Structural Studies Research Articles

Assessment of RC Frame Structure under Different Seismic Condition

Abstract: Structures in seismic zones are especially prone to collapse during significant ground motion occurrences. This susceptibility is sometimes linked to flaws in seismic design principles, notably in the selection of suitable structural systems. Equivalent static analysis, which is often employed in seismic design, may not accurately account for the structure's strength and stiffness. As a result, ground floor columns may become highly reinforced, thereby lowering ductility, and causing poor performance. This thesis offers a parametric study of an RC frame structure developed for various seismic zones. The finite element software is used to model the structure to investigate performance levels. Pushover analysis was performed to determine the structure's seismic capacity and behavior under various seismic conditions. Parametric research employing RC Frames with demand variation was done to investigate the structure's behavior in different seismicity zones across the country

SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development.

MADS transcription factors are master regulators of plant reproduction and flower development. The SEPALLATA (SEP) subfamily of MADS transcription factors is required for the development of floral organs and plays roles in inflorescence architecture and development of the floral meristem. SEPALLATAs act as organizers of MADS complexes, forming both heterodimers and heterotetramers in vitro. To date, the MADS complexes characterized in angiosperm floral organ development contain at least one SEPALLATA protein. Whether DNA-binding by SEPALLATA-containing dimeric MADS complexes is sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization--impaired SEPALLATA mutant proteins. Here, we used a combination of genome-wide binding studies, high resolution structural studies of the SEP3/AGAMOUS (AG) tetramerization domain, structure-based mutagenesis and complementation experiments in Arabidopsis (Arabidopsis thaliana) sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers can bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild-type binding sites genome-wide, tetramerization is required not only for floral meristem determinacy, but also for floral organ identity in the second, third and fourth whorls.

Effect of enzymatic modification on the structure and rheological properties of diluted alkali-soluble pectin fraction rich in RG-I

This study focuses on pectin covalently linked in cell walls from two sources, apples and carrots, that was extracted using diluted alkali, and it describes changes in the rheological properties of diluted alkali-soluble pectin (DASP) due to enzymatic treatment. Given DASP’s richness of rhamnogalacturonan I (RG-I), RG-I acetyl esterase (RGAE), rhamnogalacturonan endolyase (RGL), and arabinofuranosidase (ABF) were employed in various combinations for targeted degradation of RG-I pectin chains. Enzymatic degradations were followed by structural studies of pectin molecules using atomic force microscopy (AFM) as well as measurements of rheological and spectral properties. AFM imaging revealed a significant increase in the length of branched molecules after incubation with ABF, suggesting that arabinose side chains limit RG-I aggregation. Structural modifications were confirmed by changes in the intensity of bands in the pectin fingerprint and anomeric region on Fourier transform infrared spectra. ABF treatment led to a decrease in the stability of pectic gels, while the simultaneous use of ABF, RGAE, and RGL enzymes did not increase the degree of aggregation compared to the control sample. These findings suggest that the association of pectin chains within the DASP fraction may rely significantly on intermolecular interactions. Two mechanisms are proposed, which involve side chains as short-range attachment points or an extended linear homogalacturonan conformation favoring inter-chain interactions over self-association.

Renewable cold plasma exposed activated carbon-derived eucalyptus leaves (EL) as electrode in fabricating low-cost energy storage devices

ABSTRACT The activated carbon made from Eucalyptus leaves was created using an environmentally friendly physical activation process, and it was then subjected with the low temperature plasma to increase its surface area and porosity, as shown by structural and morphological characteristics. The nanoparticles’ surface layers are altered by the plasma treatment, improving surface characteristics like wettability, adhesion, and surface area that were investigated using structural, morphological, and electrochemical studies. The air-plasma-treated KOH exhibits a specific capacitance of 1591 F/g for 1.5 mA, which can be utilized to prepare an electrode material for the energy storage application. The electrochemical investigation was conducted for the untreated and air, oxygen-plasma-treated carbon, demonstrating the better specific capacitance for the air plasma treatment, which can be used to prepare an electrode material for the low-cost fabrication of the devices.

