Class Of Structures Research Articles

Biochemical characterization of L-asparaginase isoforms from Rhizobium etli-the boosting effect of zinc.

L-Asparaginases, divided into three structural Classes, catalyze the hydrolysis of L-asparagine to L-aspartic acid and ammonia. The members of Class 3, ReAIV and ReAV, encoded in the genome of the nitrogen fixing Rhizobium etli, have the same fold, active site, and quaternary structure, despite low sequence identity. In the present work we examined the biochemical consequences of this difference. ReAIV is almost twice as efficient as ReAV in asparagine hydrolysis at 37°C, with the kinetic KM, kcat parameters (measured in optimal buffering agent) of 1.5mM, 770s-1 and 2.1mM, 603s-1, respectively. The activity of ReAIV has a temperature optimum at 45°C-55°C, whereas the activity of ReAV, after reaching its optimum at 37°C, decreases dramatically at 45°C. The activity of both isoforms is boosted by 32 or 56%, by low and optimal concentration of zinc, which is bound three times more strongly by ReAIV then by ReAV, as reflected by the KD values of 1.2 and 3.3μM, respectively. We also demonstrate that perturbation of zinc binding by Lys→Ala point mutagenesis drastically decreases the enzyme activity but also changes the mode of response to zinc. We also examined the impact of different divalent cations on the activity, kinetics, and stability of both isoforms. It appeared that Ni2+, Cu2+, Hg2+, and Cd2+ have the potential to inhibit both isoforms in the following order (from the strongest to weakest inhibitors) Hg2+ > Cu2+ > Cd2+ > Ni2+. ReAIV is more sensitive to Cu2+ and Cd2+, while ReAV is more sensitive to Hg2+ and Ni2+, as revealed by IC50 values, melting scans, and influence on substrate specificity. Low concentration of Cd2+ improves substrate specificity of both isoforms, suggesting its role in substrate recognition. The same observation was made for Hg2+ in the case of ReAIV. The activity of the ReAV isoform is less sensitive to Cl- anions, as reflected by the IC50 value for NaCl, which is eightfold higher for ReAV relative to ReAIV. The uncovered complementary properties of the two isoforms help us better understand the inducibility of the ReAV enzyme.

Design, Synthesis, and Antifungal Activity of 3-Substituted-2(5H)-Oxaboroles.

Next generation antimicrobial therapeutics are desperately needed as new pathogens with multiple resistance mechanisms continually emerge. Two oxaboroles, tavaborole and crisaborole, were recently approved as topical treatments for onychomycosis and atopic dermatitis, respectively, warranting further studies into this privileged structural class. Herein, we report the antimicrobial properties of 3-substituted-2(5H)-oxaboroles, an unstudied family of medicinally relevant oxaboroles. Our results revealed minimum inhibitory concentrations as low as 6.25 and 5.20 μg/mL against fungal (e.g., Penicillium chrysogenum) and yeast (Saccharomyces cerevisiae) pathogens, respectively. These oxaboroles were nonhemolytic and nontoxic to rat myoblast cells (H9c2). Structure-activity relationship studies suggest that planarity is important for antimicrobial activity, possibly due to the effects of extended conjugation between the oxaborole and benzene rings.

Two-dimensional monolayer from organic molecules F4-TCNQ via DFT calculations

Conjugated microporous polymers is a class of organic nanoporous polymers in which the pores can be easily controlled by molecule design. Here we present a new class of 2D structure based on F4-TCNQ molecules. Using ab initio calculations, the possibilities for the formation of such 2D materials based on F4-TCNQ molecules are studied as well. Among considered structures only two were selected as the most preferable for 2D layer formation. Predicted monolayers were analyzed on thermal stability, electronic, optical and mechanical properties. Combination of stability, elasticity and semiconducting band gap make suggested monolayers promising candidate for fabrication of elements of flexible and controllable optoelectronics.

Finite Element modeling and convergence analysis of a new Biomimetic Branching Structure.

