Three-dimensional Structure Research Articles

Innovation, structural inspection for new mixed complexes: DNA binding, biomedical applications and molecular docking approaches

2-Guanidinobenzimidazole (BIG) and Imidiazole (I) ligands were utilized to synthesize Cu(II), VO(II), Ag(I), and Pd(II) as mixed ligand complexes. All studied molecules were characterized through various spectral, analytical and computational studies to find out their chemical structure. TGA was applied to identify the occurrence of H2O molecules besides the mono-nuclear property of isolated complexes. These complexes were proved through DFT study to confirm the coordinating site that was proposed and displays the optimal three-dimensional structures of the studied compounds. The binding affinity of the tested complexes with CT-DNA has been tested through agarose gel, electronic spectroscopy and viscosity measurements. Furthermore, the studied molecules might bind to CT-DNA electrostatically through exterior contact, replacement, intercalation and groove surface binding with good affinity. In-vitro anti-bacterial, anti-fungi, cytotoxic and antioxidant activities are performed for all studied compounds. MOE-docking simulation results indicate promising inhibitory features of BIGIPd complexes, in agreement with in-vitro results.

Facile synthesis of an acrylic acid-co-2-acrylamide-2-methylpropanesulfonic acid copolymer / polyvinylpyrrolidone semi-IPN hydrogel with excellent swelling and anti-leakage properties

Water scarcity becomes an increasingly serious problem for humankind due to climate change and population growth, especially the water leakage in arid and semi-arid areas. Hydrogel polymers show increasingly important roles on water resources utilization. A novel hydrogel copolymer, acrylic acid-co-2-acrylamide-2-methylpropanesulfonic acid copolymer / polyvinylpyrrolidone (P(AA-co-AMPS)/PVP) semi-interpenetrating network (semi-IPN) hydrogel, was designed and successfully synthesized via a facile one-pot free radical copolymerization method. The main parameters during the synthesis process were optimized, including relative contents of polymer monomers, cross-linking agent, initiator and neutralization agent. Physical characterizations demonstrate that, P(AA-co-AMPS)/PVP hydrogel shows porous three-dimensional network structure, including a crosslinked network structure in P(AA-co-AMPS) copolymers and their intermolecular hydrogen bonding interactions with linear PVP. The as-synthesized P(AA-co-AMPS)/PVP hydrogel not only can deliver superior water absorbing capability (up to 1689.95 g g−1) and good reswelling performance, but also shows excellent water anti-leakage performance when being composed with red clay, demonstrating its multi-role applications in future sustainable agriculture.

A novel nanosheets assembled porous fusiform Co2P2O7 for sensitive electrochemical detection of ultratrace As(III) ions

A facile and low-cost method was used to synthesize a novel nanosheets assembled porous fusiform Co2P2O7 for ultrasensitive electrochemical sensing detection of As(III) in water. The porous fusiform Co2P2O7 formed by small nanosheets exhibits a three-dimensional porous structure with a rough surface and good dispersion, facilitating a well-connected electron transfer path and providing numerous electroactive sites to bind with As(III). The proposed electrochemical sensor exhibited a high sensitivity of 91.04 µA µg/L cm−2 and a low detection limit of 0.087 µg/L towards As(III) in 0.1 M HAc-NaAc buffer (pH 5.0). Furthermore, it exhibited great potential for the electrochemical detection of As(III) in tap water.

Gas-Phase-Induced Engineering for Fabrication of 3D Hierarchical Porous Nickel and Its Application toward High-Performance Supercapacitors.

Commercial nickel foam (NF), which is composed of numerous interconnected ligaments and hundred-micron pores, is widely acknowledged as a current collector/electrode material for catalysis, sensing, and energy storage applications. However, the commonly used NF often does not work satisfactorily due to its smooth surface and hollow structure of the ligaments. Herein, a gas-phase-induced engineering, two-step gaseous oxidation-reduction (GOR) is presented to directly transform the thin-walled hollow ligament of NF into a three-dimensional (3D) nanoporous prism structure, resulting in the fabrication of a unique hierarchical porous nickel foam (HPNF). This 3D nanoporous architecture is achieved by utilizing the spontaneous reconstruction of nickel atoms during volume expansion and contraction in the GOR process. The process avoids the involution of acid-base corrosion and sacrificial components, which are facile, environmentally friendly, and suitable for large-scale fabrication. Furthermore, MnO2 is electrochemically deposited on the HPNF to form a supercapacitor electrode (HPNF/MnO2). Because of the fully open structure for ion transport, superhydrophilic properties, and the increased contact area between MnO2 and the current collector, the HPNF/MnO2 electrode exhibits a high specific capacitance of 997.5 F g-1 at 3 A g-1 and remarkable cycling stability with 99.6% capacitance retention after 20000 cycles in 0.1 M Na2SO4 electrolyte, outperforming most MnO2-based supercapacitor electrodes.

Hydrogel/MOF Dual-Modified Photoelectrochemical Biosensor for Antibiofouling and Biocompatible Dopamine Detection.

For accurate in vivo detection, nonspecific adsorption of biomacromolecules such as proteins and cells is a severe issue. The adsorption leads to electrode passivation, significantly compromising both the sensitivity and precision of sensing. Meanwhile, common antibiofouling modifications, such as polymer coatings, still grapple with issues related to biocompatibility, electrode passivation, and miniaturization. Herein, we propose a composite antibiofouling coating strategy based on zwitterionic metal-organic frameworks (Z-MOFs) and a combination of acrylamide hydrogels. On a well-designed TiO2/Z-MOF/hydrogel photoelectrode, we achieve highly sensitive and selective detection of dopamine in complex biological environments. The hydrogel's three-dimensional porous structure combined with unique microporous architecture of Z-MOF ensures effective sieving of interfering macromolecules while preserving efficient small molecules and electron transport. This innovative approach paves the way for constructing miniature, in vivo antibiofouling sensors for molecule monitoring in living organisms with complicated chemical environments.

Three-dimensional forest structure features extraction based on TomoSAR

Abstract. Forest structure is an important indicator for evaluating forest ecosystem and an indispensable input parameter for estimating forest carbon sink. Synthetic Aperture Radar (SAR) Tomography (TomoