Electrostatic Patterns Research Articles

Theoretical Investigations of a point mutation affecting H5 Hemagglutinin’s receptor binding preference

The avian influenza A H5N1 virus is a subtype of influenza A virus (IAV) that causes a highly infectious and severe respiratory illness in birds and poses significant economic losses in poultry farming. To infect host cell, the virus uses its surface glycoprotein named Hemagglutinin (HA) to recognize and to interact with the host cell receptor containing either α2,6- (SAα2,6 Gal) or α2,3-linked Sialic Acid (SAα2,3 Gal). The H5N1 virus has not yet acquired the capability for efficient human-to-human transmission. However, studies have demonstrated that even a single amino acid substitution in the HA can switch its glycan receptor preference from the avian-type SAα2,3 Gal to the human-type SAα2,6 Gal. The present study aims to explain the underlying mechanism of a mutation (D94N) on the H5 HA that causes the protein to change its glycan receptor-binding preference using molecular dynamics (MD) simulations. Our results reveal that the mutation alters the electrostatic interactions pattern near the HA receptor binding pocket, leading to a reduced stability for the HA-avian-type SAα2,3 Gal complex. On the other hand, the detrimental effect of the mutation D94N is not observed in the HA-human-type SAα2,6 Gal complex due to the glycan's capability to switch its topology.

Nanotube Slidetronics.

One-dimensional slidetronics is predicted for double-walled boron-nitride nanotubes. Local electrostatic polarization patterns along the body of the nanotube are found to be determined by the nature of the two nanotube walls, their relative configuration, and circumferential faceting modulation during coaxial interwall sliding. By careful choice of chiral indices, chiral polarization patterns can emerge that spiral around the nanotube circumference. The potential usage of the discovered slidetronic effect for low-dimensional nanogenerators is briefly discussed.

First detection and genome analysis of simple nosed bat polyomaviruses in Central Europe.

Polyomaviruses (PyVs) are known to infect a diverse range of vertebrate host species. We report the discovery of PyVs in vesper bats (family Vespertilionidae) from sampling in Central Europe. Seven partial VP1 sequences from different PyVs were detected in samples originating from six distinct vesper bat species. Using a methodology based on conserved segments within the major capsid virus protein 1 (VP1) among known PyVs, the complete genomes of two different novel bat PyVs were determined. The genetic distances of the large T antigen coding sequences from these PyVs compared to previously-described bat PyVs exceeded 15% meriting classification as representatives of two novel PyV species: Alphapolyomavirus epserotinus and Alphapolyomavirus myodaubentonii. Phylogenetic analysis revealed that both belong to the genus Alphapolyomavirus and clustered together with high confidence in clades including other bat alphapolyomaviruses reported from China, South America and Africa. In silico protein modeling of the VP1 subunits and capsid pentamers, and electrostatic surface potential comparison of the pentamers showed significant differences between the reference template (murine polyomavirus) and the novel bat PyVs. An electrostatic potential difference pattern between the two bat VP1 pentamers was also revealed. Disaccharide molecular docking studies showed that the reference template and both bat PyVs possess the typical shallow sialic acid-binding site located between two VP1 subunits, with relevant oligosaccharide-binding affinities. The characterisation of these novel bat PyVs and the reported properties of their capsid proteins will potentially contribute in the elucidation of the conditions creating the host-pathogen restrictions associated with these viruses.

Structure-reactivity relationships of sanshools as the key pungent dietary components in foods: A DFT study

The structural basis behind the pungency of sanshools remains largely unknown at present. Herein, the crucial geometrical, electronic and energetic properties of sanshools have been explored and correlated with the pungency computationally. Our results have revealed the preferred reactive sites or area in sanshools responsible for their degradation, as well as their probable electrostatic and hydrophobic interaction patterns with the pungent receptors. Increasing the solvent polarity in the calculations or the conjugated CC numbers increase their chemical instability. The correlation between the polar/nonpolar/negative/positive surface area and pungency indicates the necessity of the amide, CC bonds, HO groups and carbon chains. The autoxidation may occur more probably through the radical addition than hydrogen abstraction during their applications like the process of relevant foods, and increasing the conjugated CC numbers weakens the corresponding allylic CH bonds. This study would benefit the mature pungent mechanistic understanding and practical applications in the pungent foods.

High‐Resolution 3D Deposition of Electrospun Fibers on Patterned Dielectric Elastomers

Electrostatic patterning has improved the performance of devices incorporating electrospun fibers in a wide variety of applications. However, the impact of process parameters on the final fiber pattern in these systems is rarely analyzed. Herein, a systematic analytical approach is developed to define quantitative metrics related to fiber patterning. Three‐dimensional patterned dielectric elastomer collectors are fabricated via solution‐casting polydimethylsiloxane with embedded carbon black or liquid metal droplets. Fiber patterning metrics are used to evaluate the effect of collector parameters such as insulating layer thickness, electrical ground surface area, and three‐dimensional pattern geometry. Dielectric layer parameters such as conductive material concentration and particle diameter are also investigated. Using this framework, the best‐performing collector is shown to improve selectivity 30‐fold, uniformity ninefold, reproducibility eightfold, and increase fiber volume by one order of magnitude. Furthermore, eutectic gallium indium liquid metal and scaled‐up pattern geometries demonstrate the tunability of this approach and broad applicability of systematic fiber pattern analysis. This rational approach to patterned fiber development can be applied to virtually any method or pattern to better understand the fiber patterning processes.

Electrostatic discharge pattern and energy probability distribution of different polarity powders in industrial silo

Understanding the electrostatic discharge behavior of the charged powder is significant for avoiding fire or explosion in the silo. The electrostatic discharge of different polarity powders is not fully revealed, especially for the discharge pattern and the discharge energy distribution. In this study, the electrostatic discharge of different polarity powders during the filling process was examined to explore the discharge behavior in an industrial silo. The results show that the discharge of positively charged powder was compact and the discharge of negatively charged powder was divergent. The point, linear and dendrite discharge were found in the positive charging process. The discharge position and development process of different polarity powders were revealed by the electric field simulation. The relationship among the discharge period, powder polarity and heap surface area were indicated. The probability density distribution of discharge energy on the powder heap surface of 2.7 m was proposed to thoroughly understand the discharge energy of charged powder in the silo. The discharge of positively charged powder might induce more energy release, which was more dangerous than that of negatively charged powder in the silo.

Mutation of Basic Residues R283, R286, and K288 in the Matrix Protein of Newcastle Disease Virus Attenuates Viral Replication and Pathogenicity.

The matrix (M) protein of Newcastle disease virus (NDV) contains large numbers of unevenly distributed basic residues, but the precise function of most basic residues in the M protein remains enigmatic. We previously demonstrated that the C-terminus (aa 264-313) of M protein interacted with the extra-terminal (ET) domain of chicken bromodomain-containing protein 2 (chBRD2), which promoted NDV replication by downregulating chBRD2 expression and facilitating viral RNA synthesis and transcription. However, the key amino acid sites determining M's interaction with chBRD2/ET and their roles in the replication and pathogenicity of NDV are not known. In this study, three basic residues-R283, R286, and K288-in the NDV M protein were verified to be responsible for its interaction with chBRD2/ET. In addition, mutation of these basic residues (R283A/R286A/K288A) in the M protein changed its electrostatic pattern and abrogated the decreased expression of endogenic chBRD2. Moreover, a recombinant virus harboring these mutations resulted in a pathotype change of NDV and attenuated viral replication and pathogenicity in chickens due to the decreased viral RNA synthesis and transcription. Our findings therefore provide a better understanding of the crucial biological functions of M's basic residues and also aid in understanding the poorly understood pathogenesis of NDV.

Three dimensional modelling of mutant Kir2.1 channel PIP2 interactions help stratify arrhythmia severity in Andersen Tawil syndrome type 1

Abstract Background Andersen-Tawil type 1 (ATS1) is associated with loss-of-function mutations in the inward rectifier potassium channel Kir2.1, which controls cardiac excitability and impulse conduction. Phosphatidylinositol-4,5-bisphosphate (PIP2) acts as an essential cofactor regulating the opening of Kir2.1 channels. Fifty percent of reported ATS1 mutations affect Kir2.1-PIP2 interactions, leading to ECG defects, ventricular arrhythmias and sudden cardiac death (SCD) by mechanisms that are poorly understood. Purpose To test the hypothesis that the degree of arrhythmogenic severity of ATS1 mutations disrupting PIP2-Kir2.1 binding may be predicted by the level of polarization of the mutant Kir2.1 channel pore. Methods We first used a statistical mean value approach to classify the 40 known arrhythmogenic ATS1 mutations impacting Kir2.1-PIP2 interaction (N=260 individuals) according to arrhythmogenic severity, ranging from SCD through ventricular bigeminy and QT prolongation. We then generated 3D in-silico atomic models of the wildtype channel and the 10 mutant channels with the most severe arrhythmic phenotype to assess the mechanism of the structural defects associated with Kir2.1-PIP2 disruption. Results Our cardiac lethality scoring stratifying Kir2.1 mutations according to arrhythmogenic severity was validated by three additional biostatical quantitative measures. On in-silico modelling, wildtype Kir2.1 channels without PIP2 binding had transmembrane and cytoplasmic pore radius of 1.5 and 3 Å, respectively. Kir2.1-PIP2 interactions increased transmembrane and cytoplasmic pore radius to 3 and 6 Å, respectively. All 10 Kir2.1 mutations had similar transmembrane and cytoplasmic pore radius of ∼1.0 and ∼3.0 Å, respectively. The most severe mutations yielded pore channels with highly polarized electrostatic forces. Remarkably, simulations showed a descending electrostatic pattern at the transmembrane region of PIP2 binding, where the more severe the mutation, the more positive that region was. Structural changes produced by mutations correlated with cardiac severity (R2=0.51; p<0.005) in that the most drastically altered protein structure correlated with the most severe arrhythmic phenotype. Conclusions Computer simulations of mutant Kir2.1 channel structure from the most arrhythmogenic to the least arrhythmogenic predict a gradual decrease in polarization of electrostatic forces along the Kir2.1 channel pore. The results reveal a novel mechanistic stratification of arrhythmogenic severity of ATS1 mutant Kir2.1 channel-PIP2 interactions and open new pathways for developing more personalized ATS1 patient therapies. Funding Acknowledgement Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): La Caixa Banking Foundation under the project code HR18-00304Fundaciόn La Marato TV3: Ayudas a la investigaciόn en enfermedades raras 2020

Quasi-linear and Plateaus-like Tunneling Magnetoresistance in Graphene-based Tunable Magnetic Barrier Nanostructures

The effect of electrostatic and magnetic vector potentials pattern on electrical properties and the tunneling magnetoresistance in graphene junction with periodic magnetic vector potentials are theoretically investigated using the transfer matrix method. The magnetic structure on graphene can control the direction of the magnetizations which correspond to the parallel and anti-parallel (AP) configurations. In AP magnetic structures with the applied gate voltage pattern, USUBA/SUB (U₁ = U₂), the shift of the conductance-peak position as a function of Fermi energy. The peak corresponds to resonant tunneling, where the incidence energy of the tunneling electron equals the confinement energy, and the conductance peak decrease approximately linearly with increasing electrostatic potential. The peak position occurs at ESUBF/SUB = 0.5U where it is shifted to higher Fermi energy with higher gate potential, but for the case of USUBB/SUB (U₁ = -U₂), the peak height is reduced rapidly, and the width increase as gate potential increases. Because of the periodic magnetic field with zero spatial average in the antiparallel structure, we found that the minimum conductivity decreases with increasing magnetic energy. They show suppression of Klein tunneling which occurs in the zero-conductance plateaus and leads to the robust magnetoresistance plateau and large positive magnetoresistance appears below magnetic energy. For the case of USUBA/SUB and ESUBF/SUB more than magnetic energy, we found that the quasi-linear magnetoresistance feature is applied by an electric field instead of the usual magnetically driven magnetoresistance.

