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.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

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.

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.

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.

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.

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.

The electrostatic fluidic trap: a new approach to the spatial control and manipulation of matter at the nanometer scale (presentation video)

NASA Astrophysics Data System (ADS)

Krishnan, Madhavi

2014-09-01

I will describe a new technique to trap matter at the nanometer scale in fluids. Rather than apply external fields to the object of interest, our approach relies on spatial tailoring of the interaction between an object and its neighbouring surfaces in order to create spatial potential minima in three dimensions. We demonstrate how the strong and long-ranged electrostatic interaction can be modulated by tailoring substrate geometry to achieve stable spatial trapping of charged objects, as small as single proteins in solution.

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.

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.

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

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.

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

Specificity in cationic interaction with poly(N-isopropylacrylamide).

PubMed

Du, Hongbo; Wickramasinghe, Sumith Ranil; Qian, Xianghong

2013-05-02

Classical molecular dynamics (MD) simulations were conducted for PNIPAM in 1 M monovalent alkali chloride salt solutions as well as in 0.5 M divalent Mg(2+) and Ca(2+) chloride salt solutions. It was found that the strength for the direct alkali ion-amide O binding is strongly correlated with the size of the ionic radius. The smallest Li(+) ion binds strongest to amide O, and the largest Cs(+) ion has the weakest interaction with the amide bond. For the divalent Mg(2+) and Ca(2+) ions, their interactions with the amide bond are weak and appear to be mediated by the water molecules, particularly in the case of Mg(2+), resulting from their strong hydration. The direct binding between the cations and amide O requires partial desovlation of the ions that is energetically unfavorable for Mg(2+) and also to a great extent for Ca(2+). The higher cation charge makes the electrostatic interaction more favorable but the dehydration process less favorable. This competition between electrostatic interaction and the dehydration process largely dictates whether the direct binding between the cation and amide O is energetically preferred or not. For monovalent alkali ions, it is energetically preferred to bind directly with the amide O. Moreover, Li(+) ion is also found to associate strongly with the hydrophobic residues on PNIPAM.

Kubo conductivity of a strongly magnetized two-dimensional plasma.

NASA Technical Reports Server (NTRS)

Montgomery, D.; Tappert, F.

1971-01-01

The Kubo formula is used to evaluate the bulk electrical conductivity of a two-dimensional guiding-center plasma in a strong dc magnetic field. The particles interact only electrostatically. An ?anomalous' electrical conductivity is derived for this system, which parallels a recent result of Taylor and McNamara for the coefficient of spatial diffusion.

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

Adsorption of charged protein residues on an inorganic nanosheet: Computer simulation of LDH interaction with ion channel

NASA Astrophysics Data System (ADS)

Tsukanov, Alexey A.; Psakhie, Sergey G.

2016-08-01

Quasi-two-dimensional and hybrid nanomaterials based on layered double hydroxides (LDH), cationic clays, layered oxyhydroxides and hydroxides of metals possess large specific surface area and strong electrostatic properties with permanent or pH-dependent electric charge. Such nanomaterials may impact cellular electrostatics, changing the ion balance, pH and membrane potential. Selective ion adsorption/exchange may alter the transmembrane electrochemical gradient, disrupting potential-dependent cellular processes. Cellular proteins as a rule have charged residues which can be effectively adsorbed on the surface of layered hydroxide based nanomaterials. The aim of this study is to attempt to shed some light on the possibility and mechanisms of protein "adhesion" an LDH nanosheet and to propose a new direction in anticancer medicine, based on physical impact and strong electrostatics. An unbiased molecular dynamics simulation was performed and the combined process free energy estimation (COPFEE) approach was used.

Electrostatic drift instability in a magnetotail configuration: The role of bouncing electrons

NASA Astrophysics Data System (ADS)

Fruit, G.; Louarn, P.; Tur, A.

2017-03-01

To understand the possible destabilization of two-dimensional current sheets, a kinetic model is proposed to describe the resonant interaction between electrostatic modes and trapped electrons that bounce within the sheet. This work follows the initial investigation by Tur, Louarn, and Yanovsky [Phys. Plasmas 17, 102905 (2010)] and Fruit, Louarn, and Tur [Phys. Plasmas 20, 022113 (2013)] that is revised and extended. Using a quasi-dipolar equilibrium state, the linearized gyro-kinetic Vlasov equation is solved for electrostatic fluctuations with a period of the order of the electron bounce period. Using an appropriated Fourier expansion of the particle motion along the magnetic field, the complete time integration of the non-local perturbed distribution functions is performed. The dispersion relation for electrostatic modes is then obtained through the quasineutrality condition. It is found that for a mildly stretched configuration ( L ˜8 ), strongly unstable electrostatic modes may develop in the current sheet with the growth rate of the order of a few seconds provided that the background density gradient responsible for the diamagnetic drift effects is sharp enough: typical length scale over one Earth radius or less. However, when this condition in the density gradient is not met, these electrostatic modes grow too slowly to be accountable for a rapid destabilization of the magnetic structure. This strong but finely tuned instability may offer opportunities to explain features in magnetospheric substorms.

Electrostatics effects in granular materials

NASA Astrophysics Data System (ADS)

Sarkar, Saurabh; Chaudhuri, Bodhisattwa

2013-06-01

This purpose of this study is to investigate the role of physiochemical properties and operational conditions in determining the electrostatic interactions between two species on a surface under typical industrial conditions. The variables considered for the study were particle type, particle size and shape, loading mass, surface type, angle of inclination of chute, nature and concentration of additive. Triboelectrification of simple and binary mixtures in a simple hopper and chute geometry was observed to be strongly linked to work function and moisture content of the powdered material.

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.

Nuclear Stability and Nucleon-Nucleon Interactions in Introductory and General Chemistry Textbooks

ERIC Educational Resources Information Center

Millevolte, Anthony

2010-01-01

The nucleus is a highly dense and highly charged substructure of atoms. In the nuclei of all atoms beyond hydrogen, multiple protons are in close proximity to each other in spite of strong electrostatic repulsions between them. The attractive internucleon strong force is described and its origin explained by using a simple quark model for the…

Nonlinear interaction of strong microwave beam with the ionosphere MINIX rocket experiment

NASA Astrophysics Data System (ADS)

Kaya, N.; Matsumoto, H.; Miyatake, S.; Kimura, I.; Nagatomo, M.

A rocket-borne experiment called 'MINIX' was carried out to investigate the nonlinear interaction of a strong microwave energy beam with the ionosphere. The MINIX stands for Microwave-Ionosphere Nonlinear Interaction eXperiment and was carried out on August 29, 1983. The objective of the MINIX is to study possible impacts of the SPS microwave energy beam on the ionosphere, such as the ohmic heating and plasma wave excitation. The experiment showed that the microwave with f = 2.45 GHz nonlinearly excites various electrostatic plasma waves, though no ohmic heating effects were detected.

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.

MODELING PARTICULATE CHARGING IN ESPS

EPA Science Inventory

In electrostatic precipitators there is a strong interaction between the particulate space charge and the operating voltage and current of an electrical section. Calculating either the space charge or the operating point when the other is fixed is not difficult, but calculating b...

Structural properties of the promiscuous VP16 activation domain.

PubMed

Jonker, Hendrik R A; Wechselberger, Rainer W; Boelens, Rolf; Folkers, Gert E; Kaptein, Rob

2005-01-25

Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified the regions and residues involved in the interaction with the human transcriptional coactivator positive cofactor 4 (PC4) and the general transcription factor TFIIB. NMR and biochemical experiments revealed that both VP16 activation regions are required for the interaction and undergo a conformational transition from random coil to alpha-helix upon binding to its target PC4. The interaction is strongly electrostatically driven and the binding to PC4 is enhanced by the presence of its amino-terminal domain. We propose models for binding of VP16 to the core domains of PC4 and TFIIB that are based on two independent docking approaches using NMR chemical shift changes observed in titration experiments. The models are consistent with results from site-directed mutagenesis and provide an explanation for the contribution of both acidic and hydrophobic residues for transcriptional activation by VP16. Both intrinsically unstructured activation domains are attracted to their interaction partner by electrostatic interactions, and adopt an alpha-helical conformation around the important hydrophobic residues. The models showed multiple distinct binding surfaces upon interaction with various partners, providing an explanation for the promiscuous properties, cooperativity, and the high activity of this activation domain.

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.

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.

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.

Exploring Local Electrostatic Effects with Scanning Probe Microscopy: Implications for Piezoresponse Force Microscopy and Triboelectricity

DOE PAGES

Balke, Nina; Maksymovych, Petro; Jesse, Stephen; ...

2014-09-25

The implementation of contact mode Kelvin probe force microscopy (KPFM) utilizes the electrostatic interactions between tip and sample when the tip and sample are in contact with each other. Surprisingly, the electrostatic forces in contact are large enough to be measured even with tips as stiff as 4.5 N/m. As for traditional non-contact KPFM, the signal depends strongly on electrical properties of the sample, such as the dielectric constant, and the tip-properties, such as the stiffness. Since the tip is in contact with the sample, bias-induced changes in the junction potential between tip and sample can be measured with highermore » lateral and temporal resolution compared to traditional non-contact KPFM. Significant and reproducible variations of tip-surface capacitance are observed and attributed to surface electrochemical phenomena. Lastly, observations of significant surface charge states at zero bias and strong hysteretic electromechanical responses at non-ferroelectric surface have significant implications for fields such as triboelectricity and piezoresponse force microscopy.« less

Ion-Flow-Induced Excitation of Electrostatic Cyclotron Mode in Magnetized Dusty Plasma

NASA Astrophysics Data System (ADS)

Bezbaruah, P.; Das, N.

2018-05-01

The stability of electrostatic cyclotron mode is investigated in a flowing magnetized dusty plasma in the presence of strong ion-neutral collisions. In the high magnetic field limit, when the dust magnetization becomes important, it is expected that the collective behavior of magnetized dust grains suspended in the near-sheath region substantially influences the dispersion properties of electrostatic modes. The growth/damping of the collective excitation is significantly controlled by such parameters as the ion-neutral collision frequency, Mach number, and magnetic field strength. In our case, the explicit dependence of the Mach number on the magnetic field and collision frequency has been taken into account and possible implications on the stability of the mode is analyzed. Streaming instability of cyclotron modes may be important to understand issues related to the interaction mechanism between dust grains and other associated phenomena like Coulomb crystallization, phase behavior, transport properties, etc., in the relatively strong magnetic field limit, which is currently accessible in the DPD (Kiel University) and MDPX (PSL, Auburn University) experiments.

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

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1993-01-01

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

Attractive Interactions between Heteroallenes and the Cucurbituril Portal.

PubMed

Reany, Ofer; Li, Amanda; Yefet, Maayan; Gilson, Michael K; Keinan, Ehud

2017-06-21

In this paper, we report on the noteworthy attractive interaction between organic azides and the portal carbonyls of cucurbiturils. Five homologous bis-α,ω-azidoethylammonium alkanes were prepared, where the number of methylene groups between the ammonium groups ranges from 4 to 8. Their interactions with cucurbit[6]uril were studied by NMR spectroscopy, IR spectroscopy, X-ray crystallography, and computational methods. Remarkably, while the distance between the portal plane and most atoms at the guest end groups increases progressively with the molecular size, the β-nitrogen atoms maintain a constant distance from the portal plane in all homologues, pointing at a strong attractive interaction between the azide group and the portal. Both crystallography and NMR support a specific electrostatic interaction between the carbonyl and the azide β-nitrogen, which stabilizes the canonical resonance form with positive charge on the β-nitrogen and negative charge on the γ-nitrogen. Quantum computational analyses strongly support electrostatics, in the form of orthogonal dipole-dipole interaction, as the main driver for this attraction. The alternative mechanism of n → π* orbital delocalization does not seem to play a significant role in this interaction. The computational studies also indicate that the interaction is not limited to azides, but generalizes to other isoelectronic heteroallene functions, such as isocyanate and isothiocyanate. This essentially unexploited attractive interaction could be more broadly utilized as a tool not only in relation to cucurbituril chemistry, but also for the design of novel supramolecular architectures.

The role of strong electrostatic interactions at the dimer interface of human glutathione synthetase.

PubMed

De Jesus, Margarita C; Ingle, Brandall L; Barakat, Khaldoon A; Shrestha, Bisesh; Slavens, Kerri D; Cundari, Thomas R; Anderson, Mary E

2014-10-01

The obligate homodimer human glutathione synthetase (hGS) provides an ideal system for exploring the role of protein-protein interactions in the structural stability, activity and allostery of enzymes. The two active sites of hGS, which are 40 Å apart, display allosteric modulation by the substrate γ-glutamylcysteine (γ-GC) during the synthesis of glutathione, a key cellular antioxidant. The two subunits interact at a relatively small dimer interface dominated by electrostatic interactions between S42, R221, and D24. Alanine scans of these sites result in enzymes with decreased activity, altered γ-GC affinity, and decreased thermal stability. Molecular dynamics simulations indicate these mutations disrupt interchain bonding and impact the tertiary structure of hGS. While the ionic hydrogen bonds and salt bridges between S42, R221, and D24 do not mediate allosteric communication in hGS, these interactions have a dramatic impact on the activity and structural stability of the enzyme.

Modification and simulation of Rhizomucor miehei lipase: the influence of surficial electrostatic interaction on enantioselectivity.

PubMed

Xu, Gang; Meng, Xiao; Xu, Lin-Jie; Guo, Li; Wu, Jian-Ping; Yang, Li-Rong

2015-04-01

Surface residues have a significant impact on the enantioselectivity of lipases. But the molecular basis of this has never been explained. In this work, transition state complexes of Rhizomucor miehei lipase (RmL) and (R)- or (S)-n-butyl 2-phenxypropinate were studied using molecular dynamics. According to comparison between B-factor of the two simulated complexes, the β 1-β 2 loop and α 2 helix were considered the enantioselectivity-determining domains of RmL. Interaction analysis of these domains suggested an Asp(61)-Arg(86) electrostatic interaction linking the loop and helix strongly impacting enantioselectivity of RmL. Modification of Arg(86) by 1, 2-cyclohexanedione weakening this interaction decreased the E ratio from 6 to 1, modification by 1-iodo-2, 3-butanedione covalently bonding Asp(61) and Arg(86) strengthening the interaction increased the E ratio to 45. Dynamics simulation and energy calculation of the modified lipases also displayed corresponding decreases or increases of enantioselectivity.

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.

Evidences of Changes in Surface Electrostatic Charge Distribution during Stabilization of HPV16 Virus-Like Particles

PubMed Central

Vega, Juan F.; Vicente-Alique, Ernesto; Núñez-Ramírez, Rafael; Wang, Yang; Martínez-Salazar, Javier

2016-01-01

The stabilization of human papillomavirus type 16 virus-like particles has been examined by means of different techniques including dynamic and static light scattering, transmission electron microscopy and electrophoretic mobility. All these techniques provide different and often complementary perspectives about the aggregation process and generation of stabilized virus-like particles after a period of time of 48 hours at a temperature of 298 K. Interestingly, static light scattering results point towards a clear colloidal instability in the initial systems, as suggested by a negative value of the second virial coefficient. This is likely related to small repulsive electrostatic interactions among the particles, and in agreement with relatively small absolute values of the electrophoretic mobility and, hence, of the net surface charges. At this initial stage the small repulsive interactions are not able to compensate binding interactions, which tend to aggregate the particles. As time proceeds, an increase of the size of the particles is accompanied by strong increases, in absolute values, of the electrophoretic mobility and net surface charge, suggesting enhanced repulsive electrostatic interactions and, consequently, a stabilized colloidal system. These results show that electrophoretic mobility is a useful methodology that can be applied to screen the stabilization factors for virus-like particles during vaccine development. PMID:26885635

The roles of fluid motion and other transport phenomena in the morphology of materials

NASA Technical Reports Server (NTRS)

Saville, D. A.

1993-01-01

Two crystallization problems were studied: the growth of protein crystals, in particular the influence of colloidal forces and convection, and the influence of interface resistance on the growth of dendritic crystals. The protein study involved both experimental and theoretical work; the work of dendrites was entirely theoretical. In the study of protein crystallization, experiments were carried out where crystals were grown in the presence and absence of natural convection. No evidence was found that convection retards crystal growth. The theoretical study focused on the influence of colloidal forces (electrostatic and London-van der Waals) on the interaction between a protein molecule and a flat crystal surface. It was shown that the interaction is extremely sensitive to colloidal forces and that electrostatic interactions play a strong role in deciding whether or not a molecule will find a favorable site for adsorption. In the study of dendritic growth, the role of an interfacial resistance on the selection processes was examined. Using a computational scheme, it was found that the selected velocity is strongly dependent on the magnitude of the interfacial resistance to heat transfer. This is a possible explanation for discrepancies between the theoretical and experimental results on succinonitrile.

The roles of fluid motion and other transport phenomena in the morphology of materials

NASA Astrophysics Data System (ADS)

Saville, D. A.

1993-11-01

Two crystallization problems were studied: the growth of protein crystals, in particular the influence of colloidal forces and convection, and the influence of interface resistance on the growth of dendritic crystals. The protein study involved both experimental and theoretical work; the work of dendrites was entirely theoretical. In the study of protein crystallization, experiments were carried out where crystals were grown in the presence and absence of natural convection. No evidence was found that convection retards crystal growth. The theoretical study focused on the influence of colloidal forces (electrostatic and London-van der Waals) on the interaction between a protein molecule and a flat crystal surface. It was shown that the interaction is extremely sensitive to colloidal forces and that electrostatic interactions play a strong role in deciding whether or not a molecule will find a favorable site for adsorption. In the study of dendritic growth, the role of an interfacial resistance on the selection processes was examined. Using a computational scheme, it was found that the selected velocity is strongly dependent on the magnitude of the interfacial resistance to heat transfer. This is a possible explanation for discrepancies between the theoretical and experimental results on succinonitrile.

Particle Based Simulations of Complex Systems with MP2C : Hydrodynamics and Electrostatics

NASA Astrophysics Data System (ADS)

Sutmann, Godehard; Westphal, Lidia; Bolten, Matthias

2010-09-01

Particle based simulation methods are well established paths to explore system behavior on microscopic to mesoscopic time and length scales. With the development of new computer architectures it becomes more and more important to concentrate on local algorithms which do not need global data transfer or reorganisation of large arrays of data across processors. This requirement strongly addresses long-range interactions in particle systems, i.e. mainly hydrodynamic and electrostatic contributions. In this article, emphasis is given to the implementation and parallelization of the Multi-Particle Collision Dynamics method for hydrodynamic contributions and a splitting scheme based on Multigrid for electrostatic contributions. Implementations are done for massively parallel architectures and are demonstrated for the IBM Blue Gene/P architecture Jugene in Jülich.

Synthetic food additive dye "Tartrazine" triggers amorphous aggregation in cationic myoglobin.

PubMed

Al-Shabib, Nasser Abdulatif; Khan, Javed Masood; Khan, Mohd Shahnawaz; Ali, Mohd Sajid; Al-Senaidy, Abdulrahman M; Alsenaidy, Mohammad A; Husain, Fohad Mabood; Al-Lohedan, Hamad A

2017-05-01

Protein aggregation, a characteristic of several neurodegenerative diseases, displays vast conformational diversity from amorphous to amyloid-like aggregates. In this study, we have explored the interaction of tartrazine with myoglobin protein at two different pHs (7.4 and 2.0). We have utilized various spectroscopic techniques (turbidity, Rayleigh light scattering (RLS), intrinsic fluorescence, Congo Red and far-UV CD) along with microscopy techniques i.e. atomic force microscopy (AFM) and transmission electron microscopy (TEM) to characterize the tartrazine-induced aggregation in myoglobin. The results showed that higher concentrations of tartrazine (2.0-10.0mM) induced amorphous aggregation in myoglobin at pH 2.0 via electrostatic interactions. However, tartrazine was not able to induce aggregation in myoglobin at pH 7.4; because of strong electrostatic repulsion between myoglobin and tartrazine at this pH. The tartrazine-induced amorphous aggregation process is kinetically very fast, and aggregation occurred without the formation of a nucleus. These results proposed that the electrostatic interaction is responsible for tartrazine-induced amorphous aggregation. This study may help in the understanding of mechanistic insight of aggregation by tartrazine. Copyright © 2017 Elsevier B.V. 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.

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.

Electrostatic interactions between the Bni1p formin FH2 domain and actin influence actin filament nucleation

DOE PAGES

Baker, Joseph L.; Courtemanche, Naomi; Parton, Daniel L.; ...

2014-12-04

Formins catalyze nucleation and growth of actin filaments. In this paper, we study the structure and interactions of actin with the FH2 domain of budding yeast formin Bni1p. We built an all-atom model of the formin dimer on an Oda actin filament 7-mer and studied structural relaxation and interprotein interactions by molecular dynamics simulations. These simulations produced a refined model for the FH2 dimer associated with the barbed end of the filament and showed electrostatic interactions between the formin knob and actin target-binding cleft. Mutations of two formin residues contributing to these interactions (R1423N, K1467L, or both) reduced the interactionmore » energies between the proteins, and in coarse-grained simulations, the formin lost more interprotein contacts with an actin dimer than with an actin 7-mer. Finally, biochemical experiments confirmed a strong influence of these mutations on Bni1p-mediated actin filament nucleation, but not elongation, suggesting that different interactions contribute to these two functions of formins.« less

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

PubMed

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Cooperative Effects of Zwitterionic-Ionic Surfactant Mixtures on the Interfacial Water Structure Revealed by Sum Frequency Generation Vibrational Spectroscopy.

PubMed

Pan, Xuecong; Yang, Fangyuan; Chen, Shunli; Zhu, Xuefeng; Wang, Chuanyi

2018-05-08

Cooperative effects of a series of equimolar binary zwitterionic-ionic surfactant mixtures on the interfacial water structure at the air-water interfaces have been studied by sum frequency generation vibrational spectroscopy (SFG-VS). For zwitterionic surfactant palmityl sulfobetaine (SNC 16 ), anionic surfactant sodium hexadecyl sulfate (SHS), and cationic surfactant cetyltrimethylammonium bromide (CTAB) with the same length of alkyl chain, significantly enhanced ordering of interfacial water molecules was observed for the zwitterionic-anionic surfactant mixtures SNC 16 -SHS, indicating that SNC 16 interacts more strongly with SHS than with CTAB because of the strong headgroup-headgroup electrostatic attraction for SNC 16 -SHS. Meanwhile, the SFG amplitude ratio of methyl and methylene symmetric stretching modes was used to verify the stronger interaction between SNC 16 and SHS. The conformational order indicator increased from 0.64 for SNC 16 to 7.17 for SNC 16 -SHS but only 0.94 for SNC 16 -CTAB. In addition, another anionic surfactant sodium dodecyl sulfate (SDS) was introduced to study the influence of chain-chain interaction. Decreased SFG amplitude of interfacial water molecules for SNC 16 -SDS was observed. Therefore, both the headgroup-headgroup electrostatic interaction and chain-chain van der Waals attractive interaction of the surfactants play an important role in enhancing the ordering of interfacial water molecules. The results provided experimental and theoretical bases for practical applications of the surfactants.

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.

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.

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

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

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.

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.

[Influences of the mobile phase constitution, salt concentration and pH value on retention characters of proteins on the metal chelate column].

PubMed

Li, R; Di, Z M; Chen, G L

2001-09-01

The effects of the nature and concentration of salts, pH value and competitive eluent in the mobile phase on the protein retention have been systematically investigated. A mathematical expression describing the protein retention in metal chelate chromatography has been derived. It is proposed that the eluting power of the salt solution can be expressed by the eluent strength exponent epsilon. According to the retention characters of protein under different chromatographic conditions, the interaction between the various metal chelate ligands and proteins is discussed. The protein retention on the metal chelate column is a cooperative interactions of coordination, electrostatic and hydrophobic interaction. For the strong combined metal column with proteins such as IDA-Cu, the coordination is the most important, and the electrostatic interaction is secondary in chromatographic process. However, for the weak combined metal columns with proteins such as IDA-Ni, IDA-Co and IDA-Zn, the electrostatic interaction between the metal chelate ligands and proteins is the chief one, while the coordination is the next in importance. When the mobile phase contains high concentration of salt which can't form complex with the immobilized metal, the hydrophobic interaction between the protein and stationary phase will be increased. As the interaction between the metal chelate ligand and proteins relates to chromatographic operating conditions closely, different elution processes may be selected for different metal chelate columns. The gradient elution is generally performed by the low concentration of salt or different pH for weakly combined columns with proteins, however the competitive elution procedure is commonly utilized for strongly combined column. The experiment showed that NH3 is an excellent competitive eluent. It isn't only give the efficient separation of proteins, but also has the advantages of cheapness, less bleeding of the immobilized metals and ease of controlling NH3 concentration. The interaction between the metal chelate ligand and proteins and the selectivity of metal chelate chromatography can be changed through changing chromatographic conditions.

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.

Contemporary NMR Studies of Protein Electrostatics.

PubMed

Hass, Mathias A S; Mulder, Frans A A

2015-01-01

Electrostatics play an important role in many aspects of protein chemistry. However, the accurate determination of side chain proton affinity in proteins by experiment and theory remains challenging. In recent years the field of nuclear magnetic resonance spectroscopy has advanced the way that protonation states are measured, allowing researchers to examine electrostatic interactions at an unprecedented level of detail and accuracy. Experiments are now in place that follow pH-dependent (13)C and (15)N chemical shifts as spatially close as possible to the sites of protonation, allowing all titratable amino acid side chains to be probed sequence specifically. The strong and telling response of carefully selected reporter nuclei allows individual titration events to be monitored. At the same time, improved frameworks allow researchers to model multiple coupled protonation equilibria and to identify the underlying pH-dependent contributions to the chemical shifts.

Bullied no more:when and how DNA shoves proteins around

PubMed Central

Pettitt, B. Montgomery; Sumners, De Witt L.; Harris, Sarah A.; Zechiedrich, Lynn

2016-01-01

The predominant protein-centric perspective in protein–DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism. PMID:22850561

Combinatorial multispectral, thermodynamics, docking and site-directed mutagenesis reveal the cognitive characteristics of honey bee chemosensory protein to plant semiochemical.

PubMed

Tan, Jing; Song, Xinmi; Fu, Xiaobin; Wu, Fan; Hu, Fuliang; Li, Hongliang

2018-08-05

In the chemoreceptive system of insects, there are always some soluble binding proteins, such as some antennal-specific chemosensory proteins (CSPs), which are abundantly distributed in the chemosensory sensillar lymph. The antennal-specific CSPs usually have strong capability to bind diverse semiochemicals, while the detailed interaction between CSPs and the semiochemicals remain unclear. Here, by means of the combinatorial multispectral, thermodynamics, docking and site-directed mutagenesis, we detailedly interpreted a binding interaction between a plant semiochemical β-ionone and antennal-specific CSP1 from the worker honey bee. Thermodynamic parameters (ΔH < 0, ΔS > 0) indicate that the interaction is mainly driven by hydrophobic forces and electrostatic interactions. Docking prediction results showed that there are two key amino acids, Phe44 and Gln63, may be involved in the interacting process of CSP1 to β-ionone. In order to confirm the two key amino acids, site-directed mutagenesis were performed and the binding constant (K A ) for two CSP1 mutant proteins was reduced by 60.82% and 46.80% compared to wild-type CSP1. The thermodynamic analysis of mutant proteins furtherly verified that Phe44 maintained an electrostatic interaction and Gln63 contributes hydrophobic and electrostatic forces. Our investigation initially elucidates the physicochemical mechanism of the interaction between antennal-special CSPs in insects including bees to plant semiochemicals, as well as the development of twice thermodynamic analysis (wild type and mutant proteins) combined with multispectral and site-directed mutagenesis methods. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

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.

The origins of the directionality of noncovalent intermolecular interactions.

PubMed

Wang, Changwei; Guan, Liangyu; Danovich, David; Shaik, Sason; Mo, Yirong

2016-01-05

The recent σ-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds. © 2015 Wiley Periodicals, Inc.

Ultrafast and low barrier motions in the photoreactions of the green fluorescent protein.

PubMed

van Thor, Jasper J; Georgiev, Georgi Y; Towrie, Michael; Sage, J Timothy

2005-09-30

Green fluorescent protein (GFP) fluoresces efficiently under blue excitation despite major electrostatic rearrangements resulting from photoionization of the chromophore and neutralization of Glu-222. A competing phototransformation process, which ionizes the chromophore and decarboxylates Glu-222, mimics the electrostatic and structural changes in the fluorescence photocycle. Structural and spectroscopic analysis of the cryogenically stabilized photoproduct at 100 K and a structurally annealed intermediate of the phototransformed protein at 170 K reveals distinct structural relaxations involving protein, chromophore, solvent, and photogenerated CO2. Strong structural changes of the 100 K photoproduct after decarboxylation appear exclusively within 15 angstroms of the chromophore and include the electrostatically driven perturbations of Gln-69, Cys-70, and water molecules in an H-bonding network connecting the chromophore. X-ray crystallography to 1.85 angstroms resolution and static and picosecond time-resolved IR spectroscopy identify structural mechanisms common to phototransformation and to the fluorescence photocycle. In particular, the appearance of a 1697 cm(-1) (+) difference band in both photocycle and phototransformation intermediates is a spectroscopic signature for the structural perturbation of Gln-69. This is taken as evidence for an electrostatically driven dynamic response that is common to both photoreaction pathways. The interactions between the chromophore and the perturbed residues and solvent are decreased or removed in the T203H single and T203H/Q69L double mutants, resulting in a strong reduction of the fluorescence quantum yield. This suggests that the electrostatic response to the transient formation of a buried charge in the wild type is important for the bright fluorescence.

Control of strong light-matter coupling using the capacitance of metamaterial nanocavities

DOE PAGES

Benz, Alexander; Campione, Salvatore; Klem, John Frederick; ...

2015-01-27

Metallic nanocavities with deep subwavelength mode volumes can lead to dramatic changes in the behavior of emitters placed in their vicinity. The resulting collocation and interaction often leads to strong coupling. We present for the first time experimental evidence that the Rabi splitting is directly proportional to the electrostatic capacitance associated with the metallic nanocavity. As a result, the system analyzed consists of different metamaterial geometries with the same resonance wavelength coupled to intersubband transitions in quantum wells.

Interpretation of STS-3/plasma diagnostics package results in terms of large space structure plasma interactions

NASA Technical Reports Server (NTRS)

Kurth, W. S.

1984-01-01

The Plasma Diagnostics Package, which was flown aboard STS-3 recorded various chemical releases from the Orbiter. Changes in the plasma environment were observed to occur during Flash Evaporator System (FES) releases, water dumps and maneuvering thruster operations. During flash evaporator operations, broadband Orbiter-generated electro-static noise is enhanced and plasma density irregularity (delta n/N) is observed to increase by as much as 4 times and is strongly peaked below 6 Hz. In the case of water dumps, background electrostatic noise is enhanced or suppressed depending on frequency and Delta N/N is also seen to increase by as much as 4 times. Various changes in the plasma environment are effected by primary and vernier thruster operations. In addition, thruster activity stimulates electrostatic noise with a spectrum which is most intense at frequencies below 10 kHz.

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties

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

Doktorova, Milka; Heberle, Frederick A.; Kingston, Richard L.

Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein’s matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here in this paper, using a broad set of in vitro and in silico techniques we addressed molecularmore » mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.« less

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.

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties

DOE PAGES

Doktorova, Milka; Heberle, Frederick A.; Kingston, Richard L.; ...

2017-11-07

Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein’s matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here in this paper, using a broad set of in vitro and in silico techniques we addressed molecularmore » mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.« less

Electrostatic interactions between ions near Thomas-Fermi substrates and the surface energy of ionic crystal at imperfect metals

PubMed Central

Kaiser, V.; Comtet, J.; Niguès, A.; Siria, A.; Coasne, B.; Bocquet, L.

2017-01-01

The electrostatic interaction between two charged particles is strongly modified in the vicinity of a metal. This situation is usually accounted for by the celebrated image charges approach, which was further extended to account for the electronic screening properties of the metal at the level of the Thomas-Fermi description. In this paper we build upon the approach by [Kornyshev et al. Zh. Eksp. Teor. Fiz., 78(3):1008–1019, 1980] and successive works to calculate the 1-body and 2-body electrostatic energy of ions near a metal in terms of the Thomas-Fermi screening length. We propose workable approximations suitable for molecular simulations of ionic systems close to metallic walls. Furthermore, we use this framework to calculate analytically the electrostatic contribution to the surface energy of a one dimensional crystal at a metallic wall and its dependence on the Thomas-Fermi screening length. These calculations provide a simple interpretation for the surface energy in terms of image charges, which allow for an estimate of interfacial properties in more complex situations of a disordered ionic liquid close to a metal surface. A counterintuitive outcome is that electronic screening, as characterized by a molecular Thomas-Fermi length ℓTF, profoundly affects the wetting of ionic systems close to a metal, in line with the recent experimental observation of capillary freezing of ionic liquids in metallic confinement. PMID:28436506

Stigmatellin Probes the Electrostatic Potential in the QB Site of the Photosynthetic Reaction Center

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

Gerencsér, László; Boros, Bogáta; Derrien, Valerie

2015-01-01

The electrostatic potential in the secondary quinone (QB) binding site of the reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides determines the rate and free energy change (driving force) of electron transfer to QB. It is controlled by the ionization states of residues in a strongly interacting cluster around the QB site. Reduction of the QB induces change of the ionization states of residues and binding of protons from the bulk. Stigmatellin, an inhibitor of the mitochondrial and photosynthetic respiratory chain, has been proven to be a unique voltage probe of the QB binding pocket. It binds to themore » QB site with high affinity, and the pK value of its phenolic group monitors the local electrostatic potential with high sensitivity. Investigations with different types of detergent as a model system of isolated RC revealed that the pK of stigmatellin was controlled overwhelmingly by electrostatic and slightly by hydrophobic interactions. Measurements showed a high pK value (>11) of stigmatellin in the QB pocket of the dark-state wild-type RC, indicating substantial negative potential. When the local electrostatics of the QB site was modulated by a single mutation, L213Asp/Ala, or double mutations, L213Asp-L212Glu/Ala-Ala (AA), the pK of stigmatellin dropped to 7.5 and 7.4, respectively, which corresponds to a >210 mV increase in the electrostatic potential relative to the wild-type RC. This significant pK drop (DpK > 3.5) decreased dramatically to (DpK > 0.75) in the RC of the compensatory mutant (AAþM44Asn/AAþM44Asp). Our results indicate that the L213Asp is the most important actor in the control of the electrostatic potential in the QB site of the dark-state wild-type RC, in good accordance with conclusions of former studies using theoretical calculations or light-induced charge recombination assay.« less

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.

Regimes of electrostatic collapse of a highly charged polyelectrolyte in a poor solvent.

PubMed

Tom, Anvy Moly; Vemparala, Satyavani; Rajesh, R; Brilliantov, Nikolai V

2017-03-01

We perform extensive molecular dynamics simulations of a highly charged, collapsed, flexible polyelectrolyte chain in a poor solvent for the case when the electrostatic interactions, characterized by the reduced Bjerrum length l B , are strong. We find the existence of several sub-regimes in the dependence of the gyration radius of the chain R g on l B characterized by R g ∼ l. In contrast to a good solvent, the exponent γ for a poor solvent crucially depends on the size and valency of the counterions. To explain the different sub-regimes, we generalize the existing counterion fluctuation theory by including a more complete account of all possible volume interactions in the free energy of the polyelectrolyte chain. We also show that the presence of condensed counterions modifies the effective attraction among the chain monomers and modulates the sign of the second virial coefficient under poor solvent conditions.

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

Experimental investigation and DFT calculation of different amine/ammonium salts adsorption on kaolinite

NASA Astrophysics Data System (ADS)

Chen, Jun; Min, Fan-fei; Liu, Lingyun; Liu, Chunfu; Lu, Fangqin

2017-10-01

The adsorption of four different amine/ammonium salts of DDA (Dodecyl amine), MDA (N-methyldodecyl amine), DMDA (N,N-dimethyldodecyl amine) and DTAC (Dodecyl trimethyl ammonium chloride) on kaolinite particles was investigated in the study through the measurement of contact angles, zeta potentials, aggregation observation, adsorption and sedimentation. The results show that different amine/ammonium salts can adsorb on the kaolinite surface to enhance the hydrophobicity and reduce the electronegativity of kaolinite particle surface, and thus induce a strong hydrophobic aggregation of kaolinite particles which promotes the settlement of kaolinite. To explore the adsorption mechanism of these four amine/ammonium salts on kaolinite surfaces, the adsorptions of DDA+, MDA+, DMDA+ and DTAC+ on kaolinite (001) surface and (00 1 bar) surface are calculated with DFT (Density functional theory). The DFT calculation results indicate that different amine/ammonium cations can strongly adsorbed on kaolinite (001) surface and (00 1 bar) surface by forming Nsbnd H⋯O strong hydrogen bonds or Csbnd H⋯O weak hydrogen bonds, and there are strongly electrostatic attractions between different amine/ammonium cations and kaolinite surfaces. The main adsorption mechanism of amine/ammonium cations on kaolinite is hydrogen-bond interaction and electrostatic attraction.

Interactions and diffusion in fine-stranded β-lactoglobulin gels determined via FRAP and binding.

PubMed

Schuster, Erich; Hermansson, Anne-Marie; Ohgren, Camilla; Rudemo, Mats; Lorén, Niklas

2014-01-07

The effects of electrostatic interactions and obstruction by the microstructure on probe diffusion were determined in positively charged hydrogels. Probe diffusion in fine-stranded gels and solutions of β-lactoglobulin at pH 3.5 was determined using fluorescence recovery after photobleaching (FRAP) and binding, which is widely used in biophysics. The microstructures of the β-lactoglobulin gels were characterized using transmission electron microscopy. The effects of probe size and charge (negatively charged Na2-fluorescein (376Da) and weakly anionic 70kDa FITC-dextran), probe concentration (50 to 200 ppm), and β-lactoglobulin concentration (9% to 12% w/w) on the diffusion properties and the electrostatic interaction between the negatively charged probes and the positively charged gels or solutions were evaluated. The results show that the diffusion of negatively charged Na2-fluorescein is strongly influenced by electrostatic interactions in the positively charged β-lactoglobulin systems. A linear relationship between the pseudo-on binding rate constant and the β-lactoglobulin concentration for three different probe concentrations was found. This validates an important assumption of existing biophysical FRAP and binding models, namely that the pseudo-on binding rate constant equals the product of the molecular binding rate constant and the concentration of the free binding sites. Indicators were established to clarify whether FRAP data should be analyzed using a binding-diffusion model or an obstruction-diffusion model. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular origins of osmotic second virial coefficients of proteins.

PubMed Central

Neal, B L; Asthagiri, D; Lenhoff, A M

1998-01-01

The thermodynamic properties of protein solutions are determined by the molecular interactions involving both solvent and solute molecules. A quantitative understanding of the relationship would facilitate more systematic procedures for manipulating the properties in a process environment. In this work the molecular basis for the osmotic second virial coefficient, B22, is studied; osmotic effects are critical in membrane transport, and the value of B22 has also been shown to correlate with protein crystallization behavior. The calculations here account for steric, electrostatic, and short-range interactions, with the structural and functional anisotropy of the protein molecules explicitly accounted for. The orientational dependence of the protein interactions is seen to have a pronounced effect on the calculations; in particular, the relatively few protein-protein configurations in which the apposing surfaces display geometric complementarity contribute disproportionately strongly to B22. The importance of electrostatic interactions is also amplified in these high-complementarity configurations. The significance of molecular recognition in determining B22 can explain the correlation with crystallization behavior, and it suggests that alteration of local molecular geometry can help in manipulating protein solution behavior. The results also have implications for the role of protein interactions in biological self-organization. PMID:9788942

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers.

PubMed

Zhao, Jun; Wang, Qiuming; Liang, Guizhao; Zheng, Jie

2011-12-20

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface. © 2011 American Chemical Society

Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy; Kawazoe, Yoshiyuki

2017-11-01

This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH⋯O/N-H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, SO⋯H-N type interaction have strongest hydrogen bond strength with high E HB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Electrostatic interactions during acidic phospholipid reactivation of DnaA protein, the Escherichia coli initiator of chromosomal replication.

PubMed

Kitchen, J L; Li, Z; Crooke, E

1999-05-11

The initiation of Escherichia coli chromosomal replication by DnaA protein is strongly influenced by the tight binding of the nucleotides ATP and ADP. Anionic phospholipids in a fluid bilayer promote the conversion of inactive ADP-DnaA protein to replicatively active ATP-DnaA protein in vitro, and thus likely play a key role in regulating DnaA activity. Previous studies have revealed that, during this reactivation, a specific region of DnaA protein inserts into the hydrophobic portion of the lipid bilayer in an acidic phospholipid-dependent manner. To elucidate the requirement for acidic phospholipids in the reactivation process, the contribution of electrostatic forces in the interaction of DnaA and lipid was examined. DnaA-lipid binding required anionic phospholipids, and DnaA-lipid binding as well as lipid-mediated release of DnaA-bound nucleotide were inhibited by increased ionic strength, suggesting the involvement of electrostatic interactions in these processes. As the vesicular content of acidic phospholipids was increased, both nucleotide release and DnaA-lipid binding increased in a linear, parallel manner. Given that DnaA-membrane binding, the insertion of DnaA into the membrane, and the consequent nucleotide release all require anionic phospholipids, the acidic headgroup may be necessary to recruit DnaA protein to the membrane for insertion and subsequent reactivation for replication.

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.

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.

A DFT investigation on interactions between asymmetric derivatives of cisplatin and nucleobase guanine

NASA Astrophysics Data System (ADS)

Tai, Truong Ba; Nhat, Pham Vu

2017-07-01

The interactions of hydrolysis products of cisplatin and its asymmetric derivatives cis- and trans-[PtCl2(iPram)(Mepz)] with guanine were studied using DFT methods. These interactions are dominated by electrostatic effects, namely hydrogen bond contributions and there exists a charge flow from H-atoms of ligands to the O-atoms of guanine. The replacement of NH3 moieties by larger functional groups accompanies with a moderate reaction between PtII and guanine molecule, diminishing the cytotoxicity of the drug. The asymmetric and symmetric NH2 stretching modes of complexes having strong hydrogen bond interactions are red shifted importantly as compared to complexes without presence of hydrogen bond interactions.

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 effect of charged groups on hydrophilic monolithic stationary phases on their chromatographic properties.

PubMed

Li, Haibin; Liu, Chusheng; Wang, Qiqin; Zhou, Haibo; Jiang, Zhengjin

2016-10-21

In order to investigate the effect of charged groups present in hydrophilic monolithic stationary phases on their chromatographic properties, three charged hydrophilic monomers, i.e. N,N-dimethyl-N-acryloyloxyethyl-N-(3-sulfopropyl)ammonium betaine (SPDA), [2-(acryloyloxy)ethyl]trimethylammonium chloride (AETA), and 3-sulfopropyl acrylate potassium salt (SPA) were co-polymerized with the crosslinker N,N'-methylenebisacrylamide (MBA), respectively. The physicochemical properties of the three resulting charged hydrophilic monolithic columns were evaluated using scanning electron microscopy, ζ-potential analysis and micro-HPLC. High column efficiency was obtained on the three monolithic columns at a linear velocity of 1mm/s using thiourea as test compound. Comparative characterization of the three charged HILIC phases was then carried out using a set of model compounds, including nucleobases, nucleosides, benzoic acid derivatives, phenols, β-blockers and small peptides. Depending on the combination of stationary phase/mobile phase/solute, both hydrophilic interaction and other potential secondary interactions, including electrostatic interaction, hydrogen-bonding interaction, molecular shape selectivity, could contribute to the over-all retention of the analytes. Because of the strong electrostatic interaction provided by the quaternary ammonium groups in the poly (AETA-co-MBA) monolith, this cationic HILIC monolith exhibited the strongest retention for benzoic acid derivatives and small peptides with distorted peak shapes and the weakest retention for basic β-blockers. The sulfonyl groups on the poly (SPA-co-MBA) hydrophilic monolith could provide strong electrostatic attraction and hydrogen bonding for positively charged analytes and hydrogen-donor/acceptor containing analytes, respectively. Therefore, basic drugs, nucleobases and nucleotides exhibited the strongest retention on this anionic monolith. Because of the weak but distinct cation exchange properties of the zwitterionic poly (SPDA-co-MBA) hydrophilic monolith, it exhibited the best separation for most test analytes (including phenols, β-blockers and small peptides) in terms of selectivity, peak shape and analysis time. The poly (AETA-co-MBA) hydrophilic monolithic column provides the best separation of nucleobases and nucleosides. These results could guide the selection and application of these charged HILIC monoliths in the future. Copyright © 2016 Elsevier B.V. All rights reserved.

Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties.

PubMed

Doktorova, Milka; Heberle, Frederick A; Kingston, Richard L; Khelashvili, George; Cuendet, Michel A; Wen, Yi; Katsaras, John; Feigenson, Gerald W; Vogt, Volker M; Dick, Robert A

2017-11-07

Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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)].

Coupled electrostatic and material surface stresses yield anomalous particle interactions and deformation

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

Kemp, B. A., E-mail: bkemp@astate.edu; Nikolayev, I.; Sheppard, C. J.

2016-04-14

Like-charges repel, and opposite charges attract. This fundamental tenet is a result of Coulomb's law. However, the electrostatic interactions between dielectric particles remain topical due to observations of like-charged particle attraction and the self-assembly of colloidal systems. Here, we show, using both an approximate description and an exact solution of Maxwell's equations, that nonlinear charged particle forces result even for linear material systems and can be responsible for anomalous electrostatic interactions such as like-charged particle attraction and oppositely charged particle repulsion. Furthermore, these electrostatic interactions and the deformation of such particles have fundamental implications for our understanding of macroscopic electrodynamics.

Protein adsorption onto CF(3)-terminated oligo(ethylene glycol) containing self-assembled monolayers (SAMs): the influence of ionic strength and electrostatic forces.

PubMed

Bonnet, Nelly; O'Hagan, David; Hähner, Georg

2010-05-07

Oligo(ethylene glycol) (OEG) containing self-assembled monolayers (SAMs) on gold are known for their protein resistant properties. The underlying molecular mechanisms and the contributions of the interactions involved, however, are still not completely understood. It is known that electrostatic, van der Waals, hydrophobic, and hydration forces all play a role in the interaction between proteins and surfaces, but it is difficult to study their influence separately and to quantify their contributions. In the present study we investigate five different OEG containing SAMs and the influence of the ionic strength and the electrostatic component on the amount of a negatively charged protein (fibrinogen) that adsorbs onto them. Atomic force microscopy (AFM) was employed to record force-distance curves with hydrophobic probes depending on the ion concentration, and the amount of the protein that adsorbs relative to a hydrophobic surface was quantified using ellipsometry. The findings suggest that electrostatic forces can create a very low energy barrier thus only slightly decreasing the number of negatively charged proteins in solution with sufficient energy to approach the surface closely, and have a rather small influence on the amount that adsorbs. The films we investigated were not protein resistant. This supports other studies, reporting that a strong short-range repulsion as for example caused by hydration forces is required to make these films resistant to the non-specific adsorption of proteins.

Electrostatic interactions between ions near Thomas-Fermi substrates and the surface energy of ionic crystals at imperfect metals.

PubMed

Kaiser, V; Comtet, J; Niguès, A; Siria, A; Coasne, B; Bocquet, L

2017-07-01

The electrostatic interaction between two charged particles is strongly modified in the vicinity of a metal. This situation is usually accounted for by the celebrated image charges approach, which was further extended to account for the electronic screening properties of the metal at the level of the Thomas-Fermi description. In this paper we build upon a previous approach [M. A. Vorotyntsev and A. A. Kornyshev, Zh. Eksp. Teor. Fiz., 1980, 78(3), 1008-1019] and successive works to calculate the 1-body and 2-body electrostatic energy of ions near a metal in terms of the Thomas-Fermi screening length. We propose workable approximations suitable for molecular simulations of ionic systems close to metallic walls. Furthermore, we use this framework to calculate analytically the electrostatic contribution to the surface energy of a one dimensional crystal at a metallic wall and its dependence on the Thomas-Fermi screening length. These calculations provide a simple interpretation for the surface energy in terms of image charges, which allows for an estimation of the interfacial properties in more complex situations of a disordered ionic liquid close to a metal surface. The counter-intuitive outcome is that electronic screening, as characterized by a molecular Thomas-Fermi length l TF , profoundly affects the wetting of ionic systems close to a metal, in line with the recent experimental observation of capillary freezing of ionic liquids in metallic confinement.

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

Electrostatic analogy for symmetron gravity

NASA Astrophysics Data System (ADS)

Ogden, Lillie; Brown, Katherine; Mathur, Harsh; Rovelli, Kevin

2017-12-01

The symmetron model is a scalar-tensor theory of gravity with a screening mechanism that suppresses the effect of the symmetron field at high densities characteristic of the Solar System and laboratory scales but allows it to act with gravitational strength at low density on the cosmological scale. We elucidate the screening mechanism by showing that in the quasistatic Newtonian limit there are precise analogies between symmetron gravity and electrostatics for both strong and weak screening. For strong screening we find that large dense bodies behave in a manner analogous to perfect conductors in electrostatics. Based on this analogy we find that the symmetron field exhibits a lightning rod effect wherein the field gradients are enhanced near the ends of pointed or elongated objects. An ellipsoid placed in a uniform symmetron gradient is shown to experience a torque. By symmetry there is no gravitational torque in this case. Hence this effect unmasks the symmetron and might serve as the basis for future laboratory experiments. The symmetron force between a point mass and a large dense body includes a component corresponding to the interaction of the point mass with its image in the larger body. None of these effects have counterparts in the Newtonian limit of Einstein gravity. We discuss the similarities between symmetron gravity and the chameleon model as well as the differences between the two.

How ions affect the structure of water.

PubMed

Hribar, Barbara; Southall, Noel T; Vlachy, Vojko; Dill, Ken A

2002-10-16

We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.

Toward a New Chemotherapy for Breast Cancer: Structural and Functional Mechanism of the Retinoid Receptors Addressed by a Novel Computer Approach

DTIC Science & Technology

1999-05-01

substitution of the second leucine in an LxxLL core with isoleucine still permits a strong hydrophobic interaction with the liganded receptor (Table 2...through electrostatic interactions. Figure 10 illustrates that the two leucines and one isoleucine (green and cyan) of the LxxlL motif are predicted to be...RARox was carried out as described in Materials and methods. The side chains of the two leucines (green) and one isoleucine (cyan) of the LxxIL core fit

Macroion solutions in the cell model studied by field theory and Monte Carlo simulations.

PubMed

Lue, Leo; Linse, Per

2011-12-14

Aqueous solutions of charged spherical macroions with variable dielectric permittivity and their associated counterions are examined within the cell model using a field theory and Monte Carlo simulations. The field theory is based on separation of fields into short- and long-wavelength terms, which are subjected to different statistical-mechanical treatments. The simulations were performed by using a new, accurate, and fast algorithm for numerical evaluation of the electrostatic polarization interaction. The field theory provides counterion distributions outside a macroion in good agreement with the simulation results over the full range from weak to strong electrostatic coupling. A low-dielectric macroion leads to a displacement of the counterions away from the macroion. © 2011 American Institute of Physics

Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights

NASA Astrophysics Data System (ADS)

R. S., Sai Murali; R. S., Sai Siddhardha; Rajesh Babu, D.; Venketesh, S.; Basavaraju, R.; Nageswara Rao, G.

2017-06-01

The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure.

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...

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

PubMed Central

2015-01-01

The charge distribution of halogen atoms on organochlorine compounds can be highly anisotropic and even display a so-called σ-hole, which leads to strong halogen bonds with electron donors. In this paper, we have systematically investigated a series of chloromethanes with one to four chloro substituents using a polarizable multipole-based molecular mechanics model. The atomic multipoles accurately reproduced the ab initio electrostatic potential around chloromethanes, including CCl4, which has a prominent σ-hole on the Cl atom. The van der Waals parameters for Cl were fitted to the experimental density and heat of vaporization. The calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes are in good agreement with experimental and ab initio data. This study suggests that sophisticated electrostatic models, such as polarizable atomic multipoles, are needed for accurate description of electrostatics in organochlorine compounds and halogen bonds, although further improvement is necessary for better transferability. PMID:24484473

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.

GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules

PubMed Central

Bertelshofer, Franziska; Sun, Liping; Greiner, Günther; Böckmann, Rainer A.

2015-01-01

Knowledge about the electrostatic potential on the surface of biomolecules or biomembranes under physiological conditions is an important step in the attempt to characterize the physico-chemical properties of these molecules and, in particular, also their interactions with each other. Additionally, knowledge about solution electrostatics may also guide the design of molecules with specified properties. However, explicit water models come at a high computational cost, rendering them unsuitable for large design studies or for docking purposes. Implicit models with the water phase treated as a continuum require the numerical solution of the Poisson–Boltzmann equation (PBE). Here, we present a new flexible program for the numerical solution of the PBE, allowing for different geometries, and the explicit and implicit inclusion of membranes. It involves a discretization of space and the computation of the molecular surface. The PBE is solved using finite differences, the resulting set of equations is solved using a Gauss–Seidel method. It is shown for the example of the sucrose transporter ScrY that the implicit inclusion of a surrounding membrane has a strong effect also on the electrostatics within the pore region and, thus, needs to be carefully considered, e.g., in design studies on membrane proteins. PMID:26636074

Adsorption Kinetics, Conformation, and Mobility of the Growth Hormone and Lysozyme on Solid Surfaces, Studied with TIRF

PubMed

Buijs; Hlady

1997-06-01

Interactions of recombinant human growth hormone and lysozyme with solid surfaces are studied using total internal reflection fluorescence (TIRF) and monitoring the protein's intrinsic tryptophan fluorescence. The intensity, spectra, quenching, and polarization of the fluorescence emitted by the adsorbed proteins are monitored and related to adsorption kinetics, protein conformation, and fluorophore rotational mobility. To study the influence of electrostatic and hydrophobic interactions on the adsorption process, three sorbent surfaces are used which differ in charge and hydrophobicity. The chemical surface groups are silanol, methyl, and quaternary amine. Results indicate that adsorption of hGH is dominated by hydrophobic interactions. Lysozyme adsoption is strongly affected by the ionic strength. This effect is probably caused by an ionic strength dependent conformational state in solution which, in turn, influences the affinity for adsorption. Both proteins are more strongly bound to hydrophobic surfaces and this strong interaction is accompanied by a less compact conformation. Furthermore, it was seen that regardless of the characteristics of the sorbent surface, the rotational mobility of both proteins' tryptophans is largely reduced upon adsorption.

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.

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.

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.

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

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.

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

The role of surface electrostatics on the stability, function and regulation of human cystathionine β-synthase, a complex multidomain and oligomeric protein.

PubMed

Pey, Angel L; Majtan, Tomas; Kraus, Jan P

2014-09-01

Human cystathionine β-synthase (hCBS) is a key enzyme of sulfur amino acid metabolism, controlling the commitment of homocysteine to the transsulfuration pathway and antioxidant defense. Mutations in hCBS cause inherited homocystinuria (HCU), a rare inborn error of metabolism characterized by accumulation of toxic homocysteine in blood and urine. hCBS is a complex multidomain and oligomeric protein whose activity and stability are independently regulated by the binding of S-adenosyl-methionine (SAM) to two different types of sites at its C-terminal regulatory domain. Here we study the role of surface electrostatics on the complex regulation and stability of hCBS using biophysical and biochemical procedures. We show that the kinetic stability of the catalytic and regulatory domains is significantly affected by the modulation of surface electrostatics through noticeable structural and energetic changes along their denaturation pathways. We also show that surface electrostatics strongly affect SAM binding properties to those sites responsible for either enzyme activation or kinetic stabilization. Our results provide new insight into the regulation of hCBS activity and stability in vivo with implications for understanding HCU as a conformational disease. We also lend experimental support to the role of electrostatic interactions in the recently proposed binding modes of SAM leading to hCBS activation and kinetic stabilization. Copyright © 2014 Elsevier B.V. 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

Comparative Analysis of Binding Kinetics and Thermodynamics of Dipeptidyl Peptidase-4 Inhibitors and Their Relationship to Structure.

PubMed

Schnapp, Gisela; Klein, Thomas; Hoevels, Yvette; Bakker, Remko A; Nar, Herbert

2016-08-25

The binding kinetics and thermodynamics of dipeptidyl peptidase (DPP)-4 inhibitors (gliptins) were investigated using surface plasmon resonance and isothermal titration calorimetry. Binding of gliptins to DPP-4 is a rapid electrostatically driven process. Off-rates were generally slow partly because of reversible covalent bond formation by some gliptins, and partly because of strong and extensive interactions. Binding of all gliptins is enthalpy-dominated due to strong ionic interactions and strong solvent-shielded hydrogen bonds. Using a congeneric series of molecules which represented the intermediates in the lead optimization program of linagliptin, the onset of slow binding kinetics and development of the thermodynamic repertoire were analyzed in the context of incremental changes of the chemical structures. All compounds rapidly associated, and therefore the optimization of affinity and residence time is highly correlated. The major contributor to the increasing free energy of binding was a strong increase of binding enthalpy, whereas entropic contributions remained low and constant despite significant addition of lipophilicity.

Plasma waves near saturn: initial results from voyager 1.

PubMed

Gurnett, D A; Kurth, W S; Scarf, F L

1981-04-10

The Voyager 1 plasma wave instrument detected many familiar types of plasma waves during the encounter with Saturn, including ion-acoustic waves and electron plasma oscillations upstream of the bow shock, an intense burst of electrostatic noise at the shock, and chorus, hiss, electrostatic electron cyclotron waves, and upper hybrid resonance emissions in the inner magnetosphere. A clocklike Saturn rotational control of low-frequency radio emissions was observed, and evidence was obtained of possible control by the moon Dione. Strong plasma wave emissions were detected at the Titan encounter indicating the presence of a turbulent sheath extending around Titan, and upper hybrid resonance measurements of the electron density show the existence of a dense plume of plasma being carried downstream of Titan by the interaction with the rapidly rotating magnetosphere of Saturn.

Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights.

PubMed

R S, Sai Murali; R S, Sai Siddhardha; D, Rajesh Babu; S, Venketesh; R, Basavaraju; G, Nageswara Rao

2017-06-05

The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Mechanism of Coomassie Brilliant Blue G-250 binding to cetyltrimethylammonium bromide: an interference with the Bradford assay.

PubMed

Aminian, Mahdi; Nabatchian, Fariba; Vaisi-Raygani, Asad; Torabi, Mojgan

2013-03-15

The Bradford protein assay is a popular method because of its rapidity, sensitivity, and relative specificity. This method is subject to some interference by nonprotein compounds. In this study, we describe the interference of cetyltrimethylammonium bromide (CTAB) with the Bradford assay. This interference is based on the interaction of Coomassie Brilliant Blue G-250 (CBB) with this cationic detergent. This study suggests that both electrostatic and hydrophobic interactions are involved in the interaction of CTAB and CBB. The anionic and neutral forms of CBB bind to CTAB by electrostatic attraction, which accelerates hydrophobic interactions of these CBB forms and the hydrophobic tail of CTAB. Consequently, the hydrophobic regions of the dominant free cationic form of CBB dye compete for the tail of CTAB with two other forms of the dye and gradually displace the primary hydrophobic interactions and rearrange the primary CBB-CTAB complex. This interaction of CTAB and CBB dye produces a primary 650-nm-absorbing complex that then gradually rearranges to a complex that shows an absorbance shoulder at 800-950 nm. This study conclusively shows a strong response of CBB to CTAB that causes a time-dependent and nearly additive interference with the Bradford assay. This study also may promote an application of CBB for CTAB quantification. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

Biochemical enhancement of transdermal delivery with magainin peptide: modification of electrostatic interactions by changing pH.

PubMed

Kim, Yeu-Chun; Late, Sameer; Banga, Ajay K; Ludovice, Peter J; Prausnitz, Mark R

2008-10-01

Magainin is a naturally occurring, pore-forming peptide that has recently been shown to increase skin permeability. This study tested the hypothesis that electrostatic forces between magainin peptides and drugs mediate drug transport across the skin. Electrostatic interaction between positively charged magainin and a negatively charged model drug, fluorescein, was attractive at pH 7.4 and resulted in a 35-fold increase in delivery across human epidermis in vitro when formulated with 2% N-lauroylsarcosine in 50% ethanol. Increasing to pH 10 or 11 largely neutralized magainin's charge, which eliminated enhancement due to magainin. Shielding electrostatic interactions with 1-2M NaCl solution similarly eliminated enhancement. Showing the opposite dependence on pH, electrostatic interaction between magainin and a positively charged anti-nausea drug, granisetron, was largely neutralized at pH 10 and resulted in a 92-fold increase in transdermal delivery. Decreasing to pH 5 increased magainin's positive charge, which repelled granisetron and progressively decreased transdermal flux. Circular dichroism analysis, multi-photon microscopy, and FTIR spectroscopy showed no significant pH effect on magainin secondary structure, magainin deposition in stratum corneum, or stratum corneum lipid order, respectively. We conclude that magainin increases transdermal delivery by a mechanism involving electrostatic interaction between magainin peptides and drugs.

Biochemical enhancement of transdermal delivery with magainin peptide: Modification of electrostatic interactions by changing pH

PubMed Central

Kim, Yeu-Chun; Late, Sameer; Banga, Ajay K.; Ludovice, Peter J.; Prausnitz, Mark R.

2008-01-01

Magainin is a naturally occurring, pore-forming peptide that has recently been shown to increase skin permeability. This study tested the hypothesis that electrostatic forces between magainin peptides and drugs mediate drug transport across the skin. Electrostatic interaction between positively charged magainin and a negatively charged model drug, fluorescein, was attractive at pH 7.4 and resulted in a 35 fold increase in delivery across human epidermis in vitro when formulated with 2% N-lauroylsarcosine in 50% ethanol. Increasing to pH 10 or 11 largely neutralized magainin’s charge, which eliminated enhancement due to magainin. Shielding electrostatic interactions with 1–2 M NaCl solution similarly eliminated enhancement. Showing the opposite dependence on pH, electrostatic interaction between magainin and a positively charged anti-nausea drug, granisetron, was largely neutralized at pH 10 and resulted in a 59 fold increase in transdermal delivery. Decreasing to pH 5 increased magainin’s positive charge, which repelled granisetron and progressively decreased transdermal flux. Circular dichroism analysis, multi-photon microscopy, and FTIR spectroscopy showed no significant pH effect on magainin secondary structure, magainin deposition in stratum corneum, or stratum corneum lipid order, respectively. We conclude that magainin increases transdermal delivery by a mechanism involving electrostatic interaction between magainin peptides and drugs. PMID:18601987

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

The influence of actuator materials and nozzle designs on electrostatic charge of pressurised metered dose inhaler (pMDI) formulations.

PubMed

Chen, Yang; Young, Paul M; Fletcher, David F; Chan, Hak Kim; Long, Edward; Lewis, David; Church, Tanya; Traini, Daniela

2014-05-01

To investigate the influence of different actuator materials and nozzle designs on the electrostatic charge properties of a series of solution metered dose inhaler (pMDI) aerosols. Actuators were manufactured with flat and cone nozzle designs using five different materials from the triboelectric series (Nylon, Polyethylene terephthalate, Polyethylene-High density, Polypropylene copolymer and Polytetrafluoroethylene). The electrostatic charge profiles of pMDI containing beclomethasone dipropionate (BDP) as model drug in HFA-134a propellant, with different concentrations of ethanol were studied. Electrostatic measurements were taken using a modified electrical low-pressure impactor (ELPI) and the deposited drug mass assayed chemically using HPLC. The charge profiles of HFA 134a alone have shown strong electronegativity with all actuator materials and nozzle designs, at an average of -1531.34 pC ± 377.34. The presence of co-solvent ethanol significantly reduced the negative charge magnitude. BDP reduced the suppressing effect of ethanol on the negative charging of the propellant. For all tested formulations, the flat nozzle design showed no significant differences in net charge between different actuator materials, whereas the charge profiles of cone designs followed the triboelectric series. The electrostatic charging profiles from a solution pMDI containing BDP and ethanol can be significantly influenced by the actuator material, nozzle design and formulation components. Ethanol concentration appears to have the most significant impact. Furthermore, BDP interactions with ethanol and HFA have an influence on the electrostatic charge of aerosols. By choosing different combinations of actuator materials and orifice design, the fine particle fractions of formulations can be altered.

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

Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities

NASA Astrophysics Data System (ADS)

Zhou, Peng; Chen, Xiang; Shang, Zhicai

2009-03-01

In this article, the concept of multi conformation-based quantitative structure-activity relationship (MCB-QSAR) is proposed, and based upon that, we describe a new approach called the side-chain conformational space analysis (SCSA) to model and predict protein-peptide binding affinities. In SCSA, multi-conformations (rather than traditional single-conformation) have received much attention, and the statistical average information on multi-conformations of side chains is determined using self-consistent mean field theory based upon side chain rotamer library. Thereby, enthalpy contributions (including electrostatic, steric, hydrophobic interaction and hydrogen bond) and conformational entropy effects to the binding are investigated in terms of occurrence probability of residue rotamers. Then, SCSA was applied into the dataset of 419 HLA-A*0201 binding peptides, and nonbonding contributions of each position in peptide ligands are well determined. For the peptides, the hydrogen bond and electrostatic interactions of the two ends are essential to the binding specificity, van der Waals and hydrophobic interactions of all the positions ensure strong binding affinity, and the loss of conformational entropy at anchor positions partially counteracts other favorable nonbonding effects.

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.

8-Anilino-1-naphthalenesulfonate/Layered Double Hydroxide Ultrathin Films: Small Anion Assembly and Its Potential Application as a Fluorescent Biosensor.

PubMed

Zhang, Ping; Li, Ling; Zhao, Yun; Tian, Zeyun; Qin, Yumei; Lu, Jun

2016-09-06

The fluorescent dye 8-anilino-1-naphthalenesulfonate (ANS) is a widely used fluorescent probe molecule for biochemistry analysis. This paper reported the fabrication of ANS/layered double hydroxide nanosheets (ANS/LDH)n ultrathin films (UTFs) via the layer-by-layer small anion assembly technique based on electrostatic interaction and two possible weak interactions: hydrogen-bond and induced electrostatic interactions between ANS and positive-charged LDH nanosheets. The obtained UTFs show a long-range-ordered periodic layered stacking structure and weak fluorescence in dry air or water, but it split into three narrow strong peaks in a weak polarity environment induced by the two-dimensional (2D) confinement effect of the LDH laminate; the fluorescence intensity increases with decreasing the solvent polarity, concomitant with the blue shift of the emission peaks, which show good sensoring reversibility. Meanwhile, the UTFs exhibit selective fluorescence enhancement to the bovine serum albumin (BSA)-like protein biomolecules, and the rate of fluorescence enhancement with the protein concentration is significantly different with the different protein aggregate states. The (ANS/LDH)n UTF has the potential to be a novel type of biological flourescence sensor material.

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.

Modeling of protein-anion exchange resin interaction for the human growth hormone charge variants.

PubMed

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

2015-12-01

Modeling ion exchange chromatography (IEC) behavior has generated significant interest because of the wide use of IEC as an analytical technique as well as a preparative protein purification process; indeed there is a need for better understanding of what drives the unique behavior of protein charge variants. We hypothesize that a complex protein molecule, which contains both hydrophobic and charged moieties, would interact strongly with an in silico designed resin through charged electrostatic patches on the surface of the protein. In the present work, variants of recombinant human growth hormone that mimic naturally-occurring deamidation products were produced and characterized in silico. The study included these four variants: rhGH, N149D, N152D, and N149D/N152D. Poisson-Boltzmann calculations were used to determine surface electrostatic potential. Metropolis Monte Carlo simulations were carried out with the resulting variants to simulate IEC systems, examining the free energy of the interaction of the protein with an in silico anion exchange column represented by polylysine polypeptide. The results show that the charge variants have different average binding energies and the free energy of interaction can be used to predict the retention time for the different variants. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Filippov, A. V., E-mail: fav@triniti.ru

The interaction of two charged point macroparticles located in Wigner–Seitz cells of simple cubic (SC), body-centered cubic (BCC), or face-centered cubic (FCC) lattices in an equilibrium plasma has been studied within the Debye approximation or, more specifically, based on the linearized Poisson–Boltzmann model. The shape of the outer boundary is shown to exert a strong influence on the pattern of electrostatic interaction between the two macroparticles, which transforms from repulsion at small interparticle distances to attraction as the interparticle distance approaches half the length of the computational cell. The macroparticle pair interaction potential in an equilibrium plasma is shown tomore » be nevertheless the Debye one and purely repulsive for likely charged macroparticles.« less

Preparation of a novel dual-function strong cation exchange/hydrophobic interaction chromatography stationary phase for protein separation.

PubMed

Zhao, Kailou; Yang, Li; Wang, Xuejiao; Bai, Quan; Yang, Fan; Wang, Fei

2012-08-30

We have explored a novel dual-function stationary phase which combines both strong cation exchange (SCX) and hydrophobic interaction chromatography (HIC) characteristics. The novel dual-function stationary phase is based on porous and spherical silica gel functionalized with ligand containing sulfonic and benzyl groups capable of electrostatic and hydrophobic interaction functionalities, which displays HIC character in a high salt concentration, and IEC character in a low salt concentration in mobile phase employed. As a result, it can be employed to separate proteins with SCX and HIC modes, respectively. The resolution and selectivity of the dual-function stationary phase were evaluated under both HIC and SCX modes with standard proteins and can be comparable to that of conventional IEC and HIC columns. More than 96% of mass and bioactivity recoveries of proteins can be achieved in both HIC and SCX modes, respectively. The results indicated that the novel dual-function column could replace two individual SCX and HIC columns for protein separation. Mixed retention mechanism of proteins on this dual-function column based on stoichiometric displacement theory (SDT) in LC was investigated to find the optimal balance of the magnitude of electrostatic and hydrophobic interactions between protein and the ligand on the silica surface in order to obtain high resolution and selectivity for protein separation. In addition, the effects of the hydrophobicity of the ligand of the dual-function packings and pH of the mobile phase used on protein separation were also investigated in detail. The results show that the ligand with suitable hydrophobicity to match the electrostatic interaction is very important to prepare the dual-function stationary phase, and a better resolution and selectivity can be obtained at pH 6.5 in SCX mode. Therefore, the dual-function column can replace two individual SCX and HIC columns for protein separation and be used to set up two-dimensional liquid chromatography with a single column (2DLC-1C), which can also be employed to separate three kinds of active proteins completely, such as lysozyme, ovotransferrin and ovalbumin from egg white. The result is very important not only to the development of new 2DLC technology with a single column for proteomics, but also to recombinant protein drug production for saving column expense and simplifying the process in biotechnology. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

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)).

Electrostatically Driven Guest Binding in a Self-Assembled Porous Network at the Liquid/Solid Interface.

PubMed

Iritani, Kohei; Ikeda, Motoki; Yang, Anna; Tahara, Kazukuni; Anzai, Masaru; Hirose, Keiji; De Feyter, Steven; Moore, Jeffrey S; Tobe, Yoshito

2018-05-29

We present here the construction of a self-assembled two-dimensional (2D) porous monolayer bearing a highly polar 2D space to study guest co-adsorption through electrostatic interactions at the liquid/solid interface. For this purpose, a dehydrobenzo[12]annulene (DBA) derivative, DBA-TeEG, having tetraethylene glycol (TeEG) groups at the end of the three alternating alkoxy chains connected by p-phenylene linkers was synthesized. As a reference host molecule, DBA-C10, having nonpolar C 10 alkyl chains at three alternating terminals, was employed. As guest molecules, hexagonal phenylene-ethynylene macrocycles (PEMs) attached by triethylene glycol (TEG) ester and hexyl ester groups, PEM-TEG and PEM-C6, respectively, at each vertex of the macrocyclic periphery were used. Scanning tunneling microscopy observations at the 1,2,4-trichlorobenzene/highly oriented pyrolytic graphite interface revealed that PEM-TEG was immobilized in the pores formed by DBA-TeEG at higher probability because of electrostatic interactions such as dipole-dipole and hydrogen bonding interactions between oligoether units of the host and guest, in comparison to PEM-C6 with nonpolar groups. These observations are discussed based on molecular mechanics simulations to investigate the role of the polar functional groups. When a nonpolar host matrix formed by DBA-C10 was used, however, only phase separation and preferential adsorption were observed; virtually no host-guest complexation was discernible. This is ascribed to the strong affinity between the guest molecules which form by themselves densely packed van der Waals networks on the surface.

Cluster Quantum Chemical Study of the Grignard Reagent Formation

NASA Astrophysics Data System (ADS)

Tulub, A. V.; Porsev, V. V.

The main stages of the Grignard reagent formation are described in a framework of quantum chemical cluster model. We have established two kinds of the adsorption of CH3Hal on Mgn clusters, one of which leads to radical formation and the second is responsible for radical free dissociate adsorption. The charge redistribution in cluster CH3MgnHal result to the strong electrostatic interaction with ether and Grignard reagent formation without any activation barrier.

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.

Surface charge effects in protein adsorption on nanodiamonds

NASA Astrophysics Data System (ADS)

Aramesh, M.; Shimoni, O.; Ostrikov, K.; Prawer, S.; Cervenka, J.

2015-03-01

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids. Electronic supplementary information (ESI) available: The FTIR spectrum of nanodiamonds, QCM-D profiles of 50 nm nanodiamond adsorption on silica surfaces, QCM-D profiles of protein desorption after rinsing with water (rinsing experiment) and the full FTIR spectrum of proteins before and after adsorption on ND particles. See DOI: 10.1039/c5nr00250h

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.

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

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.

Plasma waves near Saturn: initial results from Voyager 1. Progress report

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

Gurnett, D.A.; Kurth, W.S.; Scarf, F.L.

1981-01-31

The Voyager 1 plasma wave instrument detected many familiar types of plasma waves during the encounter with Saturn, including ion-acoustic waves and electron plasma oscillations upstream of the bow shock, an intense burst of electrostatic noise at the shock, and chorus, hiss, electrostatic (n + 1/2)fg waves and UHR emissions in the inner magnetosphere. A clock-like Saturn rotational control of low-frequency radio emissions was observed, and evidence was obtained of possible control by the moon Dione. Strong plasma wave emissions were detected at the Titan encounter indicating the presence of a turbulent sheath extending around Titan, and UHR measurements ofmore » the electron density show the existence of a dense plume of plasma being carried downstream of Titan by the interaction with the rapidly rotating magnetosphere of Saturn.« less

Electrostatics of colloids in mixtures

NASA Astrophysics Data System (ADS)

Samin, Sela; Tsori, Yoav

2013-03-01

We examine the force between two charged colloids immersed in salty aqueous mixtures close to the coexistence curve. In an initially water-poor phase, the short-range solvation-related forces promote the condensation of a water-rich phase at a distance in the range 1-100nm. This leads to a strong long-range attraction between the colloids and hence to a deep metastable or globally stable energetic state. Our calculations are in good agreement with recent experiments on the reversible aggregation of colloids in critical mixtures. The specific nature of the solvation energy of ions can lead to some surprising effects, whereby positively charged surfaces attract while negatively charged surfaces repel. For hydrophilic anions and hydrophobic cations, a repulsive interaction is predicted between oppositely charged and hydrophilic colloids even though both the electrostatic and adsorption forces alone are attractive.

Tuning structure of oppositely charged nanoparticle and protein complexes

NASA Astrophysics Data System (ADS)

Kumar, Sugam; Aswal, V. K.; Callow, P.

2014-04-01

Small-angle neutron scattering (SANS) has been used to probe the structures of anionic silica nanoparticles (LS30) and cationic lyszyme protein (M.W. 14.7kD, I.P. ˜ 11.4) by tuning their interaction through the pH variation. The protein adsorption on nanoparticles is found to be increasing with pH and determined by the electrostatic attraction between two components as well as repulsion between protein molecules. We show the strong electrostatic attraction between nanoparticles and protein molecules leads to protein-mediated aggregation of nanoparticles which are characterized by fractal structures. At pH 5, the protein adsorption gives rise to nanoparticle aggregation having surface fractal morphology with close packing of nanoparticles. The surface fractals transform to open structures of mass fractal morphology at higher pH (7 and 9) on approaching isoelectric point (I.P.).

Deconvolution of Raman spectroscopic signals for electrostatic, H-bonding, and inner-sphere interactions between ions and dimethyl phosphate in solution

PubMed Central

Christian, Eric L; Anderson, Vernon E.; Harris, Michael E

2011-01-01

Quantitative analysis of metal ion-phosphodiester interactions is a significant experimental challenge due to the complexities introduced by inner-sphere, outer-sphere (H-bonding with coordinated water), and electrostatic interactions that are difficult to isolate in solution studies. Here, we provide evidence that inner-sphere, H-bonding and electrostatic interactions between ions and dimethyl phosphate can be deconvoluted through peak fitting in the region of the Raman spectrum for the symmetric stretch of non-bridging phosphate oxygens (νsPO 2-). An approximation of the change in vibrational spectra due to different interaction modes is achieved using ions capable of all or a subset of the three forms of metal ion interaction. Contribution of electrostatic interactions to ion-induced changes to the Raman νsPO2- signal could be modeled by monitoring attenuation of νsPO2- in the presence of tetramethylammonium, while contribution of H-bonding and inner-sphere coordination could be approximated from the intensities of altered νsPO2- vibrational modes created by an interaction with ammonia, monovalent or divalent ions. A model is proposed in which discrete spectroscopic signals for inner-sphere, H-bonding, and electrostatic interactions are sufficient to account for the total observed change in νsPO2- signal due to interaction with a specific ion capable of all three modes of interaction. Importantly, the quantitative results are consistent with relative levels of coordination predicted from absolute electronegativity and absolute hardness of alkali and alkaline earth metals. PMID:21334281

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 molecular modeling based method to predict elution behavior and binding patches of proteins in multimodal chromatography.

PubMed

Banerjee, Suvrajit; Parimal, Siddharth; Cramer, Steven M

2017-08-18

Multimodal (MM) chromatography provides a powerful means to enhance the selectivity of protein separations by taking advantage of multiple weak interactions that include electrostatic, hydrophobic and van der Waals interactions. In order to increase our understanding of such phenomena, a computationally efficient approach was developed that combines short molecular dynamics simulations and continuum solvent based coarse-grained free energy calculations in order to study the binding of proteins to Self Assembled Monolayers (SAM) presenting MM ligands. Using this method, the free energies of protein-MM SAM binding over a range of incident orientations of the protein can be determined. The resulting free energies were then examined to identify the more "strongly bound" orientations of different proteins with two multimodal surfaces. The overall free energy of protein-MM surface binding was then determined and correlated to retention factors from isocratic chromatography. This correlation, combined with analytical expressions from the literature, was then employed to predict protein gradient elution salt concentrations as well as selectivity reversals with different MM resin systems. Patches on protein surfaces that interacted strongly with MM surfaces were also identified by determining the frequency of heavy atom contacts with the atoms of the MM SAMs. A comparison of these patches to Electrostatic Potential and hydrophobicity maps indicated that while all of these patches contained significant positive charge, only the highest frequency sites also possessed hydrophobicity. The ability to identify key binding patches on proteins may have significant impact on process development for the separation of bioproduct related impurities. Copyright © 2017 Elsevier B.V. All rights reserved.

Redox equilibria in hydroxylamine oxidoreductase. Electrostatic control of electron redistribution in multielectron oxidative processes.

PubMed

Kurnikov, Igor V; Ratner, Mark A; Pacheco, A Andrew

2005-02-15

We report results of continuum electrostatics calculations of the cofactor redox potentials, and of the titratable group pK(a) values, in hydroxylamine oxidoreductase (HAO). A picture of a sophisticated multicomponent control of electron flow in the protein emerged from the studies. First, we found that neighboring heme cofactors strongly interact electrostatically, with energies of 50-100 mV. Thus, cofactor redox potentials depend on the oxidation state of other cofactors, and cofactor redox potentials in the active (partially oxidized) enzyme differ substantially from the values obtained in electrochemical redox titration experiments. We found that, together, solvent-exposed heme 1 (having a large negative redox potential) and heme 2 (having a large positive redox potential) form a lock for electrons generated during the oxidation reaction The attachment of HAO's physiological electron transfer partner cytochrome c(554) results in a positive shift in the redox potential of heme 1, and "opens the electron gate". Electrons generated as a result of hydroxylamine oxidation travel to heme 3 and heme 8, which have redox potentials close to 0 mV versus NHE (this result is in partial disagreement with an existing experimental redox potential assignment). The closeness of hemes 3 and 8 from different enzyme subunits allows redistribution of the four electrons generated as a result of hydroxylamine oxidation, among the three enzyme subunits. For the multielectron oxidation process to be maximally efficient, the redox potentials of the electron-accepting cofactors should be roughly equal, and electrostatic interactions between extra electrons on these cofactors should be minimal. The redox potential assignments presented in the paper satisfy this general rule.

Self-assembly of short aβ(16-22) peptides: effect of terminal capping and the role of electrostatic interaction.

PubMed

Tao, Kai; Wang, Jiqian; Zhou, Peng; Wang, Chengdong; Xu, Hai; Zhao, Xiubo; Lu, Jian R

2011-03-15

We report the characterization of self-assembly of two short β-amyloid (Aβ) peptides (16-22), KLVFFAE and Ac-KLVFFAE-NH2, focusing on examining the effect of terminal capping. At pH 2.0, TEM and AFM imaging revealed that the uncapped peptide self-assembled into long, straight, and unbranched nanofibrils with a diameter of 3.8 ± 1.0 nm while the capped one formed nanotapes with a width of 70.0 ± 25.0 nm. CD analysis indicated the formation of β-sheet structures in both aggregated systems, but the characteristic CD peaks were less intense and less red-shifted for the uncapped than the capped one, indicative of weaker hydrogen bonding and weaker π-π stacking. Fluorescence and rheological measurements also confirmed stronger intermolecular attraction associated with the capped nanotapes. At acidic pH 2, each uncapped KLVFFAE molecule carries two positive charges at the N-terminus, and the strong electrostatic repulsion favors interfacial curving and twisting within the β-sheet, causing weakening of hydrogen bonds and π-π stacking. In contrast, capping reduces the charge by half, and intermolecular electrostatic repulsion is drastically reduced. As a result, the lateral attraction of β-sheets favors stronger lamellar structuring, leading to the formation of rather flat nanotapes. Flat tapes with similar morphological structure were also formed by the capped peptide at pH 12.0 where the charge on the capping end was reversed. This study has thus demonstrated how self-assembled nanostructures of small peptides can be manipulated through simple molecular structure design and tuning of electrostatic interaction.

Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution.

PubMed

Elbahnsi, Ahmad; Retureau, Romain; Baaden, Marc; Hartmann, Brigitte; Oguey, Christophe

2018-02-13

The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this complex, the DNA wraps around eight histone proteins to form a superhelical double helix. The resulting bending, stronger than anything observed in free DNA, raises the question of how such a distortion is stabilized by the proteic and solvent environments. In this work, the DNA-histone interface in solution was exhaustively analyzed from nucleosome structures generated by molecular dynamics. An original Voronoi tessellation technique, measuring the topology of interacting elements without any empirical or subjective adjustment, was used to characterize the interface in terms of contact area and occurrence. Our results revealed an interface more robust than previously known, combining extensive, long-lived nonelectrostatic and electrostatic interactions between DNA and both structured and unstructured histone regions. Cation accumulation makes the proximity of juxtaposed DNA gyres in the superhelix possible by shielding the strong electrostatic repulsion of the charged phosphate groups. Overall, this study provides new insights on the nucleosome cohesion, explaining how DNA distortions can be maintained in a nucleoprotein complex.

Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

PubMed Central

Gargallo, Raimundo; Hünenberger, Philippe H.; Avilés, Francesc X.; Oliva, Baldomero

2003-01-01

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method. PMID:14500874

Bandgap renormalization and work function tuning in MoSe2/hBN/Ru(0001) heterostructures.

PubMed

Zhang, Qiang; Chen, Yuxuan; Zhang, Chendong; Pan, Chi-Ruei; Chou, Mei-Yin; Zeng, Changgan; Shih, Chih-Kang

2016-12-14

The van der Waals interaction in vertical heterostructures made of two-dimensional (2D) materials relaxes the requirement of lattice matching, therefore enabling great design flexibility to tailor novel 2D electronic systems. Here we report the successful growth of MoSe 2 on single-layer hexagonal boron nitride (hBN) on the Ru(0001) substrate using molecular beam epitaxy. Using scanning tunnelling microscopy and spectroscopy, we found that the quasi-particle bandgap of MoSe 2 on hBN/Ru is about 0.25 eV smaller than those on graphene or graphite substrates. We attribute this result to the strong interaction between hBN/Ru, which causes residual metallic screening from the substrate. In addition, the electronic structure and the work function of MoSe 2 are modulated electrostatically with an amplitude of ∼0.13 eV. Most interestingly, this electrostatic modulation is spatially in phase with the Moiré pattern of hBN on Ru(0001) whose surface also exhibits a work function modulation of the same amplitude.

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.

The changing world of G protein-coupled receptors: from monomers to dimers and receptor mosaics with allosteric receptor-receptor interactions.

PubMed

Fuxe, Kjell; Marcellino, Daniel; Borroto-Escuela, Dasiel Oscar; Frankowska, Malgorzata; Ferraro, Luca; Guidolin, Diego; Ciruela, Francisco; Agnati, Luigi F

2010-10-01

Based on indications of direct physical interactions between neuropeptide and monoamine receptors in the early 1980s, the term receptor-receptor interactions was introduced and later on the term receptor heteromerization in the early 1990s. Allosteric mechanisms allow an integrative activity to emerge either intramolecularly in G protein-coupled receptor (GPCR) monomers or intermolecularly via receptor-receptor interactions in GPCR homodimers, heterodimers, and receptor mosaics. Stable heteromers of Class A receptors may be formed that involve strong high energy arginine-phosphate electrostatic interactions. These receptor-receptor interactions markedly increase the repertoire of GPCR recognition, signaling and trafficking in which the minimal signaling unit in the GPCR homomers appears to be one receptor and one G protein. GPCR homomers and GPCR assemblies are not isolated but also directly interact with other proteins to form horizontal molecular networks at the plasma membrane.

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.

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.

Diminish electrostatic in piezoresponse force microscopy through longer or ultra-stiff tips

NASA Astrophysics Data System (ADS)

Gomez, A.; Puig, T.; Obradors, X.

2018-05-01

Piezoresponse Force Microscopy is a powerful but delicate nanoscale technique that measures the electromechanical response resulting from the application of a highly localized electric field. Though mechanical response is normally due to piezoelectricity, other physical phenomena, especially electrostatic interaction, can contribute to the signal read. We address this problematic through the use of longer ultra-stiff probes providing state of the art sensitivity, with the lowest electrostatic interaction and avoiding working in high frequency regime. In order to find this solution we develop a theoretical description addressing the effects of electrostatic contributions in the total cantilever vibration and its quantification for different setups. The theory is subsequently tested in a Periodically Poled Lithium Niobate (PPLN) crystal, a sample with well-defined 0° and 180° domains, using different commercial available conductive tips. We employ the theoretical description to compare the electrostatic contribution effects into the total phase recorded. Through experimental data our description is corroborated for each of the tested commercially available probes. We propose that a larger probe length can be a solution to avoid electrostatic forces, so the cantilever-sample electrostatic interaction is reduced. Our proposed solution has great implications into avoiding artifacts while studying soft biological samples, multiferroic oxides, and thin film ferroelectric materials.

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.

Differences in PAR-2 activating potential by king crab (Paralithodes camtschaticus), salmon (Salmo salar), and bovine (Bos taurus) trypsin.

PubMed

Larsen, Anett K; Kristiansen, Kurt; Sylte, Ingebrigt; Seternes, Ole-Morten; Bang, Berit E

2013-07-20

Salmon trypsin is shown to increase secretion of the pro-inflammatory cytokine interleukin (IL)-8 from human airway epithelial cells through activation of PAR-2. Secretion of IL-8 induced by king crab trypsin is observed in a different concentration range compared to salmon trypsin, and seems to be only partially related to PAR-2 activation. This report aim to identify differences in the molecular structure of king crab trypsin (Paralithodes camtschaticus) compared to salmon (Salmo salar) and bovine trypsin (Bos taurus) that might influence the ability to activate protease-activated receptor-2 (PAR-2). During purification king crab trypsin displayed stronger binding capacity to the anionic column used in fast protein liquid chromatography compared to fish trypsins, and was identified as a slightly bigger molecule. Measurements of enzymatic activity yielded no obvious differences between the trypsins tested. Molecular modelling showed that king crab trypsin has a large area with strong negative electrostatic potential compared to the smaller negative areas in bovine and salmon trypsins. Bovine and salmon trypsins also displayed areas with strong positive electrostatic potential, a feature lacking in the king crab trypsin. Furthermore we have identified 3 divergent positions (Asp196, Arg244, and Tyr247) located near the substrate binding pocket of king crab trypsin that might affect the binding and cleavage of PAR-2. These preliminary results indicate that electrostatic interactions could be of importance in binding, cleavage and subsequent activation of PAR-2.

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.

Impact of a nonuniform charge distribution on virus assembly

NASA Astrophysics Data System (ADS)

Li, Siyu; Erdemci-Tandogan, Gonca; Wagner, Jef; van der Schoot, Paul; Zandi, Roya

2017-08-01

Many spherical viruses encapsulate their genomes in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genomes. We model the effect of the nonuniform icosahedral charge distribution from the protein shell instead using a mean-field theory. We find that this nonuniform charge distribution strongly affects the optimal genome length and that it can explain the experimentally observed phenomenon of overcharging of virus and viruslike particles.

Electrostatic Effects in Filamentous Protein Aggregation

PubMed Central

Buell, Alexander K.; Hung, Peter; Salvatella, Xavier; Welland, Mark E.; Dobson, Christopher M.; Knowles, Tuomas P.J.

2013-01-01

Electrostatic forces play a key role in mediating interactions between proteins. However, gaining quantitative insights into the complex effects of electrostatics on protein behavior has proved challenging, due to the wide palette of scenarios through which both cations and anions can interact with polypeptide molecules in a specific manner or can result in screening in solution. In this article, we have used a variety of biophysical methods to probe the steady-state kinetics of fibrillar protein self-assembly in a highly quantitative manner to detect how it is modulated by changes in solution ionic strength. Due to the exponential modulation of the reaction rate by electrostatic forces, this reaction represents an exquisitely sensitive probe of these effects in protein-protein interactions. Our approach, which involves a combination of experimental kinetic measurements and theoretical analysis, reveals a hierarchy of electrostatic effects that control protein aggregation. Furthermore, our results provide a highly sensitive method for the estimation of the magnitude of binding of a variety of ions to protein molecules. PMID:23473495

Protonation states and pH titration in the photocycle of photoactive yellow protein.

PubMed

Demchuk, E; Genick, U K; Woo, T T; Getzoff, E D; Bashford, D

2000-02-08

Photoactive yellow protein (PYP) undergoes a light-driven cycle of color and protonation states that is part of a mechanism of bacterial phototaxis. This article concerns functionally important protonation states of PYP and the interactions that stabilize them, and changes in the protonation state during the photocycle. In particular, the chromophore pK(a) is known to be shifted down so that the chromophore is negatively charged in the ground state (dark state) even though it is buried in the protein, while nearby Glu46 has an unusually high pK(a). The photocycle involves changes of one or both of these protonation states. Calculations of pK(a) values and protonation states using a semi-macroscopic electrostatic model are presented for the wild-type and three mutants, in both the ground state and the bleached (I(2)) intermediate state. Calculations allowing multiple H-bonding arrangements around the chromophore also have been carried out. In addition, ground-state pK(a) values of the chromophore have been measured by UV-visible spectroscopy for the wild-type and the same three mutants. Because of the unusual protonation states and strong electrostatic interactions, PYP represents a severe test of the ability of theoretical models to yield correct calculations of electrostatic interactions in proteins. Good agreement between experiment and theory can be obtained for the ground state provided the protein interior is assumed to have a relatively low dielectric constant, but only partial agreement between theory and experiment is obtained for the bleached state. We also present a reinterpretation of previously published data on the pH-dependence of the recovery of the ground state from the bleached state. The new analysis implies a pK(a) value of 6.37 for Glu46 in the bleached state, which is consistent with other available experimental data, including data that only became available after this analysis. The new analysis suggests that signal transduction is modulated by the titration properties of the bleached state, which are in turn determined by electrostatic interactions. Overall, the results of this study provide a quantitative picture of the interactions responsible for the unusual protonation states of the chromophore and Glu46, and of protonation changes upon bleaching.

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

PubMed

Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin

2017-09-14

U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.

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.

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

Temperature-responsive chromatography for the separation of biomolecules.

PubMed

Kanazawa, Hideko; Okano, Teruo

2011-12-09

Temperature-responsive chromatography for the separation of biomolecules utilizing poly(N-isopropylacrylamide) (PNIPAAm) and its copolymer-modified stationary phase is performed with an aqueous mobile phase without using organic solvent. The surface properties and function of the stationary phase are controlled by external temperature changes without changing the mobile-phase composition. This analytical system is based on nonspecific adsorption by the reversible transition of a hydrophilic-hydrophobic PNIPAAm-grafted surface. The driving force for retention is hydrophobic interaction between the solute molecules and the hydrophobized polymer chains on the stationary phase surface. The separation of the biomolecules, such as nucleotides and proteins was achieved by a dual temperature- and pH-responsive chromatography system. The electrostatic and hydrophobic interactions could be modulated simultaneously with the temperature in an aqueous mobile phase, thus the separation system would have potential applications in the separation of biomolecules. Additionally, chromatographic matrices prepared by a surface-initiated atom transfer radical polymerization (ATRP) exhibit a strong interaction with analytes, because the polymerization procedure forms a densely packed polymer, called a polymer brush, on the surfaces. The copolymer brush grafted surfaces prepared by ATRP was an effective tool for separating basic biomolecules by modulating the electrostatic and hydrophobic interactions. Applications of thermally responsive columns for the separations of biomolecules are reviewed here. Copyright © 2011 Elsevier B.V. All rights reserved.

Attachment of Pathogenic Prion Protein to Model Oxide Surfaces

PubMed Central

Jacobson, Kurt H.; Kuech, Thomas R.; Pedersen, Joel A.

2014-01-01

Prions are the infectious agents in the class of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies, which affect humans, deer, sheep, and cattle. Prion diseases of deer and sheep can be transmitted via environmental routes, and soil is has been implicated in the transmission of these diseases. Interaction with soil particles is expected to govern the transport, bioavailability and persistence of prions in soil environments. A mechanistic understanding of prion interaction with soil components is critical for understanding the behavior of these proteins in the environment. Here, we report results of a study to investigate the interactions of prions with model oxide surfaces (Al2O3, SiO2) using quartz crystal microbalance with dissipation monitoring and optical waveguide light mode spectroscopy. The efficiency of prion attachment to Al2O3 and SiO2 depended strongly on pH and ionic strength in a manner consistent with electrostatic forces dominating interaction with these oxides. The N-terminal portion of the protein appeared to facilitate attachment to Al2O3 under globally electrostatically repulsive conditions. We evaluated the utility of recombinant prion protein as a surrogate for prions in attachment experiments and found that its behavior differed markedly from that of the infectious agent. Our findings suggest that prions preferentially associate with positively charged mineral surfaces in soils (e.g., iron and aluminum oxides). PMID:23611152

Accurate potentiometric determination of lipid membrane-water partition coefficients and apparent dissociation constants of ionizable drugs: electrostatic corrections.

PubMed

Elsayed, Mustafa M A; Vierl, Ulrich; Cevc, Gregor

2009-06-01

Potentiometric lipid membrane-water partition coefficient studies neglect electrostatic interactions to date; this leads to incorrect results. We herein show how to account properly for such interactions in potentiometric data analysis. We conducted potentiometric titration experiments to determine lipid membrane-water partition coefficients of four illustrative drugs, bupivacaine, diclofenac, ketoprofen and terbinafine. We then analyzed the results conventionally and with an improved analytical approach that considers Coulombic electrostatic interactions. The new analytical approach delivers robust partition coefficient values. In contrast, the conventional data analysis yields apparent partition coefficients of the ionized drug forms that depend on experimental conditions (mainly the lipid-drug ratio and the bulk ionic strength). This is due to changing electrostatic effects originating either from bound drug and/or lipid charges. A membrane comprising 10 mol-% mono-charged molecules in a 150 mM (monovalent) electrolyte solution yields results that differ by a factor of 4 from uncharged membranes results. Allowance for the Coulombic electrostatic interactions is a prerequisite for accurate and reliable determination of lipid membrane-water partition coefficients of ionizable drugs from potentiometric titration data. The same conclusion applies to all analytical methods involving drug binding to a surface.

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.

Beyond the Electrostatic Ionosphere: Dynamic Coupling of the Magnetosphere and Ionosphere

NASA Astrophysics Data System (ADS)

Lysak, R. L.; Song, Y.

2017-12-01

Many models of magnetospheric dynamics treat the ionosphere as a height-integrated slab in which the electric fields are electrostatic. However, in dynamic situations, the coupling between magnetosphere and ionosphere is achieved by the propagation of shear Alfvén waves. Hall effects lead to a coupling of shear Alfvén and fast mode waves, resulting in an inductive electric field and a compressional component of the magnetic field. It is in fact this compressional magnetic field that is largely responsible for the magnetic fields seen on the ground. A fully inductive ionosphere model is required to describe this situation. The shear Alfvén waves are affected by the strong gradient in the Alfvén speed above the ionosphere, setting up the ionospheric Alfvén resonator with wave periods in the 1-10 second range. These waves develop a parallel electric field on small scales that can produce a broadband acceleration of auroral electrons, which form the Alfvénic aurora. Since these electrons are relatively low in energy (hundreds of eV to a few keV), they produce auroral emissions as well as ionization at higher altitudes. Therefore, they can produce localized columns of ionization that lead to structuring in the auroral currents due to phase mixing or feedback interactions. This implies that the height-integrated description of the ionosphere is not appropriate in these situations. These considerations suggest that the Alfvénic aurora may, at least in some cases, act as a precursor to the development of a quasi-static auroral arc. The acceleration of electrons and ions produces a density cavity at higher altitudes that favors the formation of parallel electric fields. Furthermore, the precipitating electrons will produce secondary and backscattered electrons that provide a necessary population for the formation of double layers. These interactions strongly suggest that the simple electrostatic boundary condition often assumed is inadequate to describe auroral arc formation.

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

PubMed Central

Tan, Cheng; Takada, Shoji

2017-01-01

While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements. PMID:29194442

Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics

PubMed Central

Baumketner, Andrij

2009-01-01

The performance of reaction-field methods to treat electrostatic interactions is tested in simulations of ions solvated in water. The potential of mean force between sodium chloride pair of ions and between side chains of lysine and aspartate are computed using umbrella sampling and molecular dynamics simulations. It is found that in comparison with lattice sum calculations, the charge-group-based approaches to reaction-field treatments produce a large error in the association energy of the ions that exhibits strong systematic dependence on the size of the simulation box. The atom-based implementation of the reaction field is seen to (i) improve the overall quality of the potential of mean force and (ii) remove the dependence on the size of the simulation box. It is suggested that the atom-based truncation be used in reaction-field simulations of mixed media. PMID:19292522

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.

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

Surface charge effects in protein adsorption on nanodiamonds.

PubMed

Aramesh, M; Shimoni, O; Ostrikov, K; Prawer, S; Cervenka, J

2015-03-19

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.

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.

First-principles simulations of electrostatic interactions between dust grains

NASA Astrophysics Data System (ADS)

Itou, H.; Amano, T.; Hoshino, M.

2014-12-01

We investigated the electrostatic interaction between two identical dust grains of an infinite mass immersed in homogeneous plasma by employing first-principles N-body simulations combined with the Ewald method. We specifically tested the possibility of an attractive force due to overlapping Debye spheres (ODSs), as was suggested by Resendes et al. [Phys. Lett. A 239, 181-186 (1998)]. Our simulation results demonstrate that the electrostatic interaction is repulsive and even stronger than the standard Yukawa potential. We showed that the measured electric field acting on the grain is highly consistent with a model electrostatic potential around a single isolated grain that takes into account a correction due to the orbital motion limited theory. Our result is qualitatively consistent with the counterargument suggested by Markes and Williams [Phys. Lett. A 278, 152-158 (2000)], indicating the absence of the ODS attractive force.

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

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.

Interaction-component analysis of the hydration and urea effects on cytochrome c

NASA Astrophysics Data System (ADS)

Yamamori, Yu; Ishizuka, Ryosuke; Karino, Yasuhito; Sakuraba, Shun; Matubayasi, Nobuyuki

2016-02-01

Energetics was analyzed for cytochrome c in pure-water solvent and in a urea-water mixed solvent to elucidate the solvation effect in the structural variation of the protein. The solvation free energy was computed through all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were examined over sets of protein structures against the electrostatic and van der Waals components in the average interaction energy of the protein with the solvent and the excluded-volume component in the solvation free energy. It was observed in pure-water solvent that the solvation free energy varies in parallel to the electrostatic component with minor roles played by the van der Waals and excluded-volume components. The effect of urea on protein structure was then investigated in terms of the free-energy change upon transfer of the protein solute from pure-water solvent to the urea-water mixed solvent. The decomposition of the transfer free energy into the contributions from urea and water showed that the urea contribution is partially canceled by the water contribution and governs the total free energy of transfer. When correlated against the change in the solute-solvent interaction energy upon transfer and the corresponding changes in the electrostatic, van der Waals, and excluded-volume components, the transfer free energy exhibited strong correlations with the total change in the solute-solvent energy and its van der Waals component. The solute-solvent energy was decomposed into the contributions from the protein backbone and side chain, furthermore, and neither of the contributions was seen to be decisive in the correlation to the transfer free energy.

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.

On the theory of electric double layer with explicit account of a polarizable co-solvent.

PubMed

Budkov, Yu A; Kolesnikov, A L; Kiselev, M G

2016-05-14

We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On the contrary, a sufficiently large additive of co-solvent shifts the saturation potential to lower surface potentials. We obtain that an increase in the co-solvent polarizability makes the electrostatic potential profile longer-ranged. However, increase in the co-solvent concentration in the bulk leads to non-monotonic behavior of the electrostatic potential profile. An increase in the co-solvent concentration in the bulk at its sufficiently small values makes the electrostatic potential profile longer-ranged. Oppositely, when the co-solvent concentration in the bulk exceeds some threshold value, its further increase leads to decrease in electrostatic potential at all distances from the electrode.

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.

Interaction of a novel peptoid enhancer--arginine oligomer with bovine submaxillary mucin.

PubMed

Liang, Wei; Davalian, Dariush; Torchilin, Vladimir P

2004-12-01

To determine the thermodynamics of binding reaction of arginine oligomer (R8) to bovine submaxillary mucin (BSM) in order to provide the foundation for understanding the influence of mucin on transport of macromolecules through mucosa mediated by arginine oligomer. Ultracentrifugation sedimentation was employed to investigate the interaction of BSM-R8. The mixtures of R8 with variable concentration and constant volume of BSM were placed on a shaker under oscillation at 25 degrees C to achieve equilibriums of binding reaction, and then centrifuged. The fluorescence intensity of the supernatant was measured by spectrofluorometer. The data were described by two types of binding sites model, the binding parameters of BSM-R8 were obtained by Scatchard plots. At the low pH values < or = 4.5 and ionic strength > or = 0.2 mol x L(-1), the BSM-R8 interaction was principally electrostatic interaction, the five primary binding sites (n1) predominantly were supplied by sulfate groups, the secondary binding sites apparently depended on pH, in that percent ionization of sialic acid residues (n2) in BSM. At the low ionic strength < or = 0.2 mol x L(-1) and pH 7.0, the BSM-R8 interaction was exceedingly complex, hydrogen bonds, hydrophobic interaction and electrostatic forces were involved in the interaction between R8 and BSM, the binding sites of BSM bound R8 were markedly increased. There existed evidence that R8 interacted with BSM. The pH and the ionic strength of the binding solution strongly affected the interaction of BSM with R8. The results suggested that the enhancing efficacy of the arginine oligomer for the transport of macromolecules through different site mucosa in body might be variable.

Suppression of Pauli Spin Blockade in Few Hole Laterally Gated Double Quantum Dots

NASA Astrophysics Data System (ADS)

Gaudreau, Louis; Bogan, Alex; Studenikin, Sergei; Korkusinski, Marek; Aers, Geof; Zawadzki, Piotr; Sachrajda, Andy; Tracy, Lisa; Reno, John; Hargett, Terry; National Research Council Team; Sandia Labs Team

Hole spins have attracted increasing attention as candidates for qubits in quantum information applications. The p-type character of their wavefunction leads to smaller hyperfine interaction with the nuclei resulting in longer coherence times. Additionally, strong spin-orbit interaction allows for enhanced all-electrical manipulation of spin qubit states. Single hole spins have been electrically studied in InSb and Si nanowire quantum dots, however, electrostatically confined hole spins in a 2D hole gas have thus far been limited to the many hole regime. In this talk we will present a full description of the two-hole spin spectrum in a lateral GaAs/AlGaAs double quantum. High-bias magneto-transport spectroscopy reveals all four states of the spectrum (singlet and triplets) in both the (1,1) and (2,0) configurations, essential for spin readout based on Pauli spin blockade. We show that spin-flip tunneling between dots is as strong as spin conserving tunneling, a consequence of the strong spin-orbit interaction. This suppresses the Pauli spin blockade. Our results suggest that alternate techniques for single hole spin qubit readout need to be explored.

How Cations Can Assist DNase I in DNA Binding and Hydrolysis

PubMed Central

Guéroult, Marc; Picot, Daniel; Abi-Ghanem, Joséphine; Hartmann, Brigitte; Baaden, Marc

2010-01-01

DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA. However, the number and the location of DNase I ion-binding sites remain unclear, as well as the role of these counter-ions. Using molecular dynamics simulations, we show that bovine pancreatic (bp) DNase I contains four ion-binding pockets. Two of them strongly bind Ca2+ while the other two sites coordinate Mg2+. These theoretical results are strongly supported by revisiting crystallographic structures that contain bpDNase I. One Ca2+ stabilizes the functional DNase I structure. The presence of Mg2+ in close vicinity to the catalytic pocket of bpDNase I reinforces the idea of a cation-assisted hydrolytic mechanism. Importantly, Poisson-Boltzmann-type electrostatic potential calculations demonstrate that the divalent cations collectively control the electrostatic fit between bpDNase I and DNA. These results improve our understanding of the essential role of cations in the biological function of bpDNase I. The high degree of conservation of the amino acids involved in the identified cation-binding sites across DNase I and DNase I-like proteins from various species suggests that our findings generally apply to all DNase I-DNA interactions. PMID:21124947

Albumin-coated SPIONs: an experimental and theoretical evaluation of protein conformation, binding affinity and competition with serum proteins

NASA Astrophysics Data System (ADS)

Yu, Siming; Perálvarez-Marín, Alex; Minelli, Caterina; Faraudo, Jordi; Roig, Anna; Laromaine, Anna

2016-07-01

The variety of nanoparticles (NPs) used in biological applications is increasing and the study of their interaction with biological media is becoming more important. Proteins are commonly the first biomolecules that NPs encounter when they interact with biological systems either in vitro or in vivo. Among NPs, super-paramagnetic iron oxide nanoparticles (SPIONs) show great promise for medicine. In this work, we study in detail the formation, composition, and structure of a monolayer of bovine serum albumin (BSA) on SPIONs. We determine, both by molecular simulations and experimentally, that ten molecules of BSA form a monolayer around the outside of the SPIONs and their binding strength to the SPIONs is about 3.5 × 10-4 M, ten times higher than the adsorption of fetal bovine serum (FBS) on the same SPIONs. We elucidate a strong electrostatic interaction between BSA and the SPIONs, although the secondary structure of the protein is not affected. We present data that supports the strong binding of the BSA monolayer on SPIONs and the properties of the BSA layer as a protein-resistant coating. We believe that a complete understanding of the behavior and morphology of BSA-SPIONs and how the protein interacts with SPIONs is crucial for improving NP surface design and expanding the potential applications of SPIONs in nanomedicine.The variety of nanoparticles (NPs) used in biological applications is increasing and the study of their interaction with biological media is becoming more important. Proteins are commonly the first biomolecules that NPs encounter when they interact with biological systems either in vitro or in vivo. Among NPs, super-paramagnetic iron oxide nanoparticles (SPIONs) show great promise for medicine. In this work, we study in detail the formation, composition, and structure of a monolayer of bovine serum albumin (BSA) on SPIONs. We determine, both by molecular simulations and experimentally, that ten molecules of BSA form a monolayer around the outside of the SPIONs and their binding strength to the SPIONs is about 3.5 × 10-4 M, ten times higher than the adsorption of fetal bovine serum (FBS) on the same SPIONs. We elucidate a strong electrostatic interaction between BSA and the SPIONs, although the secondary structure of the protein is not affected. We present data that supports the strong binding of the BSA monolayer on SPIONs and the properties of the BSA layer as a protein-resistant coating. We believe that a complete understanding of the behavior and morphology of BSA-SPIONs and how the protein interacts with SPIONs is crucial for improving NP surface design and expanding the potential applications of SPIONs in nanomedicine. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01732k

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.

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.

Dendrimer-protein interactions versus dendrimer-based nanomedicine.

PubMed

Shcharbin, Dzmitry; Shcharbina, Natallia; Dzmitruk, Volha; Pedziwiatr-Werbicka, Elzbieta; Ionov, Maksim; Mignani, Serge; de la Mata, F Javier; Gómez, Rafael; Muñoz-Fernández, Maria Angeles; Majoral, Jean-Pierre; Bryszewska, Maria

2017-04-01

Dendrimers are hyperbranched polymers belonging to the huge class of nanomedical devices. Their wide application in biology and medicine requires understanding of the fundamental mechanisms of their interactions with biological systems. Summarizing, electrostatic force plays the predominant role in dendrimer-protein interactions, especially with charged dendrimers. Other kinds of interactions have been proven, such as H-bonding, van der Waals forces, and even hydrophobic interactions. These interactions depend on the characteristics of both participants: flexibility and surface charge of a dendrimer, rigidity of protein structure and the localization of charged amino acids at its surface. pH and ionic strength of solutions can significantly modulate interactions. Ligands and cofactors attached to a protein can also change dendrimer-protein interactions. Binding of dendrimers to a protein can change its secondary structure, conformation, intramolecular mobility and functional activity. However, this strongly depends on rigidity versus flexibility of a protein's structure. In addition, the potential applications of dendrimers to nanomedicine are reviwed related to dendrimer-protein interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

Lignin Films from Spruce, Eucalyptus, and Wheat Straw Studied with Electroacoustic and Optical Sensors: Effect of Composition and Electrostatic Screening on Enzyme Binding.

PubMed

Pereira, Antonio; Hoeger, Ingrid C; Ferrer, Ana; Rencoret, Jorge; Del Rio, José C; Kruus, Kristiina; Rahikainen, Jenni; Kellock, Miriam; Gutiérrez, Ana; Rojas, Orlando J

2017-04-10

Lignins were isolated from spruce, wheat straw, and eucalyptus by using the milled wood lignin (MWL) method. Functional groups and compositional analyses were assessed via 2D NMR and 31 P NMR to realize their effect on enzyme binding. Films of the lignins were fabricated and ellipsometry, atomic force microscopy, and water contact angle measurements were used for their characterization and to reveal the changes upon enzyme adsorption. Moreover, lignin thin films were deposited on quartz crystal microgravimetry (QCM) and surface plasmon (SPR) resonance sensors and used to gain further insights into the lignin-cellulase interactions. For this purpose, a commercial multicomponent enzyme system and a monocomponent Trichoderma reesei exoglucanase (CBH-I) were considered. Strong enzyme adsorption was observed on the various lignins but compared to the multicomponent cellulases, CBH-I displayed lower surface affinity and higher binding reversibility. This resolved prevalent questions related to the affinity of this enzyme with lignin. Remarkably, a strong correlation between enzyme binding and the syringyl/guaiacyl (S/G) ratio was found for the lignins, which presented a similar hydroxyl group content ( 31 P NMR): higher protein affinity was determined on isolated spruce lignin (99% G units), while the lowest adsorption occurred on isolated eucalyptus lignin (70% S units). The effect of electrostatic interactions in enzyme adsorption was investigated by SPR, which clearly indicated that the screening of charges allowed more extensive protein adsorption. Overall, this work furthers our understanding of lignin-cellulase interactions relevant to biomass that has been subjected to no or little pretreatment and highlights the widely contrasting effects of the nature of lignin, which gives guidance to improve lignocellulosic saccharification and related processes.

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.

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.

Light-scattering studies of protein solutions: role of hydration in weak protein-protein interactions.

PubMed

Paliwal, A; Asthagiri, D; Abras, D; Lenhoff, A M; Paulaitis, M E

2005-09-01

We model the hydration contribution to short-range electrostatic/dispersion protein interactions embodied in the osmotic second virial coefficient, B(2), by adopting a quasi-chemical description in which water molecules associated with the protein are identified through explicit molecular dynamics simulations. These water molecules reduce the surface complementarity of highly favorable short-range interactions, and therefore can play an important role in mediating protein-protein interactions. Here we examine this quasi-chemical view of hydration by predicting the interaction part of B(2) and comparing our results with those derived from light-scattering measurements of B(2) for staphylococcal nuclease, lysozyme, and chymotrypsinogen at 25 degrees C as a function of solution pH and ionic strength. We find that short-range protein interactions are influenced by water molecules strongly associated with a relatively small fraction of the protein surface. However, the effect of these strongly associated water molecules on the surface complementarity of short-range protein interactions is significant, and must be taken into account for an accurate description of B(2). We also observe remarkably similar hydration behavior for these proteins despite substantial differences in their three-dimensional structures and spatial charge distributions, suggesting a general characterization of protein hydration.

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.

Small-Angle Neutron Scattering Study of Interplay of Attractive and Repulsive Interactions in Nanoparticle-Polymer System.

PubMed

Kumar, Sugam; Aswal, Vinod K; Kohlbrecher, Joachim

2016-02-16

The phase behavior of nanoparticle (silica)-polymer (polyethylene glycol) system without and with an electrolyte (NaCl) has been studied. It is observed that nanoparticle-polymer system behaves very differently in the presence of electrolyte. In the absence of electrolyte, the nanoparticle-polymer system remains in one-phase even at very high polymer concentrations. On the other hand, a re-entrant phase behavior is found in the presence of electrolyte, where one-phase (individual) system undergoes two-phase (nanoparticle aggregation) and then back to one-phase with increasing polymer concentration. The regime of two-phase system has been tuned by varying the electrolyte concentration. The polymer concentration range over which the two-phase system exists is significantly enhanced with the increase in the electrolyte concentration. These systems have been characterized by small-angle neutron scattering (SANS) experiments of contrast-marching the polymer to the solvent. The data are modeled using a two-Yukawa potential accounting for both attractive and repulsive parts of the interaction between nanoparticles. The phase behavior of nanoparticle-polymer system is explained by interplay of attractive (polymer-induced attractive depletion between nanoparticles) and repulsive (nanoparticle-nanoparticle electrostatic repulsion and polymer-polymer repulsion) interactions present in the system. In the absence of electrolyte, the strong electrostatic repulsion between nanoparticles dominates over the polymer-induced depletion attraction and the nanoparticle system remains in one-phase. With addition of electrolyte, depletion attraction overcomes electrostatic repulsion at some polymer concentration, resulting into nanoparticle aggregation and two-phase system. Further addition of polymer increases the polymer-polymer repulsion which eventually reduces the strength of depletion and hence re-entrant phase behavior. The effects of varying electrolyte concentration on the phase behavior of nanoparticle-polymer system are understood in terms of modifications in nanoparticle-nanoparticle and polymer-polymer interactions. The nanoparticle aggregates in two-phase systems are found to have surface fractal morphology.

Measuring three-dimensional interaction potentials using optical interference.

PubMed

Mojarad, Nassir; Sandoghdar, Vahid; Krishnan, Madhavi

2013-04-22

We describe the application of three-dimensional (3D) scattering interferometric (iSCAT) imaging to the measurement of spatial interaction potentials for nano-objects in solution. We study electrostatically trapped gold particles in a nanofluidic device and present details on axial particle localization in the presence of a strongly reflecting interface. Our results demonstrate high-speed (~kHz) particle tracking with subnanometer localization precision in the axial and average 2.5 nm in the lateral dimension. A comparison of the measured levitation heights of trapped particles with the calculated values for traps of various geometries reveals good agreement. Our work demonstrates that iSCAT imaging delivers label-free, high-speed and accurate 3D tracking of nano-objects conducive to probing weak and long-range interaction potentials in solution.

From dipolar to multipolar interactions between ultracold Feshbach molecules

NASA Astrophysics Data System (ADS)

Quéméner, Goulven; Lepers, Maxence; Luc-Koenig, Eliane; Dulieu, Olivier

2016-05-01

Using the multipolar expansion of electrostatic and magnetostatic potential energies, we characterize the long-range interactions between two weakly-bound diatomic molecules, taking as an example the paramagnetic Er2 Feshbach molecules which were produced recently. The interaction between atomic magnetic dipoles gives rise to the usual R-3 leading term of the multipolar expansion, where R is the intermolecular distance. We show that additional terms scaling as R-5, R-7 and so on also appear, which are strongly anisotropic with respect to the orientation of the molecules. These terms can be seen as effective molecular multipole moments reflecting the spatial extension of the molecules which is non-negligible compared to R. We acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche.

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…

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.

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

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.

Competition between excluded-volume and electrostatic interactions for nanogel swelling: effects of the counterion valence and nanogel charge.