Branching structures are gaining popularity in the field of advanced structures and building design; they offer high performance in terms of strength and lightweight design, along with the flexibility and precision enabled by modern processing technologies like Additive Manufacturing. This paper provides a concise overview of a geometric design procedure for a novel ribbed class of structures which was previously developed by the authors as a biomimetic optimal Micro-architected dome. Hereinafter, linear lattice models are suggested to carry out structural calculations using the finite element method (FEM). The objective is to examine discretization thresholding and strain energy convergence criteria. Results show that convergence is reached for numbers of elements per leg, ranging from 2 to 6, depending on the geometrical configuration of the dome being studied. The strain energy balance also exposes the influence of each internal force on the total mechanical response of the structure, pinpointing bending moment and axial force as the main decisive factors. As a perspective, the study will focus on limit state design calculations and Analysis of how the local geometry influences the overall stability and strength of this new design.

Matrix product and quasi-twisted codes in one class

Many classical constructions, such as Plotkin’s and Turyn’s, were generalized by matrix product (MP) codes. Quasi-twisted (QT) codes, on the other hand, form an algebraically rich structure class that contains many codes with best-known parameters. We significantly extend the definition of MP codes to establish a broader class of generalized matrix product (GMP) codes that contains QT codes as well. We propose a generator matrix formula for any linear GMP code and provide a condition for determining the code size. We prove that any QT code has a GMP structure. Then we show how to build a generator polynomial matrix for a QT code from its GMP structure, and vice versa. Even though the class of QT codes contains many codes with best-known parameters, we present different examples of GMP codes with best-known parameters that are neither MP nor QT. Two different lower bounds on the minimum distance of GMP codes are presented; they generalize their counterparts in the MP codes literature. The second proposed lower bound replaces the non-singular by columns matrix with a less restrictive condition. Some examples are provided for comparing the two proposed bounds, as well as showing that these bounds are tight.

Data‐Driven Screening of Pivotal Subunits in Edge‐Anchored Single Atom Catalysts for Oxygen Reactions

AbstractOxygen reduction reaction (ORR) and the oxygen evolution reaction (OER) are key reactions in diverse energy conversion devices, highlighting the importance of efficient catalysts. Edge‐anchored single atom catalysts (E‐SACs) emerge as a special class of atomic structure, but the detailed configuration and its correlation with catalytic activity remain little explored. Herein, a total of 78 E‐SACs (E‐TM‐Nx‐C) have been constructed based on 26 transition metal (TM) species with three coordination patterns. Using structural stability and ORR/OER catalytic activity as the evaluation criteria, a few catalytic structures comparable to Pt (111) for ORR and IrO2 (110) for OER are screened based on high‐throughput calculations. The screening results unveil that the E‐Rh‐N4‐C configuration exhibits most efficient bifunctional activity for both ORR and OER with an overpotential of 0.38 and 0.61 V, respectively. Electronic structure analysis confirms the distinctive edge effects on the electronic properties of TM and N species, and the feature importance derived from machine learning illustrates the efficacy of E‐TM‐Nx subunit configuration in determining the catalytic activity of E‐SACs. Finally, the trained Gradient Boosting Regression (GBR) model exhibits acceptable accuracy in predicting the OH intermediates adsorption strength for E‐SACs, thereby paving the way for expanding catalytic structures based on E‐SACs.

LATTICE TILINGS OF A PLANE BY POLYOMINOS AND MOLECULAR LAYERS IN CRYSTAL STRUCTURES. STRUCTURAL CLASS CM, Z = 2(M)

Lattice partitions of a plane into polyominoes were constructed for N from 3 to 12, where N is the order of the packing space. We obtained 5191 symmetric independent lattice partitions of a plane with one polyomino in a reduced (primitive) cell, among which 122 variants belong to the structural class cm, Z = 2(m), with the elementary conventional cell being rectangular (centered). Chain partitions of planes have been derived, for which both structural class and structural subclass were identified. The results of the analysis of lattice partitions of a plane into polyominoes were illustrated with examples of real molecular layers in crystal structures.

