Identical Structural Features Research Articles

Linguistic and extralinguistic specificity of Russian and English texts of ethical codes in the diachronic aspect

The subject of the study is linguistic, extralinguistic and linguoculturological features that determine the specifics of English and Russian-language texts of ethical codes of banks in a comparative aspect throughout the XXI century. To analyze the specifics of the texts of ethical codes of banks (based on the material of English and Russian languages), descriptive and comparative methods are used in the article. The methodological basis is determined by a systematic approach based on the principle of consistency of linguistic phenomena, system analysis, as well as descriptive, inductive-deductive and comparative methods. In accordance with the systematic approach, the interrelation of structural, genre-content, linguistic and cultural features of the texts of banking discourse on the material of English and Russian languages is actualized.The scientific novelty consists in a comprehensive study and a systematic description of the structural, genre-content, linguistic features of the texts of ethical codes of leading English-speaking and Russian-speaking banks. For the first time, the analysis of the specifics of the texts of the banking discourse in a comparative aspect was carried out, as well as the specific structural, genre, semantic features of ethical codes as a new artifact of modern textual culture, and their transformation during the XXI century against the background of the realities of reality, namely before the 2020 pandemic and after. Thus, based on the analysis performed, it can be argued that bank texts in both languages, due to the active digitalization of society, are characterized by identical key structural, genre-content and language features. Nevertheless, Russian-language texts have made a huge transformational leap in terms of digital content and can be distinguished by a large spread of semiotically complicated polycode systems and the presence of creolized texts.

Assessing the thermal conductivity of amorphous SiN by approach-to-equilibrium molecular dynamics.

First-principles molecular dynamics combined with the approach-to-equilibrium molecular dynamics methodology is employed to calculate the thermal conductivity of non-stoichiometric amorphous SiN. This is achieved by implementing thermal transients in five distinct models of different sizes along the direction of the heat transport. Such models have identical structural features and are representative of the same material, thereby allowing for a reliable analysis of thermal conductivity trends as a function of the relevant cell dimension. In line with the known physical law of heat propagation at short scale, the thermal conductivity increases in size with the direction of heat transport. The observed behavior is rationalized accounting for previous results on crystalline and amorphous materials, thus providing a unified description holding for a large class of materials and spanning a wide range of heat propagation lengths.

Halide mediated modulation of magnetic interaction and anisotropy in dimeric Co(II) complexes.

The burgeoning interest in the field of molecular magnetism is to perceive the high magnetic anisotropy in different geometries of metal complexes and hence to draw a magneto-structural correlation. Despite a handful of examples to exemplify the magnetic anisotropy in various coordination geometries of mononuclear complexes, the magnetic anisotropies for two different coordination geometries are underexplored. Employing an appropriate synthetic strategy utilizing the ligand LH2 [2,2'-{(1E,1'E)-pyridine2,6-diyl-bis(methaneylylidine)}-bis(azaneylylidine)diphenol] and cobalt halide salts in a 1 : 2 stoichiometric ratio in the presence of triethylamine allowed us to report a new family of dinuclear cobalt complexes [CoII2X2(L)(P)(Q)]·S with varying terminal halides [X = Cl, P = CH3CN, Q = H2O, S = H2O (1), X = Br, P = CH3CN, Q = H2O, S = H2O (2), X = I, P = CH3CN, and Q = CH3CN (3)]. All these complexes are characterized through single crystal X-ray crystallography, which reveals their crystallization in the monoclinic system P21/n space group with nearly identical structural features. These complexes share vital components, including Co(II) centers, a fully deprotonated ligand [L]2-, halide ions, and solvent molecules. The [L]2- ligand contains two Co(II) centers, where phenolate oxygen atoms bridge the Co(II) centers, forming a Co2O2 four-membered ring. Co1 demonstrates a distorted pentagonal-bipyramidal geometry with axial positions for solvent molecules, while Co2 displays a distorted tetrahedral geometry involving phenolate oxygen atoms and halide ions. Temperature-dependent dc magnetic susceptibility measurements were conducted on 1-3 within a range of 2 to 300 K at 1 kOe. The χmT vs. T plots exhibit similar trends, with χmT values at 300 K higher than the spin-only value, signifying a significant orbital contribution. As the temperature decreases, χmT decreases smoothly in all the complexes; however, no clear saturation at low temperatures is observed. Field-dependent magnetization measurements indicate a rapid increase below 20 kOe, with no hysteresis and a low magnetic blocking temperature. DFT and CASSCF/NEVPT2 theoretical calculations were performed to perceive the magnetic interaction and single-ion anisotropies of Co(II) ions in various ligand-field environments.