PubMed

Adroher-Benítez, Irene; Martín-Molina, Alberto; Ahualli, Silvia; Quesada-Pérez, Manuel; Odriozola, Gerardo; Moncho-Jordá, Arturo

2017-03-01

In this work the equilibrium distribution of ions around a thermo-responsive charged nanogel particle in an electrolyte aqueous suspension is explored using coarse-grained Monte Carlo computer simulations and the Ornstein-Zernike integral equation theory. We explicitly consider the ionic size in both methods and study the interplay between electrostatic and excluded-volume effects for swollen and shrunken nanogels, monovalent and trivalent counterions, and for two different nanogel charges. We find good quantitative agreement between the ionic density profiles obtained using both methods when the excluded repulsive force exerted by the cross-linked polymer network is taken into account. For the shrunken conformation, the electrostatic repulsion between the charged groups provokes a heterogeneous polymer density profile, leading to a nanogel structure with an internal low density hole surrounded by a dense corona. The results show that the excluded-volume repulsion strongly hinders the ion permeation for shrunken nanogels, where volume exclusion is able to significantly reduce the concentration of counterions in the more dense regions of the nanogel. In general, we demonstrate that the thermosensitive behaviour of nanogels, as well as their internal structure, is strongly influenced by the valence of the counterions and also by the charge of the particles. On the one hand, an increase of the counterion valence moves the swelling transition to lower temperatures, and induces a major structuring of the charged monomers into internal and external layers around the crown for shrunken nanogels. On the other hand, increasing the particle charge shifts the swelling curve to larger values of the effective radius of the nanogel.

Mechanism of the dielectric enhancement in polymer-alumina nano-particle composites

NASA Astrophysics Data System (ADS)

Jacob, Rebecca; Jacob, Anne Pavitra; Mainwaring, David E.

2009-09-01

Polymer-alumina nano-composites with enhanced dielectric properties as a possibility to enable the miniaturization of devices have been reported. The enhancement of dielectric properties was found to be unique to the polymer. In the present work, the mechanism of the dielectric enhancement is established by performing ab initio molecular orbital calculations in order to study the molecular interactions in the interfacial region between the alumina-nano-particle surface and the polymer medium. The calculations predict the existence of strong electrostatic attraction between the positive charge on the aluminium of the alumina clusters and the negative charge of the oxygens of the polymer at the polymer-nano-particle interface resulting in an increase in the dipole moment and the polarization of the system leading to enhanced dielectric properties. The oxygen thus plays a dual role by involving in covalent bonding with the polymer chain and electrostatic bonding interactions with the alumina nano-particles. The unique structure of the polymer provides the highly electronegative oxygens, as carbonyl groups or ether linkages in conjugation with aromatic rings in an extended polymer chain system, facilitating this type of bonding at the interface.

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

An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy.

PubMed

Völler, Jan-Stefan; Biava, Hernan; Hildebrandt, Peter; Budisa, Nediljko

2017-11-01

To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics. Mapping the electrostatics in proteins will improve our understanding of natural catalytic processes and, in beyond, will be helpful for biocatalyst engineering. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Counterion adsorption and desorption rate of a charged macromolecule

NASA Astrophysics Data System (ADS)

Shi, Yu; Yang, Jingfa; Zhao, Jiang

The rate constant of counterion adsorption to and desorption from a synthetic polyelectrolyte, polystyrene sulfonate (PSS-), is measured in aqueous solution by single molecule fluorescence spectroscopy. The results show that both adsorption and desorption rate of counterions have strong dependence on polymer concentration, salt concentration as well as the molecular weight of polyelectrolytes. The results clearly demonstrate that the contribution of electrostatic interaction and the translational entropy to the distribution of counterions of a polyelectrolyte molecule. The information is helpful to the understanding of polyelectrolyte physics. National Natural Science Foundation of China.

Early Program Development

NASA Image and Video Library

1961-01-01

As presented by Gerhard Heller of Marshall Space Flight Center's Research Projects Division in 1961, this chart illustrates three basic types of electric propulsion systems then under consideration by NASA. The ion engine (top) utilized cesium atoms ionized by hot tungsten and accelerated by an electrostatic field to produce thrust. The arc engine (middle) achieved propulsion by heating a propellant with an electric arc and then producing an expansion of the hot gas or plasma in a convergent-divergent duct. The electromagnetic, or MFD engine (bottom) manipulated strong magnetic fields to interact with a plasma and produce acceleration.

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.

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.

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

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.

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.

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

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

pH-responsive ion transport in polyelectrolyte multilayers of poly(diallyldimethylammonium chloride) (PDADMAC) and poly(4-styrenesulfonic acid-co-maleic acid) (PSS-MA) bearing strong- and weak anionic groups.

PubMed

Maza, Eliana; Tuninetti, Jimena S; Politakos, Nikolaos; Knoll, Wolfgang; Moya, Sergio; Azzaroni, Omar

2015-11-28

The layer-by-layer construction of interfacial architectures displaying stimuli-responsive control of mass transport is attracting increasing interest in materials science. In this work, we describe the creation of interfacial architectures displaying pH-dependent ionic transport properties which until now have not been observed in polyelectrolyte multilayers. We describe a novel approach to create pH-controlled ion-rectifying systems employing polyelectrolyte multilayers assembled from a copolymer containing both weakly and strongly charged pendant groups, poly(4-styrenesulfonic acid-co-maleic acid) (PSS-MA), alternately deposited with poly(diallyldimethylammonium chloride) (PDADMAC). The conceptual framework is based on the very contrasting and differential interactions of PSS and MA units with PDADMAC. In our setting, sulfonate groups play a structural role by conferring stability to the multilayer due to the strong electrostatic interactions with the polycations, while the weakly interacting MA groups remain "silent" within the film and then act as on-demand pH-responsive units. When these multilayers are combined with a strong cationic capping layer that repels the passage of cationic probes, a pH-gateable rectified transport of anions is observed. Concomitantly, we also observed that these functional properties are significantly affected when multilayers are subjected to extensive pH cycling as a consequence of irreversible morphological changes taking place in the film. We envision that the synergy derived from combining weak and strong interactions within the same multilayer will play a key role in the construction of new interfacial architectures displaying tailorable ion transport properties.

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

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.

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.

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.

Nature of the water/aromatic parallel alignment interactions.

PubMed

Mitoraj, Mariusz P; Janjić, Goran V; Medaković, Vesna B; Veljković, Dušan Ž; Michalak, Artur; Zarić, Snežana D; Milčić, Miloš K

2015-01-30

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE(CCSD)(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O-H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.

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.

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…

Modifications in nanoparticle-protein interactions by varying the protein conformation

NASA Astrophysics Data System (ADS)

Kumar, Sugam; Yadav, I.; Aswal, V. K.; Kohlbrecher, J.

2017-05-01

Small-angle neutron scattering has been used to study the interaction of silica nanoparticle with Bovine Serum Albumin (BSA) protein without and with a protein denaturing agent urea. The measurements have been carried out at pH 7 where both the components (nanoparticle and protein) are similarly charged. We show that the interactions in nanoparticle-protein system can be modified by changing the conformation of protein through the presence of urea. In the absence of urea, the strong electrostatic repulsion between the nanoparticle and protein prevents protein adsorption on nanoparticle surface. This non-adsorption, in turn gives rise to depletion attraction between nanoparticles. However, with addition of urea the depletion attraction is completely suppressed. Urea driven denaturation of protein is utilized to expose the positively charged patched of the BSA molecules which eventually leads to adsorption of BSA on nanoparticles eliminating the depletion interaction.

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.

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.

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.

IgG1 adsorption to siliconized glass vials-influence of pH, ionic strength, and nonionic surfactants.

PubMed

Höger, Kerstin; Mathes, Johannes; Frieß, Wolfgang

2015-01-01

In this study, the adsorption of an IgG1 antibody to siliconized vials was investigated with focus on the formulation parameters pH, ionic strength, and nonionic surfactants. Electrophoretic mobility measurements were performed to investigate the charge characteristics of protein and siliconized glass particles at different pH values. Calculation of the electrokinetic charge density allowed further insight into the energetic conditions in the protein-sorbent interface. Maximum adsorption of IgG1 was found at acidic pH values and could be correlated with energetically favorable minimal ion incorporation into the interface. The importance of electrostatic interactions for IgG1 adsorption at acidic pH values was also confirmed by the efficient adsorption reduction at decreased solution ionic strength. A second adsorption maximum around the pI of the protein was assigned to hydrophobic interactions with the siliconized surface. Addition of the nonionic surfactants poloxamer 188 or polysorbate 80 resulted in almost complete suppression of adsorption at pH 7.2, and a strong but less efficient effect at pH 4 on siliconized glass vials. This adsorption suppression was much less pronounced on borosilicate glass vials. From these results, it can be concluded that electrostatic interactions contribute substantially to IgG1 adsorption to siliconized glass vials especially at acidic formulation pH. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Varieties of charge distributions in coat proteins of ssRNA+  viruses

NASA Astrophysics Data System (ADS)

Lošdorfer Božič, Anže; Podgornik, Rudolf

2018-01-01

A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong pH- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+  viruses. We examine the pH-dependent interplay of charge on both tails and CPs alike, and show that—in contrast to the charge on the CPs—the net positive charge on the N-tails persists even to very basic pH values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.

Quantum simulation of a Fermi-Hubbard model using a semiconductor quantum dot array.

PubMed

Hensgens, T; Fujita, T; Janssen, L; Li, Xiao; Van Diepen, C J; Reichl, C; Wegscheider, W; Das Sarma, S; Vandersypen, L M K

2017-08-02

Interacting fermions on a lattice can develop strong quantum correlations, which are the cause of the classical intractability of many exotic phases of matter. Current efforts are directed towards the control of artificial quantum systems that can be made to emulate the underlying Fermi-Hubbard models. Electrostatically confined conduction-band electrons define interacting quantum coherent spin and charge degrees of freedom that allow all-electrical initialization of low-entropy states and readily adhere to the Fermi-Hubbard Hamiltonian. Until now, however, the substantial electrostatic disorder of the solid state has meant that only a few attempts at emulating Fermi-Hubbard physics on solid-state platforms have been made. Here we show that for gate-defined quantum dots this disorder can be suppressed in a controlled manner. Using a semi-automated and scalable set of experimental tools, we homogeneously and independently set up the electron filling and nearest-neighbour tunnel coupling in a semiconductor quantum dot array so as to simulate a Fermi-Hubbard system. With this set-up, we realize a detailed characterization of the collective Coulomb blockade transition, which is the finite-size analogue of the interaction-driven Mott metal-to-insulator transition. As automation and device fabrication of semiconductor quantum dots continue to improve, the ideas presented here will enable the investigation of the physics of ever more complex many-body states using quantum dots.

The effect of controlled release of PDGF-BB from heparin-conjugated electrospun PCL/gelatin scaffolds on cellular bioactivity and infiltration

PubMed Central

Lee, Jongman; Yoo, James J.; Atala, Anthony; Lee, Sang Jin

2013-01-01

Heparin-conjugated electrospun poly(ε-caprolactone) (PCL)/gelatin scaffolds were developed to provide controlled release of platelet-derived growth factor-BB (PDGF-BB) and allow prolonged bioactivity of this molecule. A mixture of PCL and gelatin was electrospun into three different morphologies. Next, heparin molecules were conjugated to the reactive surface of the scaffolds. This heparin-conjugated scaffold allowed the immobilization of PDGF-BB via electrostatic interaction. In vitro PDGF-BB release profiles indicated that passive physical adsorption of PDGF-BB to non-heparinized scaffolds resulted in an initial burst release of PDGF-BB within 5 days, which then leveled off. However, electrostatic interaction between PDGF-BB and the heparin-conjugated scaffolds gave rise to a sustained release of PDGF-BB over the course of 20 days without an initial burst. Moreover, PDGF-BB that was strongly bound to the heparin-conjugated scaffolds enhanced smooth muscle cell (SMC) proliferation. In addition, scaffolds composed of 3.0 µm diameter fibers that were immobilized with PDGF-BB accelerated SMC infiltration into the scaffold when compared to scaffolds composed of smaller diameter fibers or scaffolds that did not release PDGF-BB. We concluded that the combination of the large pore structure in the scaffolds and the heparin-mediated delivery of PDGF-BB provided the most effective cellular interactions through synergistic physical and chemical cues. PMID:22770570

Phase transition transistors based on strongly-correlated materials

NASA Astrophysics Data System (ADS)

Nakano, Masaki

2013-03-01

The field-effect transistor (FET) provides electrical switching functions through linear control of the number of charges at a channel surface by external voltage. Controlling electronic phases of condensed matters in a FET geometry has long been a central issue of physical science. In particular, FET based on a strongly correlated material, namely ``Mott transistor,'' has attracted considerable interest, because it potentially provides gigantic and diverse electronic responses due to a strong interplay between charge, spin, orbital and lattice. We have investigated electric-field effects on such materials aiming at novel physical phenomena and electronic functions originating from strong correlation effects. Here we demonstrate electrical switching of bulk state of matter over the first-order metal-insulator transition. We fabricated FETs based on VO2 with use of a recently developed electric-double-layer transistor technique, and found that the electrostatically induced carriers at a channel surface drive all preexisting localized carriers of 1022 cm-3 even inside a bulk to motion, leading to bulk carrier delocalization beyond the electrostatic screening length. This non-local switching of bulk phases is achieved with just around 1 V, and moreover, a novel non-volatile memory like character emerges in a voltage-sweep measurement. These observations are apparently distinct from those of conventional FETs based on band insulators, capturing the essential feature of collective interactions in strongly correlated materials. This work was done in collaboration with K. Shibuya, D. Okuyama, T. Hatano, S. Ono, M. Kawasaki, Y. Iwasa, and Y. Tokura. This work was supported by the Japan Society for the Promotion of Science (JSAP) through its ``Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program).''

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

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.

The ‘non-Coulombic’ character of classical electrostatic interaction between charges near interfaces

NASA Astrophysics Data System (ADS)

Gabovich, A. M.; Voitenko, A. I.

2018-07-01

The textbook problem of classical electrostatics concerning the charge–charge interaction energy W in a two-layer system is revisited. In particular, the actual dependence of W on the horizontal distance L between the charges located at the same distance x from the interface is shown to substantially differ from the original Coulomb law due to image charges. The deviations are governed by the ratio L/x and the ratio between the dielectric constants of adjacent media. Thus, the dependence W(L) is never conventionally Coulombic (∼L ‑1) and may even be close to a dipole–dipole one (∼L ‑3). Although these results are implicitly contained in the well-known formulas, they are often overlooked while teaching electrostatics. The results are of interest not only from a purely academic viewpoint but are important for modern surface science, where the electrostatic contribution to the ion–ion interaction is often treated as Coulombic without any reservations.

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.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

PubMed

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Multiple internalization pathways of polyelectrolyte multilayer capsules into mammalian cells.

PubMed

Kastl, Lena; Sasse, Daniel; Wulf, Verena; Hartmann, Raimo; Mircheski, Josif; Ranke, Christiane; Carregal-Romero, Susana; Martínez-López, José Antonio; Fernández-Chacón, Rafael; Parak, Wolfgang J; Elsasser, Hans-Peter; Rivera Gil, Pilar

2013-08-27

Polyelectrolyte multilayer (PEM) capsules are carrier vehicles with great potential for biomedical applications. With the future aim of designing biocompatible, effective therapeutic delivery systems (e.g., for cancer), the pathway of internalization (uptake and fate) of PEM capsules was investigated. In particular the following experiments were performed: (i) the study of capsule co-localization with established endocytic markers, (ii) switching-off endocytotic pathways with pharmaceutical/chemical inhibitors, and (iii) characterization and quantification of capsule uptake with confocal and electron microscopy. As result, capsules co-localized with lipid rafts and with phagolysosomes, but not with other endocytic vesicles. Chemical interference of endocytosis with chemical blockers indicated that PEM capsules enter the investigated cell lines through a mechanism slightly sensitive to electrostatic interactions, independent of clathrin and caveolae, and strongly dependent on cholesterol-rich domains and organelle acidification. Microscopic characterization of cells during capsule uptake showed the formation of phagocytic cups (vesicles) to engulf the capsules, an increased number of mitochondria, and a final localization in the perinuclear cytoplasma. Combining all these indicators we conclude that PEM capsule internalization in general occurs as a combination of different sequential mechanisms. Initially, an adsorptive mechanism due to strong electrostatic interactions governs the stabilization of the capsules at the cell surface. Membrane ruffling and filopodia extensions are responsible for capsule engulfing through the formation of a phagocytic cup. Co-localization with lipid raft domains activates the cell to initiate a lipid-raft-mediated macropinocytosis. Internalization vesicles are very acidic and co-localize only with phagolysosome markers, excluding caveolin-mediated pathways and indicating that upon phagocytosis the capsules are sorted to heterophagolysosomes.

Poloidal rotation driven by nonlinear momentum transport in strong electrostatic turbulence

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

Wang, Lu; Wen, Tiliang; Diamond, P. H.

2016-08-11

Virtually, all existing theoretical works on turbulent poloidal momentum transport are based on quasilinear theory. Nonlinear poloidal momentum flux—more » $$\\langle {{\\tilde{v}}_{r}}\\tilde{n}{{\\tilde{v}}_{\\theta}}\\rangle $$ is universally neglected. However, in the strong turbulence regime where relative fluctuation amplitude is no longer small, quasilinear theory is invalid. This is true at the all-important plasma edge. In this work, nonlinear poloidal momentum flux $$\\langle {{\\tilde{v}}_{r}}\\tilde{n}{{\\tilde{v}}_{\\theta}}\\rangle $$ in strong electrostatic turbulence is calculated using the Hasegawa–Mima equation, and is compared with quasilinear poloidal Reynolds stress. A novel property is that symmetry breaking in fluctuation spectrum is not necessary for a nonlinear poloidal momentum flux. This is fundamentally different from the quasilinear Reynold stress. Furthermore, the comparison implies that the poloidal rotation drive from the radial gradient of nonlinear momentum flux is comparable to that from the quasilinear Reynolds force. Nonlinear poloidal momentum transport in strong electrostatic turbulence is thus not negligible for poloidal rotation drive, and so may be significant to transport barrier formation.« less

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.

Influence of Hofmeister ions on the structure of proline-based peptide models: A combined experimental and molecular modeling study

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

Brohl, Andreas; Albrecht, Benjamin; Zhang, Yong

Here, the influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are alsomore » able to stabilize the conformers over wide temperature ranges.« less

Influence of Hofmeister Ions on the Structure of Proline-Based Peptide Models: A Combined Experimental and Molecular Modeling Study.

PubMed

Bröhl, Andreas; Albrecht, Benjamin; Zhang, Yong; Maginn, Edward; Giernoth, Ralf

2017-03-09

The influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are also able to stabilize the conformers over wide temperature ranges.

Influence of Hofmeister ions on the structure of proline-based peptide models: A combined experimental and molecular modeling study

DOE PAGES

Brohl, Andreas; Albrecht, Benjamin; Zhang, Yong; ...

2017-02-13

Here, the influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are alsomore » able to stabilize the conformers over wide temperature ranges.« less

Electrostatics Control Actin Filament Nucleation and Elongation Kinetics*

PubMed Central

Crevenna, Alvaro H.; Naredi-Rainer, Nikolaus; Schönichen, André; Dzubiella, Joachim; Barber, Diane L.; Lamb, Don C.; Wedlich-Söldner, Roland

2013-01-01

The actin cytoskeleton is a central mediator of cellular morphogenesis, and rapid actin reorganization drives essential processes such as cell migration and cell division. Whereas several actin-binding proteins are known to be regulated by changes in intracellular pH, detailed information regarding the effect of pH on the actin dynamics itself is still lacking. Here, we combine bulk assays, total internal reflection fluorescence microscopy, fluorescence fluctuation spectroscopy techniques, and theory to comprehensively characterize the effect of pH on actin polymerization. We show that both nucleation and elongation are strongly enhanced at acidic pH, with a maximum close to the pI of actin. Monomer association rates are similarly affected by pH at both ends, although dissociation rates are differentially affected. This indicates that electrostatics control the diffusional encounter but not the dissociation rate, which is critical for the establishment of actin filament asymmetry. A generic model of protein-protein interaction, including electrostatics, explains the observed pH sensitivity as a consequence of charge repulsion. The observed pH effect on actin in vitro agrees with measurements of Listeria propulsion in pH-controlled cells. pH regulation should therefore be considered as a modulator of actin dynamics in a cellular environment. PMID:23486468

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

Kinetic recognition of the retinoblastoma tumor suppressor by a specific protein target.

PubMed

Chemes, Lucía B; Sánchez, Ignacio E; de Prat-Gay, Gonzalo

2011-09-16

The retinoblastoma tumor suppressor (Rb) plays a key role in cell cycle control and is linked to various types of human cancer. Rb binds to the LxCxE motif, present in a number of cellular and viral proteins such as AdE1A, SV40 large T-antigen and human papillomavirus (HPV) E7, all instrumental in revealing fundamental mechanisms of tumor suppression, cell cycle control and gene expression. A detailed kinetic study of RbAB binding to the HPV E7 oncoprotein shows that an LxCxE-containing E7 fragment binds through a fast two-state reaction strongly favored by electrostatic interactions. Conversely, full-length E7 binds through a multistep process involving a pre-equilibrium between E7 conformers, a fast electrostatically driven association step guided by the LxCxE motif and a slow conformational rearrangement. This kinetic complexity arises from the conformational plasticity and intrinsically disordered nature of E7 and from multiple interaction surfaces present in both proteins. Affinity differences between E7N domains from high- and low-risk types are explained by their dissociation rates. In fact, since Rb is at the center of a large protein interaction network, fast and tight recognition provides an advantage for disruption by the viral proteins, where the balance of physiological and pathological interactions is dictated by kinetic ligand competition. The localization of the LxCxE motif within an intrinsically disordered domain provides the fast, diffusion-controlled interaction that allows viral proteins to outcompete physiological targets. We describe the interaction mechanism of Rb with a protein ligand, at the same time an LxCxE-containing model target, and a paradigmatic intrinsically disordered viral oncoprotein. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Lattice model of ionic liquid confined by metal electrodes

NASA Astrophysics Data System (ADS)

Girotto, Matheus; Malossi, Rodrigo M.; dos Santos, Alexandre P.; Levin, Yan

2018-05-01

We study, using Monte Carlo simulations, the density profiles and differential capacitance of ionic liquids confined by metal electrodes. To compute the electrostatic energy, we use the recently developed approach based on periodic Green's functions. The method also allows us to easily calculate the induced charge on the electrodes permitting an efficient implementation of simulations in a constant electrostatic potential ensemble. To speed up the simulations further, we model the ionic liquid as a lattice Coulomb gas and precalculate the interaction potential between the ions. We show that the lattice model captures the transition between camel-shaped and bell-shaped capacitance curves—the latter characteristic of ionic liquids (strong coupling limit) and the former of electrolytes (weak coupling). We observe the appearance of a second peak in the differential capacitance at ≈0.5 V for 2:1 ionic liquids, as the packing fraction is increased. Finally, we show that ionic size asymmetry decreases substantially the capacitance maximum, when all other parameters are kept fixed.

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

Polyvinylpyrrolidone stabilized-Ru nanoclusters loaded onto reduced graphene oxide as high active catalyst for hydrogen evolution

NASA Astrophysics Data System (ADS)

Zhang, Jiao; Hao, Jinghao; Ma, Qianli; Li, Chuanqi; Liu, Yushan; Li, Baojun; Liu, Zhongyi

2017-06-01

Ruthenium/reduced graphene oxide nanocomposites (Ru/rGO NCs) were synthesized via an electrostatic self-assembly approach. Polyvinylpyrrolidone (PVP) stabilized and positively charged metallic ruthenium nanoclusters about 1.2 nm were synthesized and uniformly loaded onto negatively charged graphene oxide (GO) sheets via strong electrostatic interactions. The as-prepared Ru/rGO NCs exhibited superior performance in catalytic hydrolysis of sodium borohydride (NaBH4) to generate H2. The hydrogen generation rate was up to 14.87 L H2 min-1 gcat -1 at 318 K with relatively low activation energy of 38.12 kJ mol-1. Kinetics study confirmed that the hydrolysis of NaBH4 was first order with respect to concentration of catalysts. Besides, the conversion of NaBH4 remained at 97% and catalytic activity retained more than 70% after 5 reaction cycles at room temperature. These results suggested that the Ru/rGO NCs have a promising prospect in the field of clean energy.

Structure evolution of gelatin particles induced by pH and ionic strength.

PubMed

Xu, Jing; Li, Tianduo; Tao, Furong; Cui, Yuezhi; Xia, Yongmei

2013-03-01

Microstructure of gelatin particles played a key role in determining the physicochemical properties of gelatin. Ionic strength and pH as systematic manners were considered to affect gelatin particles structure on the micrometer scale. Scanning electron microscopy was used for depicting the morphologies of gelatin particles. Increasing pH to 10.0 or decreasing pH to 4.0, spherical, spindle, and irregular aggregates of gelatin particles at 2, 6, 10, and 14% solution (w/w) were all transformed to spindle aggregates. When NaCl was added to the system, the molecular chains of gelatin possibly rearranged themselves in a stretched state, and the ribbon aggregates was observed. The structural transitions of gelatin aggregates were strongly depended on the electrostatic repulsion. In the gelatin-sodium dodecyl sulfate (SDS) case, the micrometer scale of aggregates was larger and the different degrees of cross-links were induced through hydrophobic interaction and electrostatic repulsion. Copyright © 2012 Wiley Periodicals, Inc.

ATP-induced noncooperative thermal unfolding of hen lysozyme

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

Liu, Honglin; Yin, Peidong; He, Shengnan

To understand the role of ATP underlying the enhanced amyloidosis of hen egg white lysozyme (HEWL), the synchrotron radiation circular dichroism, combined with tryptophan fluorescence, dynamic light-scattering, and differential scanning calorimetry, is used to examine the alterations of the conformation and thermal unfolding pathway of the HEWL in the presence of ATP, Mg{sup 2+}-ATP, ADP, AMP, etc. It is revealed that the binding of ATP to HEWL through strong electrostatic interaction changes the secondary structures of HEWL and makes the exposed residue W62 move into hydrophobic environments. This alteration of W62 decreases the {beta}-domain stability of HEWL, induces a noncooperativemore » unfolding of the secondary structures, and produces a partially unfolded intermediate. This intermediate containing relatively rich {alpha}-helix and less {beta}-sheet structures has a great tendency to aggregate. The results imply that the ease of aggregating of HEWL is related to the extent of denaturation of the amyloidogenic region, rather than the electrostatic neutralizing effect or monomeric {beta}-sheet enriched intermediate.« less

Controlled Growth of Gigantic Swirls in a Laboratory Magnetosphere

NASA Astrophysics Data System (ADS)

Worstell, M. W.; Mauel, M. E.; Roberts, T. M.

2012-10-01

Space and laboratory plasma confined by a strong magnetic field have remarkable properties. Low frequency mixing of the plasma occurs through the interchange of long plasma-filled tubes aligned with the magnetic field. The plasma dynamics becomes two-dimensional because these tubes can only move radially or circulate around the poles of the magnetic dipole. Studies of turbulent interchange dynamics made using the Collisionless Terella Experiment (CTX) show that turbulence appears as chaotic time-varying modes with broad global mode structures that interact nonlinearly and form an inverse cascade.footnotetextB.A. Grierson, M.W. Worstell, M.E. Mauel, Phys. Plasmas 16 055902 (2009) When we drive vortex mixing through the application of electrostatic bias to multiple probes, we break the rotational symmetry of the plasma and small vortex tubes are seen to drive larger ``gigantic'' swirls. Statistical analysis of the time-evolving spectra and measurement of the bicoherence of the turbulence show an increase of three wave coupling during non-axisymmetric electrostatic drive of the probe array.

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.

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.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

PubMed

Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

2017-10-01

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

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.

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.

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.

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.

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.

Computational study of the RGD-peptide interactions with perovskite-type BFO-(1 1 1) membranes under aqueous conditions

NASA Astrophysics Data System (ADS)

Li, Hai-long; Bian, Liang; Hou, Wen-ping; Dong, Fa-Qin; Song, Mian-Xin; Zhang, Xiao-yan; Wang, Li-sheng

2016-07-01

We elucidated a number of facets regarding arginine-glycine-aspartate (RGD)-bismuth ferrite (BFO)-(1 1 1) membrane interactions and reactivity that have previously remained unexplored on a molecular level. Results demonstrate the intra-molecular interaction facilitates a ;horseshoe; structure of RGD adsorbed onto the BFO-(1 1 1) membrane, through the electrostatic (Asp-cation-Fe) and water-bridge (Osbnd H2O and H2Osbnd NH2) interactions. The effect of structural and electron-transfer interactions is attributed to the cation-valences, indicating that the divalent cations are electron-acceptors and the monovalent cations as electron-donors. Notably, the strongly bound Ca2+ ion exerts a ;gluing; effect on the Asp-side-chain, indicating a tightly packed RGD-BFO configuration. Thus, modulating the biological response of BFO-(1 1 1) membrane will allow us to design more appropriate interfaces for implantable diagnostic and therapeutic perovskite-type micro-devices.

A POSS based hydrogel with mechanical robustness, cohesiveness and a rapid self-healing ability by electrostatic interaction.

PubMed

Pu, Wanfen; Jiang, Feng; Chen, Pei; Wei, Bing

2017-08-30

A molecularly dispersed nano-material called POSS-NH 2 -AA was synthesized to construct a hybrid hydrogel with a rapid self-healing ability (stress 8 kPa) and excellent mechanical performance (a strain of 4683% and a stress of 37.8 kPa). The hydrogel also exhibits good cohesiveness to materials, such as plastics, glass and iron. The backbone of the POSS makes the hydrogel much stronger than the hydrogel without POSS, which accounts for the improvement in its properties. This process is facile and useful to construct mechanically strong and self-healable materials.

