Charged Cavity Research Articles

Ionic Competition over Adsorption into Charged Spherical Cavities Affecting the Shape of Electric Double Layer Capacitance Curve and Zeta Potential: A Density Functional Theory Study

Modified fundamental measure theory in framework of restricted primitive model is employed to investigate the formation of the electric double layer at the concave wall of a charged spherical cavity when two positive ions, A + and C 2+, are in competition. Results indicate that, compared to A + at a bulk concentration 1M, the presence of even low concentrations (0.01 M) of C 2+ leads to a remarkable change in the capacitance curve’s shape. The concentration plays an important role in ionic adsorption at low values of electric potential, EP, while the ion charge has a dominant role at high enough EPs. The mole fraction of A + ions in the cavity, shows an initial increase with EP because of their higher concentration but they are later desorbed from the cavity. Hence, shows a maximum at EP at which their substitution with C 2+ ions start. This maximum shifts to lower EP with increasing C 2+ concentration and cavity curvature. This substitution of ions leads to a remarkable change in the capacitance curve’s shape, converting the symmetric capacitance curve to an asymmetric one. The zeta potential whose value is effectively changed by this substitution, is investigated along with its role in the diffuse capacitance.

Controlling Multiple Optomechanically Induced Transparency in Charged Cavity Optomechanical System Assisted by Three-Level Atomic Ensemble

Controlling Multiple Optomechanically Induced Transparency in Charged Cavity Optomechanical System Assisted by Three-Level Atomic Ensemble

Solution Structure, Dynamics, and New Antifungal Aspects of the Cysteine-Rich Miniprotein PAFC.

The genome of Penicillium chrysogenum Q176 contains a gene coding for the 88-amino-acid (aa)-long glycine- and cysteine-rich P. chrysogenum antifungal protein C (PAFC). After maturation, the secreted antifungal miniprotein (MP) comprises 64 aa and shares 80% aa identity with the bubble protein (BP) from Penicillium brevicompactum, which has a published X-ray structure. Our team expressed isotope (15N, 13C)-labeled, recombinant PAFC in high yields, which allowed us to determine the solution structure and molecular dynamics by nuclear magnetic resonance (NMR) experiments. The primary structure of PAFC is dominated by 14 glycines, and therefore, whether the four disulfide bonds can stabilize the fold is challenging. Indeed, unlike the few published solution structures of other antifungal MPs from filamentous ascomycetes, the NMR data indicate that PAFC has shorter secondary structure elements and lacks the typical β-barrel structure, though it has a positively charged cavity and a hydrophobic core around the disulfide bonds. Some parts within the two putative γ-core motifs exhibited enhanced dynamics according to a new disorder index presentation of 15N-NMR relaxation data. Furthermore, we also provided a more detailed insight into the antifungal spectrum of PAFC, with specific emphasis on fungal plant pathogens. Our results suggest that PAFC could be an effective candidate for the development of new antifungal strategies in agriculture.

Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1

Tripartite motif (TRIM)7 is an E3 ubiquitin ligase that was first identified through its interaction with glycogenin-1 (GN1), the autoglucosyltransferase that initiates glycogen biosynthesis. A growing body of evidence indicates that TRIM7 plays an important role in cancer development, viral pathogenesis, and atherosclerosis and, thus, represents a potential therapeutic target. TRIM family proteins share a multidomain architecture with a conserved N-terminal TRIM and a variable C-terminal domain. Human TRIM7 contains the canonical TRIM motif and a B30.2 domain at the C terminus. To contribute to the understanding of the mechanism of action of TRIM7, we solved the X-ray crystal structure of its B30.2 domain (TRIM7B30.2) in two crystal forms at resolutions of 1.6 Å and 1.8 Å. TRIM7B30.2 exhibits the typical B30.2 domain fold, consisting of two antiparallel β-sheets of seven and six strands, arranged as a distorted β-sandwich. Furthermore, two long loops partially cover the concave face of the β-sandwich defined by the β-sheet of six strands, thus forming a positively charged cavity. We used sequence conservation and mutational analyses to provide evidence of a putative binding interface for GN1. These studies showed that Leu423, Ser499, and Cys501 of TRIM7B30.2 and the C-terminal 33 amino acids of GN1 are critical for this binding interaction. Molecular dynamics simulations also revealed that hydrogen bond and hydrophobic interactions play a major role in the stability of a modeled TRIM7B30.2-GN1 C-terminal peptide complex. These data provide useful information that could be used to target this interaction for the development of potential therapeutic agents.

