stacked rotameric conformation is preferred both in solution and in the solid state. Upon quaternization of both of the pyridines substituents, either by protonation or by alkylation, it is shown that the preferred rotameric conformation is one where the pyridinium groups are rotated away from the fully pi-stacked conformation. Electrostatic calculations indicate that the rotation is caused by the electrostatic repulsion between the charges. Consistently, when the pi-stacking energy is increased pi-stacked population increases, and conversely when the electrostatic repulsion is increased pi-stacked population is decreased. This work serves to provide an approximate estimate of the amount of torque that the electrostatically driven ferrocene platform can generate when incorporated into a molecular motor. The overall conclusion is that the electrostatic interaction energy between dicationic ferrocene dipyridyl systems is similar to the pi-stacking interaction energy and, consequently, at least tricationic systems are required to fully uncouple the pi-stacked pyridine substituents.

Material Science Smart Coatings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubinstein, A. I.; Sabirianov, R. F.; Namavar, Fereydoon

2014-07-01

The contribution of electrostatic interactions to the free energy of binding between model protein and a ceramic implant surface in the aqueous solvent, considered in the framework of the nonlocal electrostatic model, is calculated as a function of the implant low-frequency dielectric constant. We show that the existence of a dynamically ordered (low-dielectric) interfacial solvent layer at the protein-solvent and ceramic-solvent interface markedly increases charging energy of the protein and ceramic implant, and consequently makes the electrostatic contribution to the protein-ceramic binding energy more favorable (attractive). Our analysis shows that the corresponding electrostatic energy between protein and oxide ceramics dependsmore » nonmonotonically on the dielectric constant of ceramic, ε C. Obtained results indicate that protein can attract electrostatically to the surface if ceramic material has a moderate ε C below or about 35 (in particularly ZrO 2 or Ta 2O 5). This is in contrast to classical (local) consideration of the solvent, which demonstrates an unfavorable electrostatic interaction of protein with typical metal oxide ceramic materials (ε C>10). Thus, a solid implant coated by combining oxide ceramic with a reduced dielectric constant can be beneficial to strengthen the electrostatic binding of the protein-implant complex.« less

Bistability in Doped Organic Thin Film Transistors (Preprint)

DTIC Science & Technology

2007-03-01

small molecules (e.g. pentacene ). As such, they do not necessarily compete with these more typical organic transistors, but rather have pertinence...involves dipping a substrate between two dilute polyelectrolyte solutions of opposite charge to build up a thin film via the electrostatic interactions...recovery is due to trapped O2(g) remaining in the film, which causes the reverse of reaction (1) to occur and the concomitant increase in the level of

A Printing-Centric Approach to the Electrostatic Modification of Polymer/Clay Composites for use in 3D Direct-Ink Writing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rauzan, Brittany; Lehman, Sean; McCracken, Josell

Polymer/clay composite inks are exceptionally useful materials for fabrication processes based on 3D direct-ink writing, however, there remains an insufficient understanding of how their physiochemical dynamics impact printability. Using a model system, N-isopropylacrylamide/Laponite, the electrostatic interactions between Laponite platelets are modified to tune critical rheological properties in order to improve printability. Rheological measurements and X-ray scattering experiments are carried out to monitor the nano/micro-structural dynamics and complex physicochemical interactions of Laponite as it impacts complex modulus in the linear region, flow behavior, thixotropy, and yield stress of the composite ink. Modification of the electrostatic interactions between platelets reduces the yieldmore » stress of the material, while maintaining a complex microstructure that allows for sufficient recovery times upon removal of stress to form stable, and thus printable, filaments. A printing-centric approach is established based on a fundamental understanding of electrostatic inter-particle interactions, harnessing the innate microstructure of Laponite in 3D direct-ink writing of composites.« less

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes.

PubMed

Lee, Hochan; Lee, Gayeon; Jeon, Jonggu; Cho, Minhaeng

2012-01-12

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.

Self organization of exotic oil-in-oil phases driven by tunable electrohydrodynamics

PubMed Central

Varshney, Atul; Ghosh, Shankar; Bhattacharya, S.; Yethiraj, Anand

2012-01-01

Self organization of large-scale structures in nature - either coherent structures like crystals, or incoherent dynamic structures like clouds - is governed by long-range interactions. In many problems, hydrodynamics and electrostatics are the source of such long-range interactions. The tuning of electrostatic interactions has helped to elucidate when coherent crystalline structures or incoherent amorphous structures form in colloidal systems. However, there is little understanding of self organization in situations where both electrostatic and hydrodynamic interactions are present. We present a minimal two-component oil-in-oil model system where we can control the strength and lengthscale of the electrohydrodynamic interactions by tuning the amplitude and frequency of the imposed electric field. As a function of the hydrodynamic lengthscale, we observe a rich phenomenology of exotic structure and dynamics, from incoherent cloud-like structures and chaotic droplet dynamics, to polyhedral droplet phases, to coherent droplet arrays. PMID:23071902

Quantifying protein microstructure and electrostatic effects on the change in Gibbs free energy of binding in immobilized metal affinity chromatography.

PubMed

Pathange, Lakshmi P; Bevan, David R; Zhang, Chenming

2008-03-01

Electrostatic forces play a major role in maintaining both structural and functional properties of proteins. A major component of protein electrostatics is the interactions between the charged or titratable amino acid residues (e.g., Glu, Lys, and His), whose pK(a) (or the change of the pK(a)) value could be used to study protein electrostatics. Here, we report the study of electrostatic forces through experiments using a well-controlled model protein (T4 lysozyme) and its variants. We generated 10 T4 lysozyme variants, in which the electrostatic environment of the histidine residue was perturbed by altering charged and neutral amino acid residues at various distances from the histidine (probe) residue. The electrostatic perturbations were theoretically quantified by calculating the change in free energy (DeltaDeltaG(E)) using Coulomb's law. On the other hand, immobilized metal affinity chromatography (IMAC) was used to quantify these perturbations in terms of protein binding strength or change in free energy of binding (DeltaDeltaG(B)), which varies from -0.53 to 0.99 kcal/mol. For most of the variants, there is a good correlation (R(2) = 0.97) between the theoretical DeltaDeltaG(E) and experimental DeltaDeltaG(B) values. However, there are three deviant variants, whose histidine residue was found to be involved in site-specific interactions (e.g., ion pair and steric hindrance), which were further investigated by molecular dynamics simulation. This report demonstrates that the electrostatic (DeltaDeltaG(Elec)) and microstructural effects (DeltaDeltaG(Micro)) in a protein can be quantified by IMAC through surface histidine mediated protein-metal ion interaction and that the unique microstructure around a histidine residue can be identified by identifying the abnormal binding behaviors during IMAC.

Structural study of surfactant-dependent interaction with protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in; Kohlbrecher, Joachim

2015-06-24

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Structural study of surfactant-dependent interaction with protein

NASA Astrophysics Data System (ADS)

Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

2015-06-01

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Helping Lower Secondary Students Develop Conceptual Understanding of Electrostatic Forces

ERIC Educational Resources Information Center

Moynihan, Richard; van Kampen, Paul; Finlayson, Odilla; McLoughlin, Eilish

2016-01-01

This article describes the development of a lesson sequence that supports secondary-level students to construct an explanatory model for electrostatic attraction using a guided enquiry method. The students examine electrostatic interactions at a macro level and explain the phenomena at the atomic level. Pre-tests, post-tests, homework assignments…

Phenylboronate chromatography selectively separates glycoproteins through the manipulation of electrostatic, charge transfer, and cis-diol interactions.

PubMed

Carvalho, Rimenys J; Woo, James; Aires-Barros, M Raquel; Cramer, Steven M; Azevedo, Ana M

2014-10-01

Phenylboronate chromatography (PBC) has been applied for several years, however details regarding the mechanisms of interactions between the ligand and biomolecules are still scarce. The goal of this work is to investigate the various chemical interactions between proteins and their ligands, using a protein library containing both glycosylated and nonglycosylated proteins. Differences in the adsorption of these proteins over a pH range from 4 to 9 were related to two main properties: charge and presence of glycans. Acidic or neutral proteins were strongly adsorbed below pH 8 although the uncharged trigonal form of phenylboronate (PB) is less susceptible to forming electrostatic and cis-diol interactions with proteins. The glycosylated proteins were only adsorbed above pH 8 when the electrostatic repulsion between the boronate anion and the protein surface was mitigated (at 200 mM NaCl). All basic proteins were highly adsorbed above pH 8 with PB also acting as a cation-exchanger with binding occurring through electrostatic interactions. Batch adsorption performed at acidic conditions in the presence of Lewis base showed that charge-transfer interactions are critical for protein retention. This study demonstrates the multimodal interaction of PBC, which can be a selective tool for separation of different classes of proteins. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach.

PubMed

Rubinstein, Alexander; Sherman, Simon

The dielectric properties of the polar solvent on the protein-solvent interface at small intercharge distances are still poorly explored. To deconvolute this problem and to evaluate the pair-wise electrostatic interaction (PEI) energies of the point charges located at the protein-solvent interface we used a nonlocal (NL) electrostatic approach along with a static NL dielectric response function of water. The influence of the aqueous solvent microstructure (determined by a strong nonelectrostatic correlation effect between water dipoles within the orientational Debye polarization mode) on electrostatic interactions at the interface was studied in our work. It was shown that the PEI energies can be significantly higher than the energies evaluated by the classical (local) consideration, treating water molecules as belonging to the bulk solvent with a high dielectric constant. Our analysis points to the existence of a rather extended, effective low-dielectric interfacial water shell on the protein surface. The main dielectric properties of this shell (effective thickness together with distance- and orientation-dependent dielectric permittivity function) were evaluated. The dramatic role of this shell was demonstrated when estimating the protein association rate constants.

Optimal charges in lead progression: a structure-based neuraminidase case study.

PubMed

Armstrong, Kathryn A; Tidor, Bruce; Cheng, Alan C

2006-04-20

Collective experience in structure-based lead progression has found electrostatic interactions to be more difficult to optimize than shape-based ones. A major reason for this is that the net electrostatic contribution observed includes a significant nonintuitive desolvation component in addition to the more intuitive intermolecular interaction component. To investigate whether knowledge of the ligand optimal charge distribution can facilitate more intuitive design of electrostatic interactions, we took a series of small-molecule influenza neuraminidase inhibitors with known protein cocrystal structures and calculated the difference between the optimal and actual charge distributions. This difference from the electrostatic optimum correlates with the calculated electrostatic contribution to binding (r(2) = 0.94) despite small changes in binding modes caused by chemical substitutions, suggesting that the optimal charge distribution is a useful design goal. Furthermore, detailed suggestions for chemical modification generated by this approach are in many cases consistent with observed improvements in binding affinity, and the method appears to be useful despite discrete chemical constraints. Taken together, these results suggest that charge optimization is useful in facilitating generation of compound ideas in lead optimization. Our results also provide insight into design of neuraminidase inhibitors.

Electrostatic interaction between stereocilia: II. Influence on the mechanical properties of the hair bundle.

PubMed

Dolgobrodov, S G; Lukashkin, A N; Russell, I J

2000-12-01

This paper is based on our model [Dolgobrodov et al., 2000. Hear. Res., submitted for publication] in which we examine the significance of the polyanionic surface layers of stereocilia for electrostatic interaction between them. We analyse how electrostatic forces modify the mechanical properties of the sensory hair bundle. Different charge distribution profiles within the glycocalyx are considered. When modelling a typical experiment on bundle stiffness measurements, applying an external force to the tallest row of stereocilia shows that the asymptotic stiffness of the hair bundle for negative displacements is always larger than the asymptotic stiffness for positive displacements. This increase in stiffness is monotonic for even charge distribution and shows local minima when the negative charge is concentrated in a thinner layer within the cell coat. The minima can also originate from the co-operative effect of electrostatic repulsion and inter-ciliary links with non-linear mechanical properties. Existing experimental observations are compared with the predictions of the model. We conclude that 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, which have been recorded from the auditory periphery.

PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6

NASA Astrophysics Data System (ADS)

Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir

2015-01-01

Among critical aspects of voltage-gated potassium (Kv) channels' functioning is the effective communication between their two composing domains, the voltage sensor (VSD) and the pore. This communication, called coupling, might be transmitted directly through interactions between these domains and, as recently proposed, indirectly through interactions with phosphatidylinositol-4,5-bisphosphate (PIP2), a minor lipid of the inner plasma membrane leaflet. Here, we show how the two components of coupling, mediated by protein-protein or protein-lipid interactions, both contribute in the Kv7.1 functioning. On the one hand, using molecular dynamics simulations, we identified a Kv7.1 PIP2 binding site that involves residues playing a key role in PIP2-dependent coupling. On the other hand, combined theoretical and experimental approaches have shown that the direct interaction between the segments of the VSD (S4-S5) and the pore (S6) is weakened by electrostatic repulsion. Finally, we conclude that due to weakened protein-protein interactions, the PIP2-dependent coupling is especially prominent in Kv7.1.

PHEPS: web-based pH-dependent Protein Electrostatics Server

PubMed Central

Kantardjiev, Alexander A.; Atanasov, Boris P.

2006-01-01

PHEPS (pH-dependent Protein Electrostatics Server) is a web service for fast prediction and experiment planning support, as well as for correlation and analysis of experimentally obtained results, reflecting charge-dependent phenomena in globular proteins. Its implementation is based on long-term experience (PHEI package) and the need to explain measured physicochemical characteristics at the level of protein atomic structure. The approach is semi-empirical and based on a mean field scheme for description and evaluation of global and local pH-dependent electrostatic properties: protein proton binding; ionic sites proton population; free energy electrostatic term; ionic groups proton affinities (pKa,i) and their Coulomb interaction with whole charge multipole; electrostatic potential of whole molecule at fixed pH and pH-dependent local electrostatic potentials at user-defined set of points. The speed of calculation is based on fast determination of distance-dependent pair charge-charge interactions as empirical three exponential function that covers charge–charge, charge–dipole and dipole–dipole contributions. After atomic coordinates input, all standard parameters are used as defaults to facilitate non-experienced users. Special attention was given to interactive addition of non-polypeptide charges, extra ionizable groups with intrinsic pKas or fixed ions. The output information is given as plain-text, readable by ‘RasMol’, ‘Origin’ and the like. The PHEPS server is accessible at . PMID:16845042

Long-range electrostatic screening in ionic liquids

PubMed Central

Gebbie, Matthew A.; Dobbs, Howard A.; Valtiner, Markus; Israelachvili, Jacob N.

2015-01-01

Electrolyte solutions with high concentrations of ions are prevalent in biological systems and energy storage technologies. Nevertheless, the high interaction free energy and long-range nature of electrostatic interactions makes the development of a general conceptual picture of concentrated electrolytes a significant challenge. In this work, we study ionic liquids, single-component liquids composed solely of ions, in an attempt to provide a novel perspective on electrostatic screening in very high concentration (nonideal) electrolytes. We use temperature-dependent surface force measurements to demonstrate that the long-range, exponentially decaying diffuse double-layer forces observed across ionic liquids exhibit a pronounced temperature dependence: Increasing the temperature decreases the measured exponential (Debye) decay length, implying an increase in the thermally driven effective free-ion concentration in the bulk ionic liquids. We use our quantitative results to propose a general model of long-range electrostatic screening in ionic liquids, where thermally activated charge fluctuations, either free ions or correlated domains (quasiparticles), take on the role of ions in traditional dilute electrolyte solutions. This picture represents a crucial step toward resolving several inconsistencies surrounding electrostatic screening and charge transport in ionic liquids that have impeded progress within the interdisciplinary ionic liquids community. More broadly, our work provides a previously unidentified way of envisioning highly concentrated electrolytes, with implications for diverse areas of inquiry, ranging from designing electrochemical devices to rationalizing electrostatic interactions in biological systems. PMID:26040001

Effects of dielectric inhomogeneity on electrostatic twist rigidity of a helical biomolecule in Debye-Hückel regime

NASA Astrophysics Data System (ADS)

Rezaie-Dereshgi, Amir; Mohammad-Rafiee, Farshid

2018-04-01

The electrostatic interactions play a crucial role in biological systems. Here we consider an impermeable dielectric molecule in the solvent with a different dielectric constant. The electrostatic free energy in the problem is studied in the Debye-Hückel regime using the analytical Green function that is calculated in the paper. Using this electrostatic free energy, we study the electrostatic contribution to the twist rigidity of a double stranded helical molecule such as a DNA and an actin filament. The dependence of the electrostatic twist rigidity of the molecule to the dielectric inhomogeneity, structural parameters, and the salt concentration is studied. It is shown that, depending on the parameters, the electrostatic twist rigidity could be positive or negative.

Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers: the role of electrostatic and hydrophobic interactions.

PubMed

Xu, Qing-Hua; Gaylord, Brent S; Wang, Shu; Bazan, Guillermo C; Moses, Daniel; Heeger, Alan J

2004-08-10

We have investigated the energy transfer processes in DNA sequence detection by using cationic conjugated polymers and peptide nucleic acid (PNA) probes with ultrafast pump-dump-emission spectroscopy. Pump-dump-emission spectroscopy provides femtosecond temporal resolution and high sensitivity and avoids interference from the solvent response. The energy transfer from donor (the conjugated polymer) to acceptor (a fluorescent molecule attached to a PNA terminus) has been time resolved. The results indicate that both electrostatic and hydrophobic interactions contribute to the formation of cationic conjugated polymers/PNA-C/DNA complexes. The two interactions result in two different binding conformations. This picture is supported by the average donor-acceptor separations as estimated from time-resolved and steady-state measurements. Electrostatic interactions dominate at low concentrations and in mixed solvents.

Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers: The role of electrostatic and hydrophobic interactions

PubMed Central

Xu, Qing-Hua; Gaylord, Brent S.; Wang, Shu; Bazan, Guillermo C.; Moses, Daniel; Heeger, Alan J.

2004-01-01

We have investigated the energy transfer processes in DNA sequence detection by using cationic conjugated polymers and peptide nucleic acid (PNA) probes with ultrafast pump-dump-emission spectroscopy. Pump-dump-emission spectroscopy provides femtosecond temporal resolution and high sensitivity and avoids interference from the solvent response. The energy transfer from donor (the conjugated polymer) to acceptor (a fluorescent molecule attached to a PNA terminus) has been time resolved. The results indicate that both electrostatic and hydrophobic interactions contribute to the formation of cationic conjugated polymers/PNA-C/DNA complexes. The two interactions result in two different binding conformations. This picture is supported by the average donor–acceptor separations as estimated from time-resolved and steady-state measurements. Electrostatic interactions dominate at low concentrations and in mixed solvents. PMID:15282375

Electrocatalytic tuning of biosensing response through electrostatic or hydrophobic enzyme-graphene oxide interactions.

PubMed

Baptista-Pires, Luis; Pérez-López, Briza; Mayorga-Martinez, Carmen C; Morales-Narváez, Eden; Domingo, Neus; Esplandiu, Maria Jose; Alzina, Francesc; Sotomayor-Torres, Clivia M; Merkoçi, Arben

2014-11-15

The effect of graphene oxidative grades upon the conductivity and hydrophobicity and consequently the influence on an enzymatic biosensing response is presented. The electrochemical responses of reduced graphene oxide (rGO) have been compared with the responses obtained from the oxide form (oGO) and their performances have been accordingly discussed with various evidences obtained by optical techniques. We used tyrosinase enzyme as a proof of concept receptor with interest for phenolic compounds detection through its direct adsorption onto a screen-printed carbon electrode previously modified with oGO or rGO with a carbon-oxygen ratio of 1.07 or 1.53 respectively. Different levels of oGO directly affect the (bio)conjugation properties of the biosensor due to changes at enzyme/graphene oxide interface coming from the various electrostatic or hydrophobic interactions with biomolecules. The developed biosensor was capable of reaching a limit of detection of 0.01 nM catechol. This tuning capability of the biosensor response can be of interest for building several other biosensors, including immunosensors and DNA sensors for various applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Electrostatic Self-Assembly Enabling Integrated Bulk and Interfacial Sodium Storage in 3D Titania-Graphene Hybrid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Gui-Liang; Xiao, Lisong; Sheng, Tian

Room temperature sodium-ion batteries have attracted increased attention for energy storage due to the natural abundance of sodium. However, it remains a huge challenge to develop versatile electrode materials with favorable properties, which requires smart structure design and good mechanistic understanding. Herein, we reported a general and scalable approach to synthesize 3D titania-graphene hybrid via electrostatic-interaction-induced self-assembly. Synchrotron X-ray probe, transmission electron microscopy and computational modeling revealed that the strong interaction between Titania and graphene through comparably strong van-der-Waals forces not only facilitates bulk Na+ intercalation but also enhances the interfacial sodium storage. As a result, the titania-graphene hybrid exhibitsmore » exceptional long-term cycle stability up to 5000 cycles, and ultrahigh rate capability up to 20 C for sodium storage. Furthermore, density function theory calculation indicated that the interfacial Li+, K+, Mg2+ and Al3+ storage can be enhanced as well. The proposed general strategy opens up new avenues to create versatile materials for advanced battery systems.« less

Full-field drift Hamiltonian particle orbits in 3D geometry

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Graves, J. P.; Brunner, S.; Isaev, M. Yu

2011-02-01

A Hamiltonian/Lagrangian theory to describe guiding centre orbit drift motion which is canonical in the Boozer coordinate frame has been extended to include full electromagnetic perturbed fields in anisotropic pressure 3D equilibria with nested magnetic flux surfaces. A redefinition of the guiding centre velocity to eliminate the motion due to finite equilibrium radial magnetic fields and the choice of a gauge condition that sets the radial component of the electromagnetic vector potential to zero are invoked to guarantee that the Boozer angular coordinates retain the canonical structure. The canonical momenta are identified and the guiding centre particle radial drift motion and parallel gyroradius evolution are derived. The particle coordinate position is linearly modified by wave-particle interactions. All the nonlinear wave-wave interactions appear explicitly only in the evolution of the parallel gyroradius. The radial variation of the electrostatic potential is related to the binormal component of the displacement vector for MHD-type perturbations. The electromagnetic vector potential projections can then be determined from the electrostatic potential and the radial component of the MHD displacement vector.

Electrostatic Self-Assembly Enabling Integrated Bulk and Interfacial Sodium Storage in 3D Titania-Graphene Hybrid.

PubMed

Xu, Gui-Liang; Xiao, Lisong; Sheng, Tian; Liu, Jianzhao; Hu, Yi-Xin; Ma, Tianyuan; Amine, Rachid; Xie, Yingying; Zhang, Xiaoyi; Liu, Yuzi; Ren, Yang; Sun, Cheng-Jun; Heald, Steve M; Kovacevic, Jasmina; Sehlleier, Yee Hwa; Schulz, Christof; Mattis, Wenjuan Liu; Sun, Shi-Gang; Wiggers, Hartmut; Chen, Zonghai; Amine, Khalil

2018-01-10

Room-temperature sodium-ion batteries have attracted increased attention for energy storage due to the natural abundance of sodium. However, it remains a huge challenge to develop versatile electrode materials with favorable properties, which requires smart structure design and good mechanistic understanding. Herein, we reported a general and scalable approach to synthesize three-dimensional (3D) titania-graphene hybrid via electrostatic-interaction-induced self-assembly. Synchrotron X-ray probe, transmission electron microscopy, and computational modeling revealed that the strong interaction between titania and graphene through comparably strong van der Waals forces not only facilitates bulk Na + intercalation but also enhances the interfacial sodium storage. As a result, the titania-graphene hybrid exhibits exceptional long-term cycle stability up to 5000 cycles, and ultrahigh rate capability up to 20 C for sodium storage. Furthermore, density function theory calculation indicated that the interfacial Li + , K + , Mg 2+, and Al 3+ storage can be enhanced as well. The proposed general strategy opens up new avenues to create versatile materials for advanced battery systems.

Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

2016-10-01

In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

Roles of Long-range Electrostatic Domain Interactions and K+ in Phosphoenzyme Transition of Ca2+-ATPase*

PubMed Central

Yamasaki, Kazuo; Daiho, Takashi; Danko, Stefania; Suzuki, Hiroshi

2013-01-01

Sarcoplasmic reticulum Ca2+-ATPase couples the motions and rearrangements of three cytoplasmic domains (A, P, and N) with Ca2+ transport. We explored the role of electrostatic force in the domain dynamics in a rate-limiting phosphoenzyme (EP) transition by a systematic approach combining electrostatic screening with salts, computer analysis of electric fields in crystal structures, and mutations. Low KCl concentration activated and increasing salt above 0.1 m inhibited the EP transition. A plot of the logarithm of the transition rate versus the square of the mean activity coefficient of the protein gave a linear relationship allowing division of the activation energy into an electrostatic component and a non-electrostatic component in which the screenable electrostatic forces are shielded by salt. Results show that the structural change in the transition is sterically restricted, but that strong electrostatic forces, when K+ is specifically bound at the P domain, come into play to accelerate the reaction. Electric field analysis revealed long-range electrostatic interactions between the N and P domains around their hinge. Mutations of the residues directly involved and other charged residues at the hinge disrupted in parallel the electric field and the structural transition. Favorable electrostatics evidently provides a low energy path for the critical N domain motion toward the P domain, overcoming steric restriction. The systematic approach employed here is, in general, a powerful tool for understanding the structural mechanisms of enzymes. PMID:23737524

Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces.

PubMed

Giacomelli, Carla E; Norde, Willem

2005-05-23

The conformational change of the 39-43 residues of the amyloid beta-peptide (Abeta) toward a beta-sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the self-aggregation of Abeta is related to the different pathways the peptide may take after cleavage from the amyloid precursor proteins at cellular membranes. This work is aiming at determining the conformation of the Abeta (1-40) adsorbed on hydrophobic Teflon and hydrophilic silica particles, as model sorbent surfaces mimicking the apolar transmembrane environment and the polar, charged membrane surface, respectively. The mechanism by which the Abeta interacts with solid surfaces strongly depends on the hydrophobic/hydrophilic character of the particles. Hydrophobic and electrostatic interactions contribute differently in each case, causing a completely different conformational change of the adsorbed molecules on the two surfaces. When hydrophobic interactions between the peptide and the sorbent prevail, the adsorbed Abeta (1-40) mainly adopts an alpha-helix conformation due to H-bonding in the apolar part of the peptide that is oriented towards the surface. On the other hand, when the peptide adsorbs by electrostatic interactions beta-sheet formation is promoted due to intermolecular association between the apolar parts of the adsorbed peptide. Irrespective of the characteristics of the solid sorbent, crowding the surface results in intermolecular association between adsorbed molecules leading to a strong aggregation tendency of the Abeta (1-40). [Diagram: see text] CD spectra of Abeta (1-40) at pH 7: A) in solution ([Abeta]=0.2 mg.ml(-1)) freshly prepared (line) and after overnight incubation (symbols);B) on Teflon (Gamma=0.5 mg.m(-2)).

Protein-membrane electrostatic interactions: Application of the Lekner summation technique

NASA Astrophysics Data System (ADS)

Juffer, André H.; Shepherd, Craig M.; Vogel, Hans J.

2001-01-01

A model has been developed to calculate the electrostatic interaction between biomolecules and lipid bilayers. The effect of ionic strength is included by means of explicit ions, while water is described as a background continuum. The bilayer is considered at the atomic level. The Lekner summation technique is employed to calculate the long-range electrostatic interactions. The new method is employed to estimate the electrostatic contribution to the free energy of binding of sandostatin, a cyclic eight-residue analogue of the peptide hormone somatostatin, to lipid bilayers with thermodynamic integration. Monte Carlo simulation techniques were employed to determine ion distributions and peptide orientations. Both neutral as well as negatively charged lipid bilayers were used. An error analysis to judge the quality of the computation is also presented. The applicability of the Lekner summation technique to combine it with computer simulation models that simulate the adsorption of peptides (and proteins) into the interfacial region of lipid bilayers is discussed.

Inductive and electrostatic acceleration in relativistic jet-plasma interactions.

PubMed

Ng, Johnny S T; Noble, Robert J

2006-03-24

We report on the observation of rapid particle acceleration in numerical simulations of relativistic jet-plasma interactions and discuss the underlying mechanisms. The dynamics of a charge-neutral, narrow, electron-positron jet propagating through an unmagnetized electron-ion plasma was investigated using a three-dimensional, electromagnetic, particle-in-cell computer code. The interaction excited magnetic filamentation as well as electrostatic plasma instabilities. In some cases, the longitudinal electric fields generated inductively and electrostatically reached the cold plasma-wave-breaking limit, and the longitudinal momentum of about half the positrons increased by 50% with a maximum gain exceeding a factor of 2 during the simulation period. Particle acceleration via these mechanisms occurred when the criteria for Weibel instability were satisfied.

Polarization Coupling in Ferroelectric Multilayers as a Function of Interface Charge Concentration

NASA Astrophysics Data System (ADS)

Okatan, Mahmut; Mantese, Joseph; Alpay, Pamir

2009-03-01

Intriguing properties of multilayered and graded ferroelectrics follow from the electrostatic and electromechanical interactions. The strength of the interlayer coupling depends on the concentration of interfacial defects with short-range local electrostatic fields. Defects may locally relax polarization differences and thus reduce the commensurate bound charge concentration at the interlayer interfaces. In this talk, we develop a theoretical analysis based on non-linear thermodynamics coupled with basic electrostatic relations to understand the role of charge compensation at the interlayer interfaces. The results show multilayered ferroelectrics with systematic variations in the composition may display a colossal dielectric response depending upon the interlayer electrostatic interactions. It is expected that other properties such as the pyroelectric and piezoelectric response will yield concomitant increases through the dielectric permittivity.

Electrostatic interactions between diffuse soft multi-layered (bio)particles: beyond Debye-Hückel approximation and Deryagin formulation.

PubMed

Duval, Jérôme F L; Merlin, Jenny; Narayana, Puranam A L

2011-01-21

We report a steady-state theory for the evaluation of electrostatic interactions between identical or dissimilar spherical soft multi-layered (bio)particles, e.g. microgels or microorganisms. These generally consist of a rigid core surrounded by concentric ion-permeable layers that may differ in thickness, soft material density, chemical composition and degree of dissociation for the ionogenic groups. The formalism allows the account of diffuse interphases where distributions of ionogenic groups from one layer to the other are position-dependent. The model is valid for any number of ion-permeable layers around the core of the interacting soft particles and covers all limiting situations in terms of nature of interacting particles, i.e. homo- and hetero-interactions between hard, soft or entirely porous colloids. The theory is based on a rigorous numerical solution of the non-linearized Poisson-Boltzmann equation including radial and angular distortions of the electric field distribution within and outside the interacting soft particles in approach. The Gibbs energy of electrostatic interaction is obtained from a general expression derived following the method by Verwey and Overbeek based on appropriate electric double layer charging mechanisms. Original analytical solutions are provided here for cases where interaction takes place between soft multi-layered particles whose size and charge density are in line with Deryagin treatment and Debye-Hückel approximation. These situations include interactions between hard and soft particles, hard plate and soft particle or soft plate and soft particle. The flexibility of the formalism is highlighted by the discussion of few situations which clearly illustrate that electrostatic interaction between multi-layered particles may be partly or predominantly governed by potential distribution within the most internal layers. A major consequence is that both amplitude and sign of Gibbs electrostatic interaction energy may dramatically change depending on the interplay between characteristic Debye length, thickness of ion-permeable layers and their respective protolytic features (e.g. location, magnitude and sign of charge density). This formalism extends a recent model by Ohshima which is strictly limited to interaction between soft mono-shell particles within Deryagin and Debye-Hückel approximations under conditions where ionizable sites are completely dissociated.

BSA modification to reduce CTAB induced nonspecificity and cytotoxicity of aptamer-conjugated gold nanorods

NASA Astrophysics Data System (ADS)

Yasun, Emir; Li, Chunmei; Barut, Inci; Janvier, Denisse; Qiu, Liping; Cui, Cheng; Tan, Weihong

2015-05-01

Aptamer-conjugated gold nanorods (AuNRs) are excellent candidates for targeted hyperthermia therapy of cancer cells. However, in high concentrations of AuNRs, aptamer conjugation alone fails to result in highly cell-specific AuNRs due to the presence of positively charged cetyltrimethylammonium bromide (CTAB) as a templating surfactant. Besides causing nonspecific electrostatic interactions with the cell surfaces, CTAB can also be cytotoxic, leading to uncontrolled cell death. To avoid the nonspecific interactions and cytotoxicity triggered by CTAB, we report the further biologically inspired modification of aptamer-conjugated AuNRs with bovine serum albumin (BSA) protein. Following this modification, interaction between CTAB and the cell surface was efficiently blocked, thereby dramatically reducing the side effects of CTAB. This approach may provide a general and simple method to avoid one of the most serious issues in biomedical applications of nanomaterials: nonspecific binding of the nanomaterials with biological cells.Aptamer-conjugated gold nanorods (AuNRs) are excellent candidates for targeted hyperthermia therapy of cancer cells. However, in high concentrations of AuNRs, aptamer conjugation alone fails to result in highly cell-specific AuNRs due to the presence of positively charged cetyltrimethylammonium bromide (CTAB) as a templating surfactant. Besides causing nonspecific electrostatic interactions with the cell surfaces, CTAB can also be cytotoxic, leading to uncontrolled cell death. To avoid the nonspecific interactions and cytotoxicity triggered by CTAB, we report the further biologically inspired modification of aptamer-conjugated AuNRs with bovine serum albumin (BSA) protein. Following this modification, interaction between CTAB and the cell surface was efficiently blocked, thereby dramatically reducing the side effects of CTAB. This approach may provide a general and simple method to avoid one of the most serious issues in biomedical applications of nanomaterials: nonspecific binding of the nanomaterials with biological cells. Electronic supplementary information (ESI) available: Fig. S-1 to S-6 are included. See DOI: 10.1039/c5nr01704a

No need to be HAMLET or BAMLET to interact with histones: binding of monomeric alpha-lactalbumin to histones and basic poly-amino acids.

PubMed

Permyakov, Serge E; Pershikova, Irina V; Khokhlova, Tatyana I; Uversky, Vladimir N; Permyakov, Eugene A

2004-05-18

The ability of a specific complex of human alpha-lactalbumin with oleic acid (HAMLET) to induce cell death with selectivity for tumor and undifferentiated cells was shown recently to be mediated by interaction of HAMLET with histone proteins irreversibly disrupting chromatin structure [Duringer, C., et al. (2003) J. Biol. Chem. 278, 42131-42135]. Here we show that monomeric alpha-lactalbumin (alpha-LA) in the absence of fatty acids is also able to bind efficiently to the primary target of HAMLET, histone HIII, regardless of Ca(2+) content. Thus, the modification of alpha-LA by oleic acid is not required for binding to histones. We suggest that interaction of negatively charged alpha-LA with the basic histone stabilizes apo-alpha-LA and destabilizes the Ca(2+)-bound protein due to compensation for excess negative charge of alpha-LA's Ca(2+)-binding loop by positively charged residues of the histone. Spectrofluorimetric curves of titration of alpha-LA by histone H3 were well approximated by a scheme of cooperative binding of four alpha-LA molecules per molecule of histone, with an equilibrium dissociation constant of 1.0 microM. Such a stoichiometry of binding implies that the binding process is not site-specific with respect to histone and likely is driven by just electrostatic interactions. Co-incubation of positively charged poly-amino acids (poly-Lys and poly-Arg) with alpha-LA resulted in effects which were similar to those caused by histone HIII, confirming the electrostatic nature of the alpha-LA-histone interaction. In all cases that were studied, the binding was accompanied by aggregation. The data indicate that alpha-lactalbumin can be used as a basis for the design of antitumor agents, acting through disorganization of chromatin structure due to interaction between alpha-LA and histone proteins.

Magnetospheric electrons

NASA Technical Reports Server (NTRS)

Coroniti, F. V.; Thorne, R. M.

1972-01-01

Coupling of source, transport, and sink processes produces a fairly accurate model for the macroscopic structure and dynamics of magnetospheric electrons. Auroral electrons are controlled by convective transport from a plasma sheet source coupled with a precipitation loss due to whistler and electrostatic plasma turbulence. Outer and inner zone electrons are governed by radial diffusion transport from convection and acceleration sources external to the plasmapause and by parasitic precipitation losses arising from cyclotron and Landau interactions with whistler and ion cyclotron turbulence.

Upper-hybrid wave-driven Alfvenic turbulence in magnetized dusty plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Misra, A. P.; Banerjee, S.

The nonlinear dynamics of coupled electrostatic upper-hybrid (UH) and Alfven waves (AWs) is revisited in a magnetized electron-ion plasma with charged dust impurities. A pair of nonlinear equations that describe the interaction of UH wave envelopes (including the relativistic electron mass increase) and the density as well as the compressional magnetic field perturbations associated with the AWs are solved numerically to show that many coherent solitary patterns can be excited and saturated due to modulational instability of unstable UH waves. The evolution of these solitary patterns is also shown to appear in the states of spatiotemporal coherence, temporal as wellmore » as spatiotemporal chaos, due to collision and fusion among the patterns in stochastic motion. Furthermore, these spatiotemporal features are demonstrated by the analysis of wavelet power spectra. It is found that a redistribution of wave energy takes place to higher harmonic modes with small wavelengths, which, in turn, results in the onset of Alfvenic turbulence in dusty magnetoplasmas. Such a scenario can occur in the vicinity of Saturn's magnetosphere as many electrostatic solitary structures have been observed there by the Cassini spacecraft.« less

Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, A.; Sabirianov, R. F.; Mei, W. N.; Namavar, F.; Khoynezhad, A.

2010-08-01

Using a nonlocal electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an ordered interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach.

PubMed

Rubinstein, A; Sabirianov, R F; Mei, W N; Namavar, F; Khoynezhad, A

2010-08-01

Using a nonlocal electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an ordered interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

Optimizing pH response of affinity between protein G and IgG Fc: how electrostatic modulations affect protein-protein interactions.

PubMed

Watanabe, Hideki; Matsumaru, Hiroyuki; Ooishi, Ayako; Feng, Yanwen; Odahara, Takayuki; Suto, Kyoko; Honda, Shinya

2009-05-01

Protein-protein interaction in response to environmental conditions enables sophisticated biological and biotechnological processes. Aiming toward the rational design of a pH-sensitive protein-protein interaction, we engineered pH-sensitive mutants of streptococcal protein G B1, a binder to the IgG constant region. We systematically introduced histidine residues into the binding interface to cause electrostatic repulsion on the basis of a rigid body model. Exquisite pH sensitivity of this interaction was confirmed by surface plasmon resonance and affinity chromatography employing a clinically used human IgG. The pH-sensitive mechanism of the interaction was analyzed and evaluated from kinetic, thermodynamic, and structural viewpoints. Histidine-mediated electrostatic repulsion resulted in significant loss of exothermic heat of the binding that decreased the affinity only at acidic conditions, thereby improving the pH sensitivity. The reduced binding energy was partly recovered by "enthalpy-entropy compensation." Crystal structures of the designed mutants confirmed the validity of the rigid body model on which the effective electrostatic repulsion was based. Moreover, our data suggested that the entropy gain involved exclusion of water molecules solvated in a space formed by the introduced histidine and adjacent tryptophan residue. Our findings concerning the mechanism of histidine-introduced interactions will provide a guideline for the rational design of pH-sensitive protein-protein recognition.

Medium dependent dual turn on/turn off fluorescence sensing for Cu2 + ions using AMI/SDS assemblies

NASA Astrophysics Data System (ADS)

Gujar, Varsha B.; Ottoor, Divya

2017-02-01

Behavior of Amiloride (AMI) as a metal ion sensor in anionic surfactant assemblies of varying concentrations at different pH is depicted in this work. From a non-sensor fluorophore, AMI has been transformed in to a tunable fluorosensor for Cu2 + ions in various SDS concentrations. At premicellar concentration of SDS, ion-pair complex is expected to be formed between AMI and SDS due to electrostatic interactions between them. However at CMC concentrations of SDS, fluorescence intensity of AMI is greatly enhanced with red shift in emission, due to the incorporation of AMI molecule in the hydrophobic micellar interface. The behavior of metal sensing by AMI-SDS assemblies gives rise to several interesting observations. Micellation of SDS has been greatly enhanced by increasing copper ion concentrations, as these counter ions screens the charge on monomers of SDS which lead to the aggregation at premicellar concentrations only. Concentrations and pH dependent discrete trends of interactions between SDS-AMI and SDS-Cu2 + ions, have given tunable fluorescence responses (fluorescence turn on/turn off) of AMI for added Cu2 + ions. The electrostatic interaction between the metal cations and the anionic surfactants is the driving force for bringing the metal ions near to the vicinity of micelle where AMI resides. Thus, a comprehensive understanding of the mechanism related to the 'turn on-turn off' fluorescence response of AMI with respect to pH and SDS concentration for effective Cu2 + ion sensing is illustrated in this work.

Role of electrostatic interaction on surfactant induced protein unfolding

NASA Astrophysics Data System (ADS)

Sumit, Kumar, Sugam; Aswal, V. K.

2013-02-01

Small Angle Neutron Scattering has been used to examine the effect of electrostatic interaction on surfactant induced protein unfolding. Measurements are carried out from 1 wt% Bovine Serum Albumin (BSA) protein with 1 wt% Sodium Dodecyl Sulphate (SDS) surfactant at pH 7 in presence of varying concentration of NaCl. It is found that both the components (protein and surfactant micelle which are likely charged) exist individually without any interaction in absence of salt, whereas their interaction and protein unfolding is enhanced with the increase in salt concentration. The structure of protein-surfactant interaction is characterized by fractal bead-necklace model.

Protein nanoparticle electrostatic interaction: size dependent counterions induced conformational change of hen egg white lysozyme.

PubMed

Ghosh, Goutam; Panicker, Lata; Barick, K C

2014-06-01

In our earlier paper (Ghosh et al., 2013), we have shown that (i) the positively charged hen egg white lysozyme (HEWL), dispersed in water, binds electrostatically with the negatively functionalized iron oxide nanoparticles (IONPs), and (ii) the Na(+) counterions, associated with functionalized IONPs, diffuse into bound proteins and irreversibly unfold them. Having this information, we have extended our investigation and report here the effect of the size and the charge of alkaline metal counterions on the conformational modification of HEWL. In order to obtain a negative functional 'shell' on IONPs and the counterions of different size and charge we have functionalized IONPs with different derivatives of citrate, namely, tri-lithium citrate (TLC, Li3C6H5O7), tri-sodium citrate (TSC, Na3C6H5O7), tri-potassium citrate (TKC, K3C6H5O7) and tri-magnesium citrate (TMC, Mg3C12H10O14). The size of counterions varies as Mg(2+)

On the different roles of anions and cations in the solvation of enzymes in ionic liquids.

PubMed

Klähn, Marco; Lim, Geraldine S; Seduraman, Abirami; Wu, Ping

2011-01-28

The solvation of the enzyme Candida antarctica lipase B (CAL-B) was studied in eight different ionic liquids (ILs). The influence of enzyme-ion interactions on the solvation of CAL-B and the structure of the enzyme-IL interface are analyzed. CAL-B and ILs are described with molecular dynamics (MD) simulations in combination with an atomistic empirical force field. The considered cations are based on imidazolium or guanidinium that are paired with nitrate, tetrafluoroborate or hexafluorophosphate anions. The interactions of CAL-B with ILs are dominated by Coulomb interactions with anions, while the second largest contribution stems from van der Waals interactions with cations. The enzyme-ion interaction strength is determined by the ion size and the magnitude of the ion surface charge. The solvation of CAL-B in ILs is unfavorable compared to water because of large formation energies for the CAL-B solute cages in ILs. The internal energy in the IL and of CAL-B increases linearly with the enzyme-ion interaction strength. The average electrostatic potential on the surface of CAL-B is larger in ILs than in water, due to a weaker screening of charged enzyme residues. Ion densities increased moderately in the vicinity of charged residues and decreased close to non-polar residues. An aggregation of long alkyl chains close to non-polar regions and the active site entrance of CAL-B are observed in one IL that involved long non-polar decyl groups. In ILs that contain 1-butyl-3-methylimidazolium cations, the diffusion of one or two cations into the active site of CAL-B occurs during MD simulations. This suggests a possible obstruction of the active site in these ILs. Overall, the results indicate that small ions lead to a stronger electrostatic screening within the solvent and stronger interactions with the enzyme. Also a large ion surface charge, when more hydrophilic ions are used, increases enzyme-IL interactions. An increase of these interactions destabilizes the enzyme and impedes enzyme solvation due to an increase in solute cage formation energies.

Highly viscous antibody solutions are a consequence of network formation caused by domain-domain electrostatic complementarities: insights from coarse-grained simulations.

PubMed

Buck, Patrick M; Chaudhri, Anuj; Kumar, Sandeep; Singh, Satish K

2015-01-05

Therapeutic monoclonal antibody (mAb) candidates that form highly viscous solutions at concentrations above 100 mg/mL can lead to challenges in bioprocessing, formulation development, and subcutaneous drug delivery. Earlier studies of mAbs with concentration-dependent high viscosity have indicated that mAbs with negatively charged Fv regions have a dipole-like quality that increases the likelihood of reversible self-association. This suggests that weak electrostatic intermolecular interactions can form transient antibody networks that participate in resistance to solution deformation under shear stress. Here this hypothesis is explored by parametrizing a coarse-grained (CG) model of an antibody using the domain charges from four different mAbs that have had their concentration-dependent viscosity behaviors previously determined. Multicopy molecular dynamics simulations were performed for these four CG mAbs at several concentrations to understand the effect of surface charge on mass diffusivity, pairwise interactions, and electrostatic network formation. Diffusion coefficients computed from simulations were in qualitative agreement with experimentally determined viscosities for all four mAbs. Contact analysis revealed an overall greater number of pairwise interactions for the two mAbs in this study with high concentration viscosity issues. Further, using equilibrated solution trajectories, the two mAbs with high concentration viscosity issues quantitatively formed more features of an electrostatic network than the other mAbs. The change in the number of these network features as a function of concentration is related to the number of pairwise interactions formed by electrostatic complementarities between antibody domains. Thus, transient antibody network formation caused by domain-domain electrostatic complementarities is the most probable origin of high concentration viscosity for mAbs in this study.

Interaction of the BKCa channel gating ring with dendrotoxins

PubMed Central

Takacs, Zoltan; Imredy, John P; Bingham, Jon-Paul; Zhorov, Boris S; Moczydlowski, Edward G

2014-01-01

Two classes of small homologous basic proteins, mamba snake dendrotoxins (DTX) and bovine pancreatic trypsin inhibitor (BPTI), block the large conductance Ca2+-activated K+ channel (BKCa, KCa1.1) by production of discrete subconductance events when added to the intracellular side of the membrane. This toxin-channel interaction is unlikely to be pharmacologically relevant to the action of mamba venom, but as a fortuitous ligand-protein interaction, it has certain biophysical implications for the mechanism of BKCa channel gating. In this work we examined the subconductance behavior of 9 natural dendrotoxin homologs and 6 charge neutralization mutants of δ-dendrotoxin in the context of current structural information on the intracellular gating ring domain of the BKCa channel. Calculation of an electrostatic surface map of the BKCa gating ring based on the Poisson-Boltzmann equation reveals a predominantly electronegative surface due to an abundance of solvent-accessible side chains of negatively charged amino acids. Available structure-activity information suggests that cationic DTX/BPTI molecules bind by electrostatic attraction to site(s) on the gating ring located in or near the cytoplasmic side portals where the inactivation ball peptide of the β2 subunit enters to block the channel. Such an interaction may decrease the apparent unitary conductance by altering the dynamic balance of open versus closed states of BKCa channel activation gating. PMID:25483585

Rational modification of protein stability by targeting surface sites leads to complicated results

PubMed Central

Xiao, Shifeng; Patsalo, Vadim; Shan, Bing; Bi, Yuan; Green, David F.; Raleigh, Daniel P.

2013-01-01

The rational modification of protein stability is an important goal of protein design. Protein surface electrostatic interactions are not evolutionarily optimized for stability and are an attractive target for the rational redesign of proteins. We show that surface charge mutants can exert stabilizing effects in distinct and unanticipated ways, including ones that are not predicted by existing methods, even when only solvent-exposed sites are targeted. Individual mutation of three solvent-exposed lysines in the villin headpiece subdomain significantly stabilizes the protein, but the mechanism of stabilization is very different in each case. One mutation destabilizes native-state electrostatic interactions but has a larger destabilizing effect on the denatured state, a second removes the desolvation penalty paid by the charged residue, whereas the third introduces unanticipated native-state interactions but does not alter electrostatics. Our results show that even seemingly intuitive mutations can exert their effects through unforeseen and complex interactions. PMID:23798426

Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate.

PubMed

Plantinga, Matthew J; Korennykh, Alexei V; Piccirilli, Joseph A; Correll, Carl C

2008-08-26

Restrictocin, a member of the alpha-sarcin family of site-specific endoribonucleases, uses electrostatic interactions to bind to the ribosome and to RNA oligonucleotides, including the minimal specific substrate, the sarcin/ricin loop (SRL) of 23S-28S rRNA. Restrictocin binds to the SRL by forming a ground-state E:S complex that is stabilized predominantly by Coulomb interactions and depends on neither the sequence nor structure of the RNA, suggesting a nonspecific complex. The 22 cationic residues of restrictocin are dispersed throughout this protein surface, complicating a priori identification of a Coulomb interacting surface. Structural studies have identified an enzyme-substrate interface, which is expected to overlap with the electrostatic E:S interface. Here, we identified restrictocin residues that contribute to binding in the E:S complex by determining the salt dependence [partial differential log(k 2/ K 1/2)/ partial differential log[KCl

The role of electrostatics in protein-protein interactions of a monoclonal antibody.

PubMed

Roberts, D; Keeling, R; Tracka, M; van der Walle, C F; Uddin, S; Warwicker, J; Curtis, R

2014-07-07

Understanding how protein-protein interactions depend on the choice of buffer, salt, ionic strength, and pH is needed to have better control over protein solution behavior. Here, we have characterized the pH and ionic strength dependence of protein-protein interactions in terms of an interaction parameter kD obtained from dynamic light scattering and the osmotic second virial coefficient B22 measured by static light scattering. A simplified protein-protein interaction model based on a Baxter adhesive potential and an electric double layer force is used to separate out the contributions of longer-ranged electrostatic interactions from short-ranged attractive forces. The ionic strength dependence of protein-protein interactions for solutions at pH 6.5 and below can be accurately captured using a Deryaguin-Landau-Verwey-Overbeek (DLVO) potential to describe the double layer forces. In solutions at pH 9, attractive electrostatics occur over the ionic strength range of 5-275 mM. At intermediate pH values (7.25 to 8.5), there is a crossover effect characterized by a nonmonotonic ionic strength dependence of protein-protein interactions, which can be rationalized by the competing effects of long-ranged repulsive double layer forces at low ionic strength and a shorter ranged electrostatic attraction, which dominates above a critical ionic strength. The change of interactions from repulsive to attractive indicates a concomitant change in the angular dependence of protein-protein interaction from isotropic to anisotropic. In the second part of the paper, we show how the Baxter adhesive potential can be used to predict values of kD from fitting to B22 measurements, thus providing a molecular basis for the linear correlation between the two protein-protein interaction parameters.

Engineering Nucleotide Specificity of Succinyl-CoA Synthetase in Blastocystis: The Emerging Role of Gatekeeper Residues.

PubMed

Vashisht, Kapil; Verma, Sonia; Gupta, Sunita; Lynn, Andrew M; Dixit, Rajnikant; Mishra, Neelima; Valecha, Neena; Hamblin, Karleigh A; Maytum, Robin; Pandey, Kailash C; van der Giezen, Mark

2017-01-24

Charged, solvent-exposed residues at the entrance to the substrate binding site (gatekeeper residues) produce electrostatic dipole interactions with approaching substrates, and control their access by a novel mechanism called "electrostatic gatekeeper effect". This proof-of-concept study demonstrates that the nucleotide specificity can be engineered by altering the electrostatic properties of the gatekeeper residues outside the binding site. Using Blastocystis succinyl-CoA synthetase (SCS, EC 6.2.1.5), we demonstrated that the gatekeeper mutant (ED) resulted in ATP-specific SCS to show high GTP specificity. Moreover, nucleotide binding site mutant (LF) had no effect on GTP specificity and remained ATP-specific. However, via combination of the gatekeeper mutant with the nucleotide binding site mutant (ED+LF), a complete reversal of nucleotide specificity was obtained with GTP, but no detectable activity was obtained with ATP. This striking result of the combined mutant (ED+LF) was due to two changes; negatively charged gatekeeper residues (ED) favored GTP access, and nucleotide binding site residues (LF) altered ATP binding, which was consistent with the hypothesis of the "electrostatic gatekeeper effect". These results were further supported by molecular modeling and simulation studies. Hence, it is imperative to extend the strategy of the gatekeeper effect in a different range of crucial enzymes (synthetases, kinases, and transferases) to engineer substrate specificity for various industrial applications and substrate-based drug design.

A repertoire of pyridinium-phenyl-methyl cross-talk through a cascade of intramolecular electrostatic interactions.

PubMed

Acharya, P; Plashkevych, O; Morita, C; Yamada, S; Chattopadhyaya, J

2003-02-21

Direct intramolecular cation-pi interaction between phenyl and pyridinium moieties in 1a(+) has been experimentally evidenced through pH-dependent (1)H NMR titration. The basicity of the pyridinyl group (pK(a) 2.9) in 1a can be measured both from the pH-dependent chemical shifts of the pyridinyl protons as well as from the protons of the neighboring phenyl and methyl groups as a result of electrostatic interaction between the phenyl and the pyridinium ion in 1a(+) at the ground state. The net result of this nearest neighbor electrostatic interaction is that the pyridinium moiety in 1a becomes more basic (pK(a) 2.92) compared to that in the standard 2a (pK(a) 2.56) as a consequence of edge-to-face cation (pyridinium)-pi (phenyl) interaction, giving a free energy of stabilization (DeltaDeltaG(o)pKa) of -2.1 kJ mol(-1). The fact that the pH-dependent downfield shifts of the phenyl and methyl protons give the pK(a) of the pyridine moiety of 1a also suggests that the nearest neighbor cation (pyridinium)-pi (phenyl) interaction also steers the CH (methyl)-pi (phenyl) interaction in tandem. This means that the whole pyridine-phenyl-methyl system in 1a(+) is electronically coupled at the ground state, cross-modulating the physicochemical property of the next neighbor by using the electrostatics as the engine, and the origin of this electrostatics is a far away point in the molecule-the pyridinyl-nitrogen. The relative chemical shift changes and the pK(a) differences show that the cation (pyridinium)-pi (phenyl) interaction is indeed more stable (DeltaDeltaG(o)pKa = -2.1 kJ mol(-1)) than that of the CH (methyl)-pi (phenyl) interaction (DeltaDeltaG(o)pKa = -0.8 kJ mol(-1)). Since the pK(a) of the pyridine moiety in 1a is also obtained through the pH-dependent shifts of both phenyl and methyl protons, it suggests that the net electrostatic mediated charge transfer from the phenyl to the pyridinium and its effect on the CH (methyl)-pi (phenyl) interaction corresponds to DeltaG(o)pKa of the pyridinium ion (approximately 17.5 kJ mol(-1)), which means that the aromatic characters of the phenyl and the pyridinium rings in 1a(+) have been cross-modulated owing to the edge-to-face interaction proportional to this DeltaG(o)pKa change.

pH-dependence of single-protein adsorption and diffusion at a liquid chromatographic interface.

PubMed

Kisley, Lydia; Poongavanam, Mohan-Vivekanandan; Kourentzi, Katerina; Willson, Richard C; Landes, Christy F

2016-02-01

pH is a common mobile phase variable used to control protein separations due to the tunable nature of amino acid and adsorbent charge. Like other column variables such as column density and ligand loading density, pH is usually optimized empirically. Single-molecule spectroscopy extracts molecular-scale data to provide a framework for mechanistic optimization of pH. The adsorption and diffusion of a model globular protein, α-lactalbumin, was studied by single-molecule microscopy at a silica-aqueous interface analogous to aqueous normal phase and hydrophilic interaction chromatography and capillary electrophoresis interfaces at varied pH. Electrostatic repulsion resulting in free diffusion was observed at pH above the isoelectric point of the protein. In contrast, at low pH strong adsorption and surface diffusion with either no (D ∼ 0.01 μm(2) /s) or translational (D ∼ 0.3 μm(2) /s) motion was observed where the protein likely interacted with the surface through electrostatic, hydrophobic, and hydrogen bonding forces. The fraction of proteins immobilized could be increased by lowering the pH. These results show that retention of proteins at the silica interface cannot be viewed solely as an adsorption/desorption process and that the type of surface diffusion, which ultimately leads to ensemble chromatographic separations, can be controlled by tuning long-range electrostatic and short-range hydrophobic and hydrogen bonding forces with pH. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two-terminal conductance fluctuations in the integer quantum Hall regime

NASA Astrophysics Data System (ADS)

Ho, Chang-Ming

1999-09-01

Motivated by recent experiments on the conductance fluctuations in mesoscopic integer quantum Hall systems, we consider a model in which the Coulomb interactions are incorporated into the picture of edge-state transport through a single saddle point. The occupancies of classical localized states in the two-dimensional electron system change due to the interactions between electrons when the gate voltage on top of the device is varied. The electrostatic potential between the localized states and the saddle point causes fluctuations of the saddle-point potential and thus fluctuations of the transmission probability of edge states. This simple model is studied numerically and compared with the observation.

Assessment of environmental effects on Space Station Freedom Electrical Power System

NASA Technical Reports Server (NTRS)

Lu, Cheng-Yi; Nahra, Henry K.

1991-01-01

Analyses of EPS (electrical power system) interactions with the LEO (low earth orbit) environment are described. The results of these analyses will support EPS design so as to be compatible with the natural and induced environments and to meet power, lifetime, and performance requirements. The environmental impacts to the Space Station Freedom EPS include aerodynamic drag, atomic oxygen erosion, ultraviolet degradation, VXB effect, ionizing radiation dose and single event effects, electromagnetic interference, electrostatic discharge, plasma interactions (ion sputtering, arcing, and leakage current), meteoroid and orbital debris threats, thermal cycling effects, induced current and voltage potential differences in the SSF due to induced electric field, and contamination degradation.

Comparative theoretical study of the binding of luciferyl-adenylate and dehydroluciferyl-adenylate to firefly luciferase

NASA Astrophysics Data System (ADS)

Pinto da Silva, Luís; Vieira, João; Esteves da Silva, Joaquim C. G.

2012-08-01

This is the first report of a study employing a computational approach to study the binding of (D/L)-luciferyl-adenlyates and dehydroluciferyl-adenylate to firefly luciferase. A semi-empirical/molecular mechanics methodology was used to study the interaction between these ligands and active site molecules. All adenylates are complexed with the enzyme, mostly due to electrostatic interactions with cationic residues. Dehydroluciferyl-adenylate is expected to be a competitive inhibitor of luciferyl-adenylate, as their binding mechanism and affinity to luciferase are very similar. Both luciferyl-adenylates adopt the L-orientation in the active site of luciferase.

Effects of salinity and organic matter on the partitioning of perfluoroalkyl acid (PFAs) to clay particles.

PubMed

Jeon, Junho; Kannan, Kurunthachalam; Lim, Byung J; An, Kwang Guk; Kim, Sang Don

2011-06-01

The influence of salinity and organic matter on the distribution coefficient (K(d)) for perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) in a brackish water-clay system was studied. The distribution coefficients (K(d)) for PFAs onto inorganic clay surfaces increased with salinity, providing evidence for electrostatic interaction for the sorption of PFAs, whereas the relationship between K(d) and organic carbon content (f(oc)) suggested that hydrophobic interaction is the primary driving force for the sorption of PFAs onto organic matter. The organic carbon normalized adsorption coefficient (K(oc)) of PFAs can be slightly overestimated due to the electrostatic interaction within uncoated inorganic surfaces. In addition, the dissolved organic matter released from coated clay particles seemed to solvate PFA molecules in solution, which contributed to a decrease in K(d). A positive relationship between K(d) and salinity was apparent, but an empirical relationship for the 'salting-out' effect was not evident. The K(d) values of PFAs are relatively small compared with those reported for persistent organic pollutants. Thus, sorption may not be a significant route of mass transfer of PFAs from water columns in estuarine environments. However, enhancement of sorption of PFAs to particulate matter at high salinity values could evoke potential risks to benthic organisms in estuarine areas.

Using gold nanostars modified pencil graphite electrode as a novel substrate for design a sensitive and selective Dopamine aptasensor.

PubMed

Talemi, Rasoul Pourtaghavi; Mousavi, Seyed Mehdi; Afruzi, Hossein

2017-04-01

For the first time, gold nanostars (GNS) were applied for electrostatic and covalent immobilizing a thiol modified Dopamine aptamer on the pencil graphite electrode and signal amplification. Dopamine aptamer was immobilized on the gold nanostars through electrostatic interaction between negatively charged phosphate groups of aptamer and positively charged gold nanostars and AuS well known covalent interaction. In the presence of Dopamine in the test solution, the charge transfer resistance (R CT ) on the electrode surface increased with the increase of the Dopamine concentration due to specific interaction between Dopamine aptamer and Dopamine molecules, which made a barrier for electrons and inhibited the electron-transfer. So, the proposed approach showed a high sensitivity and a wide linearity to Dopamine in the range from 1.0 (±0.1) to 100.0 (±0.3) ngL -1 (ppt) with detection and quantification limits of 0.29 (±0.10) and 0.90 (±0.08) ngL -1 (ppt), respectively. Finally, the sensor was successfully used for determination of Dopamine in biological (human blood plasma and urine) samples. The results open up the path for manufacturing cost effective aptasensors for other biomedical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Particle transport through hydrogels is charge asymmetric.

PubMed

Zhang, Xiaolu; Hansing, Johann; Netz, Roland R; DeRouchey, Jason E

2015-02-03

Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Origins of microstructural transformations in charged vesicle suspensions: the crowding hypothesis.

PubMed

Seth, Mansi; Ramachandran, Arun; Murch, Bruce P; Leal, L Gary

2014-09-02

It is observed that charged unilamellar vesicles in a suspension can spontaneously deflate and subsequently transition to form bilamellar vesicles, even in the absence of externally applied triggers such as salt or temperature gradients. We provide strong evidence that the driving force for this deflation-induced transition is the repulsive electrostatic pressure between charged vesicles in concentrated suspensions, above a critical effective volume fraction. We use volume fraction measurements and cryogenic transmission electron microscopy imaging to quantitatively follow both the macroscopic and microstructural time-evolution of cationic diC18:1 DEEDMAC vesicle suspensions at different surfactant and salt concentrations. A simple model is developed to estimate the extent of deflation of unilamellar vesicles caused by electrostatic interactions with neighboring vesicles. It is determined that when the effective volume fraction of the suspension exceeds a critical value, charged vesicles in a suspension can experience "crowding" due to overlap of their electrical double layers, which can result in deflation and subsequent microstructural transformations to reduce the effective volume fraction of the suspension. Ordinarily in polydisperse colloidal suspensions, particles interacting via a repulsive potential transform into a glassy state above a critical volume fraction. The behavior of charged vesicle suspensions reported in this paper thus represents a new mechanism for the relaxation of repulsive interactions in crowded situations.

Electrostatic complementarity at protein/protein interfaces.

PubMed

McCoy, A J; Chandana Epa, V; Colman, P M

1997-05-02

Calculation of the electrostatic potential of protein-protein complexes has led to the general assertion that protein-protein interfaces display "charge complementarity" and "electrostatic complementarity". In this study, quantitative measures for these two terms are developed and used to investigate protein-protein interfaces in a rigorous manner. Charge complementarity (CC) was defined using the correlation of charges on nearest neighbour atoms at the interface. All 12 protein-protein interfaces studied had insignificantly small CC values. Therefore, the term charge complementarity is not appropriate for the description of protein-protein interfaces when used in the sense measured by CC. Electrostatic complementarity (EC) was defined using the correlation of surface electrostatic potential at protein-protein interfaces. All twelve protein-protein interfaces studied had significant EC values, and thus the assertion that protein-protein association involves surfaces with complementary electrostatic potential was substantially confirmed. The term electrostatic complementarity can therefore be used to describe protein-protein interfaces when used in the sense measured by EC. Taken together, the results for CC and EC demonstrate the relevance of the long-range effects of charges, as described by the electrostatic potential at the binding interface. The EC value did not partition the complexes by type such as antigen-antibody and proteinase-inhibitor, as measures of the geometrical complementarity at protein-protein interfaces have done. The EC value was also not directly related to the number of salt bridges in the interface, and neutralisation of these salt bridges showed that other charges also contributed significantly to electrostatic complementarity and electrostatic interactions between the proteins. Electrostatic complementarity as defined by EC was extended to investigate the electrostatic similarity at the surface of influenza virus neuraminidase where the epitopes of two monoclonal antibodies, NC10 and NC41, overlap. Although NC10 and NC41 both have quite high values of EC for their interaction with neuraminidase, the similarity in electrostatic potential generated by the two on the overlapping region of the epitopes is insignificant. Thus, it is possible for two antibodies to recognise the electrostatic surface of a protein in dissimilar ways.

Perspectives on electrostatics and conformational motions in enzyme catalysis.

PubMed

Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

2015-02-17

CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle. Complementary molecular dynamics simulations in conjunction with mixed quantum mechanical/molecular mechanical calculations accurately reproduced the vibrational frequency shifts in these probes and provided atomic-level insight into the residues influencing these changes. Our findings indicate that conformational and electrostatic changes are intimately related and functionally essential. This approach can be readily extended to the study of other enzyme systems to identify more general trends in the relationship between conformational fluctuations and electrostatic interactions. These results are relevant to researchers seeking to design novel enzymes as well as those seeking to develop therapeutic agents that function as enzyme inhibitors.

Perspectives on Electrostatics and Conformational Motions in Enzyme Catalysis

PubMed Central

2016-01-01

Conspectus Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle. Complementary molecular dynamics simulations in conjunction with mixed quantum mechanical/molecular mechanical calculations accurately reproduced the vibrational frequency shifts in these probes and provided atomic-level insight into the residues influencing these changes. Our findings indicate that conformational and electrostatic changes are intimately related and functionally essential. This approach can be readily extended to the study of other enzyme systems to identify more general trends in the relationship between conformational fluctuations and electrostatic interactions. These results are relevant to researchers seeking to design novel enzymes as well as those seeking to develop therapeutic agents that function as enzyme inhibitors. PMID:25565178

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

Abstract Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

Origin of attraction in p-benzoquinone complexes with benzene and p-hydroquinone.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Ono, Taizo

2017-08-30

The origin of the attraction in charge-transfer complexes (a p-hydroquinone-p-benzoquinone complex and benzene complexes with benzoquinone, tetracyanoethylene and Br 2 ) was analyzed using distributed multipole analysis and symmetry-adapted perturbation theory. Both methods show that the dispersion interactions are the primary source of the attraction in these charge-transfer complexes followed by the electrostatic interactions. The natures of the intermolecular interactions in these complexes are close to the π/π interactions of neutral aromatic molecules. The electrostatic interactions play important roles in determining the magnitude of the attraction. The contribution of charge-transfer interactions to the attraction is not large compared with the dispersion interactions in these complexes.

Intermolecular orbital interaction in π systems

NASA Astrophysics Data System (ADS)

Zhao, Rundong; Zhang, Rui-Qin

2018-04-01

Intermolecular interactions, in regard to which people tend to emphasise the noncovalent van der Waals (vdW) forces when conducting investigations throughout chemistry, can influence the structure, stability and function of molecules and materials. Despite the ubiquitous nature of vdW interactions, a simplified electrostatic model has been popularly adopted to explain common intermolecular interactions, especially those existing in π-involved systems. However, this classical model has come under fire in revealing specific issues such as substituent effects, due to its roughness; and it has been followed in past decades by sundry explanations which sometimes bring in nebulous descriptions. In this account, we try to summarise and present a unified model for describing and analysing the binding mechanism of such systems from the viewpoint of energy decomposition. We also emphasise a commonly ignored factor - orbital interaction, pointing out that the noncovalent intermolecular orbital interactions actually exhibit similar bonding and antibonding phenomena as those in covalent bonds.

The dark side of plasmonics.

PubMed

Gómez, D E; Teo, Z Q; Altissimo, M; Davis, T J; Earl, S; Roberts, A

2013-08-14

Plasmonic dark modes are pure near-field modes that can arise from the plasmon hybridization in a set of interacting nanoparticles. When compared to bright modes, dark modes have longer lifetimes due to their lack of a net dipole moment, making them attractive for a number of applications. We demonstrate the excitation and optical detection of a collective dark plasmonic mode from individual plasmonic trimers. The trimers consist of triangular arrangements of gold nanorods, and due to this symmetry, the lowest-energy dark plasmonic mode can interact with radially polarized light. The experimental data presented confirm the excitation of this mode, and its assignment is supported with an electrostatic approximation wherein these dark modes are described in terms of plasmon hybridization. The strong confinement of energy in these modes and their associated near fields hold great promise for achieving strong coupling to single photon emitters.

Effect of the ordered interfacial water layer in protein complex formation: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander; Sabirianov, Renat

2011-03-01

Using a non-local electrostatic approach that incorporates the short-range structure of the contacting media, we evaluated the electrostatic contribution to the energy of the complex formation of two model proteins. In this study, we have demonstrated that the existence of an low-dielectric interfacial water layer at the protein-solvent interface reduces the charging energy of the proteins in the aqueous solvent, and consequently increases the electrostatic contribution to the protein binding (change in free energy upon the complex formation of two proteins). This is in contrast with the finding of the continuum electrostatic model, which suggests that electrostatic interactions are not strong enough to compensate for the unfavorable desolvation effects.