Deer antler stem cells immortalization by modulation of hTERT and the small extracellular vesicles characters.

Deer antler stem cells (AnSCs) exhibit properties of both embryonic and mesenchymal stem cells, with superior self-renewal and proliferation, which drive rapid antler growth and regeneration. AnSCs and their derived small extracellular vesicles (sEVs) hold promising potential for applications in regeneration medicine. Due to the restricted proliferative capacity inherent in primary cells, the production capacity of AnSCs and their sEVs are limited. Human telomerase reverse transcriptase (hTERT) is the most important telomerase subunit, hTERT gene insertion has been successfully employed in generating immortalized cell lines. In this study, we successfully established immortalized AnSCs by transducing the hTERT gene using lentivirus. Compared to primary AnSCs, hTERT-AnSCs demonstrated extended passage potential and accelerated proliferation rates while maintaining the mesenchymal stem cell surface markers CD44 and CD90. Additionally, hTERT-AnSCs retained the capacity for osteogenic, adipogenic, and chondrogenic differentiation. sEVs derived from hTERT-AnSCs exhibited a particle size distribution similar to that of AnSCs, both displaying a cup-shaped morphology and expressing CD81, ALIX, and TSG101, while notably lacking GM130 expression. We successfully isolated primary stem cells from deer antler and established the immortalized hTERT-AnSCs. Remarkably, this cell line maintains its stem cell characteristics even after 40 passages. The sEVs derived from these cells exhibit identical morphological and structural features to those of primary AnSCs. This research provides essential technical support for the application of AnSCs and their sEVs in regenerative medicine.

Histidine Functionalized Gold Nanoparticles for Screening Aminoglycosides and Nanomolar Level Detection of Streptomycin in Water, Milk, and Whey

Aminoglycoside (AMG) antibiotics are being applied to treat infections caused by Gram-negative bacteria, mainly in livestock, and are prescribed only in severe cases because of their adverse impacts on human health and the environment. Monitoring antibiotic residues in dairy products relies on the accessibility of portable and efficient analytical techniques. Presently, high-throughput screening techniques have been proposed to detect several antimicrobial drugs having identical structural and functional features. The L-histidine functionalized gold nanoparticles (His@AuNPs) do not form a complex with other tested antibiotic classes but show high selectivity for AMG antibiotics. We used ligand-induced aggregation of His@AuNPs as a rapid and sensitive localized surface plasmon resonance (LSPR) assay for AMG antibiotics, producing longitudinal extinction shifts at 660 nm. Herein, we explore the practical application of His@AuNPs to detect streptomycin spiked in water, milk, and whey fraction of milk with nanomolar level sensitivity. The ability of the analytical method to recognize target analytes sensitively and rapidly is of great significance to perform monitoring, thus would certainly reassure widespread use of AMG antibiotics. The biosynthesis of hybrid organic–inorganic metal nanoparticles like His@AuNPs with desired size distribution, stability, and specific host–guest recognition proficiency, would further facilitate applications in various other fields.

Effect of alkali atom doping on the electronic structure and aromatic character of planar and quasi-planar Al13+ clusters.