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.

Electrostatic quadrupole array for focusing parallel beams of charged particles

DOEpatents

Brodowski, John

1982-11-23

An array of electrostatic quadrupoles, capable of providing strong electrostatic focusing simultaneously on multiple beams, is easily fabricated from a single array element comprising a support rod and multiple electrodes spaced at intervals along the rod. The rods are secured to four terminals which are isolated by only four insulators. This structure requires bias voltage to be supplied to only two terminals and eliminates the need for individual electrode bias and insulators, as well as increases life by eliminating beam plating of insulators.

Effect of ionic strength on the interfacial viscoelasticity and stability of silk fibroin at the oil/water interface.

PubMed

Tang, Xiaoxiao; Qiao, Xiuying; Miller, Reinhard; Sun, Kang

2016-12-01

The amphiphilic character and surface activity endows silk fibroin with the ability to reside at fluid interfaces and effectively stabilize emulsions. However, the influence of relevant factors and their actual effect on the interfacial viscoelasticity and stability of silk fibroin at the oil/water interface has received less attention. In the present study, the effect of ionic strength on the interfacial viscoelasticity, emulsification effectiveness and stability of silk fibroin at the oil/water interface was investigated in detail. A higher ion concentration facilitates greater adsorption, stronger molecular interaction and faster structure reorganization of silk fibroin at the oil/water interface, thus causing quicker interfacial saturation adsorption, greater interfacial strength and lower interfacial structural fracture on large deformation. However, the presence of concentrated ions screens the charges in silk fibroin molecules and the zeta potential decreases as a result of electrostatic screening and ion-binding effects, which may result in emulsion droplet coalescence and a decrease in emulsion stability. The positively-charged ions significantly affect the interfacial elasticity and stability of silk fibroin layers at the oil/water interface as a result of the strong electrostatic interactions between counter-ions and the negatively-charged groups of silk fibroin. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

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

Effects of ionic strength and sugars on the aggregation propensity of monoclonal antibodies: influence of colloidal and conformational stabilities.

PubMed

Saito, Shuntaro; Hasegawa, Jun; Kobayashi, Naoki; Tomitsuka, Toshiaki; Uchiyama, Susumu; Fukui, Kiichi

2013-05-01

To develop a general strategy for optimizing monoclonal antibody (MAb) formulations. Colloidal stabilities of four representative MAbs solutions were assessed based on the second virial coefficient (B 2) at 20°C and 40°C, and net charges at different NaCl concentrations, and/or in the presence of sugars. Conformational stabilities were evaluated from the unfolding temperatures. The aggregation propensities were determined at 40°C and after freeze-thawing. The electrostatic potential of antibody surfaces was simulated for the development of rational formulations. Similar B 2 values were obtained at 20°C and 40°C, implying little dependence on temperature. B 2 correlated quantitatively with aggregation propensities at 40°C. The net charge partly correlated with colloidal stability. Salts stabilized or destabilized MAbs, depending on repulsive or attractive interactions. Sugars improved the aggregation propensity under freeze-thaw stress through improved conformational stability. Uneven and even distributions of potential surfaces were attributed to attractive and strong repulsive electrostatic interactions. Assessment of colloidal stability at the lowest ionic strength is particularly effective for the development of formulations. If necessary, salts are added to enhance the colloidal stability. Sugars further improved aggregation propensities by enhancing conformational stability. These behaviors are rationally predictable according to the surface potentials of MAbs.

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.

Role of electrostatic interactions in the toxicity of titanium dioxide nanoparticles toward Escherichia coli.

PubMed

Pagnout, Christophe; Jomini, Stéphane; Dadhwal, Mandeep; Caillet, Céline; Thomas, Fabien; Bauda, Pascale

2012-04-01

The increasing production and use of titanium dioxide nanoparticles (NP-TiO(2)) has led to concerns about their possible impact on the environment. Bacteria play crucial roles in ecosystem processes and may be subject to the toxicity of these nanoparticles. In this study, we showed that at low ionic strength, the cell viability of Escherichia coli was more severely affected at pH 5.5 than at pH 7.0 and pH 9.5. At pH 5.5, nanoparticles (positively charged) strongly interacted with the bacterial cells (negatively charged) and accumulated on their surfaces. This phenomenon was observed in a much lower degree at pH 7.0 (NP-TiO(2) neutrally charged and cells negatively charged) and pH 9.5 (both NP-TiO(2) and cells negatively charged). It was also shown that the addition of electrolytes (NaCl, CaCl(2), Na(2)SO(4)) resulted in a gradual reduction of the NP-TiO(2) toxicity at pH 5.5 and an increase in this toxicity at pH 9.5, which was closely related to the reduction of the NP-TiO(2) and bacterial cell electrostatic charges. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

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.

Poisson-Boltzmann theory of the charge-induced adsorption of semi-flexible polyelectrolytes.

PubMed

Ubbink, Job; Khokhlov, Alexei R

2004-03-15

A model is suggested for the structure of an adsorbed layer of a highly charged semi-flexible polyelectrolyte on a weakly charged surface of opposite charge sign. The adsorbed phase is thin, owing to the effective reversal of the charge sign of the surface upon adsorption, and ordered, owing to the high surface density of polyelectrolyte strands caused by the generally strong binding between polyelectrolyte and surface. The Poisson-Boltzmann equation for the electrostatic interaction between the array of adsorbed polyelectrolytes and the charged surface is solved for a cylindrical geometry, both numerically, using a finite element method, and analytically within the weak curvature limit under the assumption of excess monovalent salt. For small separations, repulsive surface polarization and counterion osmotic pressure effects dominate over the electrostatic attraction and the resulting electrostatic interaction curve shows a minimum at nonzero separations on the Angstrom scale. The equilibrium density of the adsorbed phase is obtained by minimizing the total free energy under the condition of equality of chemical potential and osmotic pressure of the polyelectrolyte in solution and in the adsorbed phase. For a wide range of ionic conditions and charge densities of the charged surface, the interstrand separation as predicted by the Poisson-Boltzmann model and the analytical theory closely agree. For low to moderate charge densities of the adsorbing surface, the interstrand spacing decreases as a function of the charge density of the charged surface. Above about 0.1 M excess monovalent salt, it is only weakly dependent on the ionic strength. At high charge densities of the adsorbing surface, the interstrand spacing increases with increasing ionic strength, in line with the experiments by Fang and Yang [J. Phys. Chem. B 101, 441 (1997)]. (c) 2004 American Institute of Physics.

Polyelectrolytes and Their Biological Interactions

PubMed Central

Katchalsky, A.

1964-01-01

Polyelectrolytes are water-soluble electrically charged polymers. Their properties are determined by the interplay of the electrical forces, the Brownian motion of the macromolecular chain, and intermolecular Van der Waals forces. Charged polyacids or polybases are stretched by the electrostatic forces, as evidenced by increase in solution viscosity, or by the stretching of polyelectrolyte gels. The electrical field of the polyions is neutralized by a dense atmosphere of counter-ions. The counter-ion attraction to the polyions is expressed by a reduction of the osmotic activity of the polyion—the osmotic pressure being only 15 to 20 per cent of the ideal in highly charged polyelectrolytes neutralized by monovalent counter-ions, and as low as 1 to 3 per cent of the ideal for polyvalent counter-ions. Since the ionic atmosphere is only slightly dependent on added low molecular salt, the osmotic pressure of polyelectrolyte salt mixtures is approximately equal to the sum of the osmotic pressure of polyelectrolyte and salt alone. Acidic and basic polyelectrolytes interact electrostatically with precipitation at the point of polymeric electroneutrality. At higher salt concentrations the interaction is inhibited by the screening of polymeric fixed charges. The importance of these interactions in enzymatic processes is discussed. The electrical double layer is polarizable as may be deduced from dielectric and conductometric studies. The polarizability leads to strong dipole formation in an electrical field. These macromolecular dipoles may play a role in the adsorption of polyelectrolytes on charged surfaces. The final part of the paper is devoted to interactions of polyelectrolytes with cell membranes and the gluing of cells to higher aggregates by charged biocolloids. ImagesFigure 17Figure 18Figure 19Figure 20 PMID:14104085

Analysis of the mechanism of nucleosome survival during transcription

PubMed Central

Chang, Han-Wen; Kulaeva, Olga I.; Shaytan, Alexey K.; Kibanov, Mikhail; Kuznedelov, Konstantin; Severinov, Konstantin V.; Kirpichnikov, Mikhail P.; Clark, David J.; Studitsky, Vasily M.

2014-01-01

Maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that is likely required for nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. To evaluate these predictions, we analysed transcription through a nucleosome by different, structurally related RNA polymerases and mutant yeast Pol II having different histone-interacting surfaces that presumably stabilize the Ø-loop. The height of the nucleosomal barrier to transcription and efficiency of nucleosome survival correlate with the net negative charges of the histone-interacting surfaces. Molecular modeling and analysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient Ø-loop formation and nucleosome survival are mediated by electrostatic interactions between the largest subunit of Pol II and core histones. PMID:24234452

Spectroscopic and molecular modeling studies of the interaction between cytidine and human serum albumin and its analytical application.

PubMed

Cui, Fengling; Wang, Junli; Yao, Xiaojun; Wang, Li; Zhang, Qiangzhai; Qu, Guirong

In this study, the interaction between cytidine and human serum albumin (HSA) was investigated for the first time by fluorescence spectroscopy in combination with UV absorption spectrum and molecular modeling under simulative physiological conditions. Experimental results indicated that cytidine had a strong ability to quench the intrinsic fluorescence of human serum albumin. The binding constants (K) at different temperatures, thermodynamic parameter enthalpy changes (DeltaH) and entropy changes (DeltaS) of HSA-cytidine had been calculated according to the relevant fluorescence data, which indicated that the hydrophobic and electrostatic interactions played a major role, which was in agreement with the results of molecular modeling study. In addition, the effects of other ions on the binding constants were also studied. Furthermore, synchronous fluorescence technology was successfully applied to the determination of human serum albumin added into the cytidine solution.

Atomic basis for therapeutic activation of neuronal potassium channels

NASA Astrophysics Data System (ADS)

Kim, Robin Y.; Yau, Michael C.; Galpin, Jason D.; Seebohm, Guiscard; Ahern, Christopher A.; Pless, Stephan A.; Kurata, Harley T.

2015-09-01

Retigabine is a recently approved anticonvulsant that acts by potentiating neuronal M-current generated by KCNQ2-5 channels, interacting with a conserved Trp residue in the channel pore domain. Using unnatural amino-acid mutagenesis, we subtly altered the properties of this Trp to reveal specific chemical interactions required for retigabine action. Introduction of a non-natural isosteric H-bond-deficient Trp analogue abolishes channel potentiation, indicating that retigabine effects rely strongly on formation of a H-bond with the conserved pore Trp. Supporting this model, substitution with fluorinated Trp analogues, with increased H-bonding propensity, strengthens retigabine potency. In addition, potency of numerous retigabine analogues correlates with the negative electrostatic surface potential of a carbonyl/carbamate oxygen atom present in most KCNQ activators. These findings functionally pinpoint an atomic-scale interaction essential for effects of retigabine and provide stringent constraints that may guide rational improvement of the emerging drug class of KCNQ channel activators.

Dispersion of Co/CNTs via strong electrostatic adsorption method: Thermal treatment effect

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

Akbarzadeh, Omid, E-mail: omid.akbarzadeh63@gmail.com; Abdullah, Bawadi, E-mail: bawadi-abdullah@petronas.com.my; Subbarao, Duvvuri, E-mail: duvvuri-subbarao@petronas.com.my

The effect of different thermal treatment temperature on the structure of multi-walled carbon nanotubes (MWCNTs) and Co particle dispersion on CNTs support is studied using Strong electrostatic adsorption (SEA) method. The samples tested by N{sub 2}-adsorption, field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM). N{sub 2}-adsorption results showed BET surface area increased using thermal treatment and TEM images showed that increasing the thermal treatment temperature lead to flaky CNTs and defects introduced on the outer surface and Co particle dispersion increased.

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

Aggregation in charged nanoparticles solutions induced by different interactions

NASA Astrophysics Data System (ADS)

Abbas, S.; Kumar, Sugam; Aswal, V. K.; Kohlbrecher, J.

2016-05-01

Small-angle neutron scattering (SANS) has been used to study the aggregation of anionic silica nanoparticles as induced through different interactions. The nanoparticle aggregation is induced by addition of salt (NaCl), cationic protein (lysozyme) and non-ionic surfactant (C12E10) employing different kind of interactions. The results show that the interaction in presence of salt can be explained using DLVO theory whereas non-DLVO forces play important role for interaction of nanoparticles with protein and surfactant. The presence of salt screens the repulsion between charged nanoparticles giving rise to a net attraction in the DLVO potential. On the other hand, strong electrostatic attraction between nanoparticle and oppositely charged protein leads to protein-mediated nanoparticle aggregation. In case of non-ionic surfactant, the relatively long-range attractive depletion interaction is found to be responsible for the particle aggregation. Interestingly, the completely different interactions lead to similar kind of aggregate morphology. The nanoparticle aggregates formed are found to have mass fractal nature having a fractal dimension (~2.5) consistent with diffusion limited type of fractal morphology in all three cases.

Aggregation in charged nanoparticles solutions induced by different interactions

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

Abbas, S.; Kumar, Sugam; Aswal, V. K., E-mail: vkaswal@barc.gov.in

2016-05-23

Small-angle neutron scattering (SANS) has been used to study the aggregation of anionic silica nanoparticles as induced through different interactions. The nanoparticle aggregation is induced by addition of salt (NaCl), cationic protein (lysozyme) and non-ionic surfactant (C12E10) employing different kind of interactions. The results show that the interaction in presence of salt can be explained using DLVO theory whereas non-DLVO forces play important role for interaction of nanoparticles with protein and surfactant. The presence of salt screens the repulsion between charged nanoparticles giving rise to a net attraction in the DLVO potential. On the other hand, strong electrostatic attraction betweenmore » nanoparticle and oppositely charged protein leads to protein-mediated nanoparticle aggregation. In case of non-ionic surfactant, the relatively long-range attractive depletion interaction is found to be responsible for the particle aggregation. Interestingly, the completely different interactions lead to similar kind of aggregate morphology. The nanoparticle aggregates formed are found to have mass fractal nature having a fractal dimension (~2.5) consistent with diffusion limited type of fractal morphology in all three cases.« less

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.

Role of geometrical shape in like-charge attraction of DNA.

PubMed

Kuron, Michael; Arnold, Axel

2015-03-01

While the phenomenon of like-charge attraction of DNA is clearly observed experimentally and in simulations, mean-field theories fail to predict it. Kornyshev et al. argued that like-charge attraction is due to DNA's helical geometry and hydration forces. Strong-coupling (SC) theory shows that attraction of like-charged rods is possible through ion correlations alone at large coupling parameters, usually by multivalent counterions. However for SC theory to be applicable, counterion-counterion correlations perpendicular to the DNA strands need to be sufficiently small, which is not a priori the case for DNA even with trivalent counterions. We study a system containing infinitely long DNA strands and trivalent counterions by computer simulations employing varying degrees of coarse-graining. Our results show that there is always attraction between the strands, but its magnitude is indeed highly dependent on the specific shape of the strand. While discreteness of the charge distribution has little influence on the attractive forces, the role of the helical charge distribution is considerable: charged rods maintain a finite distance in equilibrium, while helices collapse to close contact with a phase shift of π, in full agreement with SC predictions. The SC limit is applicable because counterions strongly bind to the charged sites of the helices, so that helix-counterion interactions dominate over counterion-counterion interactions. Thus DNA's helical geometry is not crucial for like-charge DNA attraction, but strongly enhances it, and electrostatic interactions in the strong-coupling limit are sufficient to explain this attraction.

Quantum Hall signatures of dipolar Mahan excitons

NASA Astrophysics Data System (ADS)

Schinner, G. J.; Repp, J.; Kowalik-Seidl, K.; Schubert, E.; Stallhofer, M. P.; Rai, A. K.; Reuter, D.; Wieck, A. D.; Govorov, A. O.; Holleitner, A. W.; Kotthaus, J. P.

2013-01-01

We explore the photoluminescence of spatially indirect, dipolar Mahan excitons in a gated double quantum well diode containing a mesoscopic electrostatic trap for neutral dipolar excitons at low temperatures down to 250 mK and in quantizing magnetic fields. Mahan excitons in the surrounding of the trap, consisting of individual holes interacting with a degenerate two-dimensional electron system confined in one of the quantum wells, exhibit strong quantum Hall signatures at integer filling factors and related anomalies around filling factor ν=(2)/(3),(3)/(5), and (1)/(2), reflecting the formation of composite fermions. Interactions across the trap perimeter are found to influence the energy of the confined neutral dipolar excitons by the presence of the quantum Hall effects in the two-dimensional electron system surrounding the trap.

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

Laboratory evaluation of electrostatic spray wet scrubber to control particulate matter emissions from poultry facilities

USDA-ARS?s Scientific Manuscript database

Particulate matter (PM) is a major air pollutant emitted from animal production and has significant impacts on health and the environment. Abatement of PM emissions is imperative and effective PM control technologies are strongly needed. In this work, an electrostatic spray wet scrubber (ESWS) techn...

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

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.

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes.

PubMed

Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

2016-09-19

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.

PubMed

Beck, David A C; Armen, Roger S; Daggett, Valerie

2005-01-18

The correct treatment of van der Waals and electrostatic nonbonded interactions in molecular force fields is essential for performing realistic molecular dynamics (MD) simulations of solvated polypeptides. The most computationally tractable treatment of nonbonded interactions in MD utilizes a spherical distance cutoff (typically, 8-12 A) to reduce the number of pairwise interactions. In this work, we assess three spherical atom-based cutoff approaches for use with all-atom explicit solvent MD: abrupt truncation, a CHARMM-style electrostatic shift truncation, and our own force-shifted truncation. The chosen system for this study is an end-capped 17-residue alanine-based alpha-helical peptide, selected because of its use in previous computational and experimental studies. We compare the time-averaged helical content calculated from these MD trajectories with experiment. We also examine the effect of varying the cutoff treatment and distance on energy conservation. We find that the abrupt truncation approach is pathological in its inability to conserve energy. The CHARMM-style shift truncation performs quite well but suffers from energetic instability. On the other hand, the force-shifted spherical cutoff method conserves energy, correctly predicts the experimental helical content, and shows convergence in simulation statistics as the cutoff is increased. This work demonstrates that by using proper and rigorous techniques, it is possible to correctly model polypeptide dynamics in solution with a spherical cutoff. The inherent computational advantage of spherical cutoffs over Ewald summation (and related) techniques is essential in accessing longer MD time scales.

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.

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.

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.

Effects of imidazolium-based ionic liquids on the stability and dynamics of gramicidin A and lipid bilayers at different salt concentrations.

PubMed

Lee, Hwankyu; Kim, Sun Min; Jeon, Tae-Joon

2015-09-01

Gramicidin A (gA) dimers with bilayers, which consist of phospholipids and ionic liquids (ILs) at different molar ratios, were simulated at different salt concentrations of 0.15 and 1M NaCl. Bilayer thickness is larger than the length of a gA dimer, and hence lipids around the gA dimer are significantly disordered to adapt to the gA dimer, yielding membrane curvature. As the IL concentration increases, the bilayer thickness decreases and becomes closer to the gA length, leading to less membrane curvature. Also, ILs significantly increase lateral diffusivities of the gA dimer and lipids at 0.15M NaCl, but not at 1M NaCl because strong electrostatic interactions between salt ions and lipid head groups suppress an increase in the lateral mobility of the bilayer at high salt concentration. These findings help explain the conflicting experimental results that showed the increased ion permeability in electrophysiological experiments at 1M NaCl, but the reduced ion permeability in fluorescent experiments at 0.15M NaCl. ILs disorder lipids and make bilayers thinner, which yields less membrane curvature around the gA dimer and thus stabilizes the gA dimer, leading to the increased ion permeability. This IL effect predominantly occurs at 1M NaCl, where ILs only slightly increase the bilayer dynamics because of the strong electrostatic interactions between salt ions and lipids. In contrast, at 0.15M NaCl, ILs do not only stabilize the curved bilayer but also significantly increase the lateral mobility of gA dimers and lipids, which can reduce gA-induced pore formation, leading to the decreased ion permeability. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Nonlinear Electrostatic Steepening of Whistler Waves: The Guiding Factors and Dynamics in Inhomogeneous Systems

NASA Astrophysics Data System (ADS)

Agapitov, O.; Drake, J. F.; Vasko, I.; Mozer, F. S.; Artemyev, A.; Krasnoselskikh, V.; Angelopoulos, V.; Wygant, J.; Reeves, G. D.

2018-03-01

Whistler mode chorus waves are particularly important in outer radiation belt dynamics due to their key role in controlling the acceleration and scattering of electrons over a very wide energy range. The efficiency of wave-particle resonant interactions is defined by whistler wave properties which have been described by the approximation of plane linear waves propagating through the cold plasma of the inner magnetosphere. However, recent observations of extremely high-amplitude whistlers suggest the importance of nonlinear wave-particle interactions for the dynamics of the outer radiation belt. Oblique chorus waves observed in the inner magnetosphere often exhibit drastically nonsinusoidal (with significant power in the higher harmonics) waveforms of the parallel electric field, presumably due to the feedback from hot resonant electrons. We have considered the nature and properties of such nonlinear whistler waves observed by the Van Allen Probes and Time History of Events and Macroscale Interactions define during Substorms in the inner magnetosphere, and we show that the significant enhancement of the wave electrostatic component can result from whistler wave coupling with the beam-driven electrostatic mode through the resonant interaction with hot electron beams. Being modulated by a whistler wave, the electron beam generates a driven electrostatic mode significantly enhancing the parallel electric field of the initial whistler wave. We confirm this mechanism using a self-consistent particle-in-cell simulation. The nonlinear electrostatic component manifests properties of the beam-driven electron acoustic mode and can be responsible for effective electron acceleration in the inhomogeneous magnetic field.

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.

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.

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

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.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Kinetics of aggregation in charged nanoparticle solutions driven by different mechanisms

NASA Astrophysics Data System (ADS)

Abbas, S.; Yadav, I.; Kumar, Sugam; Aswal, V. K.; Kohlbrecher, J.

2017-05-01

The structure and kinetics during aggregation of anionic silica nanoparticles as induced through different mechanisms have been studied by dynamic light scattering (DLS) and small-angle neutron scattering (SANS). Three different additives, namely an electrolyte (NaCl), cationic protein (lysozyme) and non-ionic surfactant (C12E10) were used to initiate nanoparticle aggregation. Electrolyte induced aggregation can be explained by DLVO interaction, whereas depletion interaction (non-DLVO interaction) is found responsible for nanoparticle aggregation in case of non-ionic surfactant. Unlike these two cases, strong electrostatic attraction between nanoparticle and oppositely charged protein results into protein-mediated nanoparticle aggregation. The electrolyte induced aggregation show quite slow aggregation rate whereas protein mediated as well as surfactant induced aggregation takes place almost instantaneously. The significant differences observed in the kinetics are explained based on range of interactions responsible for the aggregation. In spite of differences in mechanism and kinetics, the nanoparticle clusters are found to have similar fractal morphology (fractal dimension ˜ 2.5) in all the three cases.

On the solvation of the phosphocholine headgroup in an aqueous propylene glycol solution

NASA Astrophysics Data System (ADS)

Rhys, Natasha H.; Al-Badri, Mohamed Ali; Ziolek, Robert M.; Gillams, Richard J.; Collins, Louise E.; Lawrence, M. Jayne; Lorenz, Christian D.; McLain, Sylvia E.

2018-04-01

The atomic-scale structure of the phosphocholine (PC) headgroup in 30 mol. % propylene glycol (PG) in an aqueous solution has been investigated using a combination of neutron diffraction with isotopic substitution experiments and computer simulation techniques—molecular dynamics and empirical potential structure refinement. Here, the hydration of the PC headgroup remains largely intact compared with the hydration of this group in a bilayer and in a bulk water solution, with the PG molecules showing limited interactions with the headgroup. When direct PG interactions with PC do occur, they are most likely to coordinate to the 3+N (CH 3 ) motifs. Further, PG does not affect the bulk water structure and the addition of PC does not perturb the PG-solvent interactions. This suggests that the reason why PG is able to penetrate into membranes easily is that it does not form strong-hydrogen bonding or electrostatic interactions with the headgroup allowing it to easily move across the membrane barrier.

Interactions of cinnamaldehyde and its metabolite cinnamic acid with human serum albumin and interference of other food additives.

PubMed

Sun, Qiaomei; Yang, Hongqin; Tang, Peixiao; Liu, Jiuyang; Wang, Wan; Li, Hui

2018-03-15

Considering the adverse effect of food additives on humans, thorough research of their physiological effects at the molecular level is important. The interactions of cinnamaldehyde (CNMA), a food perfume, and its major metabolite cinnamic acid (CA) with human serum albumin (HSA) were examined by multiple-spectroscopies. NMR analysis revealed CNMA and CA both bound to HSA, and STD-NMR experiments established CNMA and CA primarily interacted with site I and site II of HSA, respectively. The ligands caused strong quenching of HSA fluorescence through a static quenching mechanism, with hydrophobic and electrostatic interaction between CNMA/CA and HSA, respectively. UV-vis absorption and CD results showed ligands induced secondary structure changes of HSA. Binding configurations were proved by docking method. Furthermore, binding constants of CNMA/CA-HSA systems were influenced by the addition of four other food additives. These studies have increased our knowledge regarding the safety and biological action of CNMA and CA. Copyright © 2017 Elsevier Ltd. All rights reserved.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations

PubMed Central

Peter, Christine; Hummer, Gerhard

2005-01-01

Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic membrane pores by molecular dynamics simulation of model membranes formed of hexagonally packed carbon nanotubes. We focus on the factors that determine the energetics of ion translocation through such nonpolar nanopores and compare the resulting free-energy barriers for pores with different diameters corresponding to the gating regions in closed and open forms of potassium channels. Our model system also allows us to compare the results from molecular dynamics simulations directly to continuum electrostatics calculations. Both simulations and continuum calculations show that subnanometer wide pores pose a huge free-energy barrier for ions, but a small increase in the pore diameter to ∼1 nm nearly eliminates that barrier. We also find that in those wider channels the ion mobility is comparable to that in the bulk phase. By calculating local electrostatic potentials, we show that the long range Coulomb interactions of ions are strongly screened in the wide water-filled channels. Whereas continuum calculations capture the overall energetics reasonably well, the local water structure, which is not accounted for in this model, leads to interesting effects such as the preference of hydrated ions to move along the pore wall rather than through the center of the pore. PMID:16006629

Electrostatic dry powder prepregging of carbon fiber

NASA Technical Reports Server (NTRS)

Throne, James L.; Sohn, Min-Seok

1990-01-01

Ultrafine, 5-10 micron polymer-matrix resin powders are directly applied to carbon fiber tows by passing then in an air or nitrogen stream through an electrostatic potential; the particles thus charged will strongly adhere to grounded carbon fibers, and can be subsequently fused to the fiber in a continuously-fed radiant oven. This electrostatic technique derived significant end-use mechanical property advantages from the obviation of solvents, binders, and other adulterants. Additional matrix resins used to produce prepregs to date have been PMR-15, Torlon 40000, and LaRC TPI.

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

Plasma wave observations at comet giacobini-zinner.

PubMed

Scarf, F L; Coroniti, F V; Kennel, C F; Gurnett, D A; Ip, W H; Smith, E J

1986-04-18

The plasma wave instrument on the International Cometary Explorer (ICE) detected bursts of strong ion acoustic waves almost continuously when the spacecraft was within 2 million kilometers of the nucleus of comet Giacobini-Zinner. Electromagnetic whistlers and low-level electron plasma oscillations were also observed in this vast region that appears to be associated with heavy ion pickup. As ICE came closer to the anticipated location of the bow shock, the electromagnetic and electrostatic wave levels increased significantly, but even in the midst of this turbulence the wave instrument detected structures with familiar bow shock characteristics that were well correlated with observations of localized electron heating phenomena. Just beyond the visible coma, broadband waves with amplitudes as high as any ever detected by the ICE plasma wave instrument were recorded. These waves may account for the significant electron heating observed in this region by the ICE plasma probe, and these observations of strong wave-particle interactions may provide answers to longstanding questions concerning ionization processes in the vicinity of the coma. Near closest approach, the plasma wave instrument detected broadband electrostatic noise and a changing pattern of weak electron plasma oscillations that yielded a density profile for the outer layers of the cold plasma tail. Near the tail axis the plasma wave instrument also detected a nonuniform flux of dust impacts, and a preliminary profile of the Giacobini-Zinner dust distribution for micrometer-sized particles is presented.

Reynolds stress flow shear and turbulent energy transfer in reversed field pinch configuration

NASA Astrophysics Data System (ADS)

Vianello, Nicola; Spolaore, Monica; Serianni, Gianluigi; Regnoli, Giorgio; Spada, Emanuele; Antoni, Vanni; Bergsåker, Henric; Drake, James R.