Carbene-aerogen bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Sabouri, Ayda

2017-04-01

Through the use of ab initio calculations, the possibility of formation of σ-hole interaction between ZO3 (Z = Ar, Kr and Xe) and carbene species is investigated. Since singlet carbenes show a negative electrostatic potential on their divalent carbon atom, they can favourably interact with the positive electrostatic potential generated by the σ-hole of Z atom of ZO3. The characteristic of this interaction, termed as 'carbene-aerogen' bond, is analysed in terms of geometric, interaction energies and electronic features. The energy decomposition analysis indicates that for all complexes analysed here, the electrostatic energy is more negative than the polarisation or dispersion energy term. According to the electron density analysis, some partial covalent character can be ascribed to XeṡṡṡC interactions. In addition, the carbene-aerogen bond exhibits cooperative effects with the HṡṡṡO hydrogen-bonding interaction in ternary complexes where both interactions coexist. For a given carbene, the amount of these cooperative effects increases with the size of the Z atom. The results obtained in this work may be helpful for the extension and future application of σ-hole intermolecular interactions as well as coordination chemistry.

Collisionless coupling of a high- β expansion to an ambient, magnetized plasma. II. Experimental fields and measured momentum coupling

NASA Astrophysics Data System (ADS)

Bonde, Jeffrey; Vincena, Stephen; Gekelman, Walter

2018-04-01

The momentum coupled to a magnetized, ambient argon plasma from a high- β, laser-produced carbon plasma is examined in a collisionless, weakly coupled limit. The total electric field was measured by separately examining the induced component associated with the rapidly changing magnetic field of the high- β (kinetic β˜106), expanding plasma and the electrostatic component due to polarization of the expansion. Their temporal and spatial structures are discussed and their effect on the ambient argon plasma (thermal β˜10-2) is confirmed with a laser-induced fluorescence diagnostic, which directly probed the argon ion velocity distribution function. For the given experimental conditions, the electrostatic field is shown to dominate the interaction between the high- β expansion and the ambient plasma. Specifically, the expanding plasma couples energy and momentum into the ambient plasma by pulling ions inward against the flow direction.

Adhesion of liposomes: a quartz crystal microbalance study

NASA Astrophysics Data System (ADS)

Lüthgens, Eike; Herrig, Alexander; Kastl, Katja; Steinem, Claudia; Reiss, Björn; Wegener, Joachim; Pignataro, Bruno; Janshoff, Andreas

2003-11-01

Three different systems are presented, exploring the adhesion of liposomes mediated by electrostatic and lipid-protein interactions as well as molecular recognition of ligand receptor pairs. Liposomes are frequently used to gain insight into the complicated processes involving adhesion and subsequent events such as fusion and fission mainly triggered by specific proteins. We combined liposome technology with the quartz crystal microbalance (QCM) technique as a powerful tool to study the hidden interface between the membrane and functionalized surface. Electrostatic attraction and molecular recognition were employed to bind liposomes to the functionalized quartz crystal. The QCM was used to distinguish between adsorption of vesicles and rupture due to strong adhesive forces. Intact vesicles display viscoelastic behaviour, while planar lipid bilayers as a result of vesicle rupture can be modelled by a thin rigid film. Furthermore, the adhesion of cells was modelled successfully by receptor bearing liposomes. Scanning force microscopy was used to confirm the results obtained by QCM measurements.

Effect of phosphorylation of myelin basic protein by MAPK on its interactions with actin and actin binding to a lipid membrane in vitro.

PubMed

Boggs, Joan M; Rangaraj, Godha; Gao, Wen; Heng, Yew-Meng

2006-01-17

Myelin basic protein (MBP) binds to negatively charged lipids on the cytosolic surface of oligodendrocyte membranes and is most likely responsible for adhesion of these surfaces in the multilayered myelin sheath. It can also polymerize actin, bundle F-actin filaments, and bind actin filaments to lipid bilayers through electrostatic interactions. MBP consists of a number of posttranslationally modified isomers of varying charge, some resulting from phosphorylation at several sites by different kinases, including mitogen-activated protein kinase (MAPK). Phosphorylation of MBP in oligodendrocytes occurs in response to various extracellular stimuli. Phosphorylation/dephosphorylation of MBP also occurs in the myelin sheath in response to electrical activity in the brain. Here we investigate the effect of phosphorylation of MBP on its interaction with actin in vitro by phosphorylating the most highly charged unmodified isomer, C1, at two sites with MAPK. Phosphorylation decreased the ability of MBP to polymerize actin and to bundle actin filaments but had no effect on the dissociation constant of the MBP-actin complex or on the ability of Ca2+-calmodulin to dissociate the complex. The most significant effect of phosphorylation on the MBP-actin complex was a dramatic reduction in its ability to bind to negatively charged lipid bilayers. The effect was much greater than that reported earlier for another charge isomer of MBP, C8, in which six arginines were deiminated to citrulline, resulting in a reduction of net positive charge of 6. These results indicate that although average electrostatic forces are the primary determinant of the interaction of MBP with actin, phosphorylation may have an additional effect due to a site-specific electrostatic effect or to a conformational change. Thus, phosphorylation of MBP, which occurs in response to various extracellular signals in both myelin and oligodendrocytes, attenuates the ability of MBP to polymerize and bundle actin and to bind it to a negatively charged membrane.

Charge density distribution and the electrostatic moments of CTPB in the active site of p300 enzyme: a DFT and charge density study.

PubMed

Devipriya, B; Kumaradhas, P

2013-10-21

A molecular docking and charge density analysis have been carried out to understand the conformational change, charge distribution and electrostatic properties of N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide (CTPB) in the active site of p300. The nearest neighbors, shortest intermolecular contacts between CTPB-p300 and the lowest binding energy of CTPB have been analyzed from the docking analysis. Further, a charge density analysis has been carried out for the molecule in gas phase and for the corresponding molecule lifted from the active site of p300. Due to the intermolecular interaction between CTPB and the amino acids of active site, the conformation of the CTPB has been significantly altered (particularly the pentadecyl chain). CTPB forms strong interaction with the amino acid residues Tyr1397 and Trp1436 at the distance 2.12 and 2.72Å, respectively. However, the long pentadecyl alkyl chain of CTPB produces a barrier and reducing the chance of forming hydrogen bonding with p300. The electron density ρbcp(r) of the polar bonds (C-O, C-N, C-F and C-Cl) of CTPB are increased when it present in the active site. The dipole moment of CTPB in the active site is significantly less (5.73D) when compared with the gas phase (8.16D) form. In the gas phase structure, a large region of negative electrostatic potential (ESP) is found at the vicinity of O(2) and CF3 group, which is less around the O(1) atom. Whereas, in the active site, the negative ESP around the CF3 group is decreased and increased at the O(1) and O(2)-atoms. The ESP modifications of CTPB in the active site are mainly attributed to the effect of intermolecular interaction. The gas phase and active site study insights the molecular flexibility and the electrostatic properties of CTPB in the active site. © 2013 Elsevier Ltd. All rights reserved.

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

PubMed

Dolgobrodov, S G; Lukashkin, A N; Russell, I J

2000-12-01

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.

Discrete Element Modeling of Triboelectrically Charged Particles

NASA Technical Reports Server (NTRS)

Hogue, Michael D.; Calle, Carlos I.; Weitzman, Peter S.; Curry, David R.

2008-01-01

Tribocharging of particles is common in many processes including fine powder handling and mixing, printer toner transport and dust extraction. In a lunar environment with its high vacuum and lack of water, electrostatic forces are an important factor to consider when designing and operating equipment. Dust mitigation and management is critical to safe and predictable performance of people and equipment. The extreme nature of lunar conditions makes it difficult and costly to carry out experiments on earth which are necessary to better understand how particles gather and transfer charge between each other and with equipment surfaces. DEM (Discrete Element Modeling) provides an excellent virtual laboratory for studying tribocharging of particles as well as for design of devices for dust mitigation and for other purposes related to handling and processing of lunar regolith. Theoretical and experimental work has been performed pursuant to incorporating screened Coulombic electrostatic forces into EDEM, a commercial DEM software package. The DEM software is used to model the trajectories of large numbers of particles for industrial particulate handling and processing applications and can be coupled with other solvers and numerical models to calculate particle interaction with surrounding media and force fields. While simple Coulombic force between two particles is well understood, its operation in an ensemble of particles is more complex. When the tribocharging of particles and surfaces due to frictional contact is also considered, it is necessary to consider longer range of interaction of particles in response to electrostatic charging. The standard DEM algorithm accounts for particle mechanical properties and inertia as a function of particle shape and mass. If fluid drag is neglected, then particle dynamics are governed by contact between particles, between particles and equipment surfaces and gravity forces. Consideration of particle charge and any tribocharging and electric field effects requires calculation of the forces due to these effects.

Spectroscopic investigation of the effect of salt on binding of tartrazine with two homologous serum albumins: quantification by use of the Debye-Hückel limiting law and observation of enthalpy-entropy compensation.

PubMed

Bolel, Priyanka; Datta, Shubhashis; Mahapatra, Niharendu; Halder, Mintu

2012-08-30

Formation of ion pair between charged molecule and protein can lead to interesting biochemical phenomena. We report the evolution of thermodynamics of the binding of tartrazine, a negatively charged azo colorant, and serum albumins with salt. The dye binds predominantly electrostatically in low buffer strengths; however, on increasing salt concentration, affinity decreases considerably. The calculated thermodynamic parameters in high salt indicate manifestation of nonelectrostatic interactions, namely, van der Waals force and hydrogen bonding. Site-marker competitive binding studies and docking simulations indicate that the dye binds with HSA in the warfarin site and with BSA at the interface of warfarin and ibuprofen binding sites. The docked poses indicate nearby amino acid positive side chains, which are possibly responsible for electrostatic interaction. Using the Debye-Hückel interionic attraction theory for binding equilibria, it is shown that, for electrostatic binding the calculated free energy change increases linearly with square root of ionic strength. Also UV-vis, fluorescence, CD data indicate a decrease of interaction with salt concentration. This study quantitatively relates how ionic strength modulates the strength of the protein-ligand electrostatic interaction. The binding enthalpy and entropy have been found to compensate one another. The enthalpy-entropy compensation (EEC), general property of weak intermolecular interactions, has been discussed.

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

PubMed Central

Law, Michael J.; Linde, Michael E.; Chambers, Eric J.; Oubridge, Chris; Katsamba, Phinikoula S.; Nilsson, Lennart; Haworth, Ian S.; Laird-Offringa, Ite A.

2006-01-01

Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a ‘lure and lock’ model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the ‘lure’ step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on ‘top’ of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein–RNA complexes. PMID:16407334

Chemotherapy drugs form ion pores in membranes due to physical interactions with lipids.

PubMed

Ashrafuzzaman, Mohammad; Tseng, Chih-Yuan; Duszyk, Marek; Tuszynski, Jack A

2012-12-01

We demonstrate the effects on membrane of the tubulin-binding chemotherapy drugs: thiocolchicoside and taxol. Electrophysiology recordings across lipid membranes in aqueous phases containing drugs were used to investigate the drug effects on membrane conductance. Molecular dynamics simulation of the chemotherapy drug-lipid complexes was used to elucidate the mechanism at an atomistic level. Both drugs are observed to induce stable ion-flowing pores across membranes. Discrete pore current-time plots exhibit triangular conductance events in contrast to rectangular ones found for ion channels. Molecular dynamics simulations indicate that drugs and lipids experience electrostatic and van der Waals interactions for short periods of time when found within each other's proximity. The energies from these two interactions are found to be similar to the energies derived theoretically using the screened Coulomb and the van der Waals interactions between peptides and lipids due to mainly their charge properties while forming peptide-induced ion channels in lipid bilayers. Experimental and in silico studies together suggest that the chemotherapy drugs induce ion pores inside lipid membranes due to drug-lipid physical interactions. The findings reveal cytotoxic effects of drugs on the cell membrane, which may aid in novel drug development for treatment of cancer and other diseases. © 2012 John Wiley & Sons A/S.

Electrostatic Interactions and Self-Assembly in Polymeric Systems

NASA Astrophysics Data System (ADS)

Dobrynin, Andrey

Electrostatic interactions between macroions play an important role in different areas ranging from materials science to biophysics. They are main driving forces behind layer-by-layer assembly technique that allows self-assembly of multilayer films from synthetic polyelectrolytes, DNA, proteins and nanoparticles. They are responsible for complexation and reversible gelation between polyelectrolytes and proteins. In this talk, using results of the molecular dynamics simulations and analytical calculations, I will demonstrate what effect electrostatic interactions, counterion condensation and polymer solvent affinity have on a collapse of polyelectrolyte chain in a poor solvent conditions for the polymer backbone, on complexations and reversible gelation between polyelectrolytes and polyamholytes (unstructured proteins), on microphase separation transitions in spherical and planar charged brushes, and on a layer-by-layer assembly of charged nanoparticles and linear polyelectrolytes on charged surfaces. NSF DMR-1004576 DMR-1409710.

Electrostatic and hydrodynamics effects in a sedimented magnetorheological suspension.

PubMed

Domínguez-García, P; Pastor, J M; Melle, Sonia; Rubio, Miguel A

2009-08-01

We present experimental results on the equilibrium microstructure of a sedimented magnetorheological suspension, namely, an aqueous suspension of micron-sized superparamagnetic particles. We develop a study of the electrical interactions on the suspension by processing video-microscopy images of the sedimented particles. We calculate the pair distribution function, g(r), which yields the electrostatic pair potential u(r), showing an anomalous attractive interaction for distances on the order of twice the particle diameter, with characteristic parameters whose values show a dependence with the two-dimensional concentration of particles. The repulsive body of the potential is adjusted to a DLVO expression in order to calculate the Debye screening length and the effective surface charge density. Influence of confinement and variations on the Boltzmann sedimentation profile because of the electrostatic interactions appear to be essential for the interpretation of experimental results.

Kinesin motor protein as an electrostatic ratchet machine

NASA Astrophysics Data System (ADS)

Tsironis, George; Ciudad, Aleix; Sancho, Jose Maria

2008-03-01

Kinesin and related motor proteins utilize ATP fuel to propel themselves along the external surface of microtubules in a processive and directional fashion. We show that the observed step-like motion is possible through time varying charge distributions furnished by the ATP hydrolysis circle while the static charge configuration on the microtuble provides the guide for motion. Thus, while the chemical hydrolysis energy induces appropriate local conformational changes, the motor translational energy is fundamentally electrostatic. Numerical simulations of the mechanical equations of motion show that processivity and directionality are direct consequences of the ATP-dependent electrostatic interaction between the different charge distributions of kinesin and microtubule. Treating proterins as continuous dielectric media and using a Green's function formalism we find analytical expressions for the electrostatic energy in the vicinity of the protein surfaces. We calculate the Bjerrum length in the interior of the protein and analyze its dependence on the charge proximity to the protein interface. We apply these results to kinesin and estimate the pure electrostatic ATP-ADP interaction to be larger than 2k T.

Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins.

PubMed

Deb, Pranab; Haldar, Tapas; Kashid, Somnath M; Banerjee, Subhrashis; Chakrabarty, Suman; Bagchi, Sayan

2016-05-05

Noncovalent interactions, in particular the hydrogen bonds and nonspecific long-range electrostatic interactions are fundamental to biomolecular functions. A molecular understanding of the local electrostatic environment, consistently for both specific (hydrogen-bonding) and nonspecific electrostatic (local polarity) interactions, is essential for a detailed understanding of these processes. Vibrational Stark Effect (VSE) has proven to be an extremely useful method to measure the local electric field using infrared spectroscopy of carbonyl and nitrile based probes. The nitrile chemical group would be an ideal choice because of its absorption in an infrared spectral window transparent to biomolecules, ease of site-specific incorporation into proteins, and common occurrence as a substituent in various drug molecules. However, the inability of VSE to describe the dependence of IR frequency on electric field for hydrogen-bonded nitriles to date has severely limited nitrile's utility to probe the noncovalent interactions. In this work, using infrared spectroscopy and atomistic molecular dynamics simulations, we have reported for the first time a linear correlation between nitrile frequencies and electric fields in a wide range of hydrogen-bonding environments that may bridge the existing gap between VSE and H-bonding interactions. We have demonstrated the robustness of this field-frequency correlation for both aromatic nitriles and sulfur-based nitriles in a wide range of molecules of varying size and compactness, including small molecules in complex solvation environments, an amino acid, disordered peptides, and structured proteins. This correlation, when coupled to VSE, can be used to quantify noncovalent interactions, specific or nonspecific, in a consistent manner.

TEMPO Monolayers on Si(100) Electrodes: Electrostatic Effects by the Electrolyte and Semiconductor Space-Charge on the Electroactivity of a Persistent Radical.

PubMed

Zhang, Long; Vogel, Yan Boris; Noble, Benjamin B; Gonçales, Vinicius R; Darwish, Nadim; Brun, Anton Le; Gooding, J Justin; Wallace, Gordon G; Coote, Michelle L; Ciampi, Simone

2016-08-03

This work demonstrates the effect of electrostatic interactions on the electroactivity of a persistent organic free radical. This was achieved by chemisorption of molecules of 4-azido-2,2,6,6-tetramethyl-1-piperdinyloxy (4-azido-TEMPO) onto monolayer-modified Si(100) electrodes using a two-step chemical procedure to preserve the open-shell state and hence the electroactivity of the nitroxide radical. Kinetic and thermodynamic parameters for the surface electrochemical reaction are investigated experimentally and analyzed with the aid of electrochemical digital simulations and quantum-chemical calculations of a theoretical model of the tethered TEMPO system. Interactions between the electrolyte anions and the TEMPO grafted on highly doped, i.e., metallic, electrodes can be tuned to predictably manipulate the oxidizing power of surface nitroxide/oxoammonium redox couple, hence showing the practical importance of the electrostatics on the electrolyte side of the radical monolayer. Conversely, for monolayers prepared on the poorly doped electrodes, the electrostatic interactions between the tethered TEMPO units and the semiconductor-side, i.e., space-charge, become dominant and result in drastic kinetic changes to the electroactivity of the radical monolayer as well as electrochemical nonidealities that can be explained as an increase in the self-interaction "a" parameter that leads to the Frumkin isotherm.

Biofilm formation and local electrostatic force characteristics of Escherichia coli O157:H7 observed by electrostatic force microscopy

NASA Astrophysics Data System (ADS)

Oh, Y. J.; Jo, W.; Yang, Y.; Park, S.

2007-04-01

The authors report growth media dependence of electrostatic force characteristics in Escherichia coli O157:H7 biofilm through local measurement by electrostatic force microscopy (EFM). The difference values of electrostatic interaction between the bacterial surface and the abiotic surface show an exponential decay behavior during biofilm development. In the EFM data, the biofilm in the low nutrient media shows a faster decay than the biofilm in the rich media. The surface potential in the bacterial cells was changed from 957to149mV. Local characterization of extracellular materials extracted from the bacteria reveals the progress of the biofilm formation and functional complexities.

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

PubMed

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Electrostatic Similarity Analysis of Human β-Defensin Binding in the Melanocortin System

PubMed Central

Nix, Matthew A.; Kaelin, Christopher B.; Palomino, Rafael; Miller, Jillian L.; Barsh, Gregory S.; Millhauser, Glenn L.

2015-01-01

Summary The β-defensins are a class of small cationic proteins that serve as components of numerous systems in vertebrate biology, including the immune and melanocortin systems. Human β-defensin 3 (HBD3), which is produced in the skin, has been found to bind to melanocortin receptors 1 and 4 through complementary electrostatics, a unique mechanism of ligand-receptor interaction. This finding indicates that electrostatics alone, and not specific amino acid contact points, could be sufficient for function in this ligand-receptor system, and further suggests that other small peptide ligands could interact with these receptors in a similar fashion. Here, we conducted molecular-similarity analyses and functional studies of additional members of the human β-defensin family, examining their potential as ligands of melanocortin-1 receptor, through selection based on their electrostatic similarity to HBD3. Using Poisson-Boltzmann electrostatic calculations and molecular-similarity analysis, we identified members of the human β-defensin family that are both similar and dissimilar to HBD3 in terms of electrostatic potential. Synthesis and functional testing of a subset of these β-defensins showed that peptides with an HBD3-like electrostatic character bound to melanocortin receptors with high affinity, whereas those that were anticorrelated to HBD3 showed no binding affinity. These findings expand on the central role of electrostatics in the control of this ligand-receptor system and further demonstrate the utility of employing molecular-similarity analysis. Additionally, we identified several new potential ligands of melanocortin-1 receptor, which may have implications for our understanding of the role defensins play in melanocortin physiology. PMID:26536271

Electrostatic contribution to the binding stability of protein-protein complexes.

PubMed

Dong, Feng; Zhou, Huan-Xiang

2006-10-01

To investigate roles of electrostatic interactions in protein binding stability, electrostatic calculations were carried out on a set of 64 mutations over six protein-protein complexes. These mutations alter polar interactions across the interface and were selected for putative dominance of electrostatic contributions to the binding stability. Three protocols of implementing the Poisson-Boltzmann model were tested. In vdW4 the dielectric boundary between the protein low dielectric and the solvent high dielectric is defined as the protein van der Waals surface and the protein dielectric constant is set to 4. In SE4 and SE20, the dielectric boundary is defined as the surface of the protein interior inaccessible to a 1.4-A solvent probe, and the protein dielectric constant is set to 4 and 20, respectively. In line with earlier studies on the barnase-barstar complex, the vdW4 results on the large set of mutations showed the closest agreement with experimental data. The agreement between vdW4 and experiment supports the contention of dominant electrostatic contributions for the mutations, but their differences also suggest van der Waals and hydrophobic contributions. The results presented here will serve as a guide for future refinement in electrostatic calculation and inclusion of nonelectrostatic effects. Proteins 2006. (c) 2006 Wiley-Liss, Inc.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.

2014-05-01

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

Introduction of a specific binding domain on myoglobin surface by new chemical modification.

PubMed

Hayashi, T; Ando, T; Matsuda, T; Yonemura, H; Yamada, S; Hisaeda, Y

2000-11-01

A new myoglobin, reconstituted with a modified zinc protoporphyrin, having a total of four ammonium groups at the terminal of the two propionate side chains was constructed to introduce a substrate binding site. The protein with a positively charged patch on the surface formed a stable complex with negatively charged substrates, such as hexacyanoferrate(III) and anthraquinonesulfonate via an electrostatic interaction. The complexation was monitored by fluorescence quenching due to singlet electron transfer from the photoexcited reconstituted zinc myoglobin to the substrates. The binding properties were evaluated by Stern-Volmer plots from the fluorescence quenching of the zinc myoglobin by a quencher. Particularly, anthraquinone-2,7-disulfonic acid showed a high affinity with a binding constant of 1.5 x 10(5) M(-1) in 10 mM phosphate buffer, pH 7.0. In contrast, the plots upon the addition of anthraquinone-2-sulfonic acid at different ionic strengths indicated that the complex was formed not only by an electrostatic interaction but also by a hydrophobic contact. The findings from the fluorescence studies conclude that the present system is a useful model for discussion of electron transfer via non-covalently linked donor-acceptor pairing on the protein surface.

Colloidal polymer particles as catalyst carriers and phase transfer agents in multiphasic hydroformylation reactions.

PubMed

Peral, D; Stehl, D; Bibouche, B; Yu, H; Mardoukh, J; Schomäcker, R; Klitzing, R von; Vogt, D

2018-03-01

Colloidal particles have been used to covalently bind ligands for the heterogenization of homogeneous catalysts. The replacement of the covalent bonds by electrostatic interactions between particles and the catalyst could preserve the selectivity of a truly homogeneous catalytic process. Functionalized polymer particles with trimethylammonium moieties, dispersed in water, with a hydrophobic core and a hydrophilic shell have been synthesized by emulsion polymerization and have been thoroughly characterized. The ability of the particles with different monomer compositions to act as catalyst carriers has been studied. Finally, the colloidal dispersions have been applied as phase transfer agents in the multiphasic rhodium-catalyzed hydroformylation of 1-octene. The hydrodynamic radius of the particles has been shown to be around 100 nm, and a core-shell structure could be observed by atomic force microscopy. The polymer particles were proven to act as carriers for the water-soluble hydroformylation catalyst, due to electrostatic interaction between the functionalized particles bearing ammonium groups and the sulfonated ligands of the catalyst. The particles were stable under the hydroformylation conditions and the aqueous catalyst phase could be recycled three times. Copyright © 2017 Elsevier Inc. All rights reserved.

Some improvements in DNA interaction calculations

NASA Technical Reports Server (NTRS)

Egan, J. T.; Swissler, T. J.; Rein, R.

1974-01-01

Calculations are made on specific DNA-type complexes using refined expressions for electrostatic and polarization energies. Dispersion and repulsive terms are included in the evaluation of the total interaction energy. It is shown that the expansion of the electrostatic potential to include multipole moments up to octopole is necessary to achieve convergence of first-order energies. Polarization energies are not as sensitive to this expansion. The calculations also support the usefulness of the hard sphere model for DNA hydrogen bonds and indicate how stacking interactions are influenced by second-order energies.

Quantitative nanoscale electrostatics of viruses

NASA Astrophysics Data System (ADS)

Hernando-Pérez, M.; Cartagena-Rivera, A. X.; Lošdorfer Božič, A.; Carrillo, P. J. P.; San Martín, C.; Mateu, M. G.; Raman, A.; Podgornik, R.; de Pablo, P. J.

2015-10-01

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04274g

Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

NASA Astrophysics Data System (ADS)

Chen, Chun-Long; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald N.; Deyoreo, James J.

2014-09-01

In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic and hydrophobic interactions, with hydrophobic interactions playing the dominant role. While either strong electrostatic or hydrophobic interactions inhibit growth and reduces expression of the {104} faces, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate electrostatic interactions allow peptoids to weakly adsorb while moderate hydrophobic interactions cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of the {104} faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

Electrostatic interactions of colicin E1 with the surface of Escherichia coli total lipid.

PubMed

Tian, Chunhong; Tétreault, Elaine; Huang, Christopher K; Dahms, Tanya E S

2006-06-01

The surface properties of colicin E1, a 522-amino acid protein, and its interaction with monolayers of Escherichia coli (E. coli) total lipid and 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DOPC) were studied using the Langmuir-Blodgett (LB) technique. Colicin E1 is amphiphilic, forming a protein monolayer at the air/buffer interface. The protein is thought to interact with the E. coli total lipid head groups through electrostatic interactions, followed by its insertion into the lipid monolayers. Supported lipid bilayers (SLBs) of E. coli total lipid and DOPC, deposited onto mica at the cell membrane equivalence pressure for E. coli and incubated with colicin E1, were imaged by contact mode atomic force microscopy (CM-AFM). Colicin E1 formed protein aggregates on DOPC SLBs, while E. coli total lipid SLB was deformed following its incubation with colicin E1. Corresponding lateral force images, along with electrostatic surface potentials for colicin E1 P190, imply a direct interaction of colicin E1 with lipid head groups facilitating their charge neutralization.

Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

PubMed Central

Chen, Chun-Long; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald N.; DeYoreo, James J.

2014-01-01

In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic and hydrophobic interactions, with hydrophobic interactions playing the dominant role. While either strong electrostatic or hydrophobic interactions inhibit growth and reduces expression of the {104} faces, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate electrostatic interactions allow peptoids to weakly adsorb while moderate hydrophobic interactions cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of the {104} faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications. PMID:25189418

Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines.

PubMed

Li, Yang; Xu, Weixin; Mu, Yuguang; Zhang, John Z H

2013-08-07

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

Sorption of chlorophenols on microporous minerals: mechanism and influence of metal cations, solution pH, and humic acid.

PubMed

Yang, Hui; Hu, Yuanan; Cheng, Hefa

2016-10-01

Sorption of 2-chlorophenol (2-CP), 2,4-dichlorophenol (2,4-DCP), and 2,4,6-trichlorophenol (2,4,6-TCP) on a range of dealuminated zeolites were investigated to understand the mechanism of their sorption on microporous minerals, while the influence of common metal cations, solution pH, and humic acid was also studied. Sorption of chlorophenols was found to increase with the hydrophobicity of the sorbates and that of the microporous minerals, indicating the important role of hydrophobic interactions, while sorption was also stronger in the micropores of narrower sizes because of greater enhancement of the dispersion interactions. The presence of metal cations could enhance chlorophenol sorption due to the additional electrostatic attraction between metal cations exchanged into the mineral micropores and the chlorophenolates, and this effect was apparent on the mineral sorbent with a high density of surface cations (2.62 sites/nm(2)) in its micropores. Under circum-neutral or acidic conditions, neutral chlorophenol molecules adsorbed into the hydrophobic micropores through displacing the "loosely bound" water molecules, while their sorption was negligible under moderately alkaline conditions due to electrostatic repulsion between the negatively charged zeolite framework and anionic chlorophenolates. The influence of humic acid on sorption of chlorophenols on dealuminated Y zeolites suggests that its molecules did not block the micropores but created a secondary sorption sites by forming a "coating layer" on the external surface of the zeolites. These mechanistic insights could help better understand the interactions of ionizable chlorophenols and metal cations in mineral micropores and guide the selection and design of reusable microporous mineral sorbents for sorptive removal of chlorophenols from aqueous stream.

Compact electrostatic comb actuator

DOEpatents

Rodgers, M. Steven; Burg, Michael S.; Jensen, Brian D.; Miller, Samuel L.; Barnes, Stephen M.

2000-01-01

A compact electrostatic comb actuator is disclosed for microelectromechanical (MEM) applications. The actuator is based upon a plurality of meshed electrostatic combs, some of which are stationary and others of which are moveable. One or more restoring springs are fabricated within an outline of the electrostatic combs (i.e. superposed with the moveable electrostatic combs) to considerably reduce the space required for the actuator. Additionally, a truss structure is provided to support the moveable electrostatic combs and prevent bending or distortion of these combs due to unbalanced electrostatic forces or external loading. The truss structure formed about the moveable electrostatic combs allows the spacing between the interdigitated fingers of the combs to be reduced to about one micron or less, thereby substantially increasing the number of active fingers which can be provided in a given area. Finally, electrostatic shields can be used in the actuator to substantially reduce unwanted electrostatic fields to further improve performance of the device. As a result, the compact electrostatic comb actuator of the present invention occupies only a fraction of the space required for conventional electrostatic comb actuators, while providing a substantial increase in the available drive force (up to one-hundred times).

Strong coupling electrostatics for randomly charged surfaces: antifragility and effective interactions.

PubMed

Ghodrat, Malihe; Naji, Ali; Komaie-Moghaddam, Haniyeh; Podgornik, Rudolf

2015-05-07

We study the effective interaction mediated by strongly coupled Coulomb fluids between dielectric surfaces carrying quenched, random monopolar charges with equal mean and variance, both when the Coulomb fluid consists only of mobile multivalent counterions and when it consists of an asymmetric ionic mixture containing multivalent and monovalent (salt) ions in equilibrium with an aqueous bulk reservoir. We analyze the consequences that follow from the interplay between surface charge disorder, dielectric and salt image effects, and the strong electrostatic coupling that results from multivalent counterions on the distribution of these ions and the effective interaction pressure they mediate between the surfaces. In a dielectrically homogeneous system, we show that the multivalent counterions are attracted towards the surfaces with a singular, disorder-induced potential that diverges logarithmically on approach to the surfaces, creating a singular but integrable counterion density profile that exhibits an algebraic divergence at the surfaces with an exponent that depends on the surface charge (disorder) variance. This effect drives the system towards a state of lower thermal 'disorder', one that can be described by a renormalized temperature, exhibiting thus a remarkable antifragility. In the presence of an interfacial dielectric discontinuity, the singular behavior of counterion density at the surfaces is removed but multivalent counterions are still accumulated much more strongly close to randomly charged surfaces as compared with uniformly charged ones. The interaction pressure acting on the surfaces displays in general a highly non-monotonic behavior as a function of the inter-surface separation with a prominent regime of attraction at small to intermediate separations. This attraction is caused directly by the combined effects from charge disorder and strong coupling electrostatics of multivalent counterions, which dominate the surface-surface repulsion due to the (equal) mean charges on the two surfaces and the osmotic pressure of monovalent ions residing between them. These effects can be quite significant even with a small degree of surface charge disorder relative to the mean surface charge. The strong coupling, disorder-induced attraction is typically much stronger than the van der Waals interaction between the surfaces, especially within a range of several nanometers for the inter-surface separation, where such effects are predicted to be most pronounced.

Label-free biosensing with functionalized nanopipette probes.

PubMed

Umehara, Senkei; Karhanek, Miloslav; Davis, Ronald W; Pourmand, Nader

2009-03-24

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research.

Influence of the electron-cation interaction on electron mobility in dye-sensitized ZnO and TiO2 nanocrystals: a study using ultrafast terahertz spectroscopy.

PubMed

Nemec, H; Rochford, J; Taratula, O; Galoppini, E; Kuzel, P; Polívka, T; Yartsev, A; Sundström, V

2010-05-14

Charge transport and recombination in nanostructured semiconductors are poorly understood key processes in dye-sensitized solar cells. We have employed time-resolved spectroscopies in the terahertz and visible spectral regions supplemented with Monte Carlo simulations to obtain unique information on these processes. Our results show that charge transport in the active solar cell material can be very different from that in nonsensitized semiconductors, due to strong electrostatic interaction between injected electrons and dye cations at the surface of the semiconductor nanoparticle. For ZnO, this leads to formation of an electron-cation complex which causes fast charge recombination and dramatically decreases the electron mobility even after the dissociation of the complex. Sensitized TiO2 does not suffer from this problem due to its high permittivity efficiently screening the charges.

Refluxed electrons direct laser acceleration in ultrahigh laser and relativistic critical density plasma interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, J.; Science and Technology on Plasma Physics Laboratory, China Academy of Engineering Physics, P.O. Box 919-986, Mianyang 621900; Zhao, Z. Q.

2015-01-15

Refluxed electrons direct laser acceleration is proposed so as to generate a high-charge energetic electron beam. When a laser pulse is incident on a relativistic critical density target, the rising edge of the pulse heats the target and the sheath fields on the both sides of the target reflux some electrons inside the expanding target. These electrons can be trapped and accelerated due to the self-transparency and the negative longitudinal electrostatic field in the expanding target. Some of the electrons can be accelerated to energies exceeding the ponderomotive limit 1/2a{sub 0}{sup 2}mc{sup 2}. Effective temperature significantly above the ponderomotive scalingmore » is observed. Furthermore, due to the limited expanding length, the laser propagating instabilities are suppressed in the interaction. Thus, high collimated beams with tens of μC charge can be generated.« less

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

Local electrostatic interactions determine the diameter of fusion pores

PubMed Central

Guček, Alenka; Jorgačevski, Jernej; Górska, Urszula; Rituper, Boštjan; Kreft, Marko; Zorec, Robert

2015-01-01

In regulated exocytosis vesicular and plasma membranes merge to form a fusion pore in response to stimulation. The nonselective cation HCN channels are involved in the regulation of unitary exocytotic events by at least 2 mechanisms. They can affect SNARE-dependent exocytotic activity indirectly, via the modulation of free intracellular calcium; and/or directly, by altering local cation concentration, which affects fusion pore geometry likely via electrostatic interactions. By monitoring membrane capacitance, we investigated how extracellular cation concentration affects fusion pore diameter in pituitary cells and astrocytes. At low extracellular divalent cation levels predominantly transient fusion events with widely open fusion pores were detected. However, fusion events with predominately narrow fusion pores were present at elevated levels of extracellular trivalent cations. These results show that electrostatic interactions likely help determine the stability of discrete fusion pore states by affecting fusion pore membrane composition. PMID:25835258

Predicting ion specific capacitances of supercapacitors due to quantum ionic interactions.

PubMed

Parsons, Drew F

2014-08-01

A new theoretical framework is now available to help explain ion specific (Hofmeister) effects. All measurements in physical chemistry show ion specificity, inexplicable by classical electrostatic theories. These ignore ionic dispersion forces that change ionic adsorption. We explored ion specificity in supercapacitors using a modified Poisson-Boltzmann approach that includes ionic dispersion energies. We have applied ab initio quantum chemical methods to determine required ion sizes and ion polarisabilities. Our model represents graphite electrodes through their optical dielectric spectra. The electrolyte was 1.2 M Li salt in propylene carbonate, using the common battery anions, PF6(-), BF4(-) and ClO4(-). We also investigated the perhalate series with BrO4(-) and IO4(-). The capacitance C=dσ/dψ was calculated from the predicted electrode surface charge σ of each electrode with potential ψ between electrodes. Compared to the purely electrostatic calculation, the capacitance of a positively charged graphite electrode was enhanced by more than 15%, with PF6(-) showing >50% increase in capacitance. IO4(-) provided minimal enhancement. The enhancement is due to adsorption of both anions and cations, driven by ionic dispersion forces. The Hofmeister series in the single-electrode capacitance was PF6(-)>BF4(-)>ClO4(-)>BrO4(-)>IO4(-) . When the graphite electrode was negatively charged, the perhalates provided almost no enhancement of capacitance, while PF6(-) and BF4(-) decreased capacitance by about 15%. Due to the asymmetric impact of nonelectrostatic ion interactions, the capacitances of positive and negative electrodes are not equal. The capacitance of a supercapacitor should therefore be reported as two values rather than one, similar to the matrix of mutual capacitances used in multielectrode devices. Copyright © 2014 Elsevier Inc. All rights reserved.

AMOEBA 2.0: A physics-first approach to biomolecular simulations

NASA Astrophysics Data System (ADS)

Rackers, Joshua; Ponder, Jay

The goal of the AMOEBA force field project is to use classical physics to understand and predict the nature of interactions between biological molecules. While making significant advances over the past decade, the ultimate goal of predicting binding energies with ``chemical accuracy'' remains elusive. The primary source of this inaccuracy comes from the physics of how molecules interact at short range. For example, despite AMOEBA's advanced treatment of electrostatics, the force field dramatically overpredicts the electrostatic energy of DNA stacking interactions. AMOEBA 2.0 works to correct these errors by including simple, first principles physics-based terms to account for the quantum mechanical nature of these short-range molecular interactions. We have added a charge penetration term that considerably improves the description of electrostatic interactions at short range. We are reformulating the polarization term of AMOEBA in terms of basic physics assertions. And we are reevaluating the van der Waals term to match ab initio energy decompositions. These additions and changes promise to make AMOEBA more predictive. By including more physical detail of the important short-range interactions of biological molecules, we hope to move closer to the ultimate goal of true predictive power.

Effect of noncovalent interaction on the self-assembly of a designed peptide and its potential use as a carrier for controlled bFGF release

PubMed Central

Liu, Yanfei; Zhang, Ling; Wei, Wei

2017-01-01

Peptide self-assembly is one of the promising bottom-up approaches for creating synthetic supermolecular architectures. Noncovalent interactions such as hydrophobic packing, electrostatic interaction, and polypeptide chain entropy (ΔSC) are the most relevant factors that affect the folding and self-assembly of peptides and the stability of supermolecular structures. The GVGV tetrapeptide is an abundant repeat in elastin, an extracellular matrix protein. In this study, four GVGV-containing peptides were designed with the aim of understanding the effects of these weak interactions on peptide self-assembly. Transmission electron microscopy, circular dichroism spectroscopy, dynamic light scattering measurements, and rheometry assays were used to study the structural features of the peptides. Because self-assembling peptides with different amino acid sequences may significantly affect protein release, basic fibroblast growth factor (bFGF) was used as a model molecule and encapsulated within the P2 (RLDLGVGVRLDLGVGV) hydrogel to study the release kinetics. The results showed that the balance among hydrophobic effects, electrostatic interactions, and chain entropy determined the molecular state and self-assembly of the peptide. Moreover, encapsulation of bFGF within the P2 hydrogel allowed its sustained release without causing changes in the secondary structure. The release profiles could be tuned by adjusting the P2 hydrogel concentration. Cell Counting Kit-8 and Western blot assays demonstrated that the encapsulated and released bFGFs were biologically active and capable of promoting the proliferation of murine fibroblast NIH-3T3 cells, most likely due to the activation of downstream signaling pathways. PMID:28176898

Fouling of nanofiltration, reverse osmosis, and ultrafiltration membranes by protein mixtures: the role of inter-foulant-species interaction.

PubMed

Wang, Yi-Ning; Tang, Chuyang Y

2011-08-01

Protein fouling of nanofiltration (NF), reverse osmosis (RO), and ultrafiltration (UF) membranes by bovine serum albumin (BSA), lysozyme (LYS), and their mixture was investigated under cross-flow conditions. The effect of solution chemistry, membrane properties, and permeate flux level was systematically studied. When the solution pH was within the isoelectric points (IEPs) of the two proteins (i.e., pH 4.7-10.4), the mixed protein system experienced more severe flux decline compared to the respective single protein systems, which may be attributed to the electrostatic attraction between the negatively charged BSA and positively charged LYS molecules. Unlike a typical single protein system, membrane fouling by BSA-LYS mixture was only weakly dependent on solution pH within this pH range, and increased ionic strength was found to enhance the membrane flux as a result of the suppressed BSA-LYS electrostatic attraction. Membrane fouling was likely controlled by foulant-fouled-membrane interaction under severe fouling conditions (elevated flux level and unfavorable solution chemistry that promotes fouling), whereas it was likely dominated by foulant-clean-membrane interaction under mild fouling conditions. Compared to nonporous NF and RO membranes, the porous UF membrane was more susceptible to dramatic flux decline due to the increased risk of membrane pore plugging. This study reveals that membrane fouling by mixed macromolecules may behave very differently from that by typical single foulant system, especially when the inter-foulant-species interaction dominates over the intra-species interaction in the mixed foulant system.

ZnO nanoparticles modulate the ionic transport and voltage regulation of lysenin nanochannels.

PubMed

Bryant, Sheenah L; Eixenberger, Josh E; Rossland, Steven; Apsley, Holly; Hoffmann, Connor; Shrestha, Nisha; McHugh, Michael; Punnoose, Alex; Fologea, Daniel

2017-12-16

The insufficient understanding of unintended biological impacts from nanomaterials (NMs) represents a serious impediment to their use for scientific, technological, and medical applications. While previous studies have focused on understanding nanotoxicity effects mostly resulting from cellular internalization, recent work indicates that NMs may interfere with transmembrane transport mechanisms, hence enabling contributions to nanotoxicity by affecting key biological activities dependent on transmembrane transport. In this line of inquiry, we investigated the effects of charged nanoparticles (NPs) on the transport properties of lysenin, a pore-forming toxin that shares fundamental features with ion channels such as regulation and high transport rate. The macroscopic conductance of lysenin channels greatly diminished in the presence of cationic ZnO NPs. The inhibitory effects were asymmetrical relative to the direction of the electric field and addition site, suggesting electrostatic interactions between ZnO NPs and a binding site. Similar changes in the macroscopic conductance were observed when lysenin channels were reconstituted in neutral lipid membranes, implicating protein-NP interactions as the major contributor to the reduced transport capabilities. In contrast, no inhibitory effects were observed in the presence of anionic SnO 2 NPs. Additionally, we demonstrate that inhibition of ion transport is not due to the dissolution of ZnO NPs and subsequent interactions of zinc ions with lysenin channels. We conclude that electrostatic interactions between positively charged ZnO NPs and negative charges within the lysenin channels are responsible for the inhibitory effects on the transport of ions. These interactions point to a potential mechanism of cytotoxicity, which may not require NP internalization.

Adsorption and release of amino acids mixture onto apatitic calcium phosphates analogous to bone mineral

NASA Astrophysics Data System (ADS)

El Rhilassi, A.; Mourabet, M.; El Boujaady, H.; Bennani-Ziatni, M.; Hamri, R. El; Taitai, A.

2012-10-01

Study focused on the interaction of adsorbate with poorly crystalline apatitic calcium phosphates analogous to bone mineral. Calcium phosphates prepared in water-ethanol medium at physiological temperature (37 °C) and neutral pH, their Ca/P ratio was between 1.33 and 1.67. Adsorbate used in this paper takes the mixture form of two essential amino acids L-lysine and DL-leucine which have respectively a character hydrophilic and hydrophobic. Adsorption and release are investigated experimentally; they are dependent on the phosphate type and on the nature of adsorbate L-lysine, DL-leucine and their mixture. Adsorption of mixture of amino acids on the apatitic calcium phosphates is influenced by the competition between the two amino acids: L-lysine and DL-leucine which exist in the medium reaction. The adsorption kinetics is very fast while the release kinetics is slow. The chemical composition of apatite has an influence on both adsorption and release. The interactions adsorbate-adsorbent are electrostatic type. Adsorption and release reactions of the amino acid mixture are explained by the existence of the hydrated surface layer of calcium phosphate apatite. The charged sbnd COOsbnd and sbnd NH3+ of adsorbates are the strongest groups that interact with the surface of apatites, the adsorption is mainly due to the electrostatic interaction between the groups sbnd COOsbnd of amino acids and calcium Ca2+ ions of the apatite. Comparative study of interactions between adsorbates (L-lysine, DL-leucine and their mixture) and apatitic calcium phosphates is carried out in vitro by using UV-vis and infrared spectroscopy IR techniques.

Theoretical insights into the π-hole interactions in the complexes containing triphosphorus hydride (P3H3) and its derivatives.

PubMed

Wang, Yuehong; Li, Xiaoyan; Zeng, Yanli; Meng, Lingpeng; Zhang, Xueying

2017-04-01

The π-hole of triphosphorus hydride (P 3 H 3 ) and its derivatives Z 3 X 3 (Z = P, As; X = H, F, Cl, Br) was discovered and analyzed. MP2/aug-cc-pVDZ calculations were performed on the π-hole interactions in the HCN...Z 3 X 3 complexes and the mutual influence between π-hole interactions and the hydrogen bond in the HCN...HCN...Z 3 X 3 and HCN...Z 3 X 3 ...HCN complexes studied. The π-hole interaction belongs to the typical closed-shell noncovalent interaction. The linear relationship was found between the most positive electrostatic potential of the π-hole (V S,max ) and the interaction energy. Moreover, the V S,max of the π-hole was also found to be linearly correlated to the electrostatic energy term, indicating the important contribution of the electrostatic energy term to the π-hole interaction. There is positive cooperativity between the π-hole interaction and the hydrogen bond in the termolecular complexes. The π-hole interaction has a greater influence on the hydrogen bond than vice versa. The mutual enhancing effect between the π-hole interaction and the hydrogen bond in the HCN...HCN...Z 3 X 3 complexes is greater than that in the HCN...Z 3 X 3 ...HCN complexes.

Evidence that electrostatic interactions between vesicle-associated membrane protein 2 and acidic phospholipids may modulate the fusion of transport vesicles with the plasma membrane.

PubMed

Williams, Dumaine; Vicôgne, Jérome; Zaitseva, Irina; McLaughlin, Stuart; Pessin, Jeffrey E

2009-12-01

The juxtamembrane domain of vesicle-associated membrane protein (VAMP) 2 (also known as synaptobrevin2) contains a conserved cluster of basic/hydrophobic residues that may play an important role in membrane fusion. Our measurements on peptides corresponding to this domain determine the electrostatic and hydrophobic energies by which this domain of VAMP2 could bind to the adjacent lipid bilayer in an insulin granule or other transport vesicle. Mutation of residues within the juxtamembrane domain that reduce the VAMP2 net positive charge, and thus its interaction with membranes, inhibits secretion of insulin granules in beta cells. Increasing salt concentration in permeabilized cells, which reduces electrostatic interactions, also results in an inhibition of insulin secretion. Similarly, amphipathic weak bases (e.g., sphingosine) that reverse the negative electrostatic surface potential of a bilayer reverse membrane binding of the positively charged juxtamembrane domain of a reconstituted VAMP2 protein and inhibit membrane fusion. We propose a model in which the positively charged VAMP and syntaxin juxtamembrane regions facilitate fusion by bridging the negatively charged vesicle and plasma membrane leaflets.

Modeling the formation of ordered nano-assemblies comprised by dendrimers and linear polyelectrolytes: The role of Coulombic interactions

NASA Astrophysics Data System (ADS)

Eleftheriou, E.; Karatasos, K.

2012-10-01

Models of mixtures of peripherally charged dendrimers with oppositely charged linear polyelectrolytes in the presence of explicit solvent are studied by means of molecular dynamics simulations. Under the influence of varying strength of electrostatic interactions, these systems appear to form dynamically arrested film-like interconnected structures in the polymer-rich phase. Acting like a pseudo-thermodynamic inverse temperature, the increase of the strength of the Coulombic interactions drive the polymeric constituents of the mixture to a gradual dynamic freezing-in. The timescale of the average density fluctuations of the formed complexes initially increases in the weak electrostatic regime reaching a finite limit as the strength of electrostatic interactions grow. Although the models are overall electrically neutral, during this process the dendrimer/linear complexes develop a polar character with an excess charge mainly close to the periphery of the dendrimers. The morphological characteristics of the resulted pattern are found to depend on the size of the polymer chains on account of the distinct conformational features assumed by the complexed linear polyelectrolytes of different length. In addition, the length of the polymer chain appears to affect the dynamics of the counterions, thus affecting the ionic transport properties of the system. It appears, therefore, that the strength of electrostatic interactions together with the length of the linear polyelectrolytes are parameters to which these systems are particularly responsive, offering thus the possibility for a better control of the resulted structure and the electric properties of these soft-colloidal systems.

Monte Carlo simulations of flexible polyanions complexing with whey proteins at their isoelectric point

NASA Astrophysics Data System (ADS)

de Vries, R.

2004-02-01

Electrostatic complexation of flexible polyanions with the whey proteins α-lactalbumin and β-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Hückel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that α-lactalbumin complexes much more strongly than β-lactoglobulin. For α-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for β-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches.

Protein-ion binding process on finite macromolecular concentration. A Poisson-Boltzmann and Monte Carlo study.

PubMed

de Carvalho, Sidney Jurado; Fenley, Márcia O; da Silva, Fernando Luís Barroso

2008-12-25

Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.

Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80.

PubMed

Anamika; Spyracopoulos, Leo

2016-02-26

Recognition and repair of double-stranded DNA breaks (DSB) involves the targeted recruitment of BRCA tumor suppressors to damage foci through binding of both ubiquitin (Ub) and the Ub-like modifier SUMO. RAP80 is a component of the BRCA1 A complex, and plays a key role in the recruitment process through the binding of Lys(63)-linked poly-Ub chains by tandem Ub interacting motifs (UIM). RAP80 also contains a SUMO interacting motif (SIM) just upstream of the tandem UIMs that has been shown to specifically bind the SUMO-2 isoform. The RAP80 tandem UIMs and SIM function collectively for optimal recruitment of BRCA1 to DSBs, although the molecular basis of this process is not well understood. Using NMR spectroscopy, we demonstrate that the RAP80 SIM binds SUMO-2, and that both specificity and affinity are enhanced through phosphorylation of the canonical CK2 site within the SIM. The affinity increase results from an enhancement of electrostatic interactions between the phosphoserines of RAP80 and the SIM recognition module within SUMO-2. The NMR structure of the SUMO-2·phospho-RAP80 complex reveals that the molecular basis for SUMO-2 specificity is due to isoform-specific sequence differences in electrostatic SIM recognition modules. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties.

PubMed

Wennberg, Christian L; Murtola, Teemu; Hess, Berk; Lindahl, Erik

2013-08-13

The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

The physicochemical process of bacterial attachment to abiotic surfaces: Challenges for mechanistic studies, predictability and the development of control strategies.

PubMed

Wang, Yi; Lee, Sui Mae; Dykes, Gary

2015-01-01

Bacterial attachment to abiotic surfaces can be explained as a physicochemical process. Mechanisms of the process have been widely studied but are not yet well understood due to their complexity. Physicochemical processes can be influenced by various interactions and factors in attachment systems, including, but not limited to, hydrophobic interactions, electrostatic interactions and substratum surface roughness. Mechanistic models and control strategies for bacterial attachment to abiotic surfaces have been established based on the current understanding of the attachment process and the interactions involved. Due to a lack of process control and standardization in the methodologies used to study the mechanisms of bacterial attachment, however, various challenges are apparent in the development of models and control strategies. In this review, the physicochemical mechanisms, interactions and factors affecting the process of bacterial attachment to abiotic surfaces are described. Mechanistic models established based on these parameters are discussed in terms of their limitations. Currently employed methods to study these parameters and bacterial attachment are critically compared. The roles of these parameters in the development of control strategies for bacterial attachment are reviewed, and the challenges that arise in developing mechanistic models and control strategies are assessed.

A Study on the Effect of Surface Lysine to Arginine Mutagenesis on Protein Stability and Structure Using Green Fluorescent Protein

PubMed Central

Sokalingam, Sriram; Raghunathan, Govindan; Soundrarajan, Nagasundarapandian; Lee, Sun-Gu

2012-01-01

Two positively charged basic amino acids, arginine and lysine, are mostly exposed to protein surface, and play important roles in protein stability by forming electrostatic interactions. In particular, the guanidinium group of arginine allows interactions in three possible directions, which enables arginine to form a larger number of electrostatic interactions compared to lysine. The higher pKa of the basic residue in arginine may also generate more stable ionic interactions than lysine. This paper reports an investigation whether the advantageous properties of arginine over lysine can be utilized to enhance protein stability. A variant of green fluorescent protein (GFP) was created by mutating the maximum possible number of lysine residues on the surface to arginines while retaining the activity. When the stability of the variant was examined under a range of denaturing conditions, the variant was relatively more stable compared to control GFP in the presence of chemical denaturants such as urea, alkaline pH and ionic detergents, but the thermal stability of the protein was not changed. The modeled structure of the variant indicated putative new salt bridges and hydrogen bond interactions that help improve the rigidity of the protein against different chemical denaturants. Structural analyses of the electrostatic interactions also confirmed that the geometric properties of the guanidinium group in arginine had such effects. On the other hand, the altered electrostatic interactions induced by the mutagenesis of surface lysines to arginines adversely affected protein folding, which decreased the productivity of the functional form of the variant. These results suggest that the surface lysine mutagenesis to arginines can be considered one of the parameters in protein stability engineering. PMID:22792305

Bile Acid-Based Drug Delivery Systems for Enhanced Doxorubicin Encapsulation: Comparing Hydrophobic and Ionic Interactions in Drug Loading and Release.

PubMed

Cunningham, Alexander J; Robinson, Mattieu; Banquy, Xavier; Leblond, Jeanne; Zhu, X X

2018-03-05

Doxorubicin (Dox) is a drug of choice in the design of drug delivery systems directed toward breast cancers, but is often limited by loading and control over its release from polymer micelles. Bile acid-based block copolymers present certain advantages over traditional polymer-based systems for drug delivery purposes, since they can enable a higher drug loading via the formation of a reservoir through their aggregation process. In this study, hydrophobic and electrostatic interactions are compared for their influence on Dox loading inside cholic acid based block copolymers. Poly(allyl glycidyl ether) (PAGE) and poly(ethylene glycol) (PEG) were grafted from the cholic acid (CA) core yielding a star-shaped block copolymer with 4 arms (CA-(PAGE- b-PEG) 4 ) and then loaded with Dox via a nanoprecipitation technique. A high Dox loading of 14 wt % was achieved via electrostatic as opposed to hydrophobic interactions with or without oleic acid as a cosurfactant. The electrostatic interactions confer a pH responsiveness to the system. 50% of the loaded Dox was released at pH 5 in comparison to 12% at pH 7.4. The nanoparticles with Dox loaded via hydrophobic interactions did not show such a pH responsiveness. The systems with Dox loaded via electrostatic interactions showed the lowest IC 50 and highest cellular internalization, indicating the pre-eminence of this interaction in Dox loading. The blank formulations are biocompatible and did not show cytotoxicity up to 0.17 mg/mL. The new functionalized star block copolymers based on cholic acid show great potential as drug delivery carriers.

Electrostatic Phenomena on Planetary Surfaces

NASA Astrophysics Data System (ADS)

Calle, Carlos I.

2017-02-01

The diverse planetary environments in the solar system react in somewhat different ways to the encompassing influence of the Sun. These different interactions define the electrostatic phenomena that take place on and near planetary surfaces. The desire to understand the electrostatic environments of planetary surfaces goes beyond scientific inquiry. These environments have enormous implications for both human and robotic exploration of the solar system. This book describes in some detail what is known about the electrostatic environment of the solar system from early and current experiments on Earth as well as what is being learned from the instrumentation on the space exploration missions (NASA, European Space Agency, and the Japanese Space Agency) of the last few decades. It begins with a brief review of the basic principles of electrostatics.

Plasma Effects on Fast Pair Beams. II. Reactive versus Kinetic Instability of Parallel Electrostatic Waves

NASA Astrophysics Data System (ADS)

Schlickeiser, R.; Krakau, S.; Supsar, M.

2013-11-01

The interaction of TeV gamma-rays from distant blazars with the extragalactic background light produces relativistic electron-positron pair beams by the photon-photon annihilation process. Using the linear instability analysis in the kinetic limit, which properly accounts for the longitudinal and the small but finite perpendicular momentum spread in the pair momentum distribution function, the growth rate of parallel propagating electrostatic oscillations in the intergalactic medium is calculated. Contrary to the claims of Miniati and Elyiv, we find that neither the longitudinal nor the perpendicular spread in the relativistic pair distribution function significantly affect the electrostatic growth rates. The maximum kinetic growth rate for no perpendicular spread is even about an order of magnitude greater than the corresponding reactive maximum growth rate. The reduction factors in the maximum growth rate due to the finite perpendicular spread in the pair distribution function are tiny and always less than 10-4. We confirm earlier conclusions by Broderick et al. and our group that the created pair beam distribution function is quickly unstable in the unmagnetized intergalactic medium. Therefore, there is no need to require the existence of small intergalactic magnetic fields to scatter the produced pairs, so that the explanation (made by several authors) for the Fermi non-detection of the inverse Compton scattered GeV gamma-rays by a finite deflecting intergalactic magnetic field is not necessary. In particular, the various derived lower bounds for the intergalactic magnetic fields are invalid due to the pair beam instability argument.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

PubMed Central

Gunner, MR; Baker, Nathan A.

2017-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. PMID:27497160

Electrostatic Field Invisibility Cloak

NASA Astrophysics Data System (ADS)

Lan, Chuwen; Yang, Yuping; Geng, Zhaoxin; Li, Bo; Zhou, Ji

2015-11-01

The invisibility cloak has been drawing much attention due to its new concept for manipulating many physical fields, from oscillating wave fields (electromagnetic, acoustic and elastic) to static magnetic fields, dc electric fields, and diffusive fields. Here, an electrostatic field invisibility cloak has been theoretically investigated and experimentally demonstrated to perfectly hide two dimensional objects without disturbing their external electrostatic fields. The desired cloaking effect has been achieved via both cancelling technology and transformation optics (TO). This study demonstrates a novel way for manipulating electrostatic fields, which shows promise for a wide range of potential applications.

Improved Electronic Control for Electrostatic Precipitators

NASA Technical Reports Server (NTRS)

Johnston, D. F.

1986-01-01

Electrostatic precipitators remove particulate matter from smoke created by burning refuse. Smoke exposed to electrostatic field, and particles become electrically charged and migrate to electrically charged collecting surfaces. New microprocessor-based electronic control maintains precipitator power at maximum particulate-collection level. Control automatically senses changes in smoke composition due to variations in fuel or combustion and adjusts precipitator voltage and current accordingly. Also, sensitive yet stable fault detection provided.

Physical and mechanical properties of gelatin-CMC composite films under the influence of electrostatic interactions.

PubMed

Esteghlal, Sara; Niakousari, Mehrdad; Hosseini, Seyed Mohammad Hashem

2018-07-15

The objective of current study was to examine the electrostatic interactions between gelatin and carboxymethyl cellulose (CMC) as a function of pH and mixing ratio (MR) and to observe how the physical and mechanical properties of gelatin-CMC composite films are affected by these interactions. The interaction between biopolymers was studied using turbidometric analysis at different gelatin: CMC MRs and pH values. A reduction in pH and MR enhanced the electrostatic interactions; while, decreased the relative viscosity of mixed system. Physical and mechanical properties of resultant composite films were examined and compared with those of control gelatin films. Changes in the intensity of interactions between the two biopolymers resulted in films with different properties. Polymer complexation led to formation of resistant film networks of less solubility and swellability. Water vapor permeability (WVP) was not significantly (P≤0.05) influenced by incorporating CMC into continuous gelatin films. Composite films prepared at MR of 9:1 and pH opt (corresponding to the maximum amount of interaction) revealed different characteristics such as maximum amounts of WVP and swelling and minimum amounts of tensile strength and solubility. FTIR spectra of composite films confirmed that gelatin and CMC were not covalently bonded. Copyright © 2018 Elsevier B.V. All rights reserved.

Interactions regulating the head-to-tail directed assembly of biological Janus rods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greene, A. C.; Bachand, M.; Gomez, A.

We can generalize the directed, head-to-tail self-assembly of microtubule filaments in the context of Janus colloidal rods. Specifically, their assembly at the tens of micron-length scale involves a careful balance between long-range electrostatic repulsion and short-range attractive forces. We show that the addition of counterion salts increases the rate of directed assembly by screening the electrostatic forces and enhancing the effectiveness of short-range interactions at the microtubule ends.

Interactions regulating the head-to-tail directed assembly of biological Janus rods

DOE PAGES

Greene, A. C.; Bachand, M.; Gomez, A.; ...

2017-03-31

We can generalize the directed, head-to-tail self-assembly of microtubule filaments in the context of Janus colloidal rods. Specifically, their assembly at the tens of micron-length scale involves a careful balance between long-range electrostatic repulsion and short-range attractive forces. We show that the addition of counterion salts increases the rate of directed assembly by screening the electrostatic forces and enhancing the effectiveness of short-range interactions at the microtubule ends.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

NASA Astrophysics Data System (ADS)

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

2015-11-01

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase.

PubMed

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L

2015-11-07

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Electrostatic interaction of positive charges on the surface of Psb31 with photosystem II in the diatom Chaetoceros gracilis.

PubMed

Nagao, Ryo; Suzuki, Takehiro; Okumura, Akinori; Kihira, Tomohiro; Toda, Ayaka; Dohmae, Naoshi; Nakazato, Katsuyoshi; Tomo, Tatsuya

2017-09-01

Psb31, a novel extrinsic protein found in diatom photosystem II (PSII), directly binds to PSII core subunits, independent of the other extrinsic proteins, and functions to maintain optimum oxygen evolution. However, how Psb31 electrostatically interacts with PSII intrinsic proteins remains to be clarified. In this study, we examined electrostatic interaction of Psb31 with PSII complexes isolated from the diatom Chaetoceros gracilis. Positive or negative charges of isolated Psb31 proteins were modified with N-succinimidyl propionate (NSP) or glycine methyl ester (GME), respectively, resulting in formation of uncharged groups. NSP-modified Psb31 did not bind to PSII with a concomitant increase in NSP concentration, whereas GME-modified Psb31 clearly bound to PSII with retention of oxygen-evolving activity, indicating that positive charges of Lys residues and the N-terminus on the surface of Psb31 are involved in electrostatic interactions with PSII intrinsic proteins. Mass spectrometry analysis of NSP-modified Psb31 and sequence comparisons of Psb31 from C. gracilis with other chromophyte algae led to identification of three Lys residues as possible binding sites to PSII. Based on these findings, together with our previous cross-linking study in diatom PSII and a red algal PSII structure, we discuss binding properties of Psb31 with PSII core proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

Electrostatic roles in electron transfer from [NiFe] hydrogenase to cytochrome c3 from Desulfovibrio vulgaris Miyazaki F.

PubMed

Sugimoto, Yu; Kitazumi, Yuki; Shirai, Osamu; Nishikawa, Koji; Higuchi, Yoshiki; Yamamoto, Masahiro; Kano, Kenji

2017-05-01

Electrostatic interactions between proteins are key factors that govern the association and reaction rate. We spectroscopically determine the second-order reaction rate constant (k) of electron transfer from [NiFe] hydrogenase (H 2 ase) to cytochrome (cyt) c 3 at various ionic strengths (I). The k value decreases with I. To analyze the results, we develop a semi-analytical formula for I dependence of k based on the assumptions that molecules are spherical and the reaction proceeds via a transition state. Fitting of the formula to the experimental data reveals that the interaction occurs in limited regions with opposite charges and with radii much smaller than those estimated from crystal structures. This suggests that local charges in H 2 ase and cyt c 3 play important roles in the reaction. Although the crystallographic data indicate a positive electrostatic potential over almost the entire surface of the proteins, there exists a small region with negative potential on H 2 ase at which the electron transfer from H 2 ase to cyt c 3 may occur. This local negative potential region is identical to the hypothetical interaction sphere predicted by the analysis. Furthermore, I dependence of k is predicted by the Adaptive Poisson-Boltzmann Solver considering all charges of the amino acids in the proteins and the configuration of H 2 ase/cyt c 3 complex. The calculation reproduces the experimental results except at extremely low I. These results indicate that the stabilization derived from the local electrostatic interaction in the H 2 ase/cyt c 3 complex overcomes the destabilization derived from the electrostatic repulsion of the overall positive charge of both proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation of intermolecular interactions in finasteride drug crystals in view of X-ray and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Bojarska, Joanna; Maniukiewicz, Waldemar

2015-11-01

The N,N-dimethylformamide (DMF) solvate hemihydrate (1) of finasteride, has been structurally characterized by single-crystal X-ray diffraction at 100 K and compared with previously reported finasteride crystalline forms. In addition, in order to resolve ambiguity concerning H-bond interactions, the crystal structure of finasteride hemihydrate, (2), originally reported by Schultheiss et al. in 2009, has been redetermined with higher precision. The (1) and (2) pseudopolymorphs of finasteride crystallize as orthorhombic in chiral P212121 space group with two very similar host molecules in the asymmetric unit. The conformation of fused 6-membered rings are screw-boat, chair and chair for both molecules, while 5-membered rings assume chair in (1), and half-chair in (2). There is a fairly close resemblance of the molecular geometry for all analyzed compounds, arising due to the rigid host molecule. Inter- and intramolecular host-host, host-guest strong O-H⋯O, N-H⋯O hydrogen bonds and weak C-H⋯O interactions form 3D net conferring stability to the crystal packing. Finasterides can be classified as synthon pseudopolymorphs. Isostructural solvates crystallizing in the orthorhombic space group P212121, with Z‧ = 2, exhibit R22(8) C22(15) network, monoclinic solvate (Z‧ = 1) possess D11(2), while both orthorhombic and monoclinic polymorphs have C(4) motifs, respectively. The structural similarities and subtle differences have been interpreted in view of the 3D Hirshfeld surface analysis and associated 2D fingerprint plots, which enabled detailed qualitative and quantitative insight into the intermolecular interactions. The 97-100% of Hirshfeld surface areas are due to H···H, O···H/H⋯O, C···H/H⋯C and N⋯H/H⋯N contacts. Furthermore, the electrostatic potential has been mapped over the Hirshfeld surfaces to decode the electrostatic complementarities, which exist in the crystal packing.

Versatile organic (fullerene)-inorganic (CdTe nanoparticle) nanoensembles.

PubMed

Guldi, Dirk M; Zilbermann, Israel; Anderson, Greg; Kotov, Nicholas A; Tagmatarchis, Nikos; Prato, Maurizio

2004-11-10

Novel organic (positively charged fullerene)-inorganic (negatively charged CdTe nanoparticle) nanoensembles were devised through electrostatic interactions and probed as versatile donor-acceptor hybrids. Photoirradiation of their homogeneous solutions, containing the electrostatically packed components, let to very long-lived (1.3 ms) charge separated states.

Electrostatic 2D assembly of bionanoparticles on a cationic lipid monolayer.

NASA Astrophysics Data System (ADS)

Kewalramani, Sumit; Wang, Suntao; Fukuto, Masafumi; Yang, Lin; Niu, Zhongwei; Nguyen, Giang; Wang, Qian

2010-03-01

We present a grazing-incidence small-angle X-ray scattering (GISAXS) study on 2D assembly of cowpea mosaic virus (CPMV) under a mixed cationic-zwitterionic (DMTAP^+-DMPC) lipid monolayer at the air-water interface. The inter-particle and particle-lipid electrostatic interactions were varied by controlling the subphase pH and the membrane charge density. GISAXS data show that 2D crystals of CPMV are formed above a threshold membrane charge density and only in a narrow pH range just above CPMV's isoelectric point, where the charge on CPMV is expected to be weakly negative. The particle density for the 2D crystals is similar to that for the densest lattice plane in the 3D crystals of CPMV. The results show that the 2D crystallization is achieved in the part of the phase space where the electrostatic interactions are expected to maximize the adsorption of CPMV onto the lipid membrane. This electrostatics-based strategy for controlling interfacial nanoscale assembly should be generally applicable to other nanoparticles.

Quantitative nanoscale electrostatics of viruses.

PubMed

Hernando-Pérez, M; Cartagena-Rivera, A X; Lošdorfer Božič, A; Carrillo, P J P; San Martín, C; Mateu, M G; Raman, A; Podgornik, R; de Pablo, P J

2015-11-07

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed ϕ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.