Lewis acid catalysis of polydopamine electropolymerisation as a tool for shaping its morphology and electrochemical properties

AbstractOrganic–inorganic semiconductor interfaces are of utmost importance in many photoelectrochemical applications, including water splitting and photodegradation of pollutants. The current work focuses on the fabrication and characterisation of transition metal-loaded polydopamine (PDA) electropolymerised on the surface of titania nanotubes. The structural studies via X-ray photoelectron spectroscopy and electron microscopy confirmed the catalytic effect of d-metal salts on the formation of the PDA layer during electropolymerisation. Cu and Ni loading leads to a significant enhancement of the visible absorption compared to that of the pristine PDA, also confirmed by the density functional theory calculations. Although the boost is greater for the thickest coatings, an excess amount of polymer suppresses the charge transfer and thus photocurrent generation. Synthesis in acidic conditions—optimal for photosensitisation—provides structures with a strong increase in the photocurrent quantum efficiency in the visible range, equal to 20% at 400 nm. Graphical Abstract

The anthropomorphization of the human-animal bond in family dynamics: A documentary review

Introduction: The study of the interaction between humans and companion animals has become more relevant due to changes in current social dynamics. Objective: To conduct a documentary review of the evolution of research on anthropomorphizationin animals and its impact on the human-animal bond characteristic of contemporary family dynamics. Methodology: This is a documentary review study supported by the Tree of Science (ToS) web tool for literature selection. The search was conducted inScopus and Web of Science. Thirty-one studies were included in the review. Results: The results were categorized into classical, structural and recent studies. It was found that the anthropomorphization of the animal and its inclusion in the family makes it possible to modify behaviors and establish habits in family life. The role of animals in the family scenario is directly influenced by the degree to which they are anthropomorphized, which generates both advantages and disadvantages for the family, the pets and their direct caregivers. Conclusions: Anthropomorphizing practices respond to contemporary changes in human relationships and perceived loneliness and may promote bonds in human-animal and human-human interactions.

Aluminum Complexes Supported by Ph2P‐Functionalized Anilido‐Pyridine Ligand Platform: Synthesis, Structure and Evaluation as Frustrated Lewis Pairs

AbstractA simple direct condensation of 2,6‐bis(phenylamino)pyridine (1) and ClPPh2 under basic conditions allowed straightforward synthesis of the new multidentate Ph2P‐substituted anilido‐pyridine proligands 2 a and 2 b. Proligand 2 a was used in σ‐bond metathesis reactions with Me3Al affording either dinuclear product 3 a‐Al2 or mononuclear 4 a‐Al, depending on the reaction conditions. These complexes were authenticated by X‐ray crystallography, NMR spectroscopy and microanalysis. The analysis of the interaction between Me2Al and Ph2P fragments in 4 a‐Al was performed by structural and computational studies. The reactivity of 4 a‐Al was preliminary assessed in several representative reactions.

A novel variant in the FLNB gene associated with spondylocarpotarsal synostosis syndrome.

Genetic disorders involved in skeleton system arise due to the disturbance in skeletal development, growth and homeostasis. Filamin B is an actin binding protein which is large dimeric protein which cross link actin cytoskeleton filaments into dynamic structure. A single nucleotide changes in the FLNB gene causes spondylocarpotarsal synostosis syndrome, a rare bone disorder due to which the fusion of carpels and tarsals synostosis occurred along with fused vertebrae. In the current study we investigated a family residing in north-western areas of Pakistan. The whole exome sequencing of proband was performed followed by Sanger sequencing of all family members of the subject to validate the variant segregation within the family. Bioinformatics tools were utilized to assess the pathogenicity of the variant. Whole Exome Sequencing revealed a novel variant (NM_001457: c.209C>T and p.Pro70Leu) in the FLNB gene which was homozygous missense mutation in the FLNB gene. The variant was further validated and visualized by Sanger sequencing and protein structure studies respectively as mentioned before. The findings have highlighted the importance of the molecular diagnosis in SCT (spondylocarpotarsal synostosis syndrome) for genetic risk counselling in consanguineous families.