Lattice Tilings of a Plane into Polyominoes and Molecular Layers in Crystal Structures: Structural Class cm, Z = 2(m)

Lattice Tilings of a Plane into Polyominoes and Molecular Layers in Crystal Structures: Structural Class cm, Z = 2(m)

Graph Entropy for Adjacently and Non-Adjacently Configured Pentagonal Structure of Carbon Nanocones

aims: Carbon nanocones possess exceptional properties compared to other nanomaterials, such as nanotubes, graphene etc. Hence they can be used as an alternative to other nanostructures. This work helps in determining various properties of the nanocone structure through topological descriptors. In this paper, various degree based topological descriptors along with its entropy measures are evaluated for adjacently and non-adjacently configured pentagonal structure of carbon nanocones. background: Carbon nanoparticles are gaining much importance in the contemporary world. Among which carbon nanocones have wide range of acceptance in the field of nanotechnology due to its effective properties and applications. Nanocones, also known as nanohorns are carbon networks which are planar in structure and has majority of hexagonal faces along with some nonhexagonal faces, which are most commonly pentagons. Nanocones which include pentagons in their structure can be referred to as adjacently or non- adjacently configured pentagonal structure of nanocones. Various topological descriptors for few nanocone classes were derived by researchers earlier, but not for the class of nanocones in this paper. Through this work, we try to vanish the research gap in this field. objective: : The degree based descriptors and corresponding graph entropies for the adjacently and non-adjacently configured pentagonal structure of nanocones were determined, which further can be applied in quantitative structure – activity – property relationship studies. The concept of graph entropy is to assign a probability function to the edges in the chemical graph using the topological descriptor and it helps to characterise the complexity of graphs. method: We have employed the degree counting method and edge partition based on the vertices and edges of the adjacently and non-adjacently configured pentagonal nanocone structures to obtain the edge partitions and then using the corresponding mathematical expression, the degree based descriptors and its corresponding entropies were determined. result: Result: The analytically closed formulas to compute the degree based topological descriptors and graph entropies for any generation of the class of nanocone structures were obtained. conclusion: In this work, the degree based descriptors and the corresponding graph entropies for the adjacently and non-adjacently configured pentagonal structure of carbon nanocones are determined applying the degree counting method and edge partition based on the vertices and edges. Also a graphical comparative study was also done with the help of obtained results. other: end.

Integrative metabolome and transcriptome analysis characterized methyl jasmonate-elicited flavonoid metabolites of Blumea balsamifera.

As a commonly used medicinal plant, the flavonoid metabolites of Blumea balsamifera and their association with genes are still elusive. In this study, the total flavonoid content (TFC), flavonoid metabolites and biosynthetic gene expression patterns of B. balsamifera after application of exogenous methyl jasmonate (MeJA) were scrutinized. The different concentrations of exogenous MeJA increased the TFC of B. balsamifera leaves after 48 h of exposure, and there was a positive correlation between TFC and the elicitor concentration. A total of 48 flavonoid metabolites, falling into 10 structural classes, were identified, among which flavones and flavanones were predominant. After screening candidate genes by transcriptome mining, the comprehensive analysis of gene expression level and TFC suggested that FLS and MYB may be key genes that regulate the TFC in B. balsamifera leaves under exogenous MeJA treatment. This study lays a foundation for elucidating flavonoids of B. balsamifera, and navigates the breeding of flavonoid-rich B. balsamifera varieties.

Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction.