Metal nanoparticles encapsulated within charge tunable porous coordination cages for hydrogen generation reaction

Metal nanoparticles (M NPs) sometimes suffer from low stability and high aggregation, reducing their reactivity during catalytic cycles. In order to obtain stable and ultrafine noble metal (Ru/Rh/Pd) and first-row transition-metal (Co/Ni/Cu) nanoclusters, several porous coordination cages (PCCs) were applied to confine the nanoparticles within their cavities. Because of the electrostatic attraction, metal cations were only encapsulated by PCC-2a with a highly negatively charged cavity. By in situ reduction, M NPs were synthesized within the cavity of PCC-2a to form stable, ultrafine, and highly active catalyst composite. Through characterization by high resolution transmission electron microscope, the synthesized M NPs were found in face-cubic-centered single crystal form, which were rarely reported. In contrast, cages with only 6- negative charges (PCC-2b) or 12+ positive charges (PCC-3) were unable to obtain high crystalline, ultra-small M NPs, resulting in aggregation and large particle size. Finally, the M NPs@PCC catalysts exhibit different activities in methanolysis and hydrolysis of ammonium borane.

Sonochemical degradation of surfactants with different charge types: Effect of the critical micelle concentration in the interfacial region of the cavity

Ionic surfactants tend to accumulate in the interfacial region of ultrasonic cavitation bubbles (cavities) because of their surface active properties and because they are difficult to evaporate in cavitation bubbles owing to their extremely low volatilities. Hence, sonolysis of ionic surfactants is expected to occur in the interfacial region of the cavity. In this study, we performed sonochemical degradation of surfactants with different charge types: anionic, cationic, zwitterionic, and nonionic. We then estimated the degradation rates of the surfactants to clarify the surfactant behavior in the interfacial region of cavitation bubbles. For all of the surfactants investigated, the degradation rate increased with increasing initial bulk concentration and reached a maximum value. The initial bulk concentration to obtain the maximum degradation rate had a positive correlation with the critical micelle concentration (cmc). The initial bulk concentrations of the anionic surfactants were lower than their cmcs, while those of the cationic surfactants were higher than their cmcs. These results can be explained by the negatively charged cavity surface and the effect of the coexisting counterions of the surfactants.

The effect of electro-neutrality violation inside a charged spherical cavity on the capacitance curve shape in DFT approach and interpretation of mean electrostatic potential

The effect of electro-neutrality deviation in small charged cavities on the shape of the capacitance curve is investigated in this study. The data required are obtained using the modified fundamental measure theory and two models; namely, the restricted primitive model (RPM) and the primitive model (PM). The results of RPM investigations show that the capacitance curve will take on a bell shape when electro-neutrality parameter decreases with increasing surface charge, but that it exhibits a camel shape when electro-neutrality parameter shows a maximum versus surface charge. This behavior is essentially governed by both curvature and bulk concentration as it is observed that electro-neutrality parameter declines at high enough bulk concentrations and large enough curvatures. The PM study results indicate that an increase in the ratio of anion size to that of cation gives rise to higher positive values of the electric potential at zero surface charge. Moreover, it is seen that an increase in counter ion size causes more deviations from the electro-neutral condition while an increase in co-ion size relative to that of counter ions leads to the minimum value of electro-neutrality parameter versus surface charge but to a maximum for larger counter ions. Finally, it is found that, at the saturation point, the value for electro-neutrality parameter and, thereby, that for capacitance both become dependent on the size of counter ions. Base on the concept of the work in the thermodynamics and definition of mean electrostatic potential we interpreted all the terms present in the mean electrostatic potential in spherical cavity.

Enhanced piezoelectricity in twinned ferroelastics with nanocavities

Enhancing the electromechanical response by engineering domain boundaries in multiferroics has become a highly active research field in recent years. The starting point is the discovery that ferroelastic twin walls are polar inside a nonpolar matrix. The density of such twin walls is then greatly enhanced by forming complex twin patterns. Our computer simulations show that the interaction of nanocavities with differently charged configurations with twin boundaries generates strong piezoelectricity in ferroelastic (nonferroelectric) crystals. Cavity-induced domain patterns statistically break the inversion symmetry of a sample even when the cavities themselves obey inversion symmetry with relatively weak emerging piezoelectricity $(d\ensuremath{\sim}{10}^{\ensuremath{-}3}\phantom{\rule{0.16em}{0ex}}\mathrm{pm}/\mathrm{V})$ . Stronger piezoelectricity occurs in noncentrosymmetric charged cavity arrangements with a coefficient of $d\ensuremath{\sim}{10}^{\ensuremath{-}1}\mathrm{pm}/\mathrm{V}$. Structurally, the electric field polarizes and shifts the nanocavities by the displacement of trapped surface charges. The related strain fields interact with the ferroelastic domains, which act as soft bridges between the nanocavities. This leads to a significant deformation of the entire sample and hence to enhanced piezoelectricity. Our simulation results point to new directions for designing and enhancing electromechanical nanodevices based on ferroelastic templates even when the bulk material is structurally centrosymmetric.