AlZnO magnetron sputtered thin film for photovoltaic application

Aluminum zinc oxide (AZO) is a nontoxic and a low-cost material that finds application as a transparent conducting electrode in photovoltaic devices. In this study the (direct current) DC magnetron sputtering of AZO films is carried out at different deposition times of 5, 10, 15, 20 and 25 min’s at room temperature and it’s structural, optical, electrical and morphological properties are studied for its use as a front contact for thin film solar cell application. The structural study suggests that the preferred orientation of grains along (002) plane having hexagonal structure and the optical and the electrical studies suggest that the films show an average transmission of 70% and a resistivity of the order of 10-4Ωcm. On the other hand, the scanning electron microscopy (SEM) images suggest the formation of packed grains having a homogeneous surface. Moreover in order to study the optoelectronic properties of prepared samples, the electronic and optical calculations of the AZO are performed by the first-principles calculations using density functional theory (DFT).

Structural and chemical study of complex silver patterns additively manufactured by multi-photon reduction.

Multi-photon reduction (MPR) based on femtosecond laser makes rapid prototyping and molding in micro-nano scale feasible, but is limited in material selectivity due to lack of the understanding of the reaction mechanism in MPR process. In this paper, additively manufacturing of complex silver-based patterns through MPR is demonstrated. The effects of laser parameters, including laser pulse energies and scanning speeds, on the structural and chemical characteristics of the printed structures are systematically investigated. The results show that the geometric size of printed cubes deviates from the designed size further by increasing laser pulse energies or decreasing scanning speeds. The reaction mechanism of MPR is revealed by studying the elemental composition and chemical structures of printed cubes. The evolution of Raman spectra upon the laser processing parameters suggests that the MPR process mainly includes two processes: reduction and decomposition. In the MPR process, silver ions are reduced and grow into particles by accepting the electrons from ethonal molecules; meanwhile carboxyl groups in polyvinylpyrrolidone are decomposed and form amorphous carbon that is attached on the surface of silver particles. The conductivity of silver wires fabricated by MPR reaches 2×105 S/m and stays relatively constant as varying their cross section area, suggesting excellent electrical conduction. The understanding of the MPR process would accelerate the development of MPR technology and the implementation of MPR in micro-electromechanical systems could therefore be envisioned.

Highly specific aptamer trap for extremophilic RNA polymerases

During transcription initiation, the holoenzyme of bacterial RNA polymerase (RNAP) specifically recognizes promoters using a dedicated σ factor. During transcription elongation, the core enzyme of RNAP interacts with nucleic acids mainly nonspecifically, by stably locking the DNA template and RNA transcript inside the main cleft. Here, we present a synthetic DNA aptamer that is specifically recognized by both core and holoenzyme RNAPs from extremophilic bacteria of the Deinococcus-Thermus lineage. The aptamer binds RNAP with subnanomolar affinities, forming extremely stable complexes even at high ionic strength conditions, blocks RNAP interactions with the DNA template and inhibits RNAP activity during transcription elongation. We propose that the aptamer binds at a conserved site within the downstream DNA-binding cleft of RNAP and traps it in an inactive conformation. The aptamer can potentially be used for structural studies to reveal RNAP conformational states, affinity binding of RNAP and associated factors, and screening of transcriptional inhibitors.

Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A–A-Mismatch-Containing DNA

Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A–A-Mismatch-Containing DNA

Antibodies expand the scope of angiotensin receptor pharmacology.

G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often limited at the receptor, tissue and cellular levels. Antibodies have the potential to address these limitations but their properties as GPCR ligands remain poorly characterized. Here, using protein engineering, pharmacological assays and structural studies, we develop maternally selective heavy-chain-only antibody ('nanobody') antagonists against the angiotensin II type I receptor and uncover the unusual molecular basis of their receptor antagonism. We further show that our nanobodies can simultaneously bind to angiotensin II type I receptor with specific small-molecule antagonists and demonstrate that ligand selectivity can be readily tuned. Our work illustrates that antibody fragments can exhibit rich and evolvable pharmacology, attesting to their potential as next-generation GPCR modulators.