Fixing zein at the fibrillar carboxymethyl cellulose toward an amphiphilic nano-network

In this study, co-assembled protein-polysaccharide complexes (ZCs) were prepared by fixing zein nanoparticles at the fibrillar carboxymethyl cellulose (CMC) by pH-driven anti-solvent precipitation. The complexation boosted the dispersity of zein from 17.3% to 88.6%. Scanning electron microscopy and atomic force microscopy confirmed the formation of network structures where the fibrous polysaccharides inserted into the interval of granular proteins. Circular dichroism spectrum, fluorescence spectrum, and X-ray diffraction verified the electrostatic interaction pattern between zein and CMC. Besides, the ZCs presented favorable amphiphilic properties, and the electrostatic interaction between zein and CMC can be fine-tuned by the substitution degree (DS) of carboxymethyl in CMC. Therefore, the Pickering emulsions stabilized by ZCs had controllable size and long-term stability using DS as a stimulus. Our study offers a novel strategy developing bio-based materials as novel stabilizers of Pickering emulsions.

Field evaluation of two types of EDS-integrated PV modules with different configurations and surface properties

In this study, two prototypes of PV modules with integrated electrodynamic dust shield (EDS) were characterized in the lab and tested in the field to determine their effectiveness in soiling mitigation. The surface properties of the prototype modules’ front cover were measured to evaluate their effects on the EDS dust removal performance. The soiling of each EDS-PV module was assessed based on its PV power output, from which the EDS cleaning efficiency was quantified in field conditions during winter and summer periods. The dust removal efficiency of glass-surface EDS-PV modules was approximately 30%, about three times higher than that of polymer-surface modules. The EDS technology cleaned more effectively in dry and windy weather conditions. The EDS modules’ front surfaces varied significantly with respect to thickness, hydrophobicity, and the electrostatic potential pattern, contributing to the variation of the EDS efficiency of modules. The EDS-PV module with a hydrophobic polymer surface had a higher soiling rate and lower cleaning efficiency than a thinner, hydrophilic glass surface. The results of this study may help improve design and manufacturing methods for more efficient and robust EDS devices integrated into PV modules.

Absorption of Phosphonium Cations and Dications into a Hydrated POPC Phospholipid Bilayer: A Computational Study.

Molecular dynamics (MD) based on an empirical force field is applied to investigate the effect of phosphonium cations ([P6,6,6,6]+) and geminal dications ([DxC10]2+) inserted at T = 300 K into the hydration layer separating planar POPC phospholipid bilayers. Up to high concentration, nearly every added cation and dication becomes absorbed into the lipid phase. Absorption takes place during several microseconds and is virtually irreversible. The neutralizing counterions ([Cl]−, in the present simulation) remain dissolved in water, giving origin to the charge separation and the strong electrostatic double layer at the water/lipid interface. Incorporation of cations and dications changes the properties of the lipid bilayer such as diffusion, viscosity, and the electrostatic pattern. At high ionic concentration, the bilayer acquires a long-wavelength standing undulation, corresponding to a change of phase from fluid planar to ripple. All these changes are potentially able to affect processes relevant in the context of cell biology. The major difference between cations and dications concerns the kinetics of absorption, which takes place nearly two times faster in the [P6,6,6,6]+ case, and for [DxC10]2+ dications displays a marked separation into two-stages, corresponding to the easy absorption of the first phosphonium head of the dication and the somewhat more activated absorption of the second phosphonium head of each dication.

Chitosan Functionalization: Covalent and Non-Covalent Interactions and Their Characterization.

Chitosan (CS) is a natural biopolymer that has gained great interest in many research fields due to its promising biocompatibility, biodegradability, and favorable mechanical properties. The versatility of this low-cost polymer allows for a variety of chemical modifications via covalent conjugation and non-covalent interactions, which are designed to further improve the properties of interest. This review aims at presenting the broad range of functionalization strategies reported over the last five years to reflect the state-of-the art of CS derivatization. We start by describing covalent modifications performed on the CS backbone, followed by non-covalent CS modifications involving small molecules, proteins, and metal adjuvants. An overview of CS-based systems involving both covalent and electrostatic modification patterns is then presented. Finally, a special focus will be given on the characterization techniques commonly used to qualify the composition and physical properties of CS derivatives.