Electrostatic Similarities between Protein and Small Molecule Ligands Facilitate the Design of Protein-Protein Interaction Inhibitors

PubMed Central

Zhang, Kam Y. J.

2013-01-01

One of the underlying principles in drug discovery is that a biologically active compound is complimentary in shape and molecular recognition features to its receptor. This principle infers that molecules binding to the same receptor may share some common features. Here, we have investigated whether the electrostatic similarity can be used for the discovery of small molecule protein-protein interaction inhibitors (SMPPIIs). We have developed a method that can be used to evaluate the similarity of electrostatic potentials between small molecules and known protein ligands. This method was implemented in a software called EleKit. Analyses of all available (at the time of research) SMPPII structures indicate that SMPPIIs bear some similarities of electrostatic potential with the ligand proteins of the same receptor. This is especially true for the more polar SMPPIIs. Retrospective analysis of several successful SMPPIIs has shown the applicability of EleKit in the design of new SMPPIIs. PMID:24130741

Space-charge-mediated anomalous ferroelectric switching in P(VDF-TrEE) polymer films.

PubMed

Hu, Weijin; Wang, Zhihong; Du, Yuanmin; Zhang, Xi-Xiang; Wu, Tom

2014-11-12

We report on the switching dynamics of P(VDF-TrEE) copolymer devices and the realization of additional substable ferroelectric states via modulation of the coupling between polarizations and space charges. The space-charge-limited current is revealed to be the dominant leakage mechanism in such organic ferroelectric devices, and electrostatic interactions due to space charges lead to the emergence of anomalous ferroelectric loops. The reliable control of ferroelectric switching in P(VDF-TrEE) copolymers opens doors toward engineering advanced organic memories with tailored switching characteristics.

Chromium(VI) Removal from Aqueous Solution by Magnetite Coated by a Polymeric Ionic Liquid-Based Adsorbent

PubMed Central

Ferreira, Thania Alexandra; Rodriguez, Jose Antonio; Paez-Hernandez, María Elena; Guevara-Lara, Alfredo; Barrado, Enrique; Hernandez, Prisciliano

2017-01-01

An evaluation of the chromium(VI) adsorption capacity of four magnetite sorbents coated with a polymer phase containing polymethacrylic acid or polyallyl-3-methylimidazolium is presented. Factors that influence the chromium(VI) removal such as solution pH and contact time were investigated in batch experiments and in stirred tank reactor mode. Affinity and rate constants increased with the molar ratio of the imidazolium. The highest adsorption was obtained at pH 2.0 due to the contribution of electrostatic interactions. PMID:28772865

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Search for Screened Interactions Associated with Dark Energy below the 100 μm Length Scale.

PubMed

Rider, Alexander D; Moore, David C; Blakemore, Charles P; Louis, Maxime; Lu, Marie; Gratta, Giorgio

2016-09-02

We present the results of a search for unknown interactions that couple to mass between an optically levitated microsphere and a gold-coated silicon cantilever. The scale and geometry of the apparatus enable a search for new forces that appear at distances below 100  μm and which would have evaded previous searches due to screening mechanisms. The data are consistent with electrostatic backgrounds and place upper limits on the strength of new interactions at <0.1  fN in the geometry tested. For the specific example of a chameleon interaction with an inverse power law potential, these results exclude matter couplings β>5.6×10^{4} in the region of parameter space where the self-coupling Λ≳5  meV and the microspheres are not fully screened.

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Protein–Protein Interactions in Dilute to Concentrated Solutions: α-Chymotrypsinogen in Acidic Conditions

PubMed Central

2015-01-01

Protein–protein interactions were investigated for α-chymotrypsinogen by static and dynamic light scattering (SLS and DLS, respectively), as well as small-angle neutron scattering (SANS), as a function of protein and salt concentration at acidic conditions. Net protein–protein interactions were probed via the Kirkwood–Buff integral G22 and the static structure factor S(q) from SLS and SANS data. G22 was obtained by regressing the Rayleigh ratio versus protein concentration with a local Taylor series approach, which does not require one to assume the underlying form or nature of intermolecular interactions. In addition, G22 and S(q) were further analyzed by traditional methods involving fits to effective interaction potentials. Although the fitted model parameters were not always physically realistic, the numerical values for G22 and S(q → 0) were in good agreement from SLS and SANS as a function of protein concentration. In the dilute regime, fitted G22 values agreed with those obtained via the osmotic second virial coefficient B22 and showed that electrostatic interactions are the dominant contribution for colloidal interactions in α-chymotrypsinogen solutions. However, as protein concentration increases, the strength of protein–protein interactions decreases, with a more pronounced decrease at low salt concentrations. The results are consistent with an effective “crowding” or excluded volume contribution to G22 due to the long-ranged electrostatic repulsions that are prominent even at the moderate range of protein concentrations used here (<40 g/L). These apparent crowding effects were confirmed and quantified by assessing the hydrodynamic factor H(q → 0), which is obtained by combining measurements of the collective diffusion coefficient from DLS data with measurements of S(q → 0). H(q → 0) was significantly less than that for a corresponding hard-sphere system and showed that hydrodynamic nonidealities can lead to qualitatively incorrect conclusions regarding B22, G22, and static protein–protein interactions if one uses only DLS to assess protein interactions. PMID:24810917

Electrostatic energy and screened charge interaction near the surface of metals with different Fermi surface shape

NASA Astrophysics Data System (ADS)

Gabovich, A. M.; Il'chenko, L. G.; Pashitskii, E. A.; Romanov, Yu. A.

1980-04-01

Using the Poisson equation Green function for a self-consistent field in a spatially inhomogeneous system, expressions for the electrostatic energy and screened charge interaction near the surface of a semi-infinite metal and a thin quantizing film are derived. It is shown that the decrease law and Friedel oscillation amplitude of adsorbed atom indirect interaction are determined by the electron spectrum character and the Fermi surface shape. The results obtained enable us to explain, in particular, the submonolayer adsorbed film structure on the W and Mo surfaces.

The “Electrostatic-Switch” Mechanism: Monte Carlo Study of MARCKS-Membrane Interaction

PubMed Central

Tzlil, Shelly; Murray, Diana; Ben-Shaul, Avinoam

2008-01-01

The binding of the myristoylated alanine-rich C kinase substrate (MARCKS) to mixed, fluid, phospholipid membranes is modeled with a recently developed Monte Carlo simulation scheme. The central domain of MARCKS is both basic (ζ = +13) and hydrophobic (five Phe residues), and is flanked with two long chains, one ending with the myristoylated N-terminus. This natively unfolded protein is modeled as a flexible chain of “beads” representing the amino acid residues. The membranes contain neutral (ζ = 0), monovalent (ζ = −1), and tetravalent (ζ = −4) lipids, all of which are laterally mobile. MARCKS-membrane interaction is modeled by Debye-Hückel electrostatic potentials and semiempirical hydrophobic energies. In agreement with experiment, we find that membrane binding is mediated by electrostatic attraction of the basic domain to acidic lipids and membrane penetration of its hydrophobic moieties. The binding is opposed by configurational entropy losses and electrostatic membrane repulsion of the two long chains, and by lipid demixing upon adsorption. The simulations provide a physical model for how membrane-adsorbed MARCKS attracts several PIP2 lipids (ζ = −4) to its vicinity, and how phosphorylation of the central domain (ζ = +13 to ζ = +7) triggers an “electrostatic switch”, which weakens both the membrane interaction and PIP2 sequestration. This scheme captures the essence of “discreteness of charge” at membrane surfaces and can examine the formation of membrane-mediated multicomponent macromolecular complexes that function in many cellular processes. PMID:18502797

Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study

PubMed Central

2015-01-01

A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation. PMID:24393011

An anisotropic hydrogel with electrostatic repulsion between cofacially aligned nanosheets

NASA Astrophysics Data System (ADS)

Liu, Mingjie; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Takata, Masaki; Aida, Takuzo

2015-01-01

Machine technology frequently puts magnetic or electrostatic repulsive forces to practical use, as in maglev trains, vehicle suspensions or non-contact bearings. In contrast, materials design overwhelmingly focuses on attractive interactions, such as in the many advanced polymer-based composites, where inorganic fillers interact with a polymer matrix to improve mechanical properties. However, articular cartilage strikingly illustrates how electrostatic repulsion can be harnessed to achieve unparalleled functional efficiency: it permits virtually frictionless mechanical motion within joints, even under high compression. Here we describe a composite hydrogel with anisotropic mechanical properties dominated by electrostatic repulsion between negatively charged unilamellar titanate nanosheets embedded within it. Crucial to the behaviour of this hydrogel is the serendipitous discovery of cofacial nanosheet alignment in aqueous colloidal dispersions subjected to a strong magnetic field, which maximizes electrostatic repulsion and thereby induces a quasi-crystalline structural ordering over macroscopic length scales and with uniformly large face-to-face nanosheet separation. We fix this transiently induced structural order by transforming the dispersion into a hydrogel using light-triggered in situ vinyl polymerization. The resultant hydrogel, containing charged inorganic structures that align cofacially in a magnetic flux, deforms easily under shear forces applied parallel to the embedded nanosheets yet resists compressive forces applied orthogonally. We anticipate that the concept of embedding anisotropic repulsive electrostatics within a composite material, inspired by articular cartilage, will open up new possibilities for developing soft materials with unusual functions.

An anisotropic hydrogel with electrostatic repulsion between cofacially aligned nanosheets.

PubMed

Liu, Mingjie; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Takata, Masaki; Aida, Takuzo

2015-01-01

Machine technology frequently puts magnetic or electrostatic repulsive forces to practical use, as in maglev trains, vehicle suspensions or non-contact bearings. In contrast, materials design overwhelmingly focuses on attractive interactions, such as in the many advanced polymer-based composites, where inorganic fillers interact with a polymer matrix to improve mechanical properties. However, articular cartilage strikingly illustrates how electrostatic repulsion can be harnessed to achieve unparalleled functional efficiency: it permits virtually frictionless mechanical motion within joints, even under high compression. Here we describe a composite hydrogel with anisotropic mechanical properties dominated by electrostatic repulsion between negatively charged unilamellar titanate nanosheets embedded within it. Crucial to the behaviour of this hydrogel is the serendipitous discovery of cofacial nanosheet alignment in aqueous colloidal dispersions subjected to a strong magnetic field, which maximizes electrostatic repulsion and thereby induces a quasi-crystalline structural ordering over macroscopic length scales and with uniformly large face-to-face nanosheet separation. We fix this transiently induced structural order by transforming the dispersion into a hydrogel using light-triggered in situ vinyl polymerization. The resultant hydrogel, containing charged inorganic structures that align cofacially in a magnetic flux, deforms easily under shear forces applied parallel to the embedded nanosheets yet resists compressive forces applied orthogonally. We anticipate that the concept of embedding anisotropic repulsive electrostatics within a composite material, inspired by articular cartilage, will open up new possibilities for developing soft materials with unusual functions.

Interactions of molecules and the properties of crystals

NASA Astrophysics Data System (ADS)

McConnell, Thomas Daniel Leigh

In this thesis the basic theory of the lattice dynamics of molecular crystals is considered, with particular reference to the specific case of linear molecules. The objective is to carry out a critical investigation of a number of empirical potentials as models for real systems. Suitable coordinates are introduced, in particular vibrational coordinates which are used to describe the translational and rotational modes of the free molecule. The Taylor expansion of the intermolecular potential is introduced and its terms considered, in particular the (first-order) equilibrium conditions for such a system and the (second-order) lattice vibrations. The elastic properties are also considered, in particular with reference to the specific case of rhombohedral crystals. The compressibility and a number of conditions for elastic stability are introduced. The total intermolecular interaction potential is divided into three components using perturbation methods, the electrostatic energy, the repulsion energy and the dispersion energy. A number of models are introduced for these various components. The induction energy is neglected. The electrostatic interaction is represented by atomic multipole and molecular multipole models. The repulsion and dispersion energies are modelled together in a central interaction potential, either the Lennard-Jones atom-atom potential or the anisotropic Berne-Pechukas molecule-molecule potential. In each case, the Taylor expansion coefficients, used to calculate the various molecular properties, are determined. An algorithm is described which provides a relatively simple method for calculating cartesian tensors, which are found in the Taylor expansion coefficients of the multipolar potentials. This proves to be particularly useful from a computational viewpoint, both in terms of programming and calculating efficiency. The model system carbonyl sulphide is introduced and its lattice properties are described. Suitable parameters for potentials used to model the system are discussed and the simplifications to the Taylor expansion coefficients due to crystal symmetry are detailed. Four potential parameters are chosen to be fitted to four lattice properties, representing zero, first and second order Taylor expansion coefficients. The supplementary tests of a given fitted potential are detailed. A number of forms for the electrostatic interaction of carbonyl sulphide are considered, each combined with a standard atom-atom potential. The success of the molecular octupole model is considered and the inability of more complex electrostatic potentials to improve on this simple model is noted. The anisotropic Berne-Pechukas potential, which provides an increased estimate of the compressibility is considered as being an improvement on the various atom-atom potentials. The effect of varying the exponents in the atom-atom (or molecule-molecule) potential, representing a systematic variation of the repulsion and dispersion energy models, is examined and a potential which is able to reproduce all of the given lattice properties for carbonyl sulphide is obtained. The molecular crystal of cyanogen iodide is investigated. Superficially it is similar to the crystal of carbonyl sulphide and the potentials used with success for the latter are applied to cyanogen iodide to determine whether they are equally as effective models for this molecule. These potentials are found to be far less successful, in all cases yielding a number of unrealistic results. Reasons for the failure of the model are considered, in particular the 3 differences between the electrostatic properties of the two molecules are discussed. It is concluded that some of the simplifications which proved satisfactory for carbonyl sulphide are invalid for simple extension to the case of cyanogen iodide. A first estimate of the differences in the electrostatic properties is attempted, calculating the induction energies of the two molecules. The assumption that the induction energy may be neglected is justified for the case of carbonyl sulphide but found to be far less satisfactory for cyanogen iodide. Finally details of ab initio calculations are outlined. The amount of experimental data available for the electrostatic properties of the two molecules under consideration is relatively small and the experimental data which is available is supplemented by values obtained from these calculations.

Structure and dynamics of hyaluronic acid semidilute solutions: a dielectric spectroscopy study.

PubMed

Vuletić, T; Dolanski Babić, S; Ivek, T; Grgicin, D; Tomić, S; Podgornik, R

2010-07-01

Dielectric spectroscopy is used to investigate fundamental length scales describing the structure of hyaluronic acid sodium salt (Na-HA) semidilute aqueous solutions. In salt-free regime, the length scale of the relaxation mode detected in MHz range scales with HA concentration as c(HA)(-0.5) and corresponds to the de Gennes-Pfeuty-Dobrynin correlation length of polyelectrolytes in semidilute solution. The same scaling was observed for the case of long, genomic DNA. Conversely, the length scale of the mode detected in kilohertz range also varies with HA concentration as c(HA)(-0.5) which differs from the case of DNA (c(DNA)(-0.25)). The observed behavior suggests that the relaxation in the kilohertz range reveals the de Gennes-Dobrynin renormalized Debye screening length, and not the average size of the chain, as the pertinent length scale. Similarly, with increasing added salt the electrostatic contribution to the HA persistence length is observed to scale as the Debye length, contrary to scaling pertinent to the Odijk-Skolnick-Fixman electrostatic persistence length observed in the case of DNA. We argue that the observed features of the kilohertz range relaxation are due to much weaker electrostatic interactions that lead to the absence of Manning condensation as well as a rather high flexibility of HA as compared to DNA.

Electrostatic immobilization of antimicrobial peptides on polyethylenimine and their antibacterial effect against Staphylococcus epidermidis.

PubMed

Hernandez-Montelongo, J; Corrales Ureña, Y R; Machado, D; Lancelloti, M; Pinheiro, M P; Rischka, K; Lisboa-Filho, P N; Cotta, M A

2018-04-01

Staphylococcus epidermidis is a gram-positive bacterium, and one of the most prevalent causes of nosocomial infections due to its strong ability to form biofilms on catheters and surgical implants. Here we explore the antimicrobial properties of Tet-124 peptides, which are part of the innate defense against different multicellular organisms in nature. Two different Tet-124 peptides were immobilized on a polyethylenimine (PEI) film to determine their impact on the antimicrobial properties: KLWWMIRRW (Tet-124), which contains only natural amino acids, and KLWWMIRRWG-(F-Br)-G (F-Br = 4-Bromophenylalanine), a modified Tet-124 sequence with the addition of an unnatural amino acid. The immobilization was obtained as a result of the electrostatic interaction between PEI amino groups and the C-terminal carboxylic groups of tryptophan and glycine amino acids of Tet-124 and Tet-124-Br peptides, respectively. The process was monitored and studied by water contact angle, Atomic Force Microscopy (AFM), X-ray Photoelectron Spectroscopy (XPS) and Quartz Crystal Microbalance with Dissipation (QCM-D) measurements. The antibacterial effect of our samples against S. epidermis was evaluated by the spread plate counting method, and cytotoxicity was tested using fibroblast cultures. Our results indicate the feasibility to immobilize electrostatically both Tet-124 peptides for biomedical applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Predicting Electrostatic Forces in RNA Folding

PubMed Central

Tan, Zhi-Jie; Chen, Shi-Jie

2016-01-01

Metal ion-mediated electrostatic interactions are critical to RNA folding. Although considerable progress has been made in mechanistic studies, the problem of accurate predictions for the ion effects in RNA folding remains unsolved, mainly due to the complexity of several potentially important issues such as ion correlation and dehydration effects. In this chapter, after giving a brief overview of the experimental findings and theoretical approaches, we focus on a recently developed new model, the tightly bound ion (TBI) model, for ion electrostatics in RNA folding. The model is unique because it can treat ion correlation and fluctuation effects for realistic RNA 3D structures. For monovalent ion (such as Na+) solutions, where ion correlation is weak, TBI and the Poisson–Boltzmann (PB) theory give the same results and the results agree with the experimental data. For multivalent ion (such as Mg2+) solutions, where ion correlation can be strong, however, TBI gives much improved predictions than the PB. Moreover, the model suggests an ion correlation- induced mechanism for the unusual efficiency of Mg2+ ions in the stabilization of RNA tertiary folds. In this chapter, after introducing the theoretical framework of the TBI model, we will describe how to apply the model to predict ion-binding properties and ion-dependent folding stabilities. PMID:20946803

An experimental system for controlled exposure of biological samples to electrostatic discharges.

PubMed

Marjanovič, Igor; Kotnik, Tadej

2013-12-01

Electrostatic discharges occur naturally as lightning strokes, and artificially in light sources and in materials processing. When an electrostatic discharge interacts with living matter, the basic physical effects can be accompanied by biophysical and biochemical phenomena, including cell excitation, electroporation, and electrofusion. To study these phenomena, we developed an experimental system that provides easy sample insertion and removal, protection from airborne particles, observability during the experiment, accurate discharge origin positioning, discharge delivery into the sample either through an electric arc with adjustable air gap width or through direct contact, and reliable electrical insulation where required. We tested the system by assessing irreversible electroporation of Escherichia coli bacteria (15 mm discharge arc, 100 A peak current, 0.1 μs zero-to-peak time, 0.2 μs peak-to-halving time), and gene electrotransfer into CHO cells (7 mm discharge arc, 14 A peak current, 0.5 μs zero-to-peak time, 1.0 μs peak-to-halving time). Exposures to natural lightning stroke can also be studied with this system, as due to radial current dissipation, the conditions achieved by a stroke at a particular distance from its entry are also achieved by an artificial discharge with electric current downscaled in magnitude, but similar in time course, correspondingly closer to its entry. © 2013.

Explaining reaction mechanisms using the dual descriptor: a complementary tool to the molecular electrostatic potential.

PubMed

Martínez-Araya, Jorge Ignacio

2013-07-01

The intrinsic reactivity of cyanide when interacting with a silver cation was rationalized using the dual descriptor (DD) as a complement to the molecular electrostatic potential (MEP) in order to predict interactions at the local level. It was found that DD accurately explains covalent interactions that cannot be explained by MEP, which focuses on essentially ionic interactions. This allowed the rationalization of the reaction mechanism that yields silver cyanide in the gas phase. Other similar reaction mechanisms involving a silver cation interacting with water, ammonia, and thiosulfate were also explained by the combination of MEP and DD. This analysis provides another example of the usefulness of DD as a tool for gaining a deeper understanding of any reaction mechanism that is mainly governed by covalent interactions.

Combined effect of moisture and electrostatic charges on powder flow

NASA Astrophysics Data System (ADS)

Rescaglio, Antonella; Schockmel, Julien; Vandewalle, Nicolas; Lumay, Geoffroy

2017-06-01

It is well known in industrial applications involving powders and granular materials that the relative air humidity and the presence of electrostatic charges influence drastically the material flowing properties. The relative air humidity induces the formation of capillary bridges and modify the grain surface conductivity. The presence of capillary bridges produces cohesive forces. On the other hand, the apparition of electrostatic charges due to the triboelectric effect at the contacts between the grains and at the contacts between the grains and the container produces electrostatic forces. Therefore, in many cases, the powder cohesiveness is the result of the interplay between capillary and electrostatic forces. Unfortunately, the triboelectric effect is still poorly understood, in particular inside a granular material. Moreover, reproducible electrostatic measurements are difficult to perform. We developed an experimental device to measures the ability of a powder to charge electrostatically during a flow in contact with a selected material. Both electrostatic and flow measurements have been performed in different hygrometric conditions. The correlation between the powder electrostatic properties, the hygrometry and the flowing behavior are analyzed.

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach.

PubMed

Rubinstein, Alexander I; Sabirianov, Renat F; Namavar, Fereydoon

2016-10-14

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ∼80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

Effects of the dielectric properties of the ceramic-solvent interface on the binding of proteins to oxide ceramics: a non-local electrostatic approach

NASA Astrophysics Data System (ADS)

Rubinstein, Alexander I.; Sabirianov, Renat F.; Namavar, Fereydoon

2016-10-01

The rapid development of nanoscience and nanotechnology has raised many fundamental questions that significantly impede progress in these fields. In particular, understanding the physicochemical processes at the interface in aqueous solvents requires the development and application of efficient and accurate methods. In the present work we evaluate the electrostatic contribution to the energy of model protein-ceramic complex formation in an aqueous solvent. We apply a non-local (NL) electrostatic approach that accounts for the effects of the short-range structure of the solvent on the electrostatic interactions of the interfacial systems. In this approach the aqueous solvent is considered as a non-ionic liquid, with the rigid and strongly correlated dipoles of the water molecules. We have found that an ordered interfacial aqueous solvent layer at the protein- and ceramic-solvent interfaces reduces the charging energy of both the ceramic and the protein in the solvent, and significantly increases the electrostatic contribution to their association into a complex. This contribution in the presented NL approach was found to be significantly shifted with respect to the classical model at any dielectric constant value of the ceramics. This implies a significant increase of the adsorption energy in the protein-ceramic complex formation for any ceramic material. We show that for several biocompatible ceramics (for example HfO2, ZrO2, and Ta2O5) the above effect predicts electrostatically induced protein-ceramic complex formation. However, in the framework of the classical continuum electrostatic model (the aqueous solvent as a uniform dielectric medium with a high dielectric constant ˜80) the above ceramics cannot be considered as suitable for electrostatically induced complex formation. Our results also show that the protein-ceramic electrostatic interactions can be strong enough to compensate for the unfavorable desolvation effect in the process of protein-ceramic complex formation.

irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules--a GPU solver using the fast multipole method and statistical thermodynamics.

PubMed

Kantardjiev, Alexander A

2015-04-05

A cluster of strongly interacting ionization groups in protein molecules with irregular ionization behavior is suggestive for specific structure-function relationship. However, their computational treatment is unconventional (e.g., lack of convergence in naive self-consistent iterative algorithm). The stringent evaluation requires evaluation of Boltzmann averaged statistical mechanics sums and electrostatic energy estimation for each microstate. irGPU: Irregular strong interactions in proteins--a GPU solver is novel solution to a versatile problem in protein biophysics--atypical protonation behavior of coupled groups. The computational severity of the problem is alleviated by parallelization (via GPU kernels) which is applied for the electrostatic interaction evaluation (including explicit electrostatics via the fast multipole method) as well as statistical mechanics sums (partition function) estimation. Special attention is given to the ease of the service and encapsulation of theoretical details without sacrificing rigor of computational procedures. irGPU is not just a solution-in-principle but a promising practical application with potential to entice community into deeper understanding of principles governing biomolecule mechanisms. © 2015 Wiley Periodicals, Inc.

The bee, the flower, and the electric field: electric ecology and aerial electroreception.

PubMed

Clarke, Dominic; Morley, Erica; Robert, Daniel

2017-09-01

Bees and flowering plants have a long-standing and remarkable co-evolutionary history. Flowers and bees evolved traits that enable pollination, a process that is as important to plants as it is for pollinating insects. From the sensory ecological viewpoint, bee-flower interactions rely on senses such as vision, olfaction, humidity sensing, and touch. Recently, another sensory modality has been unveiled; the detection of the weak electrostatic field that arises between a flower and a bee. Here, we present our latest understanding of how these electric interactions arise and how they contribute to pollination and electroreception. Finite-element modelling and experimental evidence offer new insights into how these interactions are organised and how they can be further studied. Focussing on pollen transfer, we deconstruct some of the salient features of the three ingredients that enable electrostatic interactions, namely the atmospheric electric field, the capacity of bees to accumulate positive charge, and the propensity of plants to be relatively negatively charged. This article also aims at highlighting areas in need of further investigation, where more research is required to better understand the mechanisms of electrostatic interactions and aerial electroreception.

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

PubMed

Kato, Mitsunori; Pisliakov, Andrei V; Warshel, Arieh

2006-09-01

The origin of the barrier for proton transport through the aquaporin channel is a problem of general interest. It is becoming increasingly clear that this barrier is not attributable to the orientation of the water molecules across the channel but rather to the electrostatic penalty for moving the proton charge to the center of the channel. However, the reason for the high electrostatic barrier is still rather controversial. It has been argued by some workers that the barrier is due to the so-called NPA motif and/or to the helix macrodipole or to other specific elements. However, our works indicated that the main reason for the high barrier is the loss of the generalized solvation upon moving the proton charge from the bulk to the center of the channel and that this does not reflect a specific repulsive electrostatic interaction but the absence of sufficient electrostatic stabilization. At this stage it seems that the elucidation and clarification of the origin of the electrostatic barrier can serve as an instructive test case for electrostatic models. Thus, we reexamine the free-energy surface for proton transport in aquaporins using the microscopic free-energy perturbation/umbrella sampling (FEP/US) and the empirical valence bond/umbrella sampling (EVB/US) methods as well as the semimacroscopic protein dipole Langevin dipole model in its linear response approximation version (the PDLD/S-LRA). These extensive studies help to clarify the nature of the barrier and to establish the "reduced solvation effect" as the primary source of this barrier. That is, it is found that the barrier is associated with the loss of the generalized solvation energy (which includes of course all electrostatic effects) upon moving the proton charge from the bulk solvent to the center of the channel. It is also demonstrated that the residues in the NPA region and the helix dipole cannot be considered as the main reasons for the electrostatic barrier. Furthermore, our microscopic and semimacroscopic studies clarify the problems with incomplete alternative calculations, illustrating that the effects of various electrostatic elements are drastically overestimated by macroscopic calculations that use a low dielectric constant and do not consider the protein reorganization. Similarly, it is pointed out that microscopic potential of mean force calculations that do not evaluate the electrostatic barrier relative to the bulk water cannot be used to establish the origin of the electrostatic barrier. The relationship between the present study and calculations of pK(a)s in protein interiors is clarified, pointing out that approaches that are applied to study the aquaporin barrier should be validated by pK(a)s calculations. Such calculations also help to clarify the crucial role of solvation energies in establishing the barrier in aquaporins. (c) 2006 Wiley-Liss, Inc.

The Influence of Fluorocarbon and Hydrocarbon Acyl Groups at the Surface of Bovine Carbonic Anhydrase II on the Kinetics of Denaturation by Sodium Dodecyl Sulfate

PubMed Central

Lee, Andrew; Mirica, Katherine A.; Whitesides, George M.

2011-01-01

This paper examines the influence of acylation of the Lys-ε-NH3+ groups of bovine carbonic anhydrase (BCA, E.C. 4.2.1.1) to Lys-ε-NHCOR (R = -CH3, -CH2CH3, and -CH(CH3)2, -CF3) on the rate of denaturation of this protein in buffer containing sodium dodecyl sulfate (SDS). Analysis of the rates suggested separate effects due to electrostatic charge and hydrophobic interactions. Rates of denaturation (kAc,n) of each series of acylated derivatives depended on the number of acylations (n). Plots of log kAc,n vs. n followed U-shaped curves. Within each series of derivatives, rates of denaturation decreased as n increased to ~7; this decrease was compatible with increasingly unfavorable electrostatic interactions between SDS and protein. In this range of n, rates of denaturation also depended on the choice of the acyl group as n increased to ~7, in a manner compatible with favorable hydrophobic interactions between SDS and the -NHCOR groups. As n increased in the range 7 < n < 14 however, rates of denaturation stayed approximately constant; analysis suggested these rates were compatible with an increasingly important contribution to denaturation that depended both on the net negative charge of the protein and on the hydrophobicity of the R group. The mechanism of denaturation thus seems to change with the extent of acylation of the protein. For derivatives with the same net electrostatic charge, rates of denaturation increased with the acyl group (by a factor of ~3 for n ~ 14) in the order CH3CONH- < CH3CH2CONH- < (CH3)2CHCONH- < CF3CONH-. These results suggested that the hydrophobicity of CF3CONH- is slightly greater (by a factor of < 2) than that of RHCONH- similar in surface area. PMID:21182314

Multiscale Multiphysics and Multidomain Models I: Basic Theory

PubMed Central

Wei, Guo-Wei

2013-01-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field. PMID:25382892

Multiscale Multiphysics and Multidomain Models I: Basic Theory.

PubMed

Wei, Guo-Wei

2013-12-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.

Influence of fluorocarbon and hydrocarbon acyl groups at the surface of bovine carbonic anhydrase II on the kinetics of denaturation by sodium dodecyl sulfate.

PubMed

Lee, Andrew; Mirica, Katherine A; Whitesides, George M

2011-02-10

This paper examines the influence of acylation of the Lys-ε-NH(3)(+) groups of bovine carbonic anhydrase (BCA, EC 4.2.1.1) to Lys-ε-NHCOR (R = -CH(3), -CH(2)CH(3), and -CH(CH(3))(2), -CF(3)) on the rate of denaturation of this protein in buffer containing sodium dodecyl sulfate (SDS). Analysis of the rates suggested separate effects due to electrostatic charge and hydrophobic interactions. Rates of denaturation (k(Ac,n)) of each series of acylated derivatives depended on the number of acylations (n). Plots of log k(Ac,n) vs n followed U-shaped curves. Within each series of derivatives, rates of denaturation decreased as n increased to ∼7; this decrease was compatible with increasingly unfavorable electrostatic interactions between SDS and protein. In this range of n, rates of denaturation also depended on the choice of the acyl group as n increased to ∼7, in a manner compatible with favorable hydrophobic interactions between SDS and the -NHCOR groups. As n increased in the range 7 < n < 14, however, rates of denaturation stayed approximately constant; analysis suggested that these rates were compatible with an increasingly important contribution to denaturation that depended both on the net negative charge of the protein and on the hydrophobicity of the R group. The mechanism of denaturation thus seems to change with the extent of acylation of the protein. For derivatives with the same net electrostatic charge, rates of denaturation increased with the acyl group (by a factor of ∼3 for n ∼ 14) in the order CH(3)CONH- < CH(3)CH(2)CONH- < (CH(3))(2)CHCONH- < CF(3)CONH-. These results suggested that the hydrophobicity of CF(3)CONH- is slightly greater (by a factor of <2) than that of RHCONH- with similar surface area.

Continuum electromechanical modeling of protein-membrane interactions

NASA Astrophysics Data System (ADS)

Zhou, Y. C.; Lu, Benzhuo; Gorfe, Alemayehu A.

2010-10-01

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the dielectric interface. The model is illustrated with the systems with increasing geometry complexity and captures the sensitivity of membrane curvature to the permanent and mobile charge distributions.

Label-free biosensing with functionalized nanopipette probes

PubMed Central

Umehara, Senkei; Karhanek, Miloslav; Davis, Ronald W.; Pourmand, Nader

2009-01-01

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research. PMID:19264962

Silver-cotton nanocomposites: Nano-design of microfibrillar structure causes morphological changes and increased tenacity

PubMed Central

Nam, Sunghyun; Condon, Brian D.; Delhom, Christopher D.; Fontenot, Krystal R.

2016-01-01

The interactions of nanoparticles with polymer hosts have important implications for directing the macroscopic properties of composite fibers, yet little is known about such interactions with hierarchically ordered natural polymers due to the difficulty of achieving uniform dispersion of nanoparticles within semi-crystalline natural fiber. In this study we have homogeneously dispersed silver nanoparticles throughout an entire volume of cotton fiber. The resulting electrostatic interaction and distinct supramolecular structure of the cotton fiber provided a favorable environment for the controlled formation of nanoparticles (12 ± 3 nm in diameter). With a high surface-to-volume ratio, the extensive interfacial contacts of the nanoparticles efficiently “glued” the structural elements of microfibrils together, producing a unique inorganic-organic hybrid substructure that reinforced the multilayered architecture of the cotton fiber. PMID:27849038

A COMPUTER MODELING STUDY OF BINDING PROPERTIES OF CHIRAL NUCLEOPEPTIDE FOR BIOMEDICAL APPLICATIONS.

PubMed

Pirtskhalava, M; Egoyan, A; Mirtskhulava, M; Roviello, G

2017-12-01

Nucleopeptides often show interesting properties of molecular binding that render them good candidates for development of innovative drugs for anticancer and antiviral therapies. In this work we present results of computer modeling of interactions between the molecules of hexathymine nucleopeptide (T6) and poly rA RNA (A18). The results of geometry optimization calculated using Hyperchem software and our own computer program for molecular docking show that molecules establish stable complexes due to the complementary-nucleobase interaction and the electrostatic interaction between the negative phosphate group of poly rA and the positively-charged residues present in the cationic nucleopeptide structure. Computer modeling makes it possible to find the optimal binding configuration of the molecules of a nucleopeptide and poly rA RNA and to estimate the binding energy between the molecules.

The physics of charge separation preceding lightning strokes in thunderclouds

NASA Technical Reports Server (NTRS)

Kyrala, Ali

1987-01-01

The physics of charge separation preceding lightning strokes in thunderclouds is presented by three types of arguments: An explanation is given for the aggregation of electrical charges of like sign overcoming Coulomb repulsion by attraction due to exchange interaction. The latter is well known in quantum mechanics from the theories of the nuclear bond and the covalent bond. A classical electrostatic model of charge balls of segregated positive and negative charges in the thundercloud is presented. These charge balls can only be maintained in temporarily stable locations by a containing vortex. Because they will be of different sizes and masses, they will stabilize at different altitudes when drag forces are included with the given electrostatic force. The question of how the charges become concentrated again after lightning discharges is approached by means of the collisional Boltzmann transport equation to explain quasi-periodic recharging. It is shown that solutions cannot be separable in both position and time if they are to represent aggregation.