Orbital-overlap-driven hybridization in 3d-transition metal perovskite oxides LaMO3 (M = Ti-Ni) and La2CuO4

The wide tunability of strongly correlated transition metal (TM) oxides stems from their complex electronic properties and the coupled degrees of freedom. Among the perovskite oxides family, LaMO3 (M = Ti-Ni) allows an M-dependent systematic study of the electronic structure within the same-structure-family motif. While most of the studies have been focusing on the 3d TMs and oxygen sites, the role of the rare-earth site has been far less explored. In this work, we use resonant inelastic X-ray scattering (RIXS) at the lanthanum N4,5 edges and density functional theory (DFT) to investigate the hybridization mechanisms in LaMO3. We link the spatial-overlap-driven hybridization to energetic-overlap-driven hybridization by comparing the RIXS chemical shifts and the DFT band widths. The scope is extended to highly covalent Ruddlesden-Popper perovskite La2CuO4 by intercalating lanthanum atoms to rock-salt layers. Our work evidences an observable contribution of localized lanthanum 5p and 4f orbitals in the band structure.

The β-subunit of tryptophan synthase is a latent tyrosine synthase.

Aromatic amino acids and their derivatives are diverse primary and secondary metabolites with critical roles in protein synthesis, cell structure and integrity, defense and signaling. All de novo aromatic amino acid production relies on a set of ancient and highly conserved chemistries. Here we introduce a new enzymatic transformation for L-tyrosine synthesis by demonstrating that the β-subunit of tryptophan synthase-which natively couples indole and L-serine to form L-tryptophan-can act as a latent 'tyrosine synthase'. A single substitution of a near-universally conserved catalytic residue unlocks activity toward simple phenol analogs and yields exclusive para carbon-carbon bond formation to furnish L-tyrosines. Structural and mechanistic studies show how a new active-site water molecule orients phenols for a nonnative mechanism of alkylation, with additional directed evolution resulting in a net >30,000-fold rate enhancement. This new biocatalyst can be used to efficiently prepare valuable L-tyrosine analogs at gram scales and provides the missing chemistry for a conceptually different pathway to L-tyrosine.

Enabling nucleophilic reactivity in molecular calcium fluoride complexes.

Calcium fluoride is the ultimate source of all fluorochemicals. Current synthetic approaches rely on the use of HF, generated from naturally occurring fluorspar and sulfuric acid. Methods for constructing E-F bonds directly from CaF2 have long been frustrated by its high lattice energy, low solubility and impaired fluoride ion nucleophilicity. Little fundamental understanding of the reactivity of Ca-F moieties is available to guide methodology development; well-defined molecular species containing Ca-F bonds are extremely rare, and existing examples are strongly aggregated and evidence no nucleophilic fluoride delivery. Here, by contrast, we show that by targeting anionic systems of the type [Ln(X)2CaF]-, monomeric calcium fluoride complexes containing single Ca-F bonds can be synthesized, including via routes involving fluoride abstraction from existing C-F bonds. Comparative structural and spectroscopic studies of mono- and dinuclear systems allow us to define structure-activity relationships for E-F bond formation from molecular calcium fluorides.

Influence of thickness, Si and SiO2/Si substrate interfaces upon magnetization dynamics in RF sputtered Fe3O4 thin films

The effect of film thickness (90–220 nm), Si and SiO2/Si substrate interfaces upon structural, micro-structural and dynamic magnetic properties of RF sputtered Fe3O4 films are investigated. Structural and micro-structural studies have confirmed the polycrystalline Fe3O4 growth with a α-Fe2O3 minority phase. A systematic grain growth with thickness suggests the presence of anti-phase boundary (APB) and corresponding competing magnetic interactions. The absence of Verwey phase transition and lower effective magnetization of 283–359 emu/cm3 are attributed to the APBs. The influence of APBs and impurity states upon the magnetization dynamics has been investigated with co-planar waveguide ferromagnetic resonance spectroscopy from 9 to 33 GHz frequency range. A higher Gilbert damping of ∼0.016 is noted for Fe3O4/Si films as compared to the lower damping of ∼0.002–0.004 for Fe3O4/SiO2/Si interfaces. Further, inhomogeneity, intrinsic Gilbert damping and two-magnon scattering contributions to the damping parameter are evaluated and discussed.