Self-Complementary Zwitterionic Peptides Direct Nanoparticle Assembly and Enable Enzymatic Selection of Endocytic Pathways.

Supramolecular self-assembly in biological systems holds promise to convert and amplify disease-specific signals to physical or mechanical signals that can direct cell fate. However, it remains challenging to design physiologically stable self-assembling systems that demonstrate tunable and predictable behavior. Here, the use of zwitterionic tetrapeptide modalities to direct nanoparticle assembly under physiological conditions is reported. The self-assembly of gold nanoparticles can be activated by enzymatic unveiling of surface-bound zwitterionic tetrapeptides through matrix metalloprotease-9 (MMP-9), which is overexpressed by cancer cells. This robust nanoparticle assembly is achieved by multivalent, self-complementary interactions of the zwitterionic tetrapeptides. In cancer cells that overexpress MMP-9, the nanoparticle assembly process occurs near the cell membrane and causes size-induced selection of cellular uptake mechanism, resulting in diminished cell growth. The enzyme responsiveness, and therefore, indirectly, the uptake route of the system can be programmed by customizing the peptide sequence: a simple inversion of the two amino acids at the cleavage site completely inactivates the enzyme responsiveness, self-assembly, and consequently changes the endocytic pathway. This robust self-complementary, zwitterionic peptide design demonstrates the use of enzyme-activated electrostatic side-chain patterns as powerful and customizable peptide modalities to program nanoparticle self-assembly and alter cellular response in biological context.

Molecular electrostatic potential and pattern recognition models to design potentially active pentamidine derivatives against Trypanosoma brucei rhodesiense

Molecular electrostatic potential (MEP) and pattern recognition (PR) were used to draw potentially active pentamidine derivatives against Trypanosome brucei rhodesiense (T. b. rhodesiense). PR models: Principal Component Analysis, PCA model; Hierarchical Cluster Analysis, HCA model; K-Nearest Neighbor, KNN model; Soft Independent Modeling of Class Analogy, SIMCA model; and Stepwise Discriminant Analysis, SDA model, were built by reducing the dimensionality of a data matrix to twenty-eight pentamidine derivatives and allowed the compounds to be classified into two classes: more active and less active, according to their degrees of activity against T. b. rhodesiense. The study outlined that the properties HOMO (highest occupied molecular orbital) energy, VOL (molecular volume), and ASA_P (water accessible surface area of all polar (½qi½³0. 2) atoms) are the most relevant for the construction of the models. The key structural features required for biological activity investigated through MEP were used as guidelines in the design of thirteen new compounds, which were evaluated by PR models as more active or less active against T. b. rhodesiense. The application of PR models indicated nine promising compounds (29, 30, 31, 32, 33, 36, 37, 39, and 40) for synthesis and biological assays.

Static and Dynamic Analysis of Electrostatically Actuated MEMS Shallow Arches for Various Air-Gap Configurations.

In this research, we investigate the structural behavior, including the snap-through and pull-in instabilities, of in-plane microelectromechanical COSINE-shaped and electrically actuated clamped-clamped micro-beams resonators. The work examines various electrostatic actuation patterns including uniform and non-uniform parallel-plates airgap arrangements, which offer options to actuate the arches in the opposite and same direction of their curvature. The nonlinear equation of motion of a shallow arch is discretized into a reduced-order model based on the Galerkin’s expansion method, which is then numerically solved. Static responses are examined for various DC electrostatic loads starting from small values to large values near pull-in and snap-through instability ranges, if any. The eigenvalue problem of the micro-beam is solved revealing the variations of the first four natural frequencies as varying the DC load. Various simulations are carried out for several case studies of shallow arches of various geometrical parameters and airgap arrangements, which demonstrate rich and diverse static and dynamic behaviors. Results show few cases with multi-states and hysteresis behaviors where some with only the pull-in instability and others with both snap-through buckling and pull-in instabilities. It is found that the micro-arches behaviors are very sensitive to the electrode’s configuration. The studied configurations reveal different possibilities to control the pull-in and snap-through instabilities, which can be used for improving arches static stroke range as actuators and for realizing wide-range tunable micro-resonators.