2003-10-01

The role of Reynolds Stress tensor on flow generation in turbulent fluids and plasmas is still an open question and the comprehension of its behavior may assist the understanding of improved confinement scenario. It is generally believed that shear flow generation may occur by an interaction of the turbulent Reynolds stress with the shear flow. It is also generally believed that this mechanism may influence the generation of zonal flow shears. The evaluation of the complete Reynolds Stress tensor requires contemporary measurements of its electrostatic and magnetic part: this requirement is more restrictive for Reversed Field Pinch configuration where magnetic fluctuations are larger than in tokamak . A new diagnostic system which combines electrostatic and magnetic probes has been installed in the edge region of Extrap-T2R reversed field pinch. With this new probe the Reynolds stress tensor has been deduced and its radial profile has been reconstructed on a shot to shot basis exploring differen plasma conditions. These profiles have been compared with the naturally occurring velocity flow profile, in particular during Pulsed Poloidal Current Drive experiment, where a strong variation of ExB flow radial profile has been registered. The study of the temporal evolution of Reynolds stress reveals the appearance of strong localized bursts: these are considered in relation with global MHD relaxation phenomena, which naturally occur in the core of an RFP plasma sustaining its configuration.

A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

PubMed Central

Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew

2008-01-01

In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946

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.

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.

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.

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.

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.

Electrostatic cloaking of surface structure for dynamic wetting

NASA Astrophysics Data System (ADS)

Shiomi, Junichiro; Nita, Satoshi; Do-Quang, Minh; Wang, Jiayu; Chen, Yu-Chung; Suzuki, Yuji; Amberg, Gustav

2017-11-01

Dynamic wetting problems are fundamental to the understanding of the interaction between liquids and solids. Even in a superficially simple experimental situation, such as a droplet spreading over a dry surface, the result may depend not only on the liquid properties but also strongly on the substrate-surface properties; even for macroscopically smooth surfaces, the microscopic geometrical roughness can be important. In addition, as surfaces may often be naturally charged, or electric fields are used to manipulate fluids, electric effects are crucial components that influence wetting phenomena. Here we investigate the interplay between electric forces and surface structures in dynamic wetting. While surface microstructures can significantly hinder the spreading, we find that the electrostatics can ``cloak'' the microstructures, i.e. deactivate the hindering. We identify the physics in terms of reduction in contact-line friction, which makes the dynamic wetting inertial force dominant and insensitive to the substrate properties. This work was financially supported in part by, the Japan Society for the Promotion of Science, Swedish Governmental Agency for Innovation Systems, and the Japan Science and Technology Agency.

Electrostatic properties of the pyrimethamine-2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters.

PubMed

Faroque, Muhammad Umer; Noureen, Sajida; Ahmed, Maqsood; Tahir, Muhammad Nawaz

2018-01-01

The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C 12 H 14 ClN 4 + ·C 7 H 5 O 4 - ·CH 3 OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

Chain stiffness, salt valency, and concentration influences on titration curves of polyelectrolytes: Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Carnal, Fabrice; Stoll, Serge

2011-01-01

Monte Carlo simulations have been used to study two different models of a weak linear polyelectrolyte surrounded by explicit counterions and salt particles: (i) a rigid rod and (ii) a flexible chain. We focused on the influence of the pH, chain stiffness, salt concentration, and valency on the polyelectrolyte titration process and conformational properties. It is shown that chain acid-base properties and conformational properties are strongly modified when multivalent salt concentration variation ranges below the charge equivalence. Increasing chain stiffness allows to minimize intramolecular electrostatic monomer interactions hence improving the deprotonation process. The presence of di and trivalent salt cations clearly promotes the chain degree of ionization but has only a limited effect at very low salt concentration ranges. Moreover, folded structures of fully charged chains are only observed when multivalent salt at a concentration equal or above charge equivalence is considered. Long-range electrostatic potential is found to influence the distribution of charges along and around the polyelectrolyte backbones hence resulting in a higher degree of ionization and a lower attraction of counterions and salt particles at the chain extremities.

Chain stiffness, salt valency, and concentration influences on titration curves of polyelectrolytes: Monte Carlo simulations.

PubMed

Carnal, Fabrice; Stoll, Serge

2011-01-28

Monte Carlo simulations have been used to study two different models of a weak linear polyelectrolyte surrounded by explicit counterions and salt particles: (i) a rigid rod and (ii) a flexible chain. We focused on the influence of the pH, chain stiffness, salt concentration, and valency on the polyelectrolyte titration process and conformational properties. It is shown that chain acid-base properties and conformational properties are strongly modified when multivalent salt concentration variation ranges below the charge equivalence. Increasing chain stiffness allows to minimize intramolecular electrostatic monomer interactions hence improving the deprotonation process. The presence of di and trivalent salt cations clearly promotes the chain degree of ionization but has only a limited effect at very low salt concentration ranges. Moreover, folded structures of fully charged chains are only observed when multivalent salt at a concentration equal or above charge equivalence is considered. Long-range electrostatic potential is found to influence the distribution of charges along and around the polyelectrolyte backbones hence resulting in a higher degree of ionization and a lower attraction of counterions and salt particles at the chain extremities.

Electrostatic model for protein adsorption in ion-exchange chromatography and application to monoclonal antibodies, lysozyme and chymotrypsinogen A.

PubMed

Guélat, Bertrand; Ströhlein, Guido; Lattuada, Marco; Morbidelli, Massimo

2010-08-27

A model for the adsorption equilibrium of proteins in ion-exchange chromatography explicitly accounting for the effect of pH and salt concentration in the limit of highly diluted systems was developed. It is based on the use of DLVO theory to estimate the electrostatic interactions between the charged surface of the ion-exchanger and the proteins. The corresponding charge distributions were evaluated as a function of pH and salt concentration using a molecular approach. The model was verified for the adsorption equilibrium of lysozyme, chymotrypsinogen A and four industrial monoclonal antibodies on two strong cation-exchangers. The adsorption equilibrium constants of these proteins were determined experimentally at various pH values and salt concentrations and the model was fitted with a good agreement using three adjustable parameters for each protein in the whole range of experimental conditions. Despite the simplifications of the model regarding the geometry of the protein-ion-exchanger system, the physical meaning of the parameters was retained. 2010 Elsevier B.V. All rights reserved.

Ligand solvation in molecular docking.

PubMed

Shoichet, B K; Leach, A R; Kuntz, I D

1999-01-01

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

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

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.

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.

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.

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

Theory of type 3b solar radio bursts. [plasma interaction and electron beams

NASA Technical Reports Server (NTRS)

Smith, R. A.; Delanoee, J.

1975-01-01

During the initial space-time evolution of an electron beam injected into the corona, the strong beam-plasma interaction occurs at the head of the beam, leading to the amplification of a quasi-monochromatic large-amplitude plasma wave that stabilizes by trapping the beam particles. Oscillation of the trapped particles in the wave troughs amplifies sideband electrostatic waves. The sidebands and the main wave subsequently decay to observable transverse electromagnetic waves through the parametric decay instability. This process gives rise to the elementary striation bursts. Owing to velocity dispersion in the beam and the density gradient of the corona, the entire process may repeat at a finite number of discrete plasma levels, producing chains of elementary bursts. All the properties of the type IIIb bursts are accounted for in the context of the theory.

Controlling single-molecule junction conductance by molecular interactions

NASA Astrophysics Data System (ADS)

Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

2015-07-01

For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment.

Unmagnetized diffusion for azimuthally symmetric wave and particle distributions

NASA Technical Reports Server (NTRS)

Dusenbery, P. B.; Lyons, L. R.

1988-01-01

The quasi-linear diffusion of particles from resonant interactions with a spectrum of electrostatic waves is investigated theoretically, extending results obtained for no magnetic field and for strong magnetic fields to cases where the ambient magnetic field which organizes azimuthally symmetric wave and particle distributions does not have to be taken into consideration in evaluating the local interaction. The derivation of the governing equations is explained, and numerical results are presented in extensive graphs and characterized in detail. Slow-mode ion-acoustic waves are shown to be unstable under the plasma conditions studied, and the dependence of resonant-ion diffusion rates with pitch angle, speed, and the distribution of wave energy in wavenumber space is explored. The implications of the present findings for theoretical models of the earth bow shock and plasma-sheet boundary layer are indicated.

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.

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

Mg2+ in the Major Groove Modulates B-DNA Structure and Dynamics

PubMed Central

Guéroult, Marc; Boittin, Olivier; Mauffret, Oliver; Etchebest, Catherine; Hartmann, Brigitte

2012-01-01

This study investigates the effect of Mg2+ bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5′-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg2+ close to an ApG step. These simulations showed that the hydrated Mg2+ forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg2+. The binding of Mg2+ modulates the behavior of the 5′-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5′-phosphate group and Mg2+ strengthen both the DNA-cation binding and the BII character of the 5′-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes. PMID:22844516

Effects of substrate conductivity on cell morphogenesis and proliferation using tailored, atomic layer deposition-grown ZnO thin films

PubMed Central

Choi, Won Jin; Jung, Jongjin; Lee, Sujin; Chung, Yoon Jang; Yang, Cheol-Soo; Lee, Young Kuk; Lee, You-Seop; Park, Joung Kyu; Ko, Hyuk Wan; Lee, Jeong-O

2015-01-01

We demonstrate that ZnO films grown by atomic layer deposition (ALD) can be employed as a substrate to explore the effects of electrical conductivity on cell adhesion, proliferation, and morphogenesis. ZnO substrates with precisely tunable electrical conductivity were fabricated on glass substrates using ALD deposition. The electrical conductivity of the film increased linearly with increasing duration of the ZnO deposition cycle (thickness), whereas other physical characteristics, such as surface energy and roughness, tended to saturate at a certain value. Differences in conductivity dramatically affected the behavior of SF295 glioblastoma cells grown on ZnO films, with high conductivity (thick) ZnO films causing growth arrest and producing SF295 cell morphologies distinct from those cultured on insulating substrates. Based on simple electrostatic calculations, we propose that cells grown on highly conductive substrates may strongly adhere to the substrate without focal-adhesion complex formation, owing to the enhanced electrostatic interaction between cells and the substrate. Thus, the inactivation of focal adhesions leads to cell proliferation arrest. Taken together, the work presented here confirms that substrates with high conductivity disturb the cell-substrate interaction, producing cascading effects on cellular morphogenesis and disrupting proliferation, and suggests that ALD-grown ZnO offers a single-variable method for uniquely tailoring conductivity. PMID:25897486

Numerical simulation of photocurrent generation in bilayer organic solar cells: Comparison of master equation and kinetic Monte Carlo approaches

NASA Astrophysics Data System (ADS)

Casalegno, Mosè; Bernardi, Andrea; Raos, Guido

2013-07-01

Numerical approaches can provide useful information about the microscopic processes underlying photocurrent generation in organic solar cells (OSCs). Among them, the Kinetic Monte Carlo (KMC) method is conceptually the simplest, but computationally the most intensive. A less demanding alternative is potentially represented by so-called Master Equation (ME) approaches, where the equations describing particle dynamics rely on the mean-field approximation and their solution is attained numerically, rather than stochastically. The description of charge separation dynamics, the treatment of electrostatic interactions and numerical stability are some of the key issues which have prevented the application of these methods to OSC modelling, despite of their successes in the study of charge transport in disordered system. Here we describe a three-dimensional ME approach to photocurrent generation in OSCs which attempts to deal with these issues. The reliability of the proposed method is tested against reference KMC simulations on bilayer heterojunction solar cells. Comparison of the current-voltage curves shows that the model well approximates the exact result for most devices. The largest deviations in current densities are mainly due to the adoption of the mean-field approximation for electrostatic interactions. The presence of deep traps, in devices characterized by strong energy disorder, may also affect result quality. Comparison of the simulation times reveals that the ME algorithm runs, on the average, one order of magnitude faster than KMC.

Computational analysis of aspartic protease plasmepsin II complexed with EH58 inhibitor: a QM/MM MD study.

PubMed

de Farias Silva, Natália; Lameira, Jerônimo; Alves, Cláudio Nahum

2011-10-01

Plasmepsin (PM) II is one of four enzymes in the food vacuole of Plasmodium falciparum. It has become an attractive target for combating malaria through research regarding its importance in the P. falciparum metabolism and life cycle, making it the target of choice for structure-based drug design. This paper reports the results of hybrid quantum mechanics / molecular mechanics (QM/MM) molecular dynamics (MD) simulations employed to study the details of the interactions established between PM II and N-(3-{(2-benzo[1, 3]dioxol-5-yl-ethyl)[3-(1-methyl-3-oxo-1,3-dihydro-isoindol-2-yl) propionyl]-amino}-1-benzyl-2-(hydroxyl-propyl)-4-benzyloxy-3,5dimethoxy-benzamide (EH58), a well-known potent inhibitor for this enzyme. Electrostatic binding free energy and energy terms decomposition have been computed for PM II complexed with the EH58 inhibitor. The results reveal that there is a strong interaction between Asp34, Val78, Ser79, Tyr192 and Asp214 residues and the EH58 inhibitor. In addition, we have computed the potential of the mean force (PMF) profile in order to assign the protonation state of the two catalytic aspartates in PM II-EH58 complex. The results indicate that the protonation of Asp214 favors a stable active site structure, which is consistent with our electrostatic binding free energy calculation and with previous published works.

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.

Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi)

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

Assefa, Netsanet Gizaw; Niiranen, Laila; University of Turku, FIN-20014 Turku

2014-08-01

A structural and biophysical study of the interactions between cod and human uracil-DNA N-glycosylase (UNG) and their inhibitor Ugi is presented. The stronger interaction between cod UNG and Ugi can be explained by a greater positive electrostatic surface potential. Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme–substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi)more » has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG–Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG–Ugi complex with previously determined structures of UNG–Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (K{sub b}) which is one order of magnitude larger than that for hUNG–Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein–Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.« less

Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

PubMed

Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

2016-05-05

Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

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

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.

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.

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

Interaction between calcium and phosphate adsorption on goethite.

PubMed

Rietra, R P; Hiemstra, T; van Riemsdijk, W H

2001-08-15

Quantitatively, little is known about the ion interaction processes that are responsible for the binding of phosphate in soil, water, and sediment, which determine the bioavailability and mobility of phosphate. Studies have shown that metal hydroxides are often responsible for the binding of PO4 in soils and sediments, but the binding behavior of PO4 in these systems often differs significantly from adsorption studies on metal hydroxides in laboratory. The interaction between PO4 and Ca adsorption was studied on goethite because Ca can influence the PO4 adsorption equilibria. Since adsorption interactions are very difficult to discriminate from precipitation reactions, conditions were chosen to prevent precipitation of Ca-PO4 solids. Adsorption experiments of PO4 and Ca, individually and in combination, show a strong interaction between adsorbed Ca and PO4 on goethite for conditions below the saturation index of apatite. It is shown that it is possible to predict the adsorption and interaction of PO4 and Ca on electrostatic arguments using the model parameter values derived from the single-ion systems and without invoking ternary complex formation or precipitation. The model enables the prediction of the Ca-PO4 interaction for environmentally relevant calcium and phosphate concentrations.

Ultrafiltration of pegylated proteins

NASA Astrophysics Data System (ADS)

Molek, Jessica R.

There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine groups in the PEGylated proteins. Ultrafiltration experiments were performed using PEGylated alpha-lactalbumin, ovalbumin, and bovine serum albumin. In contrast to the size exclusion chromatography data, the sieving coefficient of the PEGylated proteins depended upon both the number and size of the attached PEG chains due to the elongation or deformation of the PEG associated with the filtrate flux. Sieving coefficients at low filtrate flux were in good agreement with predictions of available hydrodynamic models, with significant elongation occurring when the Deborah number for the PEG chain exceeded 0.001. The effects of electrostatic interactions on the ultrafiltration of PEGylated proteins were examined using electrically-charged membranes generated by covalent attachment of sulphonic acid groups to the base cellulosic membrane. Transmission of PEGylated proteins through charged membranes was dramatically reduced at low ionic strength due to strong electrostatic interactions, despite the presence of the neutral PEG. The experimental results were in good agreement with model calculations developed for the partitioning of charged spheres into charged cylindrical pores. The experimental and theoretical results provide the first quantitative analysis of the effects of PEGylation on transport through semipermeable ultrafiltration membranes. The results from small-scale ultrafiltration experiments were used to develop a two-stage diafiltration process to purify PEGylated alpha-lactalbumin. The first-stage used a neutral membrane to remove the unreacted protein by exploiting differences in size. The second stage used a negatively-charged membrane to remove hydrolyzed PEG, with the PEGylated product retained by strong electrostatic interactions. This process provided a purification factor greater than 1000 with respect to the unreacted protein and greater than 20-fold with respect to the PEG with an overall yield of PEGylated alpha-lactalbumin of 78%. These results provide the first demonstration of the potential of using ultrafiltration for the purification of protein-polymer conjugates.

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.

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.

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.

MMS Observations of Ion-Scale Magnetic Island in the Magnetosheath Turbulent Plasma

NASA Technical Reports Server (NTRS)

Huang, S. Y.; Sahraoui, F.; Retino, A.; Contel, O. Le; Yuan, Z. G.; Chasapis, A.; Aunai, N.; Breuillard, H.; Deng, X. H.; Zhou, M.;

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...

COSMIC DUST AGGREGATION WITH STOCHASTIC CHARGING

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

Matthews, Lorin S.; Hyde, Truell W.; Shotorban, Babak, E-mail: Lorin_Matthews@baylor.edu

2013-10-20

The coagulation of cosmic dust grains is a fundamental process which takes place in astrophysical environments, such as presolar nebulae and circumstellar and protoplanetary disks. Cosmic dust grains can become charged through interaction with their plasma environment or other processes, and the resultant electrostatic force between dust grains can strongly affect their coagulation rate. Since ions and electrons are collected on the surface of the dust grain at random time intervals, the electrical charge of a dust grain experiences stochastic fluctuations. In this study, a set of stochastic differential equations is developed to model these fluctuations over the surface ofmore » an irregularly shaped aggregate. Then, employing the data produced, the influence of the charge fluctuations on the coagulation process and the physical characteristics of the aggregates formed is examined. It is shown that dust with small charges (due to the small size of the dust grains or a tenuous plasma environment) is affected most strongly.« less

Gels of sodium alginate‒chitosan interpolyelectrolyte complexes

NASA Astrophysics Data System (ADS)

Brovko, O. S.; Palamarchuk, I. A.; Val'chuk, N. A.; Chukhchin, D. G.; Bogolitsyn, K. G.; Boitsova, T. A.

2017-08-01

Aspects of the formation of gels of interpolyelectrolyte complexes (IPECs) based on sodium alginate (NaAlg) and chitosan are studied. The effect the conditions of synthesis and complex composition have on the morphological structure and functional properties of these complexes is examined. It is established that complexation in this system proceeds according to a mechanism of electrostatic interaction between the oppositely charged carboxylic groups of the L-hyaluronic acid pyranose cycles of NaAlg proximal polymer chains and chitosan's amino groups, along with a multitude of hydrogen bonds and dispersion forces. We show that the mechanism of IPEC formation is strongly influenced by the conformational state of a lyophilizing component that is present in the system in excess. The inner surfaces of cryogels based on NaAlg‒chitosan IPECs is found to be strongly influenced by the degree of conversion between the parental polyelectrolytes. The most developed mesoporous structure is obtained when a denser gel forms in the system.

Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

PubMed Central

Baptista, A M; Martel, P J; Soares, C M

1999-01-01

A new method is presented for simulating the simultaneous binding equilibrium of electrons and protons on protein molecules, which makes it possible to study the full equilibrium thermodynamics of redox and protonation processes, including electron-proton coupling. The simulations using this method reflect directly the pH and electrostatic potential of the environment, thus providing a much closer and realistic connection with experimental parameters than do usual methods. By ignoring the full binding equilibrium, calculations usually overlook the twofold effect that binding fluctuations have on the behavior of redox proteins: first, they affect the energy of the system by creating partially occupied sites; second, they affect its entropy by introducing an additional empty/occupied site disorder (here named occupational entropy). The proposed method is applied to cytochrome c3 of Desulfovibrio vulgaris Hildenborough to study its redox properties and electron-proton coupling (redox-Bohr effect), using a continuum electrostatic method based on the linear Poisson-Boltzmann equation. Unlike previous studies using other methods, the full reduction order of the four hemes at physiological pH is successfully predicted. The sites more strongly involved in the redox-Bohr effect are identified by analysis of their titration curves/surfaces and the shifts of their midpoint redox potentials and pKa values. Site-site couplings are analyzed using statistical correlations, a method much more realistic than the usual analysis based on direct interactions. The site found to be more strongly involved in the redox-Bohr effect is propionate D of heme I, in agreement with previous studies; other likely candidates are His67, the N-terminus, and propionate D of heme IV. Even though the present study is limited to equilibrium conditions, the possible role of binding fluctuations in the concerted transfer of protons and electrons under nonequilibrium conditions is also discussed. The occupational entropy contributions to midpoint redox potentials and pKa values are computed and shown to be significant. PMID:10354425

Binding regularities in complexes of transcription factors with operator DNA: homeodomain family.

PubMed

Chirgadze, Yu N; Zheltukhin, E I; Polozov, R V; Sivozhelezov, V S; Ivanov, V V

2009-06-01

In order to disclose general regularities of binding in homeodomain-DNA complexes we considered five of them and extended the observed regularities over the entire homeodomain family. The five complexes have been selected by similarity of protein structures and patterns of contacting residues. Their long range interactions and interfaces were compared. The long-range stage of the recognition process was characterized by electrostatic potentials about 5 Angstrom away from molecular surfaces of protein or DNA. For proteins, clear positive potential is displayed only at the side contacting the DNA. The double-chained DNA molecule displays a rather strong negative potential, especially in their grooves. Thus, a functional role of electrostatics is a guiding of the protein into the DNA major groove, so the protein and DNA could form a loose non-specific complex. At the close-range stage, neutralization of the phosphate charges by positively charged residues is necessary for decreasing the strong electrostatic potential of DNA, allowing nucleotide bases to participate in the formation of protein-DNA atomic contacts in the interface. The recognizing alpha-helix of protein was shown to form both invariant and variable groups of contacts with DNA by means of certain specific side groups. The invariant contacts included highly specific protein-DNA hydrogen bonds between asparagine and adenine, nonpolar contacts of hydrophobic amino acids serving as a stereochemical barrier for fixing the protein factor on DNA, and an interface cluster of water molecules providing local conformational mobility necessary for the dissociation process. There is a unique water molecule within the interface that is conservative and located at the interface center. Invariant contacts of the proteins are mostly formed with the TAAT motif of the promoter DNA forward strand. While the invariant contacts specify the family of homeodomains, the variable contacts that are formed with the reverse strand of DNA provide specificity of individual complexes within the homeodomain family.

Ionisation and discharge in cloud-forming atmospheres of brown dwarfs and extrasolar planets

NASA Astrophysics Data System (ADS)

Helling, Ch; Rimmer, P. B.; Rodriguez-Barrera, I. M.; Wood, Kenneth; Robertson, G. B.; Stark, C. R.

2016-07-01

Brown dwarfs and giant gas extrasolar planets have cold atmospheres with rich chemical compositions from which mineral cloud particles form. Their properties, like particle sizes and material composition, vary with height, and the mineral cloud particles are charged due to triboelectric processes in such dynamic atmospheres. The dynamics of the atmospheric gas is driven by the irradiating host star and/or by the rotation of the objects that changes during its lifetime. Thermal gas ionisation in these ultra-cool but dense atmospheres allows electrostatic interactions and magnetic coupling of a substantial atmosphere volume. Combined with a strong magnetic field \\gg {{B}\\text{Earth}} , a chromosphere and aurorae might form as suggested by radio and x-ray observations of brown dwarfs. Non-equilibrium processes like cosmic ray ionisation and discharge processes in clouds will increase the local pool of free electrons in the gas. Cosmic rays and lighting discharges also alter the composition of the local atmospheric gas such that tracer molecules might be identified. Cosmic rays affect the atmosphere through air showers in a certain volume which was modelled with a 3D Monte Carlo radiative transfer code to be able to visualise their spacial extent. Given a certain degree of thermal ionisation of the atmospheric gas, we suggest that electron attachment to charge mineral cloud particles is too inefficient to cause an electrostatic disruption of the cloud particles. Cloud particles will therefore not be destroyed by Coulomb explosion for the local temperature in the collisional dominated brown dwarf and giant gas planet atmospheres. However, the cloud particles are destroyed electrostatically in regions with strong gas ionisation. The potential size of such cloud holes would, however, be too small and might occur too far inside the cloud to mimic the effect of, e.g. magnetic field induced star spots.

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.

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.

Changes in conformational dynamics of basic side chains upon protein–DNA association

PubMed Central

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B. Montgometry; Iwahara, Junji

2016-01-01

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. PMID:27288446

Control of Rydberg atom blockade by dc electric field orientation in a quasi-one-dimensional sample

NASA Astrophysics Data System (ADS)

Goncalves, Luís Felipe; Marcassa, Luis Gustavo

2017-04-01

Rydberg atoms posse a strong atom-atom interaction, which limits its density in an atomic sample. Such effect is known as Rydberg atom blockade. Here, we present a novel way to control such effect by direct orienting the induced atomic dipole moment using a dc external electrical field. To demonstrate it, we excite the 50S1 / 2 Rb atomic state in a quasi-one-dimensional sample held in a quasi-electrostatic trap. A pure nS state holds only van der Waals interaction at long range, but in the presence of an external electric field the state mixing leads to strong dipole-dipole interactions. We have measured the Rydberg atom population as a function of ground state atoms density for several angles between the electric field and the main axis of the unidimensional sample. The results indicate that the limit on the final Rydberg density can be controlled by electric field orientation. Besides, we have characterized the sample by using direct spatial ion imaging, demonstrating that it does behave as an unidimensional sample. This work was supported by Sao Paulo Research Foundation (FAPESP) Grants No. 2011/22309-8 and No. 2013/02816- 8, the U.S. Army Research Office Grant No. W911NF-15-1-0638 and CNPq.

High Power HF Excitation of Low Frequency Stimulated Electrostatic Waves in the Ionospheric Plasma over HAARP

NASA Astrophysics Data System (ADS)

Bernhardt, Paul; Selcher, Craig A.

High Power electromagnetic (EM) waves transmitted from the HAARP facility in Alaska can excite low frequency electrostatic waves by several processes including (1) direct magnetized stimulated Brillouin scatter (MSBS) and (2) parametric decay of high frequency electrostatic waves into electron and ion Bernstein waves. Either an ion acoustic (IA) wave with a frequency less than the ion cyclotron frequency (fCI) or an electrostatic ion cyclotron (EIC) wave just above fCI can be produced by MSBS. The coupled equations describing the MSBS instabil-ity show that the production of both IA and EIC waves is strongly influenced by the wave propagation direction relative to the background magnetic field. Experimental observations of stimulated electromagnetic emissions (SEE) using the HAARP transmitter in Alaska have confirmed the theoretical predictions that only IA waves are excited for propagation along the magnetic zenith and that EIC waves can only be detected with oblique propagation angles. The electron temperature in the heated plasma is obtained from the IA spectrum offsets from the pump frequency. The ion composition can be determined from the measured EIC frequency. Near the second harmonic of the electron cyclotron frequency, the EM pump wave is converted into an electron Bernstein (EB) wave that decays into another EB wave and an ion Bernstein (IB) wave. Strong cyclotron resonance with the EB wave leads to acceleration of the electrons. Ground based SEE observations are related to the theory of low-frequency electrostatic wave generation.

Understanding AuNP interaction with low-generation PAMAM dendrimers: a CIELab and deconvolution study

NASA Astrophysics Data System (ADS)

Jimenez-Ruiz, A.; Carnerero, J. M.; Castillo, P. M.; Prado-Gotor, R.

2017-01-01

Low-generation polyamidoamine (PAMAM) dendrimers are known to adsorb on the surface of gold nanoparticles (AuNPs) causing aggregation and color changes. In this paper, a thorough study of this affinity using absorption spectroscopy, colorimetric, and emission methods has been carried out. Results show that, for citrate-capped gold nanoparticles, interaction with the dendrimer is not only of an electrostatic character but instead occurs, at least in part, through the dendrimer's uncharged internal amino groups. The possibilities of the CIELab chromaticity system parameters' evolution have also been explored in order to quantify dendrimer interaction with the red-colored nanoparticles. By measuring and quantifying 17 nm citrate-capped AuNP color changes, which are strongly dependant on their aggregation state, binding free energies are obtained for the first time for these systems. Results are confirmed via an alternate fitting method which makes use of deconvolution parameters from absorbance spectra. Binding free energies obtained through the use of both means are in good agreement with each other.

Toward the description of electrostatic interactions between globular proteins: potential of mean force in the primitive model.

PubMed

Dahirel, Vincent; Jardat, Marie; Dufrêche, Jean-François; Turq, Pierre

2007-09-07

Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern. Contrarily to Poisson-Boltzmann predictions, attractive, and repulsive direct forces between proteins are not screened similarly. Moreover, it has been shown that the relative orientations of the charge patterns strongly influence salt-mediated interactions. More precisely, for short distances between the proteins, ions enhance the difference of the effective forces between (i) like-charged and oppositely charged proteins, (ii) attractive and repulsive relative orientations of the proteins, which may affect the selectivity of protein/protein recognition. Finally, such results observed with the simplest models are applied to a more elaborate one to demonstrate their generality.

Vibrational properties of the amide group in acetanilide: A molecular-dynamics study

NASA Astrophysics Data System (ADS)

Campa, Alessandro; Giansanti, Andrea; Tenenbaum, Alexander

1987-09-01

A simplified classical model of acetanilide crystal is built in order to study the mechanisms of vibrational energy transduction in a hydrogen-bonded solid. The intermolecular hydrogen bond is modeled by an electrostatic interaction between neighboring excess charges on hydrogen and oxygen atoms. The intramolecular interaction in the peptide group is provided by a dipole-charge interaction. Forces are calculated up to second-order terms in the atomic displacements from equilibrium positions; the model is thus a chain of nonlinear coupled oscillators. Numerical molecular-dynamics experiments are performed on chain segments of five molecules. The dynamics is ordered, at all temperatures. Energy is widely exchanged between the stretching and the bending of the N-H bond, with characteristic times of the order of 0.2 ps. Energy transduction through the H bond is somewhat slower and of smaller amplitude, and is strongly reduced when the energies of the two bound molecules are very different: This could reduce the dissipation of localized energy fluctuations.