Engineering of a Baeyer-Villiger monooxygenase to improve substrate scope, stereoselectivity and regioselectivity.

Baeyer-Villiger monooxygenases belong to a family of flavin-binding proteins that catalyze the Baeyer-Villiger (BV) oxidation of ketones to produce lactones or esters, which are important intermediates in pharmaceuticals or sustainable materials. Phenylacetone monooxygenase (PAMO) from Thermobifida fusca with moderate thermostability catalyzes the oxidation of aryl ketone substrates, but is limited by high specificity and narrow substrate scope. In the present study, we applied loop optimization by loop swapping followed by focused saturation mutagenesis in order to evolve PAMO mutants capable of catalyzing the regioselective BV oxidation of cyclohexanone and cyclobutanone derivatives with formation of either normal or abnormal esters or lactones. We further modulated PAMO to increase enantioselectivity. Crystal structure studies indicate that rotation occurs in the NADP-binding domain and that the high B-factor region is predominantly distributed in the catalytic pocket residues. Computational analyses further revealed dynamic character in the catalytic pocket and reshaped hydrogen bond interaction networks, which is more favorable for substrate binding. Our study provides useful insights for studying enzyme-substrate adaptations.

A Structural Study on Absorption of Lysozyme in Amorphous Starch Microspheres.

The potential of using proteins as drugs is held back by their low stability in the human body and challenge of delivering them to the site of function. Extensive research is focused on drug delivery systems that can protect, carry, and release proteins in a controlled manner. Of high potential are cross-linked degradable starch microspheres (DSMs), as production of these is low-cost and environmentally friendly, and the products are degradable by the human body. Here, we demonstrate that DSMs can absorb the model protein lysozyme from an aqueous solution. At low amounts of lysozyme, its concentration in starch microspheres strongly exceeds the bulk concentration in water. However, at higher protein contents, the difference between concentrations in the two phases becomes small. This indicates that, at lower lysozyme contents, the absorption is driven by protein-starch interactions, which are counteracted by protein-protein electrostatic repulsion at high concentrations. By applying small-angle X-ray scattering (SAXS) to the DSM-lysozyme system, we show that lysozyme molecules are largely unaltered by the absorption in DSM. In the same process, the starch network is slightly perturbed, as demonstrated by a decrease in the characteristic chain to chain distance. The SAXS data modeling suggests an uneven distribution of the protein within the DSM particles, which can be dependent on the internal DSM structure and on the physical interactions between the components. The results presented here show that lysozyme can be incorporated into degradable starch microspheres without any dependence on electrostatic or specific interactions, suggesting that similar absorption would be possible for pharmaceutical proteins.

Quantification of native lignin structural features with gel‐phase 2D‐HSQC0 reveals lignin structural changes during extraction

Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin’s structural features. Here, we developed a rapid elevated‐temperature 1H–13C Heteronuclear Single‐Quantum Coherence Zero (HSQC0) NMR method that enables this precise quantification of native lignin structural characteristics even with whole plant cell wall (WPCW) NMR spectroscopy, overcoming fast spin relaxation in the gel phase. We also formulated a Gaussian fitting algorithm to perform automatic and reliable spectral integration. By combining HSQC0 measurements with yield measurements following depolymerization, we can confirm the combinatorial nature of radical coupling reactions during biosynthesis leading to a random sequential organization of linkages within a largely linear lignin chain. Such analyses illustrate how this analytical method can greatly facilitate the study of native lignin structure, which can then be used for fundamental studies or to understand lignin depolymerization methods like reductive catalytic fractionation or aldehyde‐assisted fractionation.