The DNA excision repair protein ERCC1 and the DNA damage sensor protein, XPA are highly overexpressed in patient samples of cisplatin-resistant solid tumors including lung, bladder, ovarian, and testicular cancer. The repair of cisplatin-DNA crosslinks is dependent upon nucleotide excision repair (NER) that is modulated by protein-protein binding interactions of ERCC1, the endonuclease, XPF, and XPA. Thus, inhibition of their function is a potential therapeutic strategy for the selective sensitization of tumors to DNA-damaging platinum-based cancer therapy. Here, we report on new small-molecule antagonists of the ERCC1/XPA protein-protein interaction (PPI) discovered using a high-throughput competitive fluorescence polarization binding assay. We discovered a unique structural class of thiopyridine-3-carbonitrile PPI antagonists that block a truncated XPA polypeptide from binding to ERCC1. Preliminary hit-to-lead studies from compound 1 reveal structure-activity relationships (SAR) and identify lead compound 27 o with an EC50 of 4.7 μM. Furthermore, chemical shift perturbation mapping by NMR confirms that 1 binds within the same site as the truncated XPA67-80 peptide. These novel ERCC1 antagonists are useful chemical biology tools for investigating DNA damage repair pathways and provide a good starting point for medicinal chemistry optimization as therapeutics for sensitizing tumors to DNA damaging agents and overcoming resistance to platinum-based chemotherapy.

Isotropic gap formation, localization, and waveguiding in mesoscale Yukawa-potential amorphous structures

Amorphous photonic structures are mesoscopic optical structures described by electrical permittivity distributions with underlying spatial randomness. They offer a unique platform for studying a broad set of electromagnetic phenomena, including transverse Anderson localization, enhanced wave transport, and suppressed diffusion in random media. Despite this, at a more practical level, there is insufficient work on both understanding the nature of optical transport and the conditions conducive to vector-wave localization in these planar structures, as well as their potential applications to photonic nanodevices. In this study, we fill this gap by investigating experimentally and theoretically the characteristics of optical transport in a class of amorphous photonic structures and by demonstrating their use to some basic waveguiding nanostructures. We demonstrate that these 2-D structures have unique isotropic and asymmetric band gaps for in-plane propagation, controlled from first principles by varying the scattering strength and whose properties are elucidated by establishing an analogy between photon and carrier transport in amorphous semiconductors. We further observe Urbach band tails in these random structures and uncover their relation to frequency- and disorder-dependent Anderson-like localized modes through the modified Ioffe-Regel criterion and their mean free path - localization length character. Finally, we illustrate that our amorphous structures can serve as a versatile platform in which photonic devices such as disorder-localized waveguides can be readily implemented.

III. Geometrical framework for thinking about globular proteins: Turns in proteins.

We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry. α-helices and β-sheets are found to be special geometries that have systematic poking contacts in a repetitive manner with the contacts being local along the α-helix and non-local along a pair of adjacent strands within a β-sheet. Pairwise poking interactions also govern tertiary structure formation, but they are weaker and there are no special geometrical constraints as in secondary structure formation. Here we demonstrate that protein turns, the most prevalent non-repetitive structural element in proteins, are instances of local (as in α-helices) and isolated (non-repetitive) poking pairwise contacts for which the geometrical constraints are partially relaxed. This simple and purely geometrical definition of protein turns (also sometimes known as reverse turns, β-turns, β-bends, hairpin bends, 310 bends, kinks, widgets, etc.) provides a simple framework for unifying them. We present the results of a systematic analysis and identify their structural classes as well as their respective amino acid preferences.

Origami-Wrapped Structures with Corrugated Unfolded Forms

Stowage schemes based on origami wrapping patterns are useful for the design of various deployable spacecraft structures. These origami patterns allow for the compact stowage of flat sheets of small thickness. Typically, some other structure is needed to stiffen this thin sheet when it is fully deployed and flat. This paper describes a class of thin-shell structures that can be compactly stowed using origami wrapping methods but have a corrugated form when deployed. These structures cannot reach a flat state by design. The persistent corrugations provide stiffness without the need for an external structure, thus leading to overall savings in mass and complexity. The geometrical design of the corrugations is highly tunable. This paper describes a method for generating the form of these folding structures; the method guarantees that the structure can be unstrained both when compactly wrapped and when fully deployed. Test articles are fabricated to demonstrate the concept, and stowage experiments and stiffness experiments are conducted. A structural finite element modeling procedure is described to predict the deployed stiffness of these structures, and the stiffness predictions match the experimental results.