Fine Spectral Properties of Langmuir Waves Observed Upstream of the Saturn's Bowshock by the Cassini Wideband Receiver

NASA Astrophysics Data System (ADS)

Hospodarsky, G. B.; Pisa, D.; Santolik, O.; Kurth, W. S.; Soucek, J.; Basovnik, M.; Gurnett, D. A.; Arridge, C. S.

2015-12-01

Langmuir waves are commonly observed in the upstream regions of planetary and interplanetary shock. Solar wind electrons accelerated at the shock front are reflected back into the solar wind and can form electron beams. In regions with beams, the electron distribution becomes unstable and electrostatic waves can be generated. The process of generation and the evolution of electrostatic waves strongly depends on the solar wind electron distribution and generally exhibits complex behavior. Langmuir waves can be identified as intense narrowband emission at a frequency very close to the local plasma frequency and weaker broadband waves below and above the plasma frequency deeper in the downstream region. We present a detailed study of Langmuir waves detected upstream of the Saturnian bowshock by the Cassini spacecraft. Using data from the Radio and Plasma Wave Science (RPWS), Magnetometer (MAG) and Cassini Plasma Spectrometer (CAPS) instruments we have analyzed several periods containing the extended waveform captures by the Wideband Receiver. Langmuir waves are a bursty emission highly controlled by variations in solar wind conditions. Unfortunately due to a combination of instrumental field of view and sampling period, it is often difficult to identify the electron distribution function that is unstable and able to generate Langmuir waves. We used an electrostatic version of particle-in-cell simulation of the Langmuir wave generation process to reproduce some of the more subtle observed spectral features and help understand the late stages of the instability and interactions in the solar wind plasma.

Electric-field-induced forces between two surfaces filled with an insulating liquid: the role of adsorbed water

NASA Astrophysics Data System (ADS)

Wang, Yong Jian; Xu, Zuli; Sheng, Ping; Tong, Penger

2014-06-01

A systematic study of the electric-field-induced forces between a solid glass sphere and a flat gold-plated substrate filled with an insulating liquid has been carried out. Using atomic force microscopy, we measure the electrostatic force f(s, V) between the sphere and substrate as a function of the surface separation s and applied voltage V. The measured f(s, V) is found to be well described by an equation for a conducting sphere. Further force measurements for the "wet" porous glass spheres filled with an aqueous solution of urea and the dried porous glass spheres filled with (dry) air suggest that there is a water layer of a few nanometers in thickness adsorbed on the hydrophilic glass surface under ambient conditions. This adsorbed water layer is more conductive than the dielectric core of the glass sphere, making the sphere surface to be at a potential close to that of the cantilever electrode. As a result, the electric field is strongly concentrated in the gap region between the glass sphere and gold-plate substrate and thus their electrostatic attraction is enhanced. This surface conductivity effect is further supported by the thermal gravimetric analysis (TGA) and force response measurements to a time-dependent electric field. The experiment clearly demonstrates that the adsorption of a conductive water layer on a hydrophilic surface plays a dominant role in determining the electrostatic interaction between the dielectric sphere and substrate.

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.

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.

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.

Water as a matrix for life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Pratt, Lawrence

2006-01-01

"Follow the water" is the canonical strategy in searching for life in the universe. Conventionally, discussion of this topic is focused on how solvent supports organic chemistry sufficiently rich to seed life. Perhaps more importantly, solvent must promote self-organization of organic matter into functional structures capable of responding to environmental changes. This process is based on non-covalent interactions. They are constantly formed and broken in response to internal and external stimuli. This requires that their strength must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. Non-covalent interactions are strongly mediated by the solvent. Specifically, high dielectric solvents for life are needed for solubility of polar species and flexibility of biological structures stabilized by electrostatic interactions. Water exhibits a remarkable trait that it promotes solvophobic interactions between non-polar species, which are responsible for self-organization phenomena such as the formation of cellular boundary structures, and protein folding and aggregation. Unusual temperature dependence of hydrophobic interactions - they often become stronger as temperature increases - is a consequence of the temperature insensitivity of properties of the liquid water. This contributes to the existence of robust life over a wide temperature range. Water is not the only liquid with favorable properties for supporting life. Other pure liquids or their mixtures that have high dielectric constants and simultaneously support some level of self-organization will be discussed.

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 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.

Electromagnetic and electrostatic emissions at the cusp-magnetosphere interface during substorms

NASA Technical Reports Server (NTRS)

Curtis, S. A.; Fairfield, D. H.; Wu, C. S.

1979-01-01

Strongly peaked electrostatic emissions near 10.0 kHz and electromagnetic emissions near 0.56 kHz have been observed by the VLF wave detector on board Imp 6 on crossings from the earth's magnetosphere into the polar cusp during the occurrence of large magnetospheric substorms. The electrostatic emissions were observed to be closely confined to the cusp-magnetosphere interface. The electromagnetic emissions were of somewhat broader spatial extent and were seen on higher-latitude field lines within the cusp. Using these plasma wave observations and additional information provided by plasma, magnetometer and particle measurements made simultaneously on Imp 6, theories are constructed to explain each of the two classes of emission. The electromagnetic waves are modeled as whistlers, and the electrostatic waves as electron-cyclotron harmonics. The resulting growth rates predict power spectra similar to those observed for both emission classes. The electrostatic waves may play a significant role via enhanced diffusion in the relaxation of the sharp substorm time cusp-magnetosphere boundary to a more diffuse quiet time boundary.

Accurate Simulation of Parametrically Excited Micromirrors via Direct Computation of the Electrostatic Stiffness

PubMed Central

Frangi, Attilio; Guerrieri, Andrea; Boni, Nicoló

2017-01-01

Electrostatically actuated torsional micromirrors are key elements in Micro-Opto-Electro- Mechanical-Systems. When forced by means of in-plane comb-fingers, the dynamics of the main torsional response is known to be strongly non-linear and governed by parametric resonance. Here, in order to also trace unstable branches of the mirror response, we implement a simplified continuation method with arc-length control and propose an innovative technique based on Finite Elements and the concepts of material derivative in order to compute the electrostatic stiffness; i.e., the derivative of the torque with respect to the torsional angle, as required by the continuation approach. PMID:28383483

Accurate Simulation of Parametrically Excited Micromirrors via Direct Computation of the Electrostatic Stiffness.

PubMed

Frangi, Attilio; Guerrieri, Andrea; Boni, Nicoló

2017-04-06

Electrostatically actuated torsional micromirrors are key elements in Micro-Opto-Electro- Mechanical-Systems. When forced by means of in-plane comb-fingers, the dynamics of the main torsional response is known to be strongly non-linear and governed by parametric resonance. Here, in order to also trace unstable branches of the mirror response, we implement a simplified continuation method with arc-length control and propose an innovative technique based on Finite Elements and the concepts of material derivative in order to compute the electrostatic stiffness; i.e., the derivative of the torque with respect to the torsional angle, as required by the continuation approach.

A master equation for strongly interacting dipoles

NASA Astrophysics Data System (ADS)

Stokes, Adam; Nazir, Ahsan

2018-04-01

We consider a pair of dipoles such as Rydberg atoms for which direct electrostatic dipole–dipole interactions may be significantly larger than the coupling to transverse radiation. We derive a master equation using the Coulomb gauge, which naturally enables us to include the inter-dipole Coulomb energy within the system Hamiltonian rather than the interaction. In contrast, the standard master equation for a two-dipole system, which depends entirely on well-known gauge-invariant S-matrix elements, is usually derived using the multipolar gauge, wherein there is no explicit inter-dipole Coulomb interaction. We show using a generalised arbitrary-gauge light-matter Hamiltonian that this master equation is obtained in other gauges only if the inter-dipole Coulomb interaction is kept within the interaction Hamiltonian rather than the unperturbed part as in our derivation. Thus, our master equation depends on different S-matrix elements, which give separation-dependent corrections to the standard matrix elements describing resonant energy transfer and collective decay. The two master equations coincide in the large separation limit where static couplings are negligible. We provide an application of our master equation by finding separation-dependent corrections to the natural emission spectrum of the two-dipole system.

Bioinspired Design of Strong, Tough, and Highly Conductive Polyol-Polypyrrole Composites for Flexible Electronics.

PubMed

Gao, Fengxian; Zhang, Ning; Fang, Xiaodong; Ma, Mingming

2017-02-22

Inspired by the dynamic network structure of animal dermis, we have designed and synthesized a series of polyol-polypyrrole (polyol-PPy) composites. Polyols and polypyrrole are cross-linked by hydrogen bonding and electrostatic interactions to form a dynamic network, which helps to dissipate destructive energy. We have found a clear correlation between the mechanical properties of polyol-PPy composites and the polyols structure. Particularly, the PEE-PPy film shows both high strength and flexibility, leading to a remarkable tensile toughness comparable to cocoon silk. The combination of outstanding strength, ductility, and conductivity enables polyol-PPy composites (especially PEE-PPy) as potential electronic materials for making flexible electronics.

Insight into the adsorption of chloramphenicol on a vermiculite surface

NASA Astrophysics Data System (ADS)

Tri, Nguyen Ngoc; Carvalho, A. J. P.; Dordio, A. V.; Nguyen, Minh Tho; Trung, Nguyen Tien

2018-05-01

Four stable configurations were found upon adsorption of the chloramphenicol on a period slab model of the vermiculite surface, using the PBE and C09-vdW functionals in a projector-augmented wave (PAW) method approach. The adsorption is a strong chemisorption process, characterized by an adsorption energy of -106.5 kcal mol-1 at the most stable configuration. Stability of configurations contributed mainly by Mg⋯O/Cl attractive electrostatic interactions and C/Osbnd H⋯O hydrogen bonds. It is remarkable that the vermiculite is found to be a solid material with good potential to be used for adsorption and consequent removal of this type of antibiotic drugs.

A Monte Carlo (N,V,T) study of the stability of charged interfaces: A simulation on a hypersphere

NASA Astrophysics Data System (ADS)

Delville, A.; Pellenq, R. J.-M.; Caillol, J. M.

1997-05-01

We have used an exact expression of the Coulombic interactions derived on a hypersphere of an Euclidian space of dimension four to determine the swelling behavior of two infinite charged plates neutralized by exchangeable counterions. Monte Carlo simulations in the (N,V,T) ensemble allows for a derivation of short-ranged hard core repulsions and long-ranged electrostatic forces, which are the two components of the interionic forces in the context of the primitive model. Comparison with numerical results obtained by a classical Euclidian method illustrates the efficiency of the hyperspherical approach, especially at strong coupling between the charged particles, i.e., for divalent counterions and small plate separation.

Mechanisms of high-regularity periodic structuring of silicon surface by sub-MHz repetition rate ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Gnilitskyi, Iaroslav; Gruzdev, Vitaly; Bulgakova, Nadezhda M.; Mocek, Tomáš; Orazi, Leonardo

2016-10-01

Silicon is one of the most abundant materials which is used in many areas of modern research and technology. A variety of those applications require surface nanopatterning with minimum structure defects. However, the high-quality nanostructuring of large areas of silicon surface at industrially acceptable speed is still a challenge. Here, we report a rapid formation of highly regular laser-induced periodic surface structures (HR-LIPSS) in the regime of strong ablation by infrared femtosecond laser pulses at sub-MHz repetition rate. Parameters of the laser-surface interactions and obtained experimental results suggest an important role of electrostatically assisted bond softening in initiating the HR-LIPSS formation.

Investigation of the SERS Spectra of Hydroquinone Molecule Adsorbed on Titanium Dioxide

NASA Astrophysics Data System (ADS)

Polubotko, A. M.; Chelibanov, V. P.

2018-01-01

The paper analyzes the SERS spectrum of hydroquinone adsorbed on nanoparticles of titanium dioxide (TiO2). It is seen that the enhancement is stronger for a larger mean size of nanoparticles that is in agreement with an electrostatic approximation. In addition, it is found that there are the lines, which are forbidden in usual Raman spectra. There is also an enhancement caused both by the normal and tangential components of the electric field. This result is in agreement with the theory of SERS on semiconductor and dielectric substrates. The discovery of the forbidden lines indicates on the sufficiently large role of the strong quadrupole light-molecule interaction in such a system.

Antiswarming: Structure and dynamics of repulsive chemically active particles

NASA Astrophysics Data System (ADS)

Yan, Wen; Brady, John F.

2017-12-01

Chemically active Brownian particles with surface catalytic reactions may repel each other due to diffusiophoretic interactions in the reaction and product concentration fields. The system behavior can be described by a "chemical" coupling parameter Γc that compares the strength of diffusiophoretic repulsion to Brownian motion, and by a mapping to the classical electrostatic one component plasma (OCP) system. When confined to a constant-volume domain, body-centered cubic (bcc) crystals spontaneously form from random initial configurations when the repulsion is strong enough to overcome Brownian motion. Face-centered cubic (fcc) crystals may also be stable. The "melting point" of the "liquid-to-crystal transition" occurs at Γc≈140 for both bcc and fcc lattices.

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.

Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment.

PubMed

Perišić, Ognjen; Schlick, Tamar

2017-08-24

The linker histone (LH), an auxiliary protein that can bind to chromatin and interact with the linker DNA to form stem motifs, is a key element of chromatin compaction. By affecting the chromatin condensation level, it also plays an active role in gene expression. However, the presence and variable concentration of LH in chromatin fibers with different DNA linker lengths indicate that its folding and condensation are highly adaptable and dependent on the immediate nucleosome environment. Recent experimental studies revealed that the behavior of LH in mononucleosomes markedly differs from that in small nucleosome arrays, but the associated mechanism is unknown. Here we report a structural analysis of the behavior of LH in mononucleosomes and oligonucleosomes (2-6 nucleosomes) using mesoscale chromatin simulations. We show that the adapted stem configuration heavily depends on the strength of electrostatic interactions between LH and its parental DNA linkers, and that those interactions tend to be asymmetric in small oligonucleosome systems. Namely, LH in oligonucleosomes dominantly interacts with one DNA linker only, as opposed to mononucleosomes where LH has similar interactions with both linkers and forms a highly stable nucleosome stem. Although we show that the LH condensation depends sensitively on the electrostatic interactions with entering and exiting DNA linkers, other interactions, especially by nonparental cores and nonparental linkers, modulate the structural condensation by softening LH and thus making oligonucleosomes more flexible, in comparison to to mono- and dinucleosomes. We also find that the overall LH/chromatin interactions sensitively depend on the linker length because the linker length determines the maximal nucleosome stem length. For mononucleosomes with DNA linkers shorter than LH, LH condenses fully, while for DNA linkers comparable or longer than LH, the LH extension in mononucleosomes strongly follows the length of DNA linkers, unhampered by neighboring linker histones. Thus, LH is more condensed for mononucleosomes with short linkers, compared to oligonucleosomes, and its orientation is variable and highly environment-dependent. More generally, the work underscores the agility of LH whose folding dynamics critically controls genomic packaging and gene expression.

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.

The Thermodynamics of Anion Complexation to Nonpolar Pockets.

PubMed

Sullivan, Matthew R; Yao, Wei; Tang, Du; Ashbaugh, Henry S; Gibb, Bruce C

2018-02-08

The interactions between nonpolar surfaces and polarizable anions lie in a gray area between the hydrophobic and Hofmeister effects. To assess the affinity of these interactions, NMR and ITC were used to probe the thermodynamics of eight anions binding to four different hosts whose pockets each consist primarily of hydrocarbon. Two classes of host were examined: cavitands and cyclodextrins. For all hosts, anion affinity was found to follow the Hofmeister series, with associations ranging from 1.6-5.7 kcal mol -1 . Despite the fact that cavitand hosts 1 and 2 possess intrinsic negative electrostatic fields, it was determined that these more enveloping hosts generally bound anions more strongly. The observation that the four hosts each possess specific anion affinities that cannot be readily explained by their structures, points to the importance of counter cations and the solvation of the "empty" hosts, free guests, and host-guest complexes, in defining the affinity.

Graphene-induced band gap renormalization in polythiophene: a many-body perturbation study

NASA Astrophysics Data System (ADS)

Marsusi, F.; Fedorov, I. A.; Gerivani, S.

2018-01-01

Density functional theory and many-body perturbation theory at the G0W0 level are employed to study the electronic properties of polythiophene (PT) adsorbed on the graphene surface. Analysis of the charge density difference shows that substrate-adsorbate interaction leads to a strong physisorption and interfacial electric dipole moment formation. The electrostatic potential displays a  -0.19 eV shift in the graphene work function from its initial value of 4.53 eV, as the result of the interaction. The LDA band gap of the polymer does not show any change. However, the band structure exhibits weak orbital hybridizations resulting from slight overlapping between the polymer and graphene states wave functions. The interfacial polarization effects on the band gap and levels alignment are investigated at the G0W0 level and show a notable reduction of PT band gap compared to that of the isolated chain.

Structural characterization and Hirshfeld surface analysis of racemic baclofen

NASA Astrophysics Data System (ADS)

Maniukiewicz, Waldemar; Oracz, Monika; Sieroń, Lesław

2016-11-01

The crystal structure of baclofen, (R,S) [4-amino-3-(4-chlorophenyl)butanoic acid], (C10H12ClNO2, Mr = 213.66) has been determined by single crystal X-ray diffraction analysis. The title compound crystallizes in the orthorhombic space group Pbca (No. 61) with a = 9.2704(5), b = 7.0397(4), c = 30.4015(15) Å, V = 1984.0(2) Å3 and Z = 8. The molecules exist as zwitterions, adopting a gauche conformation with respect to the Cαsbnd Cβ bond, and held in a cross-linked chain arrangement by strong Nsbnd H⋯O hydrogen bonds and Csbnd Cl⋯π interactions. The electrostatic molecular potential as well as the intermolecular interactions of the title compound were analyzed by the Hirshfeld surfaces. The FT-IR spectrum is also reported. The DTA, TG and DTG results indicate that baclofen is stable up to 205 °C.

Electric papers of graphene-coated Co₃O₄ fibers for high-performance lithium-ion batteries.

PubMed

Yang, Xiaoling; Fan, Kaicai; Zhu, Yihua; Shen, Jianhua; Jiang, Xin; Zhao, Peng; Luan, Shaorong; Li, Chunzhong

2013-02-01

A facile strategy to synthesize the novel composite paper of graphene nanosheets (GNS) coated Co(3)O(4) fibers is reported as an advanced anode material for high-performance lithium-ion batteries (LIBs). The GNS were able to deposit onto Co(3)O(4) fibers and form the coating via electrostatic interactions. The unique hybrid paper is evaluated as an anode electrode for LIBs, and it exhibits a very large reversible capacity (∼840 mA h g(-1) after 40 cycles), excellent cyclic stability and good rate capacity. The substantially excellent electrochemical performance of the graphene/Co(3)O(4) composite paper is the result from its unique features. Notably, the flexible structure of graphenic scaffold and the strong interaction between graphene and Co(3)O(4) fibers are beneficial for providing excellent electronic conductivity, short transportation length for lithium ions, and elastomeric space to accommodate volume varies upon Li(+) insertion/extraction.

Electrostatics of polymer translocation events in electrolyte solutions.

PubMed

Buyukdagli, Sahin; Ala-Nissila, T

2016-07-07

We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based membranes are driven by a competition between the repulsive DNA-image-charge interactions and the attractive coupling between the DNA segments on the trans and the cis sides of the membrane. The latter effect is induced by the reduction of the coupling by the dielectric membrane. In strong salt solutions where the repulsive image-charge effects dominate the attractive trans-cis coupling, the DNA molecule encounters a translocation barrier of ≈10 kBT. In dilute electrolytes, the trans-cis coupling takes over image-charge forces and the membrane becomes a metastable attraction point that can trap translocating polymers over long time intervals. This mechanism can be used in translocation experiments in order to control DNA motion by tuning the salt concentration of the solution.

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.

The interplay between screening properties and colloid anisotropy: towards a reliable pair potential for disc-like charged particles.

PubMed

Agra, R; Trizac, E; Bocquet, L

2004-12-01

The electrostatic potential of a highly charged disc (clay platelet) in an electrolyte is investigated in detail. The corresponding non-linear Poisson-Boltzmann (PB) equation is solved numerically, and we show that the far-field behaviour (relevant for colloidal interactions in dilute suspensions) is exactly that obtained within linearized PB theory, with the surface boundary condition of a uniform potential. The latter linear problem is solved by a new semi-analytical procedure and both the potential amplitude (quantified by an effective charge) and potential anisotropy coincide closely within PB and linearized PB, provided the disc bare charge is high enough. This anisotropy remains at all scales; it is encoded in a function that may vary over several orders of magnitude depending on the azimuthal angle under which the disc is seen. The results allow to construct a pair potential for discs interaction, that is strongly orientation dependent.

Conformational reduction of DOPA in the gas phase studied by laser desorption supersonic jet laser spectroscopy.

PubMed

Ishiuchi, Shun-ichi; Mitsuda, Haruhiko; Asakawa, Toshiro; Miyazaki, Mitsuhiko; Fujii, Masaaki

2011-05-07

The conformational reduction in catecholamine neurotransmitters was studied by resonance enhanced multi photon ionization (REMPI), ultraviolet-ultraviolet (UV-UV) hole burning and infrared (IR) dip spectroscopy with applying a laser desorption supersonic jet technique to DOPA, which is one of the catecholamine neurotransmitters and has one more phenolic OH group than tyrosine. It is concluded that DOPA has a single observable conformer in the gas phase at low temperature. Quantum chemical calculations at several levels with or without the dispersion correction were also carried out to study stable conformations. From the comparison between the computational IR spectra and the experimental ones, the most stable structure was determined. It is strongly suggested that the conformational reduction is caused by electrostatic interactions, such as a dipole-dipole interaction, between the chain and OH groups. This journal is © the Owner Societies 2011

Diffuse-charge dynamics of ionic liquids in electrochemical systems.

PubMed

Zhao, Hui

2011-11-01

We employ a continuum theory of solvent-free ionic liquids accounting for both short-range electrostatic correlations and steric effects (finite ion size) [Bazant et al., Phys. Rev. Lett. 106, 046102 (2011)] to study the response of a model microelectrochemical cell to a step voltage. The model problem consists of a 1-1 symmetric ionic liquid between two parallel blocking electrodes, neglecting any transverse transport phenomena. Matched asymptotic expansions in the limit of thin double layers are applied to analyze the resulting one-dimensional equations and study the overall charge-time relation in the weakly nonlinear regime. One important conclusion is that our simple scaling analysis suggests that the length scale √(λ*(D)l*(c)) accurately characterizes the double-layer structure of ionic liquids with strong electrostatic correlations where l*(c) is the electrostatic correlation length (in contrast, the Debye screening length λ*(D) is the primary double-layer length for electrolytes) and the response time of λ(D)(*3/2)L*/(D*l(c)(1/2)) (not λ*(D)L*/D* that is the primary charging time of electrolytes) is the correct charging time scale of ionic liquids with strong electrostatic correlations where D* is the diffusivity and L* is the separation length of the cell. With these two new scales, data of both electric potential versus distance from the electrode and the total diffuse charge versus time collapse onto each individual master curve in the presence of strong electrostatic correlations. In addition, the dependance of the total diffuse charge on steric effects, short-range correlations, and driving voltages is thoroughly examined. The results from the asymptotic analysis are compared favorably with those from full numerical simulations. Finally, the absorption of excess salt by the double layer creates a depletion region outside the double layer. Such salt depletion may bring a correction to the leading order terms and break down the weakly nonlinear analysis. A criterion which justifies the weakly nonlinear analysis is verified with numerical simulations.

Parametric Excitation of Electrostatic Dust-Modes by Ion-Cyclotron Waves in a Dusty Plasma

NASA Astrophysics Data System (ADS)

Islam, M. K.; Salahuddin, M.; Ferdous, T.; Salimullah, M.

A large amplitude electrostatic ion-cyclotron wave propagating through a magnetized and collisional dusty plasma undergoes strong parametric instability off the low-frequency dust-modes. The presence of the dust-component has effect on the nonlinear coupling via the dust-modes. The ion-neutral collisions are seen to have significant effect on the damping and consequent overall growth of the parametric excitation process.

Laser Accelerator

DTIC Science & Technology

2014-09-01

hollow metal sphere. Voltages of over 10 MV can be reached if used with an insulating gas. Corona discharge limits all electrostatic accelerators to...laser field. Lasers can have strong electric fields with frequencies high enough to avoid corona formation and break- down. The key is to couple the...leading to a spark discharge in the accelerator and thus a breakdown of the electrostatic field [6], [7]. Figure 1.1: Cockroft-Walton cascade generator

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.

Adsorption of GA module onto graphene and graphene oxide: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Chen, Junlang; Wang, Xiaogang; Dai, Chaoqing; Chen, Shude; Tu, Yusong

2014-08-01

Using all-atom molecular dynamics (MD) simulation, we have investigated the adsorption of protein GA module (GA53) onto graphene oxide (GO), compared with similar adsorption onto pristine graphene (PG). We find that: (1) the protein GA53 can be easily and firmly adsorbed onto the surface of GO and PG, but the binding sites are not specific; the main difference is that the secondary structure of GA53 can be well preserved in protein-GO system, while GA53 will partially lose its secondary structure after adsorbed on PG. (2) in protein-GO system, hydroxyl and epoxy groups increase the distance between protein and GO, which weaken their vdW interactions, meanwhile, hydrogen bonds and electrostatic interactions enhance their binding affinity. In protein-PG system, strong vdW interactions between residues of GA53 and PG have destroyed its secondary structure. (3) π-π stacking interactions still exist between aromatic residues and both the basal plane of GO and PG. In comparison with PG, our results suggest that GO presents better biocompatibility to preserve protein secondary structure when simultaneously absorbing protein.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

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

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.

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.

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.

Pentavalent neptunyl ([OΞNpΞO] +) cation–cation interactions in aqueous/polar organic mixed-solvent media

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

Burn, Adam G.; Martin, Leigh R.; Nash, Kenneth L.

Bonding interactions between polyvalent cations and oxo-anions are well known and characterized by predictably favorable Gibbs energies in solution-phase coordination chemistry. In contrast, interactions between ions of like charge are generally expected to be repulsive and strongly influenced by cation solvation. An exception to this instinctive rule is found in the existence of complexes resulting from interactions of pentavalent actinyl cations ([O≡An≡O] +) with selected polyvalent cations. Such cation–cation complexes have been known to exist since the 1960s, when they were first reported by Sullivan and co-workers. The weak actinyl cation–cation complex, resulting from a bonding interaction between a pentavalentmore » linear dioxo actinyl cation donor and hexavalent actinyl or trivalent/tetravalent metal cation acceptor, has been most commonly seen in media in which water activities are reduced, principally highly-salted aqueous media. Such interactions of pentavalent actinides are of relevance in ongoing research that focuses on advanced nuclear fuel processing systems based on the upper oxidation states of americium. This investigation focuses on exploring the thermodynamic stability of complexes between selected highly-charged metal cations (Al 3+, Sc 3+, Cr 3+, Fe 3+, In 3+ and UO 2+ 2) and the pentavalent neptunyl cation (NpO + 2, whose coordination chemistry is similar to that of AmO + 2 while exhibiting significantly greater oxidation state stability) in aqueous–polar organic mixed-solvents. As a result, the Gibbs energies for the cation–cation complexation reactions are correlated with general features of electrostatic bonding models; the NpO + 2 • Cr 3+ complex exhibits unexpectedly strong interactions that may indicate significant covalency in the cation–cation bonding interaction.« less

Pentavalent neptunyl ([OΞNpΞO] +) cation–cation interactions in aqueous/polar organic mixed-solvent media

DOE PAGES

Burn, Adam G.; Martin, Leigh R.; Nash, Kenneth L.

2017-06-17

Bonding interactions between polyvalent cations and oxo-anions are well known and characterized by predictably favorable Gibbs energies in solution-phase coordination chemistry. In contrast, interactions between ions of like charge are generally expected to be repulsive and strongly influenced by cation solvation. An exception to this instinctive rule is found in the existence of complexes resulting from interactions of pentavalent actinyl cations ([O≡An≡O] +) with selected polyvalent cations. Such cation–cation complexes have been known to exist since the 1960s, when they were first reported by Sullivan and co-workers. The weak actinyl cation–cation complex, resulting from a bonding interaction between a pentavalentmore » linear dioxo actinyl cation donor and hexavalent actinyl or trivalent/tetravalent metal cation acceptor, has been most commonly seen in media in which water activities are reduced, principally highly-salted aqueous media. Such interactions of pentavalent actinides are of relevance in ongoing research that focuses on advanced nuclear fuel processing systems based on the upper oxidation states of americium. This investigation focuses on exploring the thermodynamic stability of complexes between selected highly-charged metal cations (Al 3+, Sc 3+, Cr 3+, Fe 3+, In 3+ and UO 2+ 2) and the pentavalent neptunyl cation (NpO + 2, whose coordination chemistry is similar to that of AmO + 2 while exhibiting significantly greater oxidation state stability) in aqueous–polar organic mixed-solvents. As a result, the Gibbs energies for the cation–cation complexation reactions are correlated with general features of electrostatic bonding models; the NpO + 2 • Cr 3+ complex exhibits unexpectedly strong interactions that may indicate significant covalency in the cation–cation bonding interaction.« less

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)

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