A set of three Al13+ clusters, one perfectly planar, and two quasi-planar structures, have been recently reported by our group (Guin et al. Journal of Molecular Graphics and Modeling, 2020, 97, 107544). All three clusters possess bilateral symmetry with identical structural features-a set of ten aluminum atoms encircle a triangular core. The symmetry axis passes through one of the Al atoms of the central triangular core and two Al atoms located on the periphery at two opposite ends of the cluster. This set of three aluminum clusters is an example of a rare metallo-aromatic system where highly anti-aromatic islands are embedded within an aromatic sea. In the present study, we have explored the effect of doping alkali atoms (Li, Na, and K) at the positions of the Al atoms that lie on the symmetry axis of the cluster intending to understand the structural stability and the effect on the aromatic character as compared to the undoped parent clusters. Besides the electronic structural analysis, NICS and ELF studies have also been carried out to characterize the aromatic nature of the doped clusters. Interestingly, it has been found that even with the incorporation of the alkali atoms, the bilateral symmetry of the clusters remains intact, but the alkali atoms are pushed out of the original location toward the edge of the cluster, whereas the aluminum atoms remain grouped. The dipole moment of the clusters systematically increases, and the overall aromaticity of the cluster systematically decreases with the increase in the atomic number of the doped alkali atoms. Effect of alkali atom doping to Al13+ cluster.

Scalable Synthesis of Hollow β-SiC/Si Anodes via Selective Thermal Oxidation for Lithium-Ion Batteries.

Silicon for anodes in lithium-ion batteries has received much attention owing to its superior specific capacity. There has been a rapid increase of research related to void engineering to address the silicon failure mechanism stemming from the massive volume change during (dis)charging in the past decade. Nevertheless, conventional synthetic methods require complex synthetic procedures and toxic reagents to form a void space, so they have an obvious limitation to reach practical application. Here, we introduce SiCx consisting of nanocrystallite Si embedded in the inactive matrix of β-SiC to fabricate various types of void structures using thermal etching with a scalable one-pot CVD method. The structural features of SiCx make the carbonaceous template possible to be etched selectively without Si oxidation at high temperature with an air atmosphere. Furthermore, bottom-up gas phase synthesis of SiCx ensures atomically identical structural features (e.g., homogeneously distributed Si and β-SiC) regardless of different types of sacrificial templates. For these reasons, various types of SiCx hollow structures having shells, tubes, and sheets can be synthesized by simply employing different morphologies of the carbon template. As a result, the morphological effect of different hollow structures can be deeply investigated as well as the free volume effect originating from void engineering from both a electrochemical and computational point of view. In terms of selective thermal oxidation, the SiCx hollow shell achieves a much higher initial Coulombic efficiency (>89%) than that of the Si hollow shell (65%) because of its nonoxidative property originating from structural characteristics of SiCx during thermal etching. Moreover, the findings based on the clearly observed different electrochemical features between half-cell and full-cell configuration give insight into further Si anode research.

Disruption of the CD Loop by Enzymatic Cleavage Promotes the Formation of Toxic Transthyretin Oligomers through a Common Transthyretin Misfolding Pathway.

Amyloid formation of full-length TTR involves dissociation of the native tetramers into misfolded monomers that self-assemble into amyloid. In addition to the full-length TTR, C-terminal fragments including residues 49-127 were also observed in vivo, implying the presence of additional misfolding pathways. It was previously proposed that a proteolytic cleavage might lead to the formation of the C-terminal fragment TTR amyloid. Here, we report mechanistic studies of misfolding and aggregation of a TTR variant (G53A) in the absence and presence of a serine protease. A proteolytic cleavage of G53A in the CD loop (K48 and T49) with agitation promoted TTR misfolding and aggregation, suggesting that the proteolytic cleavage may lead to the aggregation of the C-terminal fragment (residues 49-127). To gain more detailed insights into TTR misfolding promoted by proteolytic cleavage, we investigated structural changes in G53A TTR in the presence and absence of trypsin. Our combined biophysical analyses revealed that the proteolytic cleavage accelerated the formation of spherical small oligomers, which exhibited cytotoxic activities. However, the truncated TTR appeared to maintain native-like structures, rather than the C-terminal fragment (residues 49-127) being released and unfolded from the native state. In addition, our solid-state nuclear magnetic resonance and Fourier transform infrared structural studies showed that the two aggregates derived from the full-length and cleaved TTR exhibited nearly identical molecular structural features, suggesting that the proteolytic cleavage in the CD loop destabilizes the native tetrameric structure and accelerates oligomer formation through a common TTR misfolding and aggregation mechanism rather than through a distinct molecular mechanism.