Proton acceleration through a charged cavity created by ultraintense laser pulse

The potential of laser-driven ion beam applications is limited by high quality requirements. The excellent “point-source” characteristics of the laser accelerated proton beam in a broad energy range were found by using proton radiographs of a mesh. The “virtual source” of protons, the point where the proton trajectories are converging and form a waist, gradually decreases and moves asymptotically to the target with increasing particles' energy. Computer simulations confirmed that the beam profile at the center is fully conserved, the virtual source of higher energy protons gradually moves closer to the target, and if the particle energy is further increased, the virtual source will be located on the target front surface (for portions above 13 MeV, in this case) with a size comparable to the laser spot size. The laser ponderomotive force pushes the electrons deep into the target creating a bipolar charge structure, i.e., an electron cavity and spike which produces strong accelerating field, realizing a point-size source of accelerated protons. This behavior has not previously been predicted. These results contribute to the development of next generation laser-accelerators suitable for many applications.

Opto-electromechanically induced transparency in a hybrid opto-electromechanical system**Project supported by the National Natural Science Foundation of China (Grant Nos. 61605225, 11704238, and 61772295), the Higher Educational Science and Technology Program of Shandong Province, China (Grant No. J18KZ012), and the Natural Science Foundation of Shanghai, China (Grant No. 16ZR1448400).

We study opto-electromechanically induced transparency in a hybrid opto-electromechanical system made up of an optical cavity tunneling-coupled to an opto-mechanical cavity, which is capacitively coupled to a charged mechanical oscillator by a charged and moveable mechanical cavity mirror as an interface. By studying the effects of the different parameters on the output field, we propose a scheme to modulate the opto-electromechanically induced transparency (OEMIT). Our results show that the OEMIT with the transparency windows from single to double to triple can be modulated by changing the tunneling, opto-mechanical and electrical couplings. In addition, the explanation of the OEMIT with multi-windows is given by the energy level diagram based on quantum interference. Our investigation will provide an optimal platform to manipulate the transmission of optical field via microfabricated opto-electromechanical device.

The K296-D320 region of recombinant levansucrase BA-SacB can affect the sensitivity of Escherichia coli host to sucrose

A mutant BA-SacB-Del encoding BA-SacB minus K296-D320 region was constructed to analyze its effect on catalytic characteristics of the enzyme as well as help deepen understanding of the catalytic mechanism of BA-SacB and even proteins of GH68 family. Based on the comparison of levansucrases from Bacillus amyloliquefaciens (BA-SacB) and Sphingopyxis macrogoltabida (SM-Lev), a mutant BA-SacB-Del encoding BA-SacB minus K296-D320 region was constructed and its effect on catalytic characteristics of the enzyme was analyzed. Deletion of this region would undoubtedly affect the conserved structure (i.e., central negatively charged cavity surrounded by five antiparallel β-strands) shared by the GH68 family. Therefore, Escherichia coli-expressing mutant BA-SacB-Del could more efficiently catalyze the production of levan in media containing high concentration of sucrose, which is unrealizable for BA-SacB. This result should be valuable for understanding this conditional lethal mechanism. Therefore, this study should be very valuable for understanding the catalytic mechanism of BA-SacB and even proteins of the GH68 family. More importantly, levan can be conveniently produced by direct fermentation of sucrose-containing media with E. coli-expressing BA-SacB-Del which is not sensitive to sucrose.

Diffusiophoresis of a Charged Porous Particle in a Charged Cavity.

The quasi-steady diffusiophoresis of a charged porous sphere situated at the center of a charged spherical cavity filled with a liquid solution of a symmetric electrolyte is analyzed. The porous particle can represent a solvent-permeable and ion-penetrable polyelectrolyte molecule or floc of nanoparticles in which fixed charges and frictional segments are uniformly distributed, whereas the spherical cavity can denote a charged pore involved in microfluidic or drug-delivery systems. The linearized electrokinetic differential equations governing the ionic concentration, electric potential, and fluid velocity distributions in the system are solved by using a perturbation method with the fixed charge density of the particle and the ζ-potential of the cavity wall as the small perturbation parameters. An expression for the diffusiophoretic (electrophoretic and chemiphoretic) mobility of the confined particle with arbitrary values of a/ b, κ a, and λ a is obtained in closed form, where a and b are the radii of the particle and cavity, respectively; κ and λ are the reciprocals of the Debye screening length and the length characterizing the extent of flow penetration into the porous particle, respectively. The presence of the charged cavity wall significantly affects the diffusiophoretic motion of the particle in typical cases. The diffusio-osmotic (electro-osmotic and chemiosmotic) flow occurring at the cavity wall can substantially alter the particle velocity and even reverse the direction of diffusiophoresis. In general, the particle velocity decreases with an increase in a/ b, increases with an increase in κ a, and decreases with an increase in λ a, but exceptions exist.