Synthesis, Structural Characterization, and Magnetic Properties of Lanthanide Arsolyl Sandwich Complexes.

A series of trivalent lanthanide sandwich complexes [(η5-C4R4As)Ln(η8-C8H8)] using three different arsolyl ligands are reported. The complexes were obtained via salt elimination reactions between potassium arsolyl salts and lanthanide precursors [LnI(COT)(THF)2] (Ln = Sm, Dy, Er; COT = η8-C8H8). The resulting compounds exhibit classical sandwich complex structures with one notable exception. Characterization was conducted in both the solid state using single-crystal X-ray diffraction and in solution for the Sm compounds using NMR spectroscopy. Furthermore, the magnetic properties of an Er complex were investigated, revealing distinctive single-molecule-magnet behavior characterized by an energy barrier of Ueff = 323.3 K. Theoretical calculations were employed to support and interpret the experimental findings, with a comparative analysis performed against previously reported complexes.

A note on minimax robustness of designs against correlated or heteroscedastic responses

Abstract We present a result according to which certain functions of covariance matrices are maximized at scalar multiples of the identity matrix. This is used to show that experimental designs that are optimal under an assumption of independent, homoscedastic responses can be minimax robust, in broad classes of alternate covariance structures. In particular, it can justify the common practice of disregarding possible dependence, or heteroscedasticity, at the design stage of an experiment.

Investigating the applicability of deep learning and machine learning models in predicting the structural performance of V-shaped RC folded plates

Reinforced concrete folded plates (RC-FPs), which are a special class of shell structures, have recently become very popular in modern architectural and engineering applications because of the need for lightweight and aesthetic structures to cover large areas. However, it is known that studies on the structural performance of RC-FPs are insufficient. Therefore, this article presents a study on the development and comparison of different deep learning (DL) and machine learning (ML) models for the prediction of the structural performance of full-scale V-shaped RC-FPs produced from hybrid fiber-reinforced self-consolidating concrete (HFR-SCC) having different plate thicknesses (50, 60, 70, and 80 mm), fiber volumes (1.00% and 1.25%), and combinations (single, binary, and ternary). While vanilla long short-term memory (VLSTM) and bidirectional long short-term memory (BILSTM) are used as DL models, random forest (RF), extremely randomized trees (ERT), and adaptive boosting (AdaBoost) are preferred for ML models. To construct the models, the structural performance results of a total of 44 full-scale V-shaped RC-FPs subjected to four-point bending loading were adopted as the database. In addition to all these, the AdaBoost model is used to determine the relative feature importance of the input parameters. Based on the results, among the DL models, the BILSTM has the best ability to predict the structural performance values of V-shaped RC-FPs (such as R-squared values for maximum load-bearing capacity, cracking load, toughness, and deflection ductility are 0.934, 0.987, 0.972, and 0.812, respectively), while in ML models, this is valid for the ERT (such as R-square values are 0.917 for maximum load-bearing capacity, 0.936 for cracking load, 0.947 for toughness and 0.825 for deflection ductility). On the other hand, DL models predicted all other structural performance values better than ML models, except for deflection ductility. Besides, the most relative important input features for maximum load-bearing capacity and toughness values is plate thickness, whereas for cracking load and deflection ductility values compressive strength is important. In conclusion, it can be emphasized that the use of DL models can provide significant advantages in engineering applications, such as predicting the structural performance of V-shaped RC-FPs.

Biomimetic Synthesis and Chemical Proteomics Reveal the Mechanism of Action and Functional Targets of Phloroglucinol Meroterpenoids.