Enzymatic Conversion of CO2 to Bicarbonate in Functionalized Mesoporous Silica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Yuehua; Chen, Baowei; Qi, Wen N.

2012-05-01

We report here that carbonic anhydrase (CA), the fastest enzyme that can covert carbon dioxide to bicarbonate, can be spontaneously entrapped in functionalized mesoporous silica (FMS) with super-high loading density (up to 0.5 mg of protein/mg of FMS) due to the dominant electrostatic interaction. The binding of CA to HOOC-FMS can result in the protein’s conformational change comparing to the enzyme free in solution, but can be overcome with increased protein loading density. The higher the protein loading density, the less conformational change, hence the higher enzymatic activity and the higher enzyme immobilization efficiency. The electrostatically bound CA can bemore » released by changing pH. The released enzyme still displayed the native conformational structure and the same high enzymatic activity as that prior to the enzyme entrapment. This work opens up a new approach converting carbon dioxide to biocarbonate in a biomimetic nanoconfiguration that can be integrated with the other part of biosynthesis process for the assimilation of carbon dioxide.« less

The potential of cashew gum functionalization as building blocks for layer-by-layer films.

PubMed

Leite, Álvaro J; Costa, Rui R; Costa, Ana M S; Maciel, Jeanny S; Costa, José F G; de Paula, Regina C M; Mano, João F

2017-10-15

Cashew gum (CG), an exudate polysaccharide from Anacardium occidentale trees, was carboxymethylated (CGCm) and oxidized (CGO). These derivatives were characterized by FTIR and zeta potential measurements confirming the success of carboxymethylation and oxidation reactions. Nanostructured multilayered films were then produced through layer-by-layer (LbL) assembly in conjugation with chitosan via electrostatic interactions or Schiff bases covalent bonds. The films were analyzed by QCM-D and AFM. CG functionalization increased the film thickness, with the highest thickness being achieved for the lowest oxidation degree. The roughest surface was obtained for the CGO with the highest oxidation degree due to the predominance of covalent Schiff bases. This work shows that nanostructured films can be assembled and stabilized by covalent bonds in alternative to the conventional electrostatic ones. Moreover, the functionalization of CG can increase its feasibility in multilayers films, widening its potential in biomedical, food industry, or environmental applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurement of Cohesion in Asteroid Regolith Materials

NASA Technical Reports Server (NTRS)

Kleinhenz, Julie; Gaier, James; Waters, Deborah; Harvey, Ralph; Zeszut, Zoe; Carreno, Brandon; Shober, Patrick

2017-01-01

There is increasing evidence that a large fraction of asteroids, and even Phobos, have such low densities (<2 g/cu cm) that the are unlikely to be consolidated rocks in space.-Water is unlikely due to close orbits to the sun. Instead, many of these asteroids are thought to be made up of unconsolidated smaller particles of varying size referred to as rubble piles. Images of the asteroid Itokawa reinforce this hypothesis. What holds the rubble piles together? Gravitational forces alone are not strong enough to hold together rubble pile asteroids, at least not those that are rapidly spinning Van der Waals forces and or Electrostatic forces must therefore be responsible for holding them together. Previous work suggests that electrostatic forces, which are orders of magnitude stronger are far more likely. Charge build-up is a likely consequence of the interaction of airless bodies with the solar wind plasma, analogous to what has been proposed to occur on the moon. Objective: Experimentally measure cohesive forces relevant to those holding rubble pile asteroids together

Degradation of Organics in a Glow Discharge Under Martian Conditions

NASA Technical Reports Server (NTRS)

Hintze, P. E.; Calle, L. M.; Calle, C. I.; Buhler, C. R.; Trigwell, S.; Starnes, J. W.; Schuerger, A. C.

2006-01-01

The primary objective of this project is to understand the consequences of glow electrical discharges on the chemistry and biology of Mars. The possibility was raised some time ago that the absence of organic material and carbonaceous matter in the Martian soil samples studied by the VikinG Landers might be due in part to an intrinsic atmospheric mechanism such as glow discharge. The high probability for dust interactions during Martian dust storms and dust devils, combined with the cold, dry climate of Mars most likely results in airborne dust that is highly charged. Such high electrostatic potentials generated during dust storms on Earth are not permitted in the low-pressure CO2 environment on Mars; therefore electrostatic energy released in the form of glow discharges is a highly likely phenomenon. Since glow discharge methods are used for cleaning and sterilizing surfaces throughout industry, the idea that dust in the Martian atmosphere undergoes a cleaning action many times over geologic time scales appears to be a plausible one.

Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

PubMed

Gunner, M R; Baker, N A

2016-01-01

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. © 2016 Elsevier Inc. All rights reserved.

Impact of short range hydrophobic interactions and long range electrostatic forces on the aggregation kinetics of a monoclonal antibody and a dual-variable domain immunoglobulin at low and high concentrations.

PubMed

Kumar, Vineet; Dixit, Nitin; Zhou, Liqiang Lisa; Fraunhofer, Wolfgang

2011-12-12

The purpose of this work was to determine the nature of long and short-range forces governing protein aggregation kinetics at low and high concentrations for a monoclonal antibody (IgG1) and a dual-variable-domain immunoglobulin (DVD-Ig). Protein-protein interactions (PPI) were studied under dilute conditions by utilizing the methods of static (B(22)) and dynamic light scattering (k(D)). PPI in solutions containing minimal ionic strengths were characterized to get detailed insights into the impact of ionic strength on aggregation. Microcalorimetry and susceptibility to denature at air-liquid interface were used to assess the tertiary structure and quiescent stability studies were conducted to study aggregation characteristics. Results for IgG1 showed that electrostatic interactions governed protein aggregation kinetics both under dilute and concentrated conditions (i.e., 5 mg/mL and 150 mg/mL). For DVD-Ig molecules, on the other hand, although electrostatic interactions governed protein aggregation under dilute conditions, hydrophobic forces clearly determined the kinetics at high concentrations. This manuscript shows for the first time that short-range hydrophobic interactions can outweigh electrostatic forces and play an important role in determining protein aggregation at high concentrations. Additionally, results show that although higher-order virial coefficients become significant under low ionic strength conditions, removal of added charges may be used to enhance the aggregation stability of dilute protein formulations. Copyright © 2011 Elsevier B.V. All rights reserved.

Charge tuning of nonresonant magnetoexciton phonon interactions in graphene.

PubMed

Rémi, Sebastian; Goldberg, Bennett B; Swan, Anna K

2014-02-07

Far from resonance, the coupling of the G-band phonon to magnetoexcitons in single layer graphene displays kinks and splittings versus filling factor that are well described by Pauli blocking and unblocking of inter- and intra-Landau level transitions. We explore the nonresonant electron-phonon coupling by high-magnetic field Raman scattering while electrostatic tuning of the carrier density controls the filling factor. We show qualitative and quantitative agreement between spectra and a linearized model of electron-phonon interactions in magnetic fields. The splitting is caused by dichroism of left- and right-handed circular polarized light due to lifting of the G-band phonon degeneracy, and the piecewise linear slopes are caused by the linear occupancy of sequential Landau levels versus ν.

Face-to-face stacks of trinuclear gold(I) trihalides with benzene, hexafluorobenzene, and borazine: impact of aromaticity on stacking interactions.

PubMed

Tsipis, Athanassios C; Stalikas, Alexandros V

2013-01-18

The interplay of electrostatics, charge transfer, and dispersion forces contributing to the interaction energies in 1:1, 1:2, and 2:1 binary stacks of the c-Au(3)(μ(2)-X)(3) (X = F, Cl, Br, I) clusters with benzene, hexafluorobenzene, or borazine were investigated by employing a multitude of electronic structure computational techniques. The molecular and electronic structures, stabilities, bonding features, and magnetotropicity of [c-Au(3)(μ(2)-X)(3)](n)(L)(m) (X = halide; L = C(6)H(6), C(6)F(6), B(3)N(3)H(6); n, m ≤ 2) columnar binary stacks have been investigated by DFT calculations employing the M05-2X functional. The novel binary stacks could be considered as the building blocks of extended columnar supramolecular assemblies formulated as {[c-Au(3)(μ(2)-X)(3)](C(6)H(6))}(∞), {[c-Au(3)(μ(2)-X)(3)](2)(C(6)F(6))}(∞), and {[c-Au(3)(μ(2)-X)(3)](B(3)N(3)H(6))(2)}(∞). In all binary stacks, with a few exceptions, the plane of the alternating c-Au(3)(μ(2)-X)(3) and L (C(6)H(6), C(6)F(6), B(3)N(3)H(6)) stacking participants adopt an almost parallel face-to-face (pff) orientation. The observed trends in the intermolecular distances R in the [c-Au(3)(μ(2)-X)(3)](n)(L)(m) (X = halide; L = C(6)H(6), C(6)F(6), B(3)N(3)H(6); n, m ≤ 2) columnar binary stacks are explained by the diverse intermolecular interactions characterizing the stacks, since the three ligands L and the c-Au(3)(μ(2)-X)(3) cyclic trinuclear clusters (CTCs) exhibit diverse physical properties being important determinants of the intermolecular interactions (consisting of covalent, electrostatic, and dispersion forces). The properties considered are the zz tensor components of quadrupole moment, Q(zz), polarizability, α(zz), nucleus-independent chemical shift, NICS(zz)(1), along with the molecular electrostatic potential, MEP(0), and surface area (S). Energy decomposition analysis (EDA) at the revPBE-D3/TZ2P level revealed that the dominant term in the stacking interactions arises mainly from dispersion and electrostatic forces, while the contribution of covalent interactions are predicted to be small. On the other hand, charge decomposition analysis (CDA) illustrated very small charge transfer from the L stacking participants toward the c-Au(3)(μ(2)-X)(3) clusters. Excellent linear correlations of the interaction energy, ΔE(int), and its components (ΔE(disp), ΔE(elstat), ΔE(orb), and ΔE(Pauli)) with calculated physical properties related to dispersion, covalent, and electrostatic forces have been established. The most important finding is the excellent linear relationship between ΔE(int) and the NICS(zz)(1) magnetic criterion of aromaticity, indicating that ΔE(int) is also affected by the coupling of the induced magnetic fields of the interacting stacking participants. The magnetotropicity of the binary stacks evaluated by the NICS(zz)-scan curves indicated an enhancement of the diatropicity in the space between the interacting inorganic and organic rings, probably due to the superposition of the diamagnetic ring currents of the interacting ring systems. The energy splitting in dimer (ESID) model was employed to estimate the charge transport of electrons and holes between the ligands L and the [c-Au(3)(μ(2)-X)(3)] clusters in [c-Au(3)(μ(2)-X)(3)](L) 1:1 binary stacks.

INTERACTIVE COMPUTER MODEL FOR CALCULATING V-I CURVES IN ESPS (ELECTROSTATIC PRECIPITATORS) VERSION 1.0

EPA Science Inventory

The manual describes two microcomputer programs written to estimate the performance of electrostatic precipitators (ESPs): the first, to estimate the electrical conditions for round discharge electrodes in the ESP; and the second, a modification of the EPA/SRI ESP model, to estim...

The role of electrostatics and temperature on morphological transitions of hydrogel nanostructures self-assembled by peptide amphiphiles via molecular dynamics simulations.

PubMed

Fu, Iris W; Markegard, Cade B; Chu, Brian K; Nguyen, Hung D

2013-10-01

Smart biomaterials that are self-assembled from peptide amphiphiles (PA) are known to undergo morphological transitions in response to specific physiological stimuli. The design of such customizable hydrogels is of significant interest due to their potential applications in tissue engineering, biomedical imaging, and drug delivery. Using a novel coarse-grained peptide/polymer model, which has been validated by comparison of equilibrium conformations from atomistic simulations, large-scale molecular dynamics simulations are performed to examine the spontaneous self-assembly process. Starting from initial random configurations, these simulations result in the formation of nanostructures of various sizes and shapes as a function of the electrostatics and temperature. At optimal conditions, the self-assembly mechanism for the formation of cylindrical nanofibers is deciphered involving a series of steps: (1) PA molecules quickly undergo micellization whose driving force is the hydrophobic interactions between alkyl tails; (2) neighboring peptide residues within a micelle engage in a slow ordering process that leads to the formation of β-sheets exposing the hydrophobic core; (3) spherical micelles merge together through an end-to-end mechanism to form cylindrical nanofibers that exhibit high structural fidelity to the proposed structure based on experimental data. As the temperature and electrostatics vary, PA molecules undergo alternative kinetic mechanisms, resulting in the formation of a wide spectrum of nanostructures. A phase diagram in the electrostatics-temperature plane is constructed delineating regions of morphological transitions in response to external stimuli. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diclofenac removal in urine using strong-base anion exchange polymer resins.

PubMed

Landry, Kelly A; Boyer, Treavor H

2013-11-01

One of the major sources of pharmaceuticals in the environment is wastewater effluent of which human urine contributes the majority of pharmaceuticals. Urine source separation has the potential to isolate pharmaceuticals at a higher concentration for efficient removal as well as produce a nutrient byproduct. This research investigated the efficacy of using strong-base anion exchange polymer resins to remove the widely detected and abundant pharmaceutical, diclofenac, from synthetic human urine under fresh and ureolyzed conditions. The majority of experiments were conducted using a strong-base, macroporous, polystyrene resin (Purolite A520E). Ion-exchange followed a two-step removal rate with rapid removal in 1 h and equilibrium removal in 24 h. Diclofenac removal was >90% at a resin dose of 8 mL/L in both fresh and ureolyzed urine. Sorption of diclofenac onto A520E resin was concurrent with desorption of an equivalent amount of chloride, which indicates the ion-exchange mechanism is occurring. The presence of competing ions such as phosphate and citrate did not significantly impact diclofenac removal. Comparisons of three polystyrene resins (A520E, Dowex 22, Dowex Marathon 11) as well as one polyacrylic resin (IRA958) were conducted to determine the major interactions between anion exchange resin and diclofenac. The results showed that polystyrene resins provide the highest level of diclofenac removal due to electrostatic interactions between quaternary ammonium functional groups of resin and carboxylic acid of diclofenac and non-electrostatic interactions between resin matrix and benzene rings of diclofenac. Diclofenac was effectively desorbed from A520E resin using a regeneration solution that contained 4.5% (m/m) NaCl in an equal-volume mixture of methanol and water. The greater regeneration efficiency of the NaCl/methanol-water mixture over the aqueous NaCl solution supports the importance of non-electrostatic interactions between resin matrix and benzene rings of diclofenac. Experiments with ketoprofen, in addition to diclofenac, suggest that polystyrene anion exchange resins can be used to selectively remove other acidic pharmaceuticals from urine. Copyright © 2013 Elsevier Ltd. All rights reserved.

Surface charge accumulation of particles containing radionuclides in open air

DOE PAGES

Kim, Yong-ha; Yiacoumi, Sotira; Tsouris, Costas

2015-05-01

Radioactivity can induce charge accumulation on radioactive particles. But, electrostatic interactions caused by radioactivity are typically neglected in transport modeling of radioactive plumes because it is assumed that ionizing radiation leads to charge neutralization. The assumption that electrostatic interactions caused by radioactivity are negligible is evaluated here by examining charge accumulation and neutralization on particles containing radionuclides in open air. Moreover, a charge-balance model is employed to predict charge accumulation on radioactive particles. It is shown that particles containing short-lived radionuclides can be charged with multiple elementary charges through radioactive decay. The presence of radioactive particles can significantly modify themore » particle charge distribution in open air and yield an asymmetric bimodal charge distribution, suggesting that strong electrostatic particle interactions may occur during short- and long-range transport of radioactive particles. Possible effects of transported radioactive particles on electrical properties of the local atmosphere are reported. Our study offers insight into transport characteristics of airborne radionuclides. Results are useful in atmospheric transport modeling of radioactive plumes.« less

Effect of cholesterol on electrostatics in lipid-protein films of a pulmonary surfactant.

PubMed

Finot, Eric; Leonenko, Yuri; Moores, Brad; Eng, Lukas; Amrein, Matthias; Leonenko, Zoya

2010-02-02

We report the changes in the electrical properties of the lipid-protein film of pulmonary surfactant produced by excess cholesterol. Pulmonary surfactant (PS) is a complex lipid-protein mixture that forms a molecular film at the interface of the lung's epithelia. The defined molecular arrangement of the lipids and proteins of the surfactant film gives rise to the locally highly variable electrical surface potential of the interface, which becomes considerably altered in the presence of cholesterol. With frequency modulation Kelvin probe force microscopy (FM-KPFM) and force measurements, complemented by theoretical analysis, we showed that excess cholesterol significantly changes the electric field around a PS film because of the presence of nanometer-sized electrostatic domains and affects the electrostatic interaction of an AFM probe with a PS film. These changes in the local electrical field would greatly alter the interaction of the surfactant film with charged species and would immediately impact the manner in which inhaled (often charged) airborne nanoparticles and fibers might interact with the lung interface.

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

Sorption of poly(hexamethylenebiguanide) on cellulose: mechanism of binding and molecular recognition.

PubMed

Blackburn, Richard S; Harvey, Anna; Kettle, Lorna L; Payne, John D; Russell, Stephen J

2006-06-20

Antimicrobial agents such as poly(hexamethylene biguanide) (PHMB) find application in medical, apparel, and household textile sectors; although it is understood that certain concentrations need to be applied to achieve suitable performance, there has been very little work published concerning the interactions of the polymer and its adsorption mechanism on cellulose. In this paper, such physical chemistry parameters are examined and related to computational chemistry studies. Adsorption isotherms were constructed: at low concentrations, these were typical Langmuir isotherms; at higher concentrations, they were more indicative of Freundlich isotherms, attributed to a combination of electrostatic and hydrogen-bonding forces, which endorsed computational chemistry proposals. At lower concentrations, electrostatic interactions between PHMB and carboxylic acid groups in the cellulose dominate with a contribution to binding through hydrogen bonding; as the concentration of PHMB increases, hydrogen bonding with cellulose becomes increasingly dominant. At high PHMB concentrations, observations of increasing PHMB adsorption are attributed to monolayer aggregation and multilayer stacking of PHMB through electrostatic interactions with counterions and hydrogen bonding of biguanide groups.

Molecular Structure and Equilibrium Forces of Bovine Submaxillary Mucin Adsorbed at a Solid-Liquid Interface.

PubMed

Zappone, Bruno; Patil, Navinkumar J; Madsen, Jan B; Pakkanen, Kirsi I; Lee, Seunghwan

2015-04-21

By combining dynamic light scattering, circular dichroism spectroscopy, atomic force microscopy, and surface force apparatus, the conformation of bovine submaxillary mucin in dilute solution and nanomechanical properties of mucin layers adsorbed on mica have been investigated. The samples were prepared by additional chromatographic purification of commercially available products. The mucin molecule was found to have a z-average hydrodynamic diameter of ca. 35 nm in phosphate buffered solution, without any particular secondary or tertiary structure. The contour length of the mucin is larger than, yet of the same order of magnitude as the diameter, indicating that the molecule can be modeled as a relatively rigid polymeric chain due to the large persistence length of the central glycosylated domain. Mucin molecules adsorbed abundantly onto mica from saline buffer, generating polymer-like, long-ranged, repulsive, and nonhysteretic forces upon compression of the adsorbed layers. Detailed analysis of such forces suggests that adsorbed mucins had an elongated conformation favored by the stiffness of the central domain. Acidification of aqueous media was chosen as means to reduce mucin-mucin and mucin-substrate electrostatic interactions. The hydrodynamic diameter in solution did not significantly change when the pH was lowered, showing that the large persistence length of the mucin molecule is due to steric hindrance between sugar chains, rather than electrostatic interactions. Remarkably, the force generated by an adsorbed layer with a fixed surface coverage also remained unaltered upon acidification. This observation can be linked to the surface-protective, pH-resistant role of bovine submaxillary mucin in the variable environmental conditions of the oral cavity.

Surfactant-cobalt(III) complexes: The impact of hydrophobicity on interaction with HSA and DNA - insights from experimental and theoretical approach.

PubMed

Veeralakshmi, Selvakumar; Sabapathi, Gopal; Nehru, Selvan; Venuvanalingam, Ponnambalam; Arunachalam, Sankaralingam

2017-05-01

To develop surfactant-based metallodrugs, it is very important to know about their hydrophobicity, micelle forming capacity, their interaction with biomacromolecules such as proteins and nucleic acids, and biological activities. Here, diethylenetriamine (dien) and tetradecylamine ligand (TA) based surfactant-cobalt(III) complexes with single chain domain, [Co(dien)(TA)Cl 2 ]ClO 4 (1) and double chain domain [Co(dien)(TA) 2 Cl](ClO 4 ) 2 (2) were chosen to study the effect of hydrophobicity on the interaction with human serum albumin and calf thymus DNA. The obtained results showed that (i) single chain surfactant-cobalt(III) complex (1) interact with HSA and DNA via electrostatic interaction and groove binding, respectively; (ii) double chain surfactant-cobalt(III) complex (2) interact with HSA and DNA via hydrophobic interaction and partial intercalation, respectively, due to the play of hydrophobicity by single and double chain domains. Further it is noted that, double chain surfactant-cobalt(III) complex interact strongly with HSA and DNA, compared single chain surfactant-cobalt(III) complex due to their more hydrophobicity nature. DFT and molecular docking studies offer insights into the mechanism and mode of binding towards the molecular target CT-DNA and HSA. Hence, the present findings will create new avenue towards the use of hydrophobic metallodrugs for various therapeutic applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Intramolecular interactions contributing for the conformational preference of bioactive diphenhydramine: Manifestation of the gauche effect

NASA Astrophysics Data System (ADS)

de Rezende, Fátima M. P.; Andrade, Laize A. F.; Freitas, Matheus P.

2015-08-01

Diphenhydramine is an antihistamine used to treat some symptoms of allergies and the common cold. It is usually marketed as the hydrochloride salt, and both the neutral and cation forms have the O-C-C-N fragment. The gauche effect is well known in fluorine-containing chains, because its main origin is hyperconjugative and the σ∗C-F is a low-lying acceptor orbital, allowing electron delocalization in the conformation where F and an adjacent electronegative substituent in an ethane fragment are in the gauche orientation. Our experimental (NMR) and theoretical findings indicate that diphenhydramine exhibits the gauche effect, since the preferential conformations have the O-C-C-N moiety in this orientation due especially to antiperiplanar σC-H → σ∗C-O and σC-H → σ∗C-N interactions. This conformational preference is strengthened in the protonated form due to an incremental electrostatic gauche effect. Because the gauche conformation matches the bioactive structure of diphenhydramine complexed with histamine methyltransferase, it is suggested that intramolecular interactions, and not only induced fit, rule its bioactive form.

Hands-on-Entropy, Energy Balance with Biological Relevance

NASA Astrophysics Data System (ADS)

Reeves, Mark

2015-03-01

Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is important contribution of the entropy in driving fundamental biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy). This has enabled students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce complex biological processes and structures in order model them mathematically to account for both deterministic and probabilistic processes. The students test these models in simulations and in laboratory experiments that are biologically relevant such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront random forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk will present a number of these exercises, with particular focus on the hands-on experiments done by the students, and will give examples of the tangible material that our students work with throughout the two-semester sequence of their course on introductory physics with a bio focus. Supported by NSF DUE.

Stereochemistry and solvent role in protein folding: nuclear magnetic resonance and molecular dynamics studies of poly-L and alternating-L,D homopolypeptides in dimethyl sulfoxide.

PubMed

Srivastava, Kinshuk Raj; Kumar, Anil; Goyal, Bhupesh; Durani, Susheel

2011-05-26

The competing interactions folding and unfolding protein structure remain obscure. Using homopolypeptides, we ask if poly-L structure may have a role. We mutate the structure to alternating-L,D stereochemistry and substitute water as the fold-promoting solvent with methanol and dimethyl sulfoxide (DMSO) as the fold-denaturing solvents. Circular dichroism and molecular dynamics established previously that, while both isomers were folded in water, the poly-L isomer was unfolded and alternating-L,D isomer folded in methanol. Nuclear magnetic resonance and molecular dynamics establish now that both isomers are unfolded in DMSO. We calculated energetics of folding-unfolding equilibrium with water and methanol as solvents. We have now calculated interactions of unfolded polypeptide structures with DMSO as solvent. Methanol was found to unfold and water fold poly-L structure as a dielectric. DMSO has now been found to unfold both poly-L and alternating-L,D structures by strong solvation of peptides to disrupt their hydrogen bonds. Accordingly, we propose that while linked peptides fold protein structure with hydrogen bonds they unfold the structure electrostatically due to the stereochemical effect of the poly-L structure. Protein folding to ordering of peptide hydrogen bonds with water as canonical solvent may thus involve two specific and independent solvent effects-one, strong screening of electrostatics of poly-L linked peptides, and two, weak dipolar solvation of peptides. Correspondingly, protein denaturation may involve two independent solvent effects-one, weak dielectric to unfold poly-L structure electrostatically, and two, strong polarity to disrupt peptide hydrogen bonds by solvation of peptides.

Effect of electrostatic interaction on the location of molecular probe in polymer-surfactant supramolecular assembly: a solvent relaxation study.

PubMed

Singh, Prabhat K; Kumbhakar, Manoj; Pal, Haridas; Nath, Sukhendu

2008-07-03

Effect of electrostatic interaction on the location of a solubilized molecular probe with ionic character in a supramolecular assembly composed of a triblock copolymer, P123 ((ethylene oxide) 20-(propylene oxide) 70-(ethylene oxide) 20) and a cosurfactant cetyltrimethylammonium chloride (CTAC) in aqueous medium has been studied using steady-state and time-resolved fluorescence measurements. Coumarin-343 dye in its anionic form has been used as the molecular probe. In the absence of the surfactant, CTAC, the probe C343 prefers to reside at the surface region of the P123 micelle, showing a relatively less dynamic Stokes' shift, as a large part of the Stokes' shift is missed in the present measurements due to faster solvent relaxation at micellar surface region. As the concentration of CTAC is increased in the solution, the percentage of the total dynamic Stokes' shift observed from time-resolved measurements gradually increases until it reaches a saturation value. Observed results have been rationalized on the basis of the mixed micellar structure of the supramolecular assembly, where the hydrocarbon chain of the CTAC surfactant dissolves into the nonpolar poly(propylene oxide) (PPO) core of the P123 micelle and the positively charged headgroup of CTAC resides at the interfacial region between the central PPO core and the surrounding hydrated poly(ethylene oxide) (PEO) shell or the corona region. The electrostatic attraction between the anionic probe molecule and the positively charged surface of the PPO core developed by the presence of CTAC results in a gradual shift of the probe in the deeper region of the micellar corona region with an increase in the CTAC concentration, as clearly manifested from the solvation dynamics results.

Optimizing energy functions for protein-protein interface design.

PubMed

Sharabi, Oz; Yanover, Chen; Dekel, Ayelet; Shifman, Julia M

2011-01-15

Protein design methods have been originally developed for the design of monomeric proteins. When applied to the more challenging task of protein–protein complex design, these methods yield suboptimal results. In particular, they often fail to recapitulate favorable hydrogen bonds and electrostatic interactions across the interface. In this work, we aim to improve the energy function of the protein design program ORBIT to better account for binding interactions between proteins. By using the advanced machine learning framework of conditional random fields, we optimize the relative importance of all the terms in the energy function, attempting to reproduce the native side-chain conformations in protein–protein interfaces. We evaluate the performance of several optimized energy functions, each describes the van der Waals interactions using a different potential. In comparison with the original energy function, our best energy function (a) incorporates a much “softer” repulsive van der Waals potential, suitable for the discrete rotameric representation of amino acid side chains; (b) does not penalize burial of polar atoms, reflecting the frequent occurrence of polar buried residues in protein–protein interfaces; and (c) significantly up-weights the electrostatic term, attesting to the high importance of these interactions for protein–protein complex formation. Using this energy function considerably improves side chain placement accuracy for interface residues in a large test set of protein–protein complexes. Moreover, the optimized energy function recovers the native sequences of protein–protein interface at a higher rate than the default function and performs substantially better in predicting changes in free energy of binding due to mutations.

Electrical interactions in the cell: Asymmetric screening in a watery antiverse.

PubMed

Doerr, T P; Yu, Yi-Kuo

2014-05-01

The problem of electrostatics in biomolecular systems presents an excellent opportunity for cross-disciplinary science and a context in which fundamental physics is called for to answer complex questions. Due to the large density in biological cells of charged biomacromolecules such as protein factors and DNA, it is challenging to understand quantitatively the electric forces in these systems. Two questions are especially puzzling. First, how is it that such a dense system of charged molecules does not simply aggregate in random and non-functional ways? Second, since some mechanism apparently prevents such aggregation, how is it that binding of biomolecules still occurs so reliably? Recognizing the role of water as a universal solvent in living systems is key to understanding these questions. We present a simplified physical model in which water is regarded as a medium of high dielectric constant that nevertheless exhibits the key features essential for answering the two questions presented. The answer to the first question lies in the strong screening ability of water, which reduces the energy scale of the electrostatic interactions. Furthermore, our model reveals the existence of asymmetric screening, a pronounced asymmetry between the screening for a system with like charges and that for a system with opposite charges, and this provides an answer to the second question.

Electrical interactions in the cell: Asymmetric screening in a watery antiverse

PubMed Central

Doerr, T. P.; Yu, Yi-Kuo

2014-01-01

The problem of electrostatics in biomolecular systems presents an excellent opportunity for cross-disciplinary science and a context in which fundamental physics is called for to answer complex questions. Due to the large density in biological cells of charged biomacromolecules such as protein factors and DNA, it is challenging to understand quantitatively the electric forces in these systems. Two questions are especially puzzling. First, how is it that such a dense system of charged molecules does not simply aggregate in random and non-functional ways? Second, since some mechanism apparently prevents such aggregation, how is it that binding of biomolecules still occurs so reliably? Recognizing the role of water as a universal solvent in living systems is key to understanding these questions. We present a simplified physical model in which water is regarded as a medium of high dielectric constant that nevertheless exhibits the key features essential for answering the two questions presented. The answer to the first question lies in the strong screening ability of water, which reduces the energy scale of the electrostatic interactions. Furthermore, our model reveals the existence of asymmetric screening, a pronounced asymmetry between the screening for a system with like charges and that for a system with opposite charges, and this provides an answer to the second question. PMID:25125701

Quantitative structure-cytotoxicity relationship of piperic acid amides.

PubMed

Shimada, Chiyako; Uesawa, Yoshihiro; Ishihara, Mariko; Kagaya, Hajime; Kanamoto, Taisei; Terakubo, Shigemi; Nakashima, Hideki; Takao, Koichi; Miyashiro, Takaki; Sugita, Yoshiaki; Sakagami, Hiroshi

2014-09-01

A total of 12 piperic acid amides, including piperine, were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity, tumor selectivity and anti-HIV activity, in order to find new biological activities. Cytotoxicity against four human oral squamous cell carcinoma (OSCC) cell lines and three human oral normal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor selectivity was evaluated by the ratio of the mean 50% cytotoxic concentration (CC50) against normal oral cells to that against OSCC cell lines. Anti-HIV activity was evaluated by the ratio of the CC50 to 50% HIV infection-cytoprotective concentration (EC50). Physicochemical, structural, and quantum-chemical parameters were calculated based on the conformations optimized by LowModeMD method followed by density functional theory method. All compounds showed low-to-moderate tumor selectivity, but no anti-HIV activity. N-Piperoyldopamine ( 8: ) which has a catechol moiety, showed the highest tumor selectivity, possibly due to its unique molecular shape and electrostatic interaction, especially its largest partial equalization of orbital electronegativities and vsurf descriptors. The present study suggests that molecular shape and ability for electrostatic interaction are useful parameters for estimating the tumor selectivity of piperic acid amides. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

2016-12-01

Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

Effects of feed solution chemistry on low pressure reverse osmosis filtration of cesium and strontium.

PubMed

Ding, Shiyuan; Yang, Yu; Huang, Haiou; Liu, Hengchen; Hou, Li-an

2015-08-30

The objective of this study was to identify the removal mechanisms of radionuclides by reverse osmosis (RO) membranes under conditions relevant to full-scale water treatment. For this purpose, the effects of feed solution chemistry on the removal of Cs and Sr by a low pressure RO system was investigated by systematically varying membrane surface charge, ionic composition, and organic matter concentrations. The results showed that the effects of solution chemistry on the filtration of Cs and Sr were related to their hydrated ionic radius, resulting in the predominance of the Donnan's effect and electrostatic interactions, respectively. Consequently, the rejection of Cs increased more pronouncedly than Sr with the increases of feed concentration. Due to the Donnan's effect, different anions decreased the rejection of Cs to different extents in accordance to the order of anions' radii as SO4(2-)>Cl(-)>NO3(-)>F(-). The variations in Sr rejection were influenced by the electrostatic interactions between Sr(2+) and the membrane. In addition, humic acid (HA) lowered the rejection of Cs and caused significant membrane flux decline, but did not change the rejection of Sr. Sr also aggravated HA fouling of the membrane. Copyright © 2015 Elsevier B.V. All rights reserved.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

Interaction of Antiinflammatory Drugs with EPC Liposomes: Calorimetric Study in a Broad Concentration Range

PubMed Central

Matos, Carla; Lima, José L. C.; Reis, Salette; Lopes, António; Bastos, Margarida

2004-01-01

Isothermal titration calorimetry was used to characterize and quantify the partition of indomethacin and acemetacin between the bulk aqueous phase and the membrane of egg phosphatidylcholine vesicles. Significant electrostatic effects were observed due to binding of the charged drugs to the membrane, which implied the use of the Gouy-Chapman theory to calculate the interfacial concentrations. The binding/partition phenomenon was quantified in terms of the partition coefficient (Kp), and/or the equilibrium constant (Kb). Mathematical expressions were developed, either to encompass the electrostatic effects in the partition model, or to numerically relate partition coefficients and binding constants. Calorimetric titrations conducted under a lipid/drug ratio >100:1 lead to a constant heat release and were used to directly calculate the enthalpy of the process, ΔH, and indirectly, ΔG and ΔS. As the lipid/drug ratio decreased, the constancy of reaction enthalpy was tested in the fitting process. Under low lipid/drug ratio conditions simple partition was no longer valid and the interaction phenomenon was interpreted in terms of binding isotherms. A mathematical expression was deduced for quantification of the binding constants and the number of lipid molecules associated with one drug molecule. The broad range of concentrations used stressed the biphasic nature of the interaction under study. As the lipid/drug ratio was varied, the results showed that the interaction of both drugs does not present a unique behavior in all studied regimes: the extent of the interaction, as well as the binding stoichiometry, is affected by the lipid/drug ratio. The change in these parameters reflects the biphasic behavior of the interaction—possibly the consequence of a modification of the membrane's physical properties as it becomes saturated with the drug. PMID:14747330

Noncovalent PEGylation through Protein-Polyelectrolyte Interaction: Kinetic Experiment and Molecular Dynamics Simulation.