Structural and Biochemical Analysis of the Citrate-Responsive Mechanism of the Regulatory Domain of Catabolite Control Protein E from Staphylococcus aureus.

Catabolite control protein E (CcpE) is a LysR-type transcriptional regulator that positively regulates the transcription of the first two enzymes of the TCA cycle, namely, citZ and citB, by sensing accumulated intracellular citrate. CcpE comprises an N-terminal DNA-binding domain and a C-terminal regulatory domain (RD) and senses citrate with conserved arginine residues in the RD. Although the crystal structure of the apo SaCcpE-RD has been reported, the citrate-responsive and DNA-binding mechanisms by which CcpE regulates TCA activity remain unclear. Here, we report the crystal structure of the apo and citrate-bound SaCcpE-RDs. The SaCcpE-RD exhibits conformational changes between the two subdomains via hinge motion of the central β4 and β10 strands. The citrate molecule is located in a positively charged cavity between the two subdomains and interacts with the highly conserved Ser98, Leu100, Arg145, and Arg256 residues. Compared with that of the apo SaCcpE-RD, the distance between the two subdomains of the citrate-bound SaCcpE-RD is more than ∼3 Å due to the binding of the citrate molecule, and this form exhibits a closed structure. The SaCcpE-RD exhibits various citrate-binding-independent conformational changes at the contacting interface. The SaCcpE-RD prefers the dimeric state in solution, whereas the SaCcpE-FL prefers the tetrameric state. Our results provide insight into the molecular function of SaCcpE.

2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop

YidC/Alb3/Oxa1 family proteins are involved in the insertion and assembly of membrane proteins. The core five transmembrane regions of YidC, which are conserved in the protein family, form a positively charged cavity open to the cytoplasmic side. The cavity plays an important role in membrane protein insertion. In all reported structural studies of YidC, the second cytoplasmic loop (C2 loop) was disordered, limiting the understanding of its role. Here, we determined the crystal structure of YidC including the C2 loop at 2.8 Å resolution with R/Rfree = 21.8/27.5. This structure and subsequent molecular dynamics simulation indicated that the intrinsic flexible C2 loop covered the positively charged cavity. This crystal structure provides the coordinates of the complete core region including the C2 loop, which is valuable for further analyses of YidC.

Diffusiophoresis of a charged particle in a charged cavity with arbitrary electric double layer thickness

An analysis is presented for the diffusiophoretic motion of a charged colloidal sphere located at the center of a charged spherical cavity filled with an electrolyte solution at the quasisteady state for the case of arbitrary electric double layers. The electrokinetic equations governing the ionic concentration, electric potential, and velocity distributions in the fluid are linearized with assumption that the system is slightly distorted from equilibrium. These linearized differential equations are solved using a perturbation method with the zeta potentials of the particle and cavity as the small perturbation parameters. An explicit formula for the diffusiophoretic velocity of the particle as a combination of the electrophoretic and chemiphoretic contributions valid for arbitrary values of $$\kappa a$$ and $$a/b$$ is obtained by balancing the electrostatic and hydrodynamic forces exerted on it, where $$\kappa$$ is the Debye screening parameter, $$a$$ is the radius of the particle, and $$b$$ is the radius of the cavity. The effect of the charged cavity wall on the diffusiophoresis of the particle is interesting and can be significant. The contributions from the diffusioosmotic (electroosmotic and chemiosmotic) flow taking place along the cavity wall and from the wall-corrected diffusiophoretic force to the particle velocity are comparably important, and this diffusioosmotic flow can reverse the direction of diffusiophoresis. The particle velocity in general increases with an increase in $$\kappa a$$ and decreases with an increase in $$a/b$$ , but exceptions exist.