Electrostatic patterning on graphene with dipolar self-assembly.

We have investigated the influence of electric dipole moment in different periodic two-dimensional network on the electronic structure properties of graphene. Although the control of doping level in graphene within a van der Waals heterostructure constitutes a difficult task, the dipolar nature of the different molecular stacks can be used to control its electrostatic properties. First, we demonstrate that the orientation and magnitude of the adsorbed molecular dipole moments allow to control the electrical behaviour of graphene, and acts as an electrostatic gate that shifts neutrality point of graphene to behave as n- or p-doped materials. Then, we show that the presence of local dipole moment in SAN induces an electrostatic potential in graphene that creates well-defined patterned regions with different electronic characteristics that would influence the confinement of molecular species.

Electromechanical coupling in elastomers: a correlation between electrostatic potential and fatigue failure.

The recent discovery of electromechanical coupling in elastomers showed periodic electrification in phase with rubber stretching but following different electrostatic potential patterns. In this work, a Kelvin electrode monitored silicone and natural rubber electrification for extended periods until the rubber tubing underwent rupture. The electric potential of the rubber follows regular, quasi-sinusoidal patterns at the beginning and during the whole run, except when close to rubber fatigue failure, changing into complex waveforms. The attractors on natural latex and silicone rubber become chaotic at roughly 50 seconds before rubber rupture when the nearby orbits diverge wildly. Thus, mechanical-to-electrical transduction in rubber alerts fatigue failure nearly one minute ahead of the breakdown. Moreover, electrostatic potential maps of stretched rubbers show the electrification of the rupture sites, evidencing the electrostatic contribution to the breakdown. These results show the convenient features of electromechanical coupling in rubbers for the non-contact, real-time prediction of the rubber fatigue failure, adding to the possibility of environmental energy harvesting.

Whole Genome Identification of Potential G-Quadruplexes and Analysis of the G-Quadruplex Binding Domain for SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about the G-quadruplexes of the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes in both positive and negative-sense viral strands. The identified potential G-quadruplexes exhibited similar features to the G-quadruplexes detected in the human transcriptome. Within some bat- and pangolin-related betacoronaviruses, the G-tracts rather than the loops were under heightened selective constraints. We also found that the amino acid sequence similar to SUD (SARS-unique domain) was retained in SARS-CoV-2 but depleted in some other coronaviruses that can infect humans. Further analysis revealed that the amino acid residues related to the binding affinity of G-quadruplexes were conserved among 16,466 SARS-CoV-2 samples. Moreover, the dimer of the SUD-homology structure in SARS-CoV-2 displayed similar electrostatic potential patterns to the SUD dimer from SARS. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.

Metal ions shape \u03b1-synuclein

α-Synuclein is an intrinsically disordered protein that can self-aggregate and plays a major role in Parkinson’s disease (PD). Elevated levels of certain metal ions are found in protein aggregates in neurons of people suffering from PD, and environmental exposure has also been linked with neurodegeneration. Importantly, cellular interactions with metal ions, particularly Ca2+, have recently been reported as key for α-synuclein’s physiological function at the pre-synapse. Here we study effects of metal ion interaction with α-synuclein at the molecular level, observing changes in the conformational behaviour of monomers, with a possible link to aggregation pathways and toxicity. Using native nano-electrospray ionisation ion mobility-mass spectrometry (nESI-IM-MS), we characterize the heterogeneous interactions of alkali, alkaline earth, transition and other metal ions and their global structural effects on α-synuclein. Different binding stoichiometries found upon titration with metal ions correlate with their specific binding affinity and capacity. Subtle conformational effects seen for singly charged metals differ profoundly from binding of multiply charged ions, often leading to overall compaction of the protein depending on the preferred binding sites. This study illustrates specific effects of metal coordination, and the associated electrostatic charge patterns, on the complex structural space of the intrinsically disordered protein α-synuclein.