Natural products perennially serve as prolific sources of drug leads and chemical probes, fueling the development of numerous therapeutics. Despite their scarcity, natural products that modulate protein function through covalent interactions with lysine residues hold immense potential to unlock new therapeutic interventions and advance our understanding of the biological processes governed by these modifications. Phloroglucinol meroterpenoids constitute one of the most expansive classes of natural products, displaying a plethora of biological activities. However, their mechanism of action and cellular targets have, until now, remained elusive. In this study, we detail the concise biomimetic synthesis, computational mechanistic insights, physicochemical attributes, kinetic parameters, molecular mechanism of action, and functional cellular targets of several phloroglucinol meroterpenoids. We harness synthetic clickable analogues of natural products to probe their disparate proteome-wide reactivity and subcellular localization through in-gel fluorescence scanning and cell imaging. By implementing sample multiplexing and a redesigned lysine-targeting probe, we streamline a quantitative activity-based protein profiling, enabling the direct mapping of global reactivity and ligandability of proteinaceous lysines in human cells. Leveraging this framework, we identify numerous lysine-meroterpenoid interactions in breast cancer cells at tractable protein sites across diverse structural and functional classes, including those historically deemed undruggable. We validate that phloroglucinol meroterpenoids perturb biochemical functions through stereoselective and site-specific modification of lysines in proteins vital for breast cancer metabolism, including lipid signaling, mitochondrial respiration, and glycolysis. These findings underscore the broad potential of phloroglucinol meroterpenoids for targeting functional lysines in the human proteome.

Review on the Applications of Selected Metal-Based Complexes on Infectious Diseases.

Fatalities caused by infectious diseases (i.e., diseases caused by parasite, bacteria, and viruses) have become reinstated as a major public health threat globally. Factors such as antimicrobial resistance and viral complications are the key contributors to the death numbers. As a result, new compounds with structural diversity classes are critical for controlling the virulence of pathogens that are multi-drug resistant. Derivatization of bio-active organic molecules with organometallic synthons is a promising strategy for modifying the inherent and enhanced properties of biomolecules. Due to their redox chemistry, bioactivity, and structural diversity, organometallic moieties make excellent candidates for lead structures in drug development. Furthermore, organometallic compounds open an array of potential in therapy that existing organic molecules lack, i.e., their ability to fulfill drug availability and resolve the frequent succumbing of organic molecules to drug resistance. Additionally, metal complexes have the potential towards metal-specific modes of action, preventing bacteria from developing resistance mechanisms. This review's main contribution is to provide a thorough account of the biological efficacy (in vitro and in vitro) of metal-based complexes against infectious diseases. This resource can also be utilized in conjunction with corresponding journals on metal-based complexes investigated against infectious diseases.

Direct Heterocycle C-H Alkenylation via Dual Catalysis Using a Palladacycle Precatalyst: Multifactor Optimization and Scope Exploration Enabled by High-Throughput Experimentation.

One of the major challenges in developing catalytic methods for C-C bond formation is the identification of generally applicable reaction conditions, particularly if multiple substrate structural classes are involved. Pd-catalyzed direct arylation reactions are powerful transformations that enable direct functionalization of C-H bonds; however, the corresponding direct alkenylation reactions, using vinyl (pseudo) halide electrophiles, are less well developed. Inspired by process development efforts toward GSK3368715, an investigational active pharmaceutical ingredient, we report that a Pd(II) palladacycle derived from tri-tert-butylphosphine and Pd(OAc)2 is an effective single-component precatalyst for a variety of direct alkenylation reactions. High-throughput experimentation identified optimal solvent/base combinations for a variety of HetAr-H substrate classes undergoing C-H activation without the need for cocatalysts or stoichiometric silver bases (e.g., Ag2CO3). We propose this reaction proceeds via a dual cooperative catalytic mechanism, where in situ-generated Pd(0) supports a canonical Pd(0)/(II) cross-coupling cycle and the palladacycle effects C-H activation via CMD in a redox-neutral cycle. In all, 192 substrate combinations were tested with a hit rate of approximately 40% and 24 isolated examples. Importantly, this method was applied to prepare a key intermediate in the synthesis of GSK3368715 on multigram scale.