PubMed

Kurinomaru, Takaaki; Kuwada, Kengo; Tomita, Shunsuke; Kameda, Tomoshi; Shiraki, Kentaro

2017-07-20

Noncovalent binding of polyethylene glycol (PEG) to a protein surface is a unique protein handling technique to control protein function and stability. A diblock copolymer containing PEG and polyelectrolyte chains (PEGylated polyelectrolyte) is a promising candidate for noncovalent attachment of PEG to a protein surface because of the binding through multiple electrostatic interactions without protein denaturation. To obtain a deeper understanding of protein-polyelectrolyte interaction at the molecular level, we investigated the manner in which cationic PEGylated polyelectrolyte binds to anionic α-amylase in enzyme kinetic experiments and molecular dynamics (MD) simulations. Cationic PEG-block-poly(N,N-dimethylaminoethyl) (PEG-b-PAMA) inhibited the enzyme activity of anionic α-amylase due to binding of PAMA chains. Enzyme kinetics revealed that the inhibition of α-amylase activity by PEG-b-PAMA is noncompetitive inhibition manner. In MD simulations, the PEG-b-PAMA molecule was initially located at six different placements of the x-, y-, and z-axis ±20 Å from the center of α-amylase, which showed that the PEG-b-PAMA nonspecifically bound to the α-amylase surface, corresponding to the noncompetitive inhibition manner that stems from the polymer binding to an enzyme surface other than the active site. In addition, the enzyme activity of α-amylase in the presence of PEG-b-PAMA was not inhibited by increasing the ionic strength, consistent with the MD simulation; i.e., PEG-b-PAMA did not interact with α-amylase in high ionic strength conditions. The results reported in this paper suggest that enzyme inhibition by PEGylated polyelectrolyte can be attributed to the random electrostatic interaction between protein and polyelectrolyte.

Symmetry-adapted perturbation theory interaction energy decomposition for some noble gas complexes

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Sadlej, Joanna

2008-06-01

This Letter contains a study of the interaction energy in HArF⋯N 2 and HArF⋯P 2 complexes. Symmetry-adapted perturbation theory (SAPT) has been applied to analyze the electrostatic, induction, dispersion and exchange contributions to the total interaction energy. The interaction energy has also been obtained by supermolecular method at the MP2, MP4, CCSD, CCSD(T) levels. The interaction energy for the studied complexes results from a partial cancelation of large attractive electrostatic, induction, dispersion terms by a strong repulsive exchange contribution. The induction and dispersion effects proved to be crucial in establishing the preference for the colinear HArF⋯N 2 and HArF⋯P 2 structures and shift direction of νHAr stretching vibrations.

Heteroaromatic π-Stacking Energy Landscapes

PubMed Central

2014-01-01

In this study we investigate π-stacking interactions of a variety of aromatic heterocycles with benzene using dispersion corrected density functional theory. We calculate extensive potential energy surfaces for parallel-displaced interaction geometries. We find that dispersion contributes significantly to the interaction energy and is complemented by a varying degree of electrostatic interactions. We identify geometric preferences and minimum interaction energies for a set of 13 5- and 6-membered aromatic heterocycles frequently encountered in small drug-like molecules. We demonstrate that the electrostatic properties of these systems are a key determinant for their orientational preferences. The results of this study can be applied in lead optimization for the improvement of stacking interactions, as it provides detailed energy landscapes for a wide range of coplanar heteroaromatic geometries. These energy landscapes can serve as a guide for ring replacement in structure-based drug design. PMID:24773380

Statistical field theory description of inhomogeneous polarizable soft matter

NASA Astrophysics Data System (ADS)

Martin, Jonathan M.; Li, Wei; Delaney, Kris T.; Fredrickson, Glenn H.

2016-10-01

We present a new molecularly informed statistical field theory model of inhomogeneous polarizable soft matter. The model is based on fluid elements, referred to as beads, that can carry a net monopole of charge at their center of mass and a fixed or induced dipole through a Drude-type distributed charge approach. The beads are thus polarizable and naturally manifest attractive van der Waals interactions. Beyond electrostatic interactions, beads can be given soft repulsions to sustain fluid phases at arbitrary densities. Beads of different types can be mixed or linked into polymers with arbitrary chain models and sequences of charged and uncharged beads. By such an approach, it is possible to construct models suitable for describing a vast range of soft-matter systems including electrolyte and polyelectrolyte solutions, ionic liquids, polymerized ionic liquids, polymer blends, ionomers, and block copolymers, among others. These bead models can be constructed in virtually any ensemble and converted to complex-valued statistical field theories by Hubbard-Stratonovich transforms. One of the fields entering the resulting theories is a fluctuating electrostatic potential; other fields are necessary to decouple non-electrostatic interactions. We elucidate the structure of these field theories, their consistency with macroscopic electrostatic theory in the absence and presence of external electric fields, and the way in which they embed van der Waals interactions and non-uniform dielectric properties. Their suitability as a framework for computational studies of heterogeneous soft matter systems using field-theoretic simulation techniques is discussed.

Electrostatically Accelerated Coupled Binding and Folding of Intrinsically Disordered Proteins

PubMed Central

Ganguly, Debabani; Otieno, Steve; Waddell, Brett; Iconaru, Luigi; Kriwacki, Richard W.; Chen, Jianhan

2012-01-01

Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and many potential functional benefits have been discussed. However, the frequent requirement of peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be overcome only by efficient folding upon encounter. Intriguingly, existing kinetic data suggest that specific binding of IDPs is generally no slower than that of globular proteins. Here, we exploited the cell cycle regulator p27Kip1 (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for facile recognition. Combining experiments and coarse-grained modeling, we demonstrate that long-range electrostatic interactions between enriched charges on p27 and near its binding site on cyclin A not only enhance the encounter rate (i.e., electrostatic steering), but also promote folding-competent topologies in the encounter complexes, allowing rapid subsequent formation of short-range native interactions en route to the specific complex. In contrast, nonspecific hydrophobic interactions, while hardly affecting the encounter rate, can significantly reduce the efficiency of folding upon encounter and lead to slower binding kinetics. Further analysis of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared to the rest of the target surface, their vicinities are frequently enriched with charges to complement those on IDPs. This observation suggests that electrostatically accelerated encounter and induced folding might represent a prevalent mechanism for promoting facile IDP recognition. PMID:22721951

Statistical field theory description of inhomogeneous polarizable soft matter.

PubMed

Martin, Jonathan M; Li, Wei; Delaney, Kris T; Fredrickson, Glenn H

2016-10-21

We present a new molecularly informed statistical field theory model of inhomogeneous polarizable soft matter. The model is based on fluid elements, referred to as beads, that can carry a net monopole of charge at their center of mass and a fixed or induced dipole through a Drude-type distributed charge approach. The beads are thus polarizable and naturally manifest attractive van der Waals interactions. Beyond electrostatic interactions, beads can be given soft repulsions to sustain fluid phases at arbitrary densities. Beads of different types can be mixed or linked into polymers with arbitrary chain models and sequences of charged and uncharged beads. By such an approach, it is possible to construct models suitable for describing a vast range of soft-matter systems including electrolyte and polyelectrolyte solutions, ionic liquids, polymerized ionic liquids, polymer blends, ionomers, and block copolymers, among others. These bead models can be constructed in virtually any ensemble and converted to complex-valued statistical field theories by Hubbard-Stratonovich transforms. One of the fields entering the resulting theories is a fluctuating electrostatic potential; other fields are necessary to decouple non-electrostatic interactions. We elucidate the structure of these field theories, their consistency with macroscopic electrostatic theory in the absence and presence of external electric fields, and the way in which they embed van der Waals interactions and non-uniform dielectric properties. Their suitability as a framework for computational studies of heterogeneous soft matter systems using field-theoretic simulation techniques is discussed.

Molecular electrostatic potential and "atoms-in-molecules" analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions.

PubMed

Bauzá, Antonio; Seth, Saikat Kumar; Frontera, Antonio

2018-04-05

Using ab initio calculations, we analyze the interplay between π-hole interactions involving the nitro group of 1,4-dinitrobenzene and lone pair···π (lp···π), C-H···π or metal(M)···π noncovalent interactions. Moreover, we have also used 1,4-phenylenebis(phosphine dioxide) for comparison purposes. Interesting cooperativity effects are found when π-hole (F···N,P) and lp···π/C-H···π/M···π interactions coexist in the same supramolecular assembly. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods (RI-MP2/def2-TZVP). A charge density analysis using the Bader's theory of "atoms in molecules" is carried out to characterize the interactions and to analyze their strengthening or weakening depending on the variation of charge density at critical points. The importance of electrostatic effects on the mutual influence of the interaction is studied by means of molecular electrostatic potential calculations. By taking advantage of these computational tools, the present study examines interplay of these interactions. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Monte Carlo simulations of flexible polyanions complexing with whey proteins at their isoelectric point.

PubMed

de Vries, R

2004-02-15

Electrostatic complexation of flexible polyanions with the whey proteins alpha-lactalbumin and beta-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Huckel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that alpha-lactalbumin complexes much more strongly than beta-lactoglobulin. For alpha-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for beta-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches. Copyright 2004 American Institute of Physics

Origin of selenium–gold interaction in F{sub 2}CSe⋯AuY (Y = CN, F, Cl, Br, OH, and CH{sub 3}): Synergistic effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xin; Yang, Yu-Ping; Li, Qing-Zhong, E-mail: liqingzhong1990@sina.com, E-mail: lihaibei@sdu.edu.cn

Selenium–gold interaction plays an important role in crystal materials, molecular self-assembly, and pharmacochemistry involving gold. In this paper, we unveiled the mechanism and nature of selenium–gold interaction by studying complexes F{sub 2}CSe⋯AuY (Y = CN, F, Cl, Br, OH, and CH{sub 3}). The results showed that the formation of selenium–gold interaction is mainly attributed to the charge transfer from the lone pair of Se atom to the Au—Y anti-bonding orbital. Energy decomposition analysis indicated that the polarization energy is nearly equivalent to or exceeds the electrostatic term in the selenium–gold interaction. Interestingly, the chalcogen–gold interaction becomes stronger with the increasemore » of chalcogen atomic mass in F{sub 2}CX⋯AuCN (X = O, S, Se, and Te). The cyclic ternary complexes are formed with the introduction of NH{sub 3} into F{sub 2}CSe⋯AuY, in which selenium–gold interaction is weakened and selenium–nitrogen interaction is strengthened due to the synergistic effects.« less

Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

PubMed

Yuan, Yongna; Mills, Matthew J L; Popelier, Paul L A

2014-02-15

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. Copyright © 2013 Wiley Periodicals, Inc.

Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations.

PubMed

Chakravorty, Dhruva K; Hammes-Schiffer, Sharon

2010-06-02

The two proton transfer reactions catalyzed by ketosteroid isomerase (KSI) involve a dienolate intermediate stabilized by hydrogen bonds with Tyr14 and Asp99. Molecular dynamics simulations based on an empirical valence bond model are used to examine the impact of mutating these residues on the hydrogen-bonding patterns, conformational changes, and van der Waals and electrostatic interactions during the proton transfer reactions. While the rate constants for the two proton transfer steps are similar for wild-type (WT) KSI, the simulations suggest that the rate constant for the first proton transfer step is smaller in the mutants due to the significantly higher free energy of the dienolate intermediate relative to the reactant. The calculated rate constants for the mutants D99L, Y14F, and Y14F/D99L relative to WT KSI are qualitatively consistent with the kinetic experiments indicating a significant reduction in the catalytic rates along the series of mutants. In the simulations, WT KSI retained two hydrogen-bonding interactions between the substrate and the active site, while the mutants typically retained only one hydrogen-bonding interaction. A new hydrogen-bonding interaction between the substrate and Tyr55 was observed in the double mutant, leading to the prediction that mutation of Tyr55 will have a greater impact on the proton transfer rate constants for the double mutant than for WT KSI. The electrostatic stabilization of the dienolate intermediate relative to the reactant was greater for WT KSI than for the mutants, providing a qualitative explanation for the significantly reduced rates of the mutants. The active site exhibited restricted motion during the proton transfer reactions, but small conformational changes occurred to facilitate the proton transfer reactions by strengthening the hydrogen-bonding interactions and by bringing the proton donor and acceptor closer to each other with the proper orientation for proton transfer. Thus, these calculations suggest that KSI forms a preorganized active site but that the structure of this preorganized active site is altered upon mutation. Moreover, small conformational changes due to stochastic thermal motions are required within this preorganized active site to facilitate the proton transfer reactions.

Lone pair-π interactions in biological systems: occurrence, function, and physical origin.

PubMed

Kozelka, Jiří

2017-12-01

Lone pair-π interactions are now recognized as a supramolecular bond whose existence in biological systems is documented by a growing number of examples. They are commonly attributed to electrostatic forces. This review attempts to highlight some recent discoveries evidencing the important role which lone pair-π interactions, and anion-π interactions in particular, play in stabilizing the structure and affecting the function of biomolecules. Special attention is paid to studies exploring the physical origin of these at first glance counterintuitive interactions between a lone pair of electrons of one residue and the π-cloud of another. Recent theoretical work went beyond the popular electrostatic model and inquired the extent to which orbital interactions have to be taken into account. In at least one biologically relevant case-that of anion-flavin interactions-a substantial charge-transfer component has been shown to operate.

Electrostatic atomization--Experiment, theory and industrial applications

NASA Astrophysics Data System (ADS)

Okuda, H.; Kelly, Arnold J.

1996-05-01

Experimental and theoretical research has been initiated at the Princeton Plasma Physics Laboratory on the electrostatic atomization process in collaboration with Charged Injection Corporation. The goal of this collaboration is to set up a comprehensive research and development program on the electrostatic atomization at the Princeton Plasma Physics Laboratory so that both institutions can benefit from the collaboration. Experimental, theoretical and numerical simulation approaches are used for this purpose. An experiment consisting of a capillary sprayer combined with a quadrupole mass filter and a charge detector was installed at the Electrostatic Atomization Laboratory to study fundamental properties of the charged droplets such as the distribution of charges with respect to the droplet radius. In addition, a numerical simulation model is used to study interaction of beam electrons with atmospheric pressure water vapor, supporting an effort to develop an electrostatic water mist fire-fighting nozzle.

Electrostatic attraction between neutral microdroplets by ion fluctuations

NASA Astrophysics Data System (ADS)

Sheng, Yu-Jane; Tsao, Heng-Kwong

2004-06-01

The interaction between two aqueous droplets containing ions is investigated. The ion-fluctuation correlation gives rise to attraction between two neutral microdroplets, similar to the van der Waals interaction between neutral atoms. Electrostatic attraction consists of contributions from various induced multipole-multipole interactions, including dipole-dipole < P2z >2 r-6 , dipole-quadrupole < P2z > < Q 2zz > r-8 , dipole-octupole < P2z > < O 2zzz > r-10 , and quadrupole-quadrupole interactions < Q 2zz >2 r-10 . The mean-square multipole moments are determined analytically by linear response theory. The fluctuation-driven attraction is so strong at short distance that it may dominate over the Coulomb repulsion between like-charged droplets. These theoretical results are confirmed by Monte Carlo simulations.

Electrostatic attraction between neutral microdroplets by ion fluctuations.

PubMed

Sheng, Yu-Jane; Tsao, Heng-Kwong

2004-06-01

The interaction between two aqueous droplets containing ions is investigated. The ion-fluctuation correlation gives rise to attraction between two neutral microdroplets, similar to the van der Waals interaction between neutral atoms. Electrostatic attraction consists of contributions from various induced multipole-multipole interactions, including dipole-dipole < P(2)(z) >(2) r(-6), dipole-quadrupole < P(2)(z) > < Q (2)(zz ) > r(-8), dipole-octupole < P(2)(z) > < O (2)(zzz ) > r(-10), and quadrupole-quadrupole interactions < Q (2)(zz ) >(2) r(-10). The mean-square multipole moments are determined analytically by linear response theory. The fluctuation-driven attraction is so strong at short distance that it may dominate over the Coulomb repulsion between like-charged droplets. These theoretical results are confirmed by Monte Carlo simulations.

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

PubMed

Beard, D A; Schlick, T

2001-01-01

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels. Copyright 2000 John Wiley & Sons, Inc.

A small-gap electrostatic micro-actuator for large deflections

PubMed Central

Conrad, Holger; Schenk, Harald; Kaiser, Bert; Langa, Sergiu; Gaudet, Matthieu; Schimmanz, Klaus; Stolz, Michael; Lenz, Miriam

2015-01-01

Common quasi-static electrostatic micro actuators have significant limitations in deflection due to electrode separation and unstable drive regions. State-of-the-art electrostatic actuators achieve maximum deflections of approximately one third of the electrode separation. Large electrode separation and high driving voltages are normally required to achieve large actuator movements. Here we report on an electrostatic actuator class, fabricated in a CMOS-compatible process, which allows high deflections with small electrode separation. The concept presented makes the huge electrostatic forces within nanometre small electrode separation accessible for large deflections. Electrostatic actuations that are larger than the electrode separation were measured. An analytical theory is compared with measurement and simulation results and enables closer understanding of these actuators. The scaling behaviour discussed indicates significant future improvement on actuator deflection. The presented driving concept enables the investigation and development of novel micro systems with a high potential for improved device and system performance. PMID:26655557

The establishment and application of direct coupled electrostatic-structural field model in electrostatically controlled deployable membrane antenna

NASA Astrophysics Data System (ADS)

Gu, Yongzhen; Duan, Baoyan; Du, Jingli

2018-05-01

The electrostatically controlled deployable membrane antenna (ECDMA) is a promising space structure due to its low weight, large aperture and high precision characteristics. However, it is an extreme challenge to describe the coupled field between electrostatic and membrane structure accurately. A direct coupled method is applied to solve the coupled problem in this paper. Firstly, the membrane structure and electrostatic field are uniformly described by energy, considering the coupled problem is an energy conservation phenomenon. Then the direct coupled electrostatic-structural field governing equilibrium equations are obtained by energy variation approach. Numerical results show that the direct coupled method improves the computing efficiency by 36% compared with the traditional indirect coupled method with the same level accuracy. Finally, the prototype has been manufactured and tested and the ECDMA finite element simulations show good agreement with the experiment results as the maximum surface error difference is 6%.

Steric, Quantum, and Electrostatic Effects on SN2 Reaction Barriers in Gas Phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Shubin; Hu, Hao; Pedersen, Lee G.

2010-05-13

Biomolecular nucleophilic substitution reactions, S{sub N}2, are fundamental and commonplace in chemistry. It is the well-documented experimental finding in the literature that vicinal substitution with bulkier groups near the reaction center significantly slows the reaction due to steric hindrance, but theoretical understanding in the quantitative manner about factors dictating the S{sub N}2 reaction barrier height is still controversial. In this work, employing the new quantification approach that we recently proposed for the steric effect from the density functional theory framework, we investigate the relative contribution of three independent effects—steric, electrostatic, and quantum—to the S{sub N}2 barrier heights in gas phasemore » for substituted methyl halide systems, R{sub 1}R{sub 2}R{sub 3}CX, reacting with the fluorine anion, where R{sub 1}, R{sub 2}, and R{sub 3} denote substituting groups and X = F or Cl. We found that in accordance with the experimental finding, for these systems, the steric effect dominates the transition state barrier, contributing positively to barrier heights, but this contribution is largely compensated by the negative, stabilizing contribution from the quantum effect due to the exchange-correlation interactions. Moreover, we find that it is the component from the electrostatic effect that is linearly correlated with the S{sub N}2 barrier height for the systems investigated in the present study. In addition, we compared our approach with the conventional method of energy decomposition in density functional theory as well as examined the steric effect from the wave function theory for these systems via natural bond orbital analysis.« less

Hierarchy of the Collective Effects in Water Clusters.

PubMed

Bakó, Imre; Mayer, István

2016-02-04

The results of dipole moment as well as of intra- and intermolecular bond order calculations indicate the big importance of collective electrostatic effects caused by the nonimmediate environment in liquid water models. It is also discussed how these collective effects are built up as consequences of the electrostatic and quantum chemical interactions in water clusters.

Charge regulation at semiconductor-electrolyte interfaces.

PubMed

Fleharty, Mark E; van Swol, Frank; Petsev, Dimiter N

2015-07-01

The interface between a semiconductor material and an electrolyte solution has interesting and complex electrostatic properties. Its behavior will depend on the density of mobile charge carriers that are present in both phases as well as on the surface chemistry at the interface through local charge regulation. The latter is driven by chemical equilibria involving the immobile surface groups and the potential determining ions in the electrolyte solution. All these lead to an electrostatic potential distribution that propagate such that the electrolyte and the semiconductor are dependent on each other. Hence, any variation in the charge density in one phase will lead to a response in the other. This has significant implications on the physical properties of single semiconductor-electrolyte interfaces and on the electrostatic interactions between semiconductor particles suspended in electrolyte solutions. The present paper expands on our previous publication (Fleharty et al., 2014) and offers new results on the electrostatics of single semiconductor interfaces as well as on the interaction of charged semiconductor colloids suspended in electrolyte solution. Copyright © 2014 Elsevier Inc. All rights reserved.

Unveiling the stimulatory effects of tartrazine on human and bovine serum albumin fibrillogenesis: Spectroscopic and microscopic study

NASA Astrophysics Data System (ADS)

Al-Shabib, Nasser Abdulatif; Khan, Javed Masood; Alsenaidy, Mohammad A.; Alsenaidy, Abdulrahman M.; Khan, Mohd Shahnawaz; Husain, Fohad Mabood; Khan, Mohammad Rashid; Naseem, Mohammad; Sen, Priyankar; Alam, Parvez; Khan, Rizwan Hasan

2018-02-01

Amyloid fibrils are playing key role in the pathogenesis of various neurodegenerative diseases. Generally anionic molecules are known to induce amyloid fibril in several proteins. In this work, we have studied the effect of anionic food additive dye i.e., tartrazine (TZ) on the amyloid fibril formation of human serum albumins (HSA) and bovine serum albumin (BSA) at pHs 7.4 and 3.5. We have employed various biophysical methods like, turbidity measurements, Rayleigh Light Scattering (RLS), Dynamic Light Scattering (DLS), intrinsic fluorescence, Congo red assay, far-UV CD, transmission electron microscopy (TEM) and atomic force microscopy (AFM) to decipher the mechanism of TZ-induce amyloid fibril formation in both the serum albumins at pHs 7.4 and 3.5. The obtained results suggest that both the albumins forms amyloid-like aggregates in the presence of 1.0 to 15.0 mM of TZ at pH 3.5, but no amyloid fibril were seen at pH 7.4. The possible cause of TZ-induced amyloid fibril formation is electrostatic and hydrophobic interaction because sulfate group of TZ may have interacted electrostatically with positively charged amino acids of the albumins at pH 3.5 and increased protein-protein and protein-TZ interactions leading to amyloid fibril formation. The TEM, RLS and DLS results are suggesting that BSA forms bigger size amyloids compared to HSA, may be due to high surface hydrophobicity of BSA.

Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi.

PubMed

Li, Chuan; Petukh, Marharyta; Li, Lin; Alexov, Emil

2013-08-15

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. Copyright © 2013 Wiley Periodicals, Inc.

Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

PubMed Central

Yang, Pei-Kun

2013-01-01

To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD) simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes. PMID:23852018

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues

NASA Astrophysics Data System (ADS)

Liwo, Adam; Tempczyk, Anna; Grzonka, Zbigniew

1989-09-01

Continuing our theoretical studies of the oxytocin and vasopressin analogues, we have analysed the molecular electrostatic potential (MEP) and the norm of the molecular electrostatic field (MEF) of [1- β-mercaptopropionic acid]-arginine-vasopressin ([Mpa1]-AVP), [1-( β-mercapto- β,β-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp']-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths']-AVP) whose low-energy conformations were calculated in our previous work. These compounds are known from experiment to exhibit different biological activity. The scalar fields mentioned determine the energy of interaction with either charged (MEP) or polar (MEF) species, the energy being in the second case either optimal or Boltzmann-averaged over all the possible orientations of the dipole moment versus the electrostatic field. The electrostatic interactions slowly vanish with distance and can therefore be considered to be the factor determining the molecular shape at greater distances, which can help in both predicting the interactions with the receptor at the stage of remote recognition and in finding the preferred directions of solvation by a polar solvent. In the analysis of the fields three techniques have been used: (i) the construction of maps in certain planes; (ii) the construction of maps on spheres centered in the charge center of the molecule under study and of poles chosen according to the main axes of the quadrupole moment; and (iii) the construction of surfaces corresponding to a given value of potential. The results obtained show that the shapes of both MEP and MEF are similar in the case of [Mpa1]-AVP and [Cpp1-AVP (biologically active), while some differences emerge when comparing these compounds with [Ths1]-AVP (inactive). It has also been found that both MEP and MEF depend even more strongly on conformation.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations.

PubMed

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-14

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-01

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Electrostatic and electromagnetic gyroharmonic emissions due to energetic electrons in magnetospheric plasma

NASA Technical Reports Server (NTRS)

Curtis, S. A.; Wu, C. S.

1979-01-01

The paper derives the growth rates and growth lengths of the electrostatic emission for spatially homogeneous and inhomogeneous energetic electrons, and numerically evaluates the growth rate and growth length spectra for several parameter sets representative of magnetospheric plasmas. In addition, the growth rates are derived for the case of electromagnetic emission modeled by the ordinary mode. The numerical results of the electromagnetic and electrostatic cases are compared with observations made by satellites in the earth's magnetosphere. It is concluded that the electrostatic gyroharmonic excitation is possible without the cold composition of plasma which is often postulated in the existing literature.

Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging.

PubMed

Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A

2015-02-05

As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1). Copyright © 2013 Elsevier B.V. All rights reserved.

Theoretical assessment of the disparity in the electrostatic forces between two point charges and two conductive spheres of equal radii

NASA Astrophysics Data System (ADS)

Kolikov, Kiril

2016-11-01

The Coulomb's formula for the force FC of electrostatic interaction between two point charges is well known. In reality, however, interactions occur not between point charges, but between charged bodies of certain geometric form, size and physical structure. This leads to deviation of the estimated force FC from the real force F of electrostatic interaction, thus imposing the task to evaluate the disparity. In the present paper the problem is being solved theoretically for two charged conductive spheres of equal radii and arbitrary electric charges. Assessment of the deviation is given as a function of the ratio of the distance R between the spheres centers to the sum of their radii. For the purpose, relations between FC and F derived in a preceding work of ours, are employed to generalize the Coulomb's interactions. At relatively short distances between the spheres, the Coulomb force FC, as estimated to be induced by charges situated at the centers of the spheres, differ significantly from the real force F of interaction between the spheres. In the case of zero and non-zero charge we prove that with increasing the distance between the two spheres, the force F decrease rapidly, virtually to zero values, i.e. it appears to be short-acting force.

Electromagnetic theory of the nuclear interaction. Application to the deuteron {sup 2}H

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaeffer, Bernard

2012-06-20

Bieler of the Rutherford laboratory imagined in 1924 a magnetic attraction equilibrating an electrostatic repulsion between the protons. Since the discovery of the neutron and the magnetic moments of the nucleons proving that the neutron contains electric charges, nobody, as far as I know, has tried to apply electromagnetism to the nuclear interaction. The electrostatic and magnetic interactions are completely neglected except for a mean Coulomb repulsion. As it is well known, there is an attraction between an electric charge and a neutral conductor. In the neutron, the positive charges are repelled and the negative charges attracted by a nearbymore » proton. There is a net attraction explaining quantitatively the so-called strong force as it is shown in this paper. In the deuteron, the magnetic repulsion equilibrates the electrostatically induced neutron-proton attraction. The experimental value (- 2.2 MeV) is surrounded by - 1.6 MeV and - 2.5 MeV, depending on the calculation method. No arbitrary fitting parameter is used, only physical constants: it is a true ab initio calculation. The theoretical ratio between nuclear and chemical energies has been found to be (m{sub p}/m{sub e}{alpha}), proving that the usual assumption that the electromagnetic interaction is too feeble to predict the nuclear interaction is incorrect.« less

Interactions between charged nanoparticles and giant vesicles fabricated from inverted-headgroup lipids

NASA Astrophysics Data System (ADS)

Wang, Lu; Malmstadt, Noah

2017-10-01

The surface chemistry of the cell membrane plays an important role in how cells interact with particulate species. These interactions are dictated in large part by lipid headgroup charge. To investigate the nature of electrostatic interactions between lipid bilayers and nanoparticles in solution, we studied nanoparticles interacting with the zwitterionic lipid 1,2-dioleoyl-glycero-3-phosphocholine (DOPC), and its inverted-headgroup analog DOCP. These interactions were investigated by fabricating giant unilamellar vesicles (GUVs) with DOPC lipids and DOCP lipids respectively, and introducing nanoparticles to suspensions of both. GUVs displayed various deformational modes depending on the charge and size of the nanoparticles as well as the compositions of the GUVs. The differences in the responses of the two lipid species illuminate how the phosphate and choline groups on the lipid interact with charged nanoparticles. This study suggests that the phosphate group dominates the lipid-nanoparticle electrostatic interaction. We speculate that the formation of water clathrate structures around the choline group inhibits interactions between negatively charged nanoparticles and the positively charged choline.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

PubMed

Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

2016-08-19

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

NASA Astrophysics Data System (ADS)

Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

2016-08-01

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Fluorescence studies on binding of pyrene and its derivatives to humic acid

NASA Astrophysics Data System (ADS)

Nakashima, K.; Maki, M.; Ishikawa, F.; Yoshikawa, T.; Gong, Y.-K.; Miyajima, T.

2007-07-01

Binding of pyrene (PyH) and its derivatives to humic acid (HA) has been studied by fluorescence spectroscopy. The nature of the interaction between HA and pyrene derivatives are extensively investigated by employing three derivatives ranging from anionic to cationic compounds: 1-pyrenebutylic acid (PyA), 1-pyrenemethanol (PyM), and 1-pyrenebutyltrimethylammonium bromide (PyB). Binding constants between HA and PyX (X = H, A, M, B) are obtained by steady-state fluorescence quenching techniques, and it is found that PyB has a markedly large binding constant among the pyrene family. This is attributed to a strong electrostatic interaction between cationic PyB and anionic HA. The result suggests that an electrostatic interaction plays a dominant role in binding of pyrenes to humic acid. The importance of electrostatic interaction was also confirmed by a salt effect on the binding constant. Influence of collisional quenching on the binding constant, which causes overestimation of the binding constant, was examined by time-resolved fluorescence spectroscopy as well as temperature effect in steady-state fluorescence measurements. It is elucidated that collisional quenching does not much bring overestimation into the binding constants.

Comparative studies on group III σ-hole and π-hole interactions.

PubMed

Gao, Lei; Zeng, Yanli; Zhang, Xueying; Meng, Lingpeng

2016-05-30

The σ-hole of M2 H6 (M = Al, Ga, In) and π-hole of MH3 (M = Al, Ga, In) were discovered and analyzed, the bimolecular complexes M2 H6 ···NH3 and MH3 ···N2 P2 F4 (M = Al, Ga, In) were constructed to carry out comparative studies on the group III σ-hole interactions and π-hole interactions. The two types of interactions are all partial-covalent interactions; the π-hole interactions are stronger than σ-hole interactions. The electrostatic energy is the largest contribution for forming the σ-hole and π-hole interaction, the polarization energy is also an important factor to form the M···N interaction. The electrostatic energy contributions to the interaction energy of the σ-hole interactions are somewhat greater than those of the π-hole interactions. However, the polarization contributions for the π-hole interactions are somewhat greater than those for the σ-hole interactions. © 2016 Wiley Periodicals, Inc.

Teaching Ion-Ion, Ion-Dipole, and Dipole-Dipole Interactions

ERIC Educational Resources Information Center

Yoder, Claude H.

1977-01-01

Discusses how electrostatic interactions can be taught quantitatively through Coulomb's Law at a variety of points in a chemistry curriculum. Each type of interaction is shown at both the intramolecular and the inter-"molecular" levels. (MR)

Effect of Surfaces on Amyloid Fibril Formation

PubMed Central

Moores, Bradley; Drolle, Elizabeth; Attwood, Simon J.; Simons, Janet; Leonenko, Zoya

2011-01-01

Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Aβ) (1–42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid with cell membrane surfaces. We compared the structure and density of Aβ fibrils on positively and negatively charged as well as hydrophobic chemically-modified surfaces at physiologically relevant conditions. We report that due to the complex distribution of charge and hydrophobicity amyloid oligomers bind to all types of surfaces investigated (CH3, COOH, and NH2) although the charge and hydrophobicity of surfaces affected the structure and size of amyloid deposits as well as surface coverage. Hydrophobic surfaces promote formation of spherical amorphous clusters, while charged surfaces promote protofibril formation. We used the nonlinear Poisson-Boltzmann equation (PBE) approach to analyze the electrostatic interactions of amyloid monomers and oligomers with modified surfaces to complement our AFM data. PMID:22016789

Photophysical study of the interaction between ZnO nanoparticles and globular protein bovine serum albumin in solution and in a layer-by-layer self-assembled film

NASA Astrophysics Data System (ADS)

Hansda, Chaitali; Maiti, Pradip; Singha, Tanmoy; Pal, Manisha; Hussain, Syed Arshad; Paul, Sharmistha; Paul, Pabitra Kumar

2018-10-01

In this study, we investigated the spectroscopic properties of the water-soluble globular protein bovine serum albumin (BSA) while interacting with zinc oxide (ZnO) semiconductor nanoparticles (NPs) in aqueous medium and in a ZnO/BSA layer-by-layer (LbL) self-assembled film fabricated on poly (acrylic acid) (PAA)-coated quartz or a Si substrate via electrostatic interactions. BSA formed a ground state complex due to its interaction with ZnO NPs, which was confirmed by ultraviolet-visible absorption, and steady state and time-resolved fluorescence emission spectroscopic techniques. However, due to its interaction with ZnO, the photophysical properties of BSA depend significantly on the concentration of ZnO NPs in the mixed solution. The quenching of the fluorescence intensity of BSA in the presence of ZnO NPs was due to the interaction between ZnO and BSA, and the formation of their stable ground state complex, as well as energy transfer from the excited BSA to ZnO NPs in the complex nano-bioconjugated species. Multilayer growth of the ZnO/BSA LbL self-assembled film on the quartz substrate was confirmed by monitoring the characteristic absorption band of BSA (280 nm), where the nature of the film growth depends on the number of bilayers deposited on the quartz substrate. BSA formed a well-ordered molecular network-type morphology due to its adsorption onto the surface of the ZnO nanostructure in the backbone of the PAA-coated Si substrate in the LbL film according to atomic force microscopic study. The as-synthesized ZnO NPs were characterized by field emission scanning electron microscopy, X-ray powder diffraction, and dynamic light scattering techniques.