A PAM-Induced Signalling Activates the Communication between HNH and RUVC in CRISPR-Cas9

CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 is a bacterial immune system, which has revolutionized life sciences through the introduction of a facile genome editing technology. In this system, the endonuclease Cas9 associates with guide RNAs to match and cleave complementary DNA sequences, forming an RNA:DNA hybrid and a displaced non-target DNA strand. Thanks to a key DNA recognition element, a Protospacer Adjacent Motif (PAM), Cas9 performs site-specific DNA cleavages, enabling to engineer biological systems with unique efficiency and resulting in numerous applications in medicine and biotechnology. However, the mechanistic basis underlying the CRISPR-Cas9 function is unclear, preventing rational engineering of the system toward improved genome editing. We report on extensive molecular dynamics studies, including multi-microsecond and accelerated methods probing displacements over micro-to-milliseconds, characterizing the mechanism of conformational activation of Cas9, from its apo form up to the nucleic acid binding. These simulations disclosed a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. As well, we revealed the formation of a catalytically competent Cas9, which is prone for the catalysis of DNA. We showed how, upon DNA binding, the relocation of the catalytic HNH domain, assisted by conformational changes of the non-target DNA strand, activates Cas9 for catalysis. Finally, a mechanism of allosteric regulation, triggered by PAM binding and activating the catalytic domains for concerted catalysis has been discovered. Overall, our outcomes address the lack of mechanistic information on CRISPR-Cas9, improving our understanding of the activation process. This information is critical for structure-based design of the CRISPR-Cas9 system, which could impact the development of improved genome editing tools.

Measurement back action and spin noise spectroscopy in a charged cavity QED device in the strong coupling regime

We study theoretically the spin-induced and photon-induced fluctuations of optical signals from a singly-charged quantum dot-microcavity structure. We identify the respective contributions of the photon-polariton interactions, in the strong light-matter coupling regime, and of the quantum back-action induced by photon detection on the spin system. Strong spin projection by a single photon is shown to be achievable, allowing the initialization and measurement of a fully-polarized Larmor precession. The spectrum of second-order correlations is deduced, displaying information on both spin and quantum dot-cavity dynamics. The presented theory thus bridges the gap between the fields of spin noise spectroscopy and quantum optics.

Vacuum-induced quantum memory in an opto-electromechanical system

We propose a scheme to implement electrically controlled quantum memory based on vacuum-induced transparency (VIT) in a high-Q tunable cavity, which is capacitively coupled to a mechanically variable capacitor by a charged mechanical cavity mirror as an interface. We analyze the changes of the cavity photons arising from vacuum-induced-Raman process and discuss VIT in an atomic ensemble trapped in the cavity. By slowly adjusting the voltage on the capacitor, the VIT can be adiabatically switched on or off, meanwhile, the transfer between the probe photon state and the atomic spin state can be electrically and adiabatically modulated. Therefore, we demonstrate a vacuum-induced quantum memory by electrically manipulating the mechanical mirror of the cavity based on electromagnetically induced transparency mechanism.

Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes.

The divergence of archaea, bacteria and eukaryotes was a fundamental step in evolution. One marker of this event is a major difference in membrane lipid chemistry between these kingdoms. Whereas the membranes of bacteria and eukaryotes primarily consist of straight fatty acids ester-bonded to glycerol-3-phosphate, archaeal phospholipids consist of isoprenoid chains ether-bonded to glycerol-1-phosphate. Notably, the mechanisms underlying the biosynthesis of these lipids remain elusive. Here, we report the structure of the CDP-archaeol synthase (CarS) of Aeropyrum pernix (ApCarS) in the CTP- and Mg2+-bound state at a resolution of 2.4 Å. The enzyme comprises a transmembrane domain with five helices and cytoplasmic loops that together form a large charged cavity providing a binding site for CTP. Identification of the binding location of CTP and Mg2+ enabled modeling of the specific lipophilic substrate-binding site, which was supported by site-directed mutagenesis, substrate-binding affinity analyses, and enzyme assays. We propose that archaeol binds within two hydrophobic membrane-embedded grooves formed by the flexible transmembrane helix 5 (TM5), together with TM1 and TM4. Collectively, structural comparisons and analyses, combined with functional studies, not only elucidated the mechanism governing the biosynthesis of phospholipids with ether-bonded isoprenoid chains by CTP transferase, but also provided insights into the evolution of this enzyme superfamily from archaea to bacteria and eukaryotes.

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. GaMD also reveals the conformation of a catalytically competent Cas9, which is prone for catalysis and whose experimental characterization is still limited. We show that, upon DNA binding, the conformational dynamics of the HNH domain triggers the formation of the active state, explaining how the HNH domain exerts a conformational control domain over DNA cleavage [Sternberg SH et al. (2015) Nature, 527, 110-113]. These results provide atomic-level information on the molecular mechanism of CRISPR-Cas9 that will inspire future experimental investigations aimed at fully clarifying the biophysics of this unique genome editing machinery and at developing new tools for nucleic acid manipulation based on CRISPR-Cas9.