Size-Related Electrochemical Performance in Active Carbon Nanostructures: A MOFs-Derived Carbons Case Study.

Metal–organic framework–derived carbon nanostructures have generated significant interest in electrochemical capacitors and oxygen/hydrogen catalysis reactions. However, they appear to show considerably varied structural properties, and thus exhibit complex electrochemical–activity relationships. Herein, a series of carbon polyhedrons of different sizes, between 50 nm and µm, are synthesized from zeolitic imidazolate frameworks, ZIF‐8 (ZIF‐derived carbon polyhedrons, ZDCPs) and their activity is studied for capacitance and the oxygen reduction reaction (ORR). Interestingly, a well‐correlated performance relationship with respect to the particle size of ZDCPs is evidenced. Here, the identical structural features, such as specific surface area (SSA), microporosity, and its distribution, nitrogen doping, and graphitization are all strictly maintained in the ZDCPs, thus allowing identification of the effect of particle size on electrochemical performance. Supercapacitors show a capacity enhancement of 50 F g−1 when the ZDCPs size is reduced from micrometers to ≤200 nm. The carbonization further shows a considerable effect on rate capacitance—ZDCPs of increased particle size lead to drastically reduced charge transportability and thus inhibit their performance for both the charge storage and the ORR. Guidelines for the capacitance variation with respect to the particle size and SSA in such carbon nanostructures from literature are presented.

Metal–Organic Frameworks Based on a Bent Triazole Dicarboxylic Acid: Magnetic Behaviors and Selective Luminescence Sensing Properties

Four new metal–organic frameworks (MOFs) constructed from the bent triazole dicarboxylic acid ligand 3,5-bis(4′-carboxyphenyl)-1,2,4-triazole (H2bct) have been discovered by a solvothermal method. These MOFs, [M5(μ2-H2O)2(μ3-OH)2(bct)4(H2O)8]·4H2O}n (1, M = Co; 2, M = Ni), {[Cd2(bct)2(bipy)]·5H2O}n (3) (bipy = 4,4′-bipyridine), and {[Cd(bct)(tib)]·H2O·DMF}n (4) (tib = 1,3,5-tris(1-imidazolyl)benzene), exhibit diverse coordination modes and fascinating crystal structures. The crystallographic structures, thermal stabilities, photoluminescence, and magnetic properties have been studied. 1 and 2 share the identical structural features based on planar pentanuclear clusters except for the central ions, where the one-dimensional chain structures are constructed from the pentanuclear secondary building units linked with bct2– ligands, while 3 and 4 have similar layered structures. Magnetic analyses of 1 and 2 reveal that an overall antiferromagnetic coupling within the pentanuclear Co(II) cluster nodes are observed, which can be switched to strong ferromagnetic coupling when using Ni(II) to replace the Co(II) sites. Both 3 and 4 show intense blue emission under ultraviolet excitation. Moreover, 4 can be applied as a selective sensor for quantitatively testing the concentration of acetone in water based on the luminescence quenching effect, with a quenching constant (Ksv) value of 12.89 L mol–1 in water.

Structural characterization and gas-phase studies of the [Ag10H8(L)6]2+ nanocluster dication.

The reactions between silver salts and borohydrides produce a rich set of products that range from discrete mononuclear compounds through to silver nanoparticles and colloids. Previous studies using electrospray ionization mass spectrometry (ESI-MS) to track the cationic products in solutions containing sodium borohydride, silver(i) tetrafluoroborate and the bisphosphine ligands, L, bis(diphenylphosphino)methane (dppm) and bis(diphenylphosphino)amine (dppa) have identified the dications [Ag10H8(L)6]2+. Here we isolate and structurally characterize [Ag10H8(dppa)6](BF4)2, and [Ag10H8(dppa)6](NO3)2via X-ray crystallography. Both dications have nearly identical structural features consisting of a Ag10 scaffold with the atoms lying on vertices of a bicapped square antiprism. DFT calculations were carried out to suggest potential sites for the hydrides. Ion-mobility mass spectrometry experiments revealed that [Ag10H8(dppa)6]2+ and [Ag10H8(dppm)6]2+ have similar collision cross sections, while multistage mass spectrometry experiments were used to compare their unimolecular gas-phase chemistry. Although the same initial sequential ligand loss followed by cluster fission and H2 evolution is observed, the more acidic N-H of the dppa provides a more labile H for H2 loss and H/D scrambling processes as revealed by isotope labelled experiments.

Patterns of reactions: a card sort task to investigate students’ organization of organic chemistry reactions

Research has shown that within a traditional organic chemistry curriculum, organic chemistry students struggle to develop deep conceptual understanding of reactions and attribute little meaning to the electron-pushing formalism. At the University of Ottawa, a new curriculum was developed for organic chemistry in which students are taught the language of the electron-pushing formalism prior to learning about specific reactions. Reactions are then organized by governing pattern of mechanism rather than by functional group and are taught in a gradient of complexity. To investigate how students are making connections across reactions within the new curriculum, a card sort task was developed. The card sort task consisted of 25 cards, each depicting the reactants and solvent for a reaction taught during the two-semester organic chemistry sequence. The first part of the task asked participants to sort 15 of 25 cards into categories. Then, participants were given the 10 remaining cards to incorporate into categories with the previous 15. Participants were asked to explain the characteristics of each category and their sorting process. Students (N= 16) in an organic chemistry course were interviewed while enrolled in the second semester course. We analyzed the students’ sorts based on which cards were sorted frequently together, the underlying characteristics used to form the categories, and the participants’ sorting processes. Participants created categories based on different levels of interpreting the reactions on the cards, with levels ranging from recognizing identical structural features to identifying similar types of mechanisms. Based on this study, if we want students to develop mechanistic thinking, we think students need to be more explicitly directed to the patterns present in organic reaction mechanisms and given opportunities to uncover and identify patterns on their own, during both summative and formative assessments.

Depth image super-resolution algorithm based on structural features and non-local means

The resolution and quality of the depth map captured by depth cameras are limited due to sensor hardware limitations, which becomes a roadblock for further computer vision applications. In order to solve this problem, we propose a new method to enhance low-resolution depth maps using high-resolution color images. The structural-aware term is introduced because of the availability of structural information in color images and the assumption of identical structural features within local neighborhoods of color images and depth images captured from the same scene. We integrate the structural-aware term with color similarity and depth similarity within local neighborhoods to design a local weighting filter based on structural features. To use non-local self-similarity of images, the local weighting filter is combined with the concept of non-local means, and then a non-local weighting filter based on structural features is designed. Some experimental results show that super-resolution depth image can be reconstructed well by the process of the non-local filter and the local filter based on structural features. The proposed method can reconstruct much better high-resolution depth images compared with previously reported methods.

Universal molecular structures in natural dissolved organic matter

Natural dissolved organic matter (DOM) comprises a broad range of dissolved organic molecules in aquatic systems and is among the most complex molecular mixtures known. Here we show, by comparing detailed structural fingerprints of individual molecular formulae in DOM from a set of four marine and one freshwater environments, that a major component of DOM is molecularly indistinguishable in these diverse samples. Molecular conformity was not only apparent by the co-occurrence of thousands of identical molecular formulae, but also by identical structural features of those isomers that collectively represent a molecular formula. The presence of a large pool of compounds with identical structural features in DOM is likely the result of a cascade of degradation processes or common synthetic pathways that ultimately lead to the formation of a universal background, regardless of origin and history of the organic material. This novel insight impacts our understanding of long-term turnover of DOM as the underlying mechanisms are possibly universal.

(Aceto-nitrile-κN)aqua-[N,N'-bis-(pyridin-2-yl-methyl)ethane-1,2-di-amine-κ4N,N',N'',N''']zinc(II) perchlorate.

The structure of the title compound, [Zn(C14H18N4)(C2H3N)(H2O)](ClO4)2, contains a six-coordinate cation consisting of the tetra-dentate bis-picen ligand, coordinated water, and coordinated aceto-nitrile, with the latter two ligands adopting a cis configuration. There are two formula units in the asymmetric unit. Both cations show almost identical structural features with the bis-picen ligand adopting the more common cis-β conformation. One of the four perchlorate anions is disordered over two positions, with occupancies of 0.9090 (15) and 0.0910 (15). There is extensive inter-ionic hydrogen bonding between the perchlorate anions and O-H and N-H groups in the cations, including a bifurcated hydrogen bond between an N-H group and two O atoms of one perchlorate anion. As a result of this extended hydrogen-bond network, the ions are linked into a complex three-dimensional array.

Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies

An Abstraction Network is a compact summary of an ontology’s structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its associated QA methodologies, however, is a labor-intensive process that previously was applicable only to one ontology at a time. To improve the efficiency of the Abstraction-Network-based QA methodology, we introduced a QA framework that uses uniform Abstraction Network derivation techniques and QA methodologies that are applicable to whole families of structurally similar ontologies. For the family-based framework to be successful, it is necessary to develop a method for classifying ontologies into structurally similar families. We now describe a structural meta-ontology that classifies ontologies according to certain structural features that are commonly used in the modeling of ontologies (e.g., object properties) and that are important for Abstraction Network derivation. Each class of the structural meta-ontology represents a family of ontologies with identical structural features, indicating which types of Abstraction Networks and QA methodologies are potentially applicable to all of the ontologies in the family. We derive a collection of 81 families, corresponding to classes of the structural meta-ontology, that enable a flexible, streamlined family-based QA methodology, offering multiple choices for classifying an ontology. The structure of 373 ontologies from the NCBO BioPortal is analyzed and each ontology is classified into multiple families modeled by the structural meta-ontology.

Multiple vitellogenins and product yolk proteins in European sea bass (Dicentrarchus labrax): Molecular characterization, quantification in plasma, liver and ovary, and maturational proteolysis.

Three complete vitellogenin (Vtg) polypeptides of European sea bass (Dicentrarchus labrax), an acanthomorph teleost spawning pelagic eggs in seawater, were deduced from cDNA and identified as VtgAa, VtgAb and VtgC based on current Vtg nomenclature and phylogeny. Label free quantitative mass spectrometry verified the presence of the three sea bass Vtgs or their product yolk proteins (YPs) in liver, plasma and ovary of postvitellogenic females. As evidenced by normalized spectral counts, VtgAb-derived protein was 2- to 5-fold more abundant, depending on sample type, than for VtgAa, while VtgC-derived protein was less abundant, albeit only 3-fold lower than for VtgAb in the ovary. Western blotting with Vtg type-specific antisera raised against corresponding gray mullet (Mugil cephalus) lipovitellins (Lvs) detected all three types of sea bass Vtg in the blood plasma of gravid females and/or estrogenized males and showed that all three forms of sea bass Lv undergo limited partial degradation during oocyte maturation. The comparatively high levels of VtgC-derived YPs in fully-grown oocytes and the maturational proteolysis of all three types of Lv differ from what has been reported for other teleosts spawning pelagic eggs in seawater but are similar to recent findings for two species of North American Moronidae, the striped bass (Morone saxatilis) and white perch (Morone americana), which spawn pelagic and demersal eggs, respectively in fresh water. Together with the high Vtg sequence homologies and virtually identical structural features of each type of Vtg between species, these findings indicate that the moronid multiple Vtg systems do not substantially vary with reproductive environment.

Thermoelectric Properties of p‐Type Semiconducting NaB5C with Hexaboride‐Type Structure, Compared to Layered MB2C2 (M = La, Ce)

AbstractWhile hexaborides are known to exhibit n‐type semi‐conducting or metallic properties, the carbaboride NaB5C that crystallizes with the hexaboride‐structure type was found to be p‐type. It thus complements n‐type CaB6, which has almost identical structural features [s.g. Pm$\bar{3}$m, a = 409.25 pm and z/c(B) = 0.2034 for NaB5C and a = 415.37 and z/c(B) = 0.201 for CaB6]. Mono‐phasic samples were synthesized via solid state reactions of the elements and compacted by spark plasma sintering at high pressures. The thermoelectric properties (thermal diffusivities, electrical conductivities, Seebeck coefficients) were measured up to temperatures as high as 873 K (S = 80 μV·K–1) and compared to that of LaB2C2 and CeB2C2. These have layered structures and are metallic.

Distinctive Nanoscale Organization of Dicationic versus Monocationic Ionic Liquids

The distinctive structural organization of dicationic ionic liquids (DILs) with varying alkyl linkage chain lengths is systematically investigated using classical molecular dynamics (MD) simulations. In comparison with their counterparts, monocationic ionic liquids (MILs) with free alkyl chains, the DILs with short linkage chains exhibit almost identical structural features regardless of anion types, whereas the long-chain DILs display a relatively insignificant prepeak and low heterogeneity order parameter (HOP), which are accompanied by the less evident structural heterogeneity. Moreover, the predominant role of anion type in the structure of DILs was verified, similar to what is observed in MILs. Finally, the different nanoscale organizations in DILs and MILs are rationalized by the relatively unfavorable straight and folded chain models proposed for the nanoaggregates in DILs and the favorable micelle-like arrangement for those in MILs.

A 3D structural model and dynamics of hepatitis C virus NS3/4A protease (genotype 4a, strain ED43) suggest conformational instability of the catalytic triad: implications in catalysis and drug resistivity

Egypt has the highest prevalence of hepatitis C virus (HCV) infection worldwide with a frequency of 15%. More than 90% of these infections are due to genotype 4, and the subtype 4a (HCV-4a) predominates. Moreover, due to the increased mobility of people, HCV-4a has recently spread to several European countries. The protease domain of the HCV nonstructural protein 3 (NS3) has been targeted for inhibition by several drugs. This approach has had marked success in inhibiting genotype 1 (HCV-1), the predominant genotype in the USA, Europe, and Japan. However, HCV-4a was found to resist inhibition by a number of these drugs, and little progress has been made to understand the structural basis of its drug resistivity. As a step forward, we sequenced the NS3 HCV-4a protease gene (strain ED43) and subsequently built a 3D structural model threaded through a template crystal structure of HCV-1b NS3 protease. The model protease, HCV-4a, shares 83% sequence identity with the template protease, HCV-1b, and has nearly identical rigid structural features. Molecular dynamics simulations predict similar overall dynamics of the two proteases. However, local dynamics and 4D analysis of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) indicate conformational instability of the catalytic site in HCV-4a NS3 protease. These results suggest that the divergent dynamics behavior, more than the rigid structure, could be related to the altered catalytic activity and drug resistivity seen in HCV-4a.