Investigation of plasma-surface interaction effects on pulsed electrostatic manipulation for reentry blackout alleviation

NASA Astrophysics Data System (ADS)

Krishnamoorthy, S.; Close, S.

2017-03-01

The reentry blackout phenomenon affects most spacecraft entering a dense planetary atmosphere from space, due to the presence of a plasma layer that surrounds the spacecraft. This plasma layer is created by ionization of ambient air due to shock and frictional heating, and in some cases is further enhanced due to contamination by ablation products. This layer causes a strong attenuation of incoming and outgoing electromagnetic waves including those used for command and control, communication and telemetry over a period referred to as the ‘blackout period’. The blackout period may last up to several minutes and is a major contributor to the landing error ellipse at best, and a serious safety hazard in the worst case, especially in the context of human spaceflight. In this work, we present a possible method for alleviation of reentry blackout using electronegative DC pulses applied from insulated electrodes on the reentry vehicle’s surface. We study the reentry plasma’s interaction with a DC pulse using a particle-in-cell (PIC) model. Detailed models of plasma-insulator interaction are included in our simulations. The absorption and scattering of ions and electrons at the plasma-dielectric interface are taken into account. Secondary emission from the insulating surface is also considered, and its implications on various design issues is studied. Furthermore, we explore the effect of changing the applied voltage and the impact of surface physics on the creation and stabilization of communication windows. The primary aim of this analysis is to examine the possibility of restoring L- and S-band communication from the spacecraft to a ground station. Our results provide insight into the effect of key design variables on the response of the plasma to the applied voltage pulse. Simulations show the creation of pockets where electron density in the plasma layer is reduced three orders of magnitude or more in the vicinity of the electrodes. These pockets extend to distances up to three times the electrode length normal to the vehicle surface. Based on our results, we postulate that pulsed electrostatic manipulation (PEM) may be a viable candidate for reentry blackout alleviation in the future.

Electrostatic potential of B-DNA: effect of interionic correlations.

PubMed Central

Gavryushov, S; Zielenkiewicz, P

1998-01-01

Modified Poisson-Boltzmann (MPB) equations have been numerically solved to study ionic distributions and mean electrostatic potentials around a macromolecule of arbitrarily complex shape and charge distribution. Results for DNA are compared with those obtained by classical Poisson-Boltzmann (PB) calculations. The comparisons were made for 1:1 and 2:1 electrolytes at ionic strengths up to 1 M. It is found that ion-image charge interactions and interionic correlations, which are neglected by the PB equation, have relatively weak effects on the electrostatic potential at charged groups of the DNA. The PB equation predicts errors in the long-range electrostatic part of the free energy that are only approximately 1.5 kJ/mol per nucleotide even in the case of an asymmetrical electrolyte. In contrast, the spatial correlations between ions drastically affect the electrostatic potential at significant separations from the macromolecule leading to a clearly predicted effect of charge overneutralization. PMID:9826596

Contribution of electrostatics to the binding of pancreatic-type ribonucleases to membranes.

PubMed

Sundlass, Nadia K; Eller, Chelcie H; Cui, Qiang; Raines, Ronald T

2013-09-17

Pancreatic-type ribonucleases show clinical promise as chemotherapeutic agents but are limited in efficacy by the inefficiency of their uptake by human cells. Cellular uptake can be increased by the addition of positive charges to the surface of ribonucleases, either by site-directed mutagenesis or by chemical modification. This observation has led to the hypothesis that ribonuclease uptake by cells depends on electrostatics. Here, we use a combination of experimental and computational methods to ascertain the contribution of electrostatics to the cellular uptake of ribonucleases. We focus on three homologous ribonucleases: Onconase (frog), ribonuclease A (cow), and ribonuclease 1 (human). Our results support the hypothesis that electrostatics are necessary for the cellular uptake of Onconase. In contrast, specific interactions with cell-surface components likely contribute more to the cellular uptake of ribonuclease A and ribonuclease 1 than do electrostatics. These findings provide insight for the design of new cytotoxic ribonucleases.

On the electrostatic and steric similarity of lactam compounds and the natural substrate for bacterial cell-wall biosynthesis

NASA Astrophysics Data System (ADS)

Frau, J.; Price, S. L.

1996-04-01

Electrostatic and structural properties of a set of β-lactam, γ-lactam and nonlactam compounds have been analyzed and compared with those of a model of the natural substrate d-alanyl- d-alanine for the carboxy- and transpeptidase enzymes. This first comparison of the electrostatic properties has been based on a distributed multipole analysis of high-quality ab initio wave functions of the substrate and potential antibiotics. The electrostatic similarity of the substrate and active compounds is apparent, and contrasts with the electrostatic properties of the noninhibitors. This has been quantified to give a reasonable correlation with the MIC (Minimum Concentration for Inhibition) and with kinetic data (k2/K) in accordance with the model for interaction of the lactam compounds with dd-peptidase. These correlations provide a better prediction of antibacterial activity than purely structural criteria.

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

PubMed

Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

2017-11-15

Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Energy decomposition analysis of the interactions in adduct ions of acetophenone and Na+, NH4+ and H+ in the gas phase

NASA Astrophysics Data System (ADS)

Sugimura, Natsuhiko; Igarashi, Yoko; Aoyama, Reiko; Shibue, Toshimichi

2017-09-01

The physical origins of the interactions in the acetophenone cation adducts [M+Na]+, [M+NH4]+, and [M+H]+ were explored by localized molecular orbital-energy decomposition analysis and density functional theory. The analyses highlighted the differences in the interactions in the three adduct ions. Electrostatic energy was important in [M+Na]+ and there was little change in the acetophenone orbital shape. Both electrostatic and polarization energy were important in [M+NH4]+, and a considerable change in the orbital shape occurred to maximize the strength of the hydrogen bond. Polarization energy was the major attractive force in [M+H]+.

Effects of electrostatic interactions on ligand dissociation kinetics

NASA Astrophysics Data System (ADS)

Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

2018-02-01

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Counting the ions surrounding nucleic acids

PubMed Central

2017-01-01

Abstract Nucleic acids are strongly negatively charged, and thus electrostatic interactions—screened by ions in solution—play an important role in governing their ability to fold and participate in biomolecular interactions. The negative charge creates a region, known as the ion atmosphere, in which cation and anion concentrations are perturbed from their bulk values. Ion counting experiments quantify the ion atmosphere by measuring the preferential ion interaction coefficient: the net total number of excess ions above, or below, the number expected due to the bulk concentration. The results of such studies provide important constraints on theories, which typically predict the full three-dimensional distribution of the screening cloud. This article reviews the state of nucleic acid ion counting measurements and critically analyzes their ability to test both analytical and simulation-based models. PMID:28034959

Wave-particle interactions on the FAST satellite

NASA Technical Reports Server (NTRS)

Temerin, M. A.; Carlson, C. W.; Cattell, C. A.; Ergun, R. E.; Mcfadden, J. P.

1990-01-01

NASA's Fast Auroral Snapshot, or 'FAST' satellite, scheduled for launch in 1993, will investigate the plasma physics of the low altitude auroral zone from a 3500-km apogee polar orbit. FAST will give attention to wave, double-layer, and soliton production processes due to electrons and ions, as well as to wave-wave interactions, and the acceleration of electrons and ions by waves and electric fields. FAST will employ an intelligent data-handling system capacle of data acquisition at rates of up to 1 Mb/sec, in addition to a 1-Gbit solid-state memory. The data need be gathered for only a few minutes during passes through the auroral zone, since the most interesting auroral phenomena occur in such narrow regions as auroral arcs, electrostatic shocks, and superthermal electron bursts.

Modeling the Electrostatics of Hollow Shell Suspensions: Ion Distribution, Pair Interactions, and Many-Body Effects.

PubMed

Hallez, Yannick; Meireles, Martine

2016-10-11

Electrostatic interactions play a key role in hollow shell suspensions as they determine their structure, stability, thermodynamics, and rheology and also the loading capacity of small charged species for nanoreservoir applications. In this work, fast, reliable modeling strategies aimed at predicting the electrostatics of hollow shells for one, two, and many colloids are proposed and validated. The electrostatic potential inside and outside a hollow shell with a finite thickness and a specific permittivity is determined analytically in the Debye-Hückel (DH) limit. An expression for the interaction potential between two such hollow shells is then derived and validated numerically. It follows a classical Yukawa form with an effective charge depending on the shell geometry, permittivity, and inner and outer surface charge densities. The predictions of the Ornstein-Zernike (OZ) equation with this pair potential to determine equations of state are then evaluated by comparison to results obtained with a Brownian dynamics algorithm coupled to the resolution of the linearized Poisson-Boltzmann and Laplace equations (PB-BD simulations). The OZ equation based on the DLVO-like potential performs very well in the dilute regime as expected, but also quite well, and more surprisingly, in the concentrated regime in which full spheres exhibit significant many-body effects. These effects are shown to vanish for shells with small thickness and high permittivity. For highly charged hollow shells, we propose and validate a charge renormalization procedure. Finally, using PB-BD simulations, we show that the cell model predicts the ion distribution inside and outside hollow shells accurately in both electrostatically dilute and concentrated suspensions. We then determine the shell loading capacity as a function of salt concentration, volume fraction, and surface charge density for nanoreservoir applications such as drug delivery, sensing, or smart coatings.

An ionic-chemical-mechanical model for muscle contraction.

PubMed

Manning, Gerald S

2016-12-01

The dynamic process underlying muscle contraction is the parallel sliding of thin actin filaments along an immobile thick myosin fiber powered by oar-like movements of protruding myosin cross bridges (myosin heads). The free energy for functioning of the myosin nanomotor comes from the hydrolysis of ATP bound to the myosin heads. The unit step of translational movement is based on a mechanical-chemical cycle involving ATP binding to myosin, hydrolysis of the bound ATP with ultimate release of the hydrolysis products, stress-generating conformational changes in the myosin cross bridge, and relief of built-up stress in the myosin power stroke. The cycle is regulated by a transition between weak and strong actin-myosin binding affinities. The dissociation of the weakly bound complex by addition of salt indicates the electrostatic basis for the weak affinity, while structural studies demonstrate that electrostatic interactions among negatively charged amino acid residues of actin and positively charged residues of myosin are involved in the strong binding interface. We therefore conjecture that intermediate states of increasing actin-myosin engagement during the weak-to-strong binding transition also involve electrostatic interactions. Methods of polymer solution physics have shown that the thin actin filament can be regarded in some of its aspects as a net negatively charged polyelectrolyte. Here we employ polyelectrolyte theory to suggest how actin-myosin electrostatic interactions might be of significance in the intermediate stages of binding, ensuring an engaged power stroke of the myosin motor that transmits force to the actin filament, and preventing the motor from getting stuck in a metastable pre-power stroke state. We provide electrostatic force estimates that are in the pN range known to operate in the cycle. © 2016 Wiley Periodicals, Inc.

Electrostatic potential calculation for biomolecules--creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures.

PubMed

Rocchia, W; Neshich, G

2007-10-05

STING and Java Protein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and Java Protein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. BlueStar STING is available at http://www.cbi.cnptia.embrapa.br.

Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation

NASA Astrophysics Data System (ADS)

Lee, Joonseong; Kim, Seonghoon; Chang, Rakwoo; Jayanthi, Lakshmi; Gebremichael, Yeshitila

2013-01-01

The present study examines the effects of the model dependence, ionic strength, divalent ions, and hydrophobic interaction on the structural organization of the human neurofilament (NF) brush, using canonical ensemble Monte Carlo (MC) simulations of a coarse-grained model with the amino-acid resolution. The model simplifies the interactions between the NF core and the sidearm or between the sidearms by the sum of excluded volume, electrostatic, and hydrophobic interactions, where both monovalent salt ions and solvents are implicitly incorporated into the electrostatic interaction potential. Several important observations are made from the MC simulations of the coarse-grained model NF systems. First, the mean-field type description of monovalent salt ions works reasonably well in the NF system. Second, the manner by which the NF sidearms are arranged on the surface of the NF backbone core has little influence on the lateral extension of NF sidearms. Third, the lateral extension of the NF sidearms is highly affected by the ionic strength of the system: at low ionic strength, NF-M is most extended but at high ionic strength, NF-H is more stretched out because of the effective screening of the electrostatic interaction. Fourth, the presence of Ca2 + ions induces the attraction between negatively charged residues, which leads to the contraction of the overall NF extension. Finally, the introduction of hydrophobic interaction does not change the general structural organization of the NF sidearms except that the overall extension is contracted.

Potential effect of cationic liposomes on interactions with oral bacterial cells and biofilms.

PubMed

Sugano, Marika; Morisaki, Hirobumi; Negishi, Yoichi; Endo-Takahashi, Yoko; Kuwata, Hirotaka; Miyazaki, Takashi; Yamamoto, Matsuo

2016-01-01

Although oral infectious diseases have been attributed to bacteria, drug treatments remain ineffective because bacteria and their products exist as biofilms. Cationic liposomes have been suggested to electrostatically interact with the negative charge on the bacterial surface, thereby improving the effects of conventional drug therapies. However, the electrostatic interaction between oral bacteria and cationic liposomes has not yet been examined in detail. The aim of the present study was to examine the behavior of cationic liposomes and Streptococcus mutans in planktonic cells and biofilms. Liposomes with or without cationic lipid were prepared using a reverse-phase evaporation method. The zeta potentials of conventional liposomes (without cationic lipid) and cationic liposomes were -13 and 8 mV, respectively, and both had a mean particle size of approximately 180 nm. We first assessed the interaction between liposomes and planktonic bacterial cells with a flow cytometer. We then used a surface plasmon resonance method to examine the binding of liposomes to biofilms. We confirmed the binding behavior of liposomes with biofilms using confocal laser scanning microscopy. The interactions between cationic liposomes and S. mutans cells and biofilms were stronger than those of conventional liposomes. Microscopic observations revealed that many cationic liposomes interacted with the bacterial mass and penetrated the deep layers of biofilms. In this study, we demonstrated that cationic liposomes had higher affinity not only to oral bacterial cells, but also biofilms than conventional liposomes. This electrostatic interaction may be useful as a potential drug delivery system to biofilms.

A theoretical study of complexes formed between cations and curved aromatic systems: electrostatics does not always control cation-π interaction.

PubMed

Carrazana-García, Jorge A; Cabaleiro-Lago, Enrique M; Rodríguez-Otero, Jesús

2017-04-19

The present work studies the interaction of two extended curved π-systems (corannulene and sumanene) with various cations (sodium, potassium, ammonium, tetramethylammonium, guanidinium and imidazolium). Polyatomic cations are models of groups found in important biomolecules in which cation-π interaction plays a fundamental role. The results indicate an important size effect: with extended π systems and cations of the size of potassium and larger, dispersion is much more important than has been generally recognized for cation-π interactions. In most of the systems studied here, the stability of the cation-π complexes is the result of a balanced combination of electrostatic, induction and dispersion contributions. None of the systems studied here owes its stability to the electrostatic interaction more than 42%. Induction dominates stabilization in complexes with sodium, and in some of the potassium and ammonium complexes. In complexes with large cations and with flat cations dispersion is the major stabilizing contribution and can provide more than 50% of the stabilization energy. This implies that theoretical studies of the cation-π interaction involving large or even medium-size fragments require a level of calculation capable of properly modelling dispersion. The separation between the cation and the π system is another important factor to take into account, especially when the fragments of the cation-π complex are bound (for example, to a protein backbone) and cannot interact at the most favourable distance.

Acidic pH retards the fibrillization of human islet amyloid polypeptide due to electrostatic repulsion of histidines

NASA Astrophysics Data System (ADS)

Li, Yang; Xu, Weixin; Mu, Yuguang; Zhang, John Z. H.

2013-08-01

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], 10.1021/ja205007j, which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

DNA binding studies of Sunset Yellow FCF using spectroscopy, viscometry and electrochemical techniques

NASA Astrophysics Data System (ADS)

Asaadi, Sara; Hajian, Reza

2017-10-01

Color is one of the important factors in food industry. All food companies use synthetic pigments to improve the aesthetic of products. Studies on the interaction between deoxyribonucleic acid (DNA) and food dye molecules is important because DNA is responsible for some processes including replication and transcription of cells, mutations, genetic diseases, and some synthetic chemical nucleases. In this study, the molecular interaction between Sunset Yellow FCF (SY) as a common food coloring additive and calf thymus DNA (ct-DNA) has been studied using UV-Vis spectrophotometry, spectrofluorometry, Fourier transform infrared (FTIR) spectroscopy, cyclic voltammetry and viscometry techniques. The binding constant between ct-DNA and SY in phosphate buffer solution (pH 7.4) was calculated as 2.09 × 103 L mol-1. The non-electrostatic bonding constant (K0t) was almost consistent and the ratio of K0t/Kb increased by increasing the ionic strength in the range of 0.01-0.1 mol L-1 of KCl. This observation shows that, the molecular bonding of SY to ct-DNA is a combination of electrostatic and intercalation interactions. In the electrochemical studies, an oxidation peak at 0.71 V and a reduction peak at about 0.63 V was observed with the peak potential difference (ΔEp) of 0.08 V, showing a reversible process. The oxidation and reduction peaks were significantly decreased in the presence of ct-DNA and the reduction peak current shifted to negative values. In spectrofluorometric study, the fluorescence intensity of SY increased dramatically after successive addition of DNA due to the increasing of molecular surface area and decreasing of impact frequency between solvent and SY-DNA adduct. Moreover, viscometric study shows that the increasing of viscosity for SY solution in the presence of DNA is due to the intercalation mechanism with double strand DNA (ds-DNA).

Solar wind interaction with dusty plasmas produces instabilities and solitary structures

NASA Astrophysics Data System (ADS)

Saleem, H.; Ali, S.

2017-12-01

It is pointed out that the solar wind interaction with dusty magnetospheres of the planets can give rise to purely growing instabilities as well as nonlinear electric field structures. Linear dispersion relation of the low frequency electrostatic ion-acoustic wave (IAW) is modified in the presence of stationary dust and its frequency becomes larger than its frequency in usual electron ion plasma even if ion temperature is equal to the electron temperature. This dust-ion-acoustic wave (DIAW) either becomes a purely growing electrostatic instability or turns out to be the modified dust-ion-acoustic wave (mDIAW) depending upon the magnitude of shear flow scale length and its direction. Growth rate of shear flow-driven electrostatic instability in a plasma having negatively charged stationary dust is larger than the usual D'Angelo instability of electron-ion plasma. It is shown that shear modified dust ion acoustic wave (mDIAW) produces electrostatic solitons in the nonlinear regime. The fluid theory predicts the existence of electrostatic solitons in the dusty plasmas in those regions where the inhomogeneous solar wind flow is parallel to the planetary or cometary magnetic field lines. The amplitude and width of the solitary structure depends upon dust density and magnitude of shear in the flow. This is a general theoretical model which is applied to dusty plasma of Saturn's F-ring for illustration.

Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding

PubMed Central

Basu, Sankar; Bhattacharyya, Dhananjay; Banerjee, Rahul

2012-01-01

Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors. PMID:22713576

The self-consistent parallel electric field due to electrostatic ion-cyclotron turbulence in downward auroral-current regions of the Earth's magnetosphere. IV

NASA Astrophysics Data System (ADS)

Jasperse, John R.; Basu, Bamandas; Lund, Eric J.; Grossbard, Neil

2010-06-01

The physical processes that determine the self-consistent electric field (E∥) parallel to the magnetic field have been an unresolved problem in magnetospheric physics for over 40 years. Recently, a new multimoment fluid theory was developed for inhomogeneous, nonuniformly magnetized plasma in the guiding-center and gyrotropic approximation that includes the effect of electrostatic, turbulent, wave-particle interactions (see Jasperse et al. [Phys. Plasmas 13, 072903 (2006); Jasperse et al., Phys. Plasmas13, 112902 (2006)]). In the present paper and its companion paper [Jasperse et al., Phys. Plasmas 17, 062903 (2010)], which are intended as sequels to the earlier work, a fundamental model for downward, magnetic field-aligned (Birkeland) currents for quasisteady conditions is presented. The model includes the production of electrostatic ion-cyclotron turbulence in the long-range potential region by an electron, bump-on-tail-driven ion-cyclotron instability. Anomalous momentum transfer (anomalous resistivity) by itself is found to produce a very small contribution to E∥; however, the presence of electrostatic, ion-cyclotron turbulence has a very large effect on the altitude dependence of the entire quasisteady solution. Anomalous energy transfer (anomalous heating and cooling) modifies the density, drift, and temperature altitude profiles and hence the generalized parallel-pressure gradients and mirror forces in the electron and ion momentum-balance equations. As a result, |E∥| is enhanced by nearly a factor of 40 compared to its value when turbulence is absent. The space-averaged potential increase associated with the strong double layer at the bottom of the downward-current sheet is estimated using the FAST satellite data and the multimoment fluid theory.

Self-complementarity within proteins: bridging the gap between binding and folding.

PubMed

Basu, Sankar; Bhattacharyya, Dhananjay; Banerjee, Rahul

2012-06-06

Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A smoothed particle hydrodynamics model for electrostatic transport of charged lunar dust on the moon surface

NASA Astrophysics Data System (ADS)

Mao, Zirui; Liu, G. R.

2018-02-01

The behavior of lunar dust on the Moon surface is quite complicated compared to that on the Earth surface due to the small lunar gravity and the significant influence of the complicated electrostatic filed in the Universe. Understanding such behavior is critical for the exploration of the Moon. This work develops a smoothed particle hydrodynamics (SPH) model with the elastic-perfectly plastic constitutive equation and Drucker-Prager yield criterion to simulate the electrostatic transporting of multiple charged lunar dust particles. The initial electric field is generated based on the particle-in-cell method and then is superposed with the additional electric field from the charged dust particles to obtain the resultant electric field in the following process. Simulations of cohesive soil's natural failure and electrostatic transport of charged soil under the given electric force and gravity were carried out using the SPH model. Results obtained in this paper show that the negatively charged dust particles levitate and transport to the shadow area with a higher potential from the light area with a lower potential. The motion of soil particles finally comes to a stable state. The numerical result for final distribution of soil particles and potential profile above planar surface by the SPH method matches well with the experimental result, and the SPH solution looks sound in the maximum levitation height prediction of lunar dust under an uniform electric field compared to theoretical solution, which prove that SPH is a reliable method in describing the behavior of soil particles under a complicated electric field and small gravity field with the consideration of interactions among soil particles.

Molecular origins of fluorocarbon hydrophobicity

PubMed Central

Dalvi, Vishwanath H.; Rossky, Peter J.

2010-01-01

We have undertaken atomistic molecular simulations to systematically determine the structural contributions to the hydrophobicity of fluorinated solutes and surfaces compared to the corresponding hydrocarbon, yielding a unified explanation for these phenomena. We have transformed a short chain alkane, n-octane, to n-perfluorooctane in stages. The free-energy changes and the entropic components calculated for each transformation stage yield considerable insight into the relevant physics. To evaluate the effect of a surface, we have also conducted contact-angle simulations of water on self-assembled monolayers of hydrocarbon and fluorocarbon thiols. Our results, which are consistent with experimental observations, indicate that the hydrophobicity of the fluorocarbon, whether the interaction with water is as solute or as surface, is due to its “fatness.” In solution, the extra work of cavity formation to accommodate a fluorocarbon, compared to a hydrocarbon, is not offset by enhanced energetic interactions with water. The enhanced hydrophobicity of fluorinated surfaces arises because fluorocarbons pack less densely on surfaces leading to poorer van der Waals interactions with water. We find that interaction of water with a hydrophobic solute/surface is primarily a function of van der Waals interactions and is substantially independent of electrostatic interactions. This independence is primarily due to the strong tendency of water at room temperature to maintain its hydrogen bonding network structure at an interface lacking hydrophilic sites. PMID:20643968

Electrostatic wrapping of doxorubicin with curdlan to construct an efficient pH-responsive drug delivery system

NASA Astrophysics Data System (ADS)

Zhou, Jiang-Ling; Song, Fei; Tian, Jia-Feng; Nie, Wu-Cheng; Wang, Xiu-Li; Wang, Yu-Zhong

2017-07-01

The development of environmentally responsive drug delivery systems for the treatment of cancer has attracted particular interest in recent years. However, the enhancement of drug loading capacity and realization of pH-responsive drug delivery remain challenging. Herein, we employ carboxymethyl curdlan as a hydrophilic carrier to wrap doxorubicin (DOX) directly via electrostatic interaction. The sizes of the formed nanoparticles can be simply tuned by changing their feeding ratios. In particular, the nanoparticles are highly stable in aqueous solution without size variation. In vitro drug release and cytotoxicity assays illustrate that this delivery system can release DOX differentially under various environmental conditions and transport it into cell nuclei efficiently, with comparable therapeutic effect to the free drug. These results suggest that the carrying of antitumor drugs by polysaccharide via electrostatic interaction is a simple but effective way to construct a pH-dependent drug delivery platform.

Electrostatics-Driven Hierarchical Buckling of Charged Flexible Ribbons.

PubMed

Yao, Zhenwei; Olvera de la Cruz, Monica

2016-04-08

We investigate the rich morphologies of an electrically charged flexible ribbon, which is a prototype for many beltlike structures in biology and nanomaterials. Long-range electrostatic repulsion is found to govern the hierarchical buckling of the ribbon from its initially flat shape to its undulated and out-of-plane twisted conformations. In this process, the screening length is the key controlling parameter, suggesting that a convenient way to manipulate the ribbon morphology is simply to change the salt concentration. We find that these shapes originate from the geometric effect of the electrostatic interaction, which fundamentally changes the metric over the ribbon surface. We also identify the basic modes by which the ribbon reshapes itself in order to lower the energy. The geometric effect of the physical interaction revealed in this Letter has implications for the shape design of extensive ribbonlike materials in nano- and biomaterials.

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

PubMed Central

Kornyshev, Alexei A.; Leikin, Sergey

2013-01-01

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation. PMID:23663846

Study of the electrostatic effects of mutations on the surface of dehaloperoxidase-hemoglobin A.

PubMed

Zhao, Junjie; Rowe, Jennifer; Franzen, Jocelyn; He, Chi; Franzen, Stefan

2012-04-20

Point mutations of dehaloperoxidase-hemoglobin A (DHP A) that affect the surface charge have been prepared to study the interaction between DHP A with its substrate 2,4,6-trichlorophenol (TCP). Kinetic studies of these surface mutations showed a correlation, in which the more positively charged mutants have increased catalytic efficiency compared with wild type DHP A. As a result, the hypothesis of this study is that there is a global electrostatic interaction between DHP A and TCP. The electrostatic nature of substrate binding was further confirmed by the result that kinetic assays of DHP A were affected by ionic strength. Furthermore, isoelectric focusing (IEF) gel study showed that the pI-6.8 for DHP A, which indicates that DHP A has a slight negative charge pH 7, consistent with the kinetic observations. Copyright © 2012 Elsevier Inc. All rights reserved.

Electrostatic-Assisted Liquefaction of Porous Carbons

DOE PAGES

Li, Peipei; Schott, Jennifer A.; Zhang, Jinshui; ...

2017-10-10

Porous liquids are a newly developed porous material that combine unique fluidity with permanent porosity, which exhibit promising functionalities for a variety of applications. However, the apparent incompatibility between fluidity and permanent porosity makes the stabilization of porous nanoparticle with still empty pores in the dense liquid phase a significant challenging. For this study, by exploiting the electrostatic interaction between carbon networks and polymerized ionic liquids, we demonstrate that carbon-based porous nanoarchitectures can be well stabilized in liquids to afford permanent porosity, and thus opens up a new approach to prepare porous carbon liquids. Furthermore, we hope this facile synthesismore » strategy can be widely applicated to fabricate other types of porous liquids, such as those (e.g., carbon nitride, boron nitride, metal–organic frameworks, covalent organic frameworks etc.) also having the electrostatic interaction with polymerized ionic liquids, evidently advancing the development and understanding of porous liquids.« less

Coarse-graining, Electrostatics and pH effects in phospholipid systems

NASA Astrophysics Data System (ADS)

Travesset, Alex; Vangaveti, Sweta

2010-03-01

We introduce a minimal free energy describing the interaction of charged groups and counterions including both classical electrostatic and specific interactions. The predictions of the model are compared against the standard model for describing ions next to charged interfaces, consisting of Poisson-Boltzmann theory with additional constants describing ion binding, which are specific to the counterion and the interfacial charge (``chemical binding''). It is shown that the ``chemical'' model can be appropriately described by an underlying ``physical'' model over several decades in concentration, but the extracted binding constants are not uniquely defined, as they differ depending on the particular observable quantity being studied. It is also shown that electrostatic correlations for divalent (or higher valence) ions enhance the surface charge by increasing deprotonation, an effect not properly accounted within chemical models. The model is applied to the charged phospholipids phosphatidylserine, Phosphatidc acid and Phosphoinositides and implications for different biological processes are discussed.

QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines

NASA Astrophysics Data System (ADS)

Hagiwara, Yohsuke; Ohta, Takehiro; Tateno, Masaru

2009-02-01

An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and a molecular mechanics (MM) calculation engine, AMBER, has been developed for QM/MM hybrid calculations. A protein-DNA complex is used as a test system to investigate the following two types of QM/MM schemes. In a 'subtractive' scheme, electrostatic interactions between QM/MM regions are truncated in QM calculations; in an 'additive' scheme, long-range electrostatic interactions within a cut-off distance from QM regions are introduced into one-electron integration terms of a QM Hamiltonian. In these calculations, 338 atoms are assigned as QM atoms using Hartree-Fock (HF)/density functional theory (DFT) hybrid all-electron calculations. By comparing the results of the additive and subtractive schemes, it is found that electronic structures are perturbed significantly by the introduction of MM partial charges surrounding QM regions, suggesting that biological processes occurring in functional sites are modulated by the surrounding structures. This also indicates that the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of biological macromolecules.

Binding interactions of halogenated bisphenol A with mouse PPARα: In vitro investigation and molecular dynamics simulation.

PubMed

Zhang, Jie; Li, Tiezhu; Wang, Tuoyi; Guan, Tianzhu; Yu, Hansong; Li, Zhuolin; Wang, Yongzhi; Wang, Yongjun; Zhang, Tiehua

2018-02-01

The binding of bisphenol A (BPA) and its halogenated derivatives (halogenated BPAs) to mouse peroxisome proliferator-activated receptor α ligand binding domain (mPPARα-LBD) was examined by a combination of in vitro investigation and in silico simulation. Fluorescence polarization (FP) assay showed that halogenated BPAs could bind to mPPARα-LBD* as the affinity ligands. The calculated electrostatic potential (ESP) illustrated the different charge distributions of halogenated BPAs with altered halogenation patterns. As electron-attracting substituents, halogens decrease the positive electrostatic potential and thereby have a significant influence on the electrostatic interactions of halogenated BPAs with mPPARα-LBD*. The docking results elucidated that hydrophobic and hydrogen-bonding interactions may also contribute to stabilize the binding of the halogenated BPAs to their receptor molecule. Comparison of the calculated binding energies with the experimentally determined affinities yielded a good correlation (R 2 =0.6659) that could provide a rational basis for designing environmentally benign chemicals with reduced toxicities. This work can potentially be used for preliminary screening of halogenated BPAs. Copyright © 2017 Elsevier B.V. All rights reserved.

Electrostatic stabilization in sperm whale and harbor seal myoglobins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gurd, F.R.N.; Friend, S.H.; Rothgeb, T.M.

1980-10-01

The compact, largely helical structure of sperm whale and harbor seal myoglobins undergoes an abrupt one-step transition between pH 4.5 and 3.5 as monitored by changes in either the heme Soret band absorbance or circular dichroism probes of secondary structure, for which a modified Tanford-Kirkwood theory provides identification of certain dominant electrostatic interactions responsible for the loss of stability. A similar treatment permits identification of the electrostatic interactions primarily responsible for a process in which the anchoring of the A helix to other parts of the molecule is weakened. This process is detected with both myoglobins, in a pH rangemore » approx. 1 unit higher than the onset of the overall unfolding process, through changes in the circular dichroic spectra near 295 nm which correspond to the L/sub a/O-O band of the only two tryptophan residues in these proteins, residues 7 and 14. In each case protonation of certain sites in neighboring parts of the molecule can be identified as producing destabilizing interactions with components of the A helix, particularly with lysine 16.« less

Counterion effects in protein nanoparticle electrostatic binding: a theoretical study.

PubMed

Ghosh, Goutam

2015-04-01

Effects of counterions on the folding conformation of proteins, bound electrostatically on the surface of charge-ligand functionalized nanoparticles, have been investigated based on the protein folding energy calculation. The folding energy of a protein has been taken as a sum of the short range interaction energies, like, the van der Waals attraction and the hydrogen bond energies, and the long range coulomb interaction energy. On electrostatic binding, counterions associated with surface ligands of nanoparticles diffuse into bound proteins through the medium of dispersion. As a result, bound proteins partially unfold, as observed in circular dichroism experiments, which has been realized using the "charge-dipole" and the "charge-induced dipole" interactions of counterions with polar and non-polar residues, respectively. The effect of counterions solvation in the dispersing medium, e.g., water, which causes water molecules to polarize around the counterions, has also been considered. The folding energy of bound proteins has been seen to decrease proportionally with the increasing number of diffusion of counterions and their polarizability. Copyright © 2015 Elsevier B.V. All rights reserved.

Surface charge accumulation of particles containing radionuclides in open air.

PubMed

Kim, Yong-Ha; Yiacoumi, Sotira; Tsouris, Costas

2015-05-01

Radioactivity can induce charge accumulation on radioactive particles. However, electrostatic interactions caused by radioactivity are typically neglected in transport modeling of radioactive plumes because it is assumed that ionizing radiation leads to charge neutralization. The assumption that electrostatic interactions caused by radioactivity are negligible is evaluated here by examining charge accumulation and neutralization on particles containing radionuclides in open air. A charge-balance model is employed to predict charge accumulation on radioactive particles. It is shown that particles containing short-lived radionuclides can be charged with multiple elementary charges through radioactive decay. The presence of radioactive particles can significantly modify the particle charge distribution in open air and yield an asymmetric bimodal charge distribution, suggesting that strong electrostatic particle interactions may occur during short- and long-range transport of radioactive particles. Possible effects of transported radioactive particles on electrical properties of the local atmosphere are reported. The study offers insight into transport characteristics of airborne radionuclides. Results are useful in atmospheric transport modeling of radioactive plumes. Copyright © 2015 Elsevier Ltd. All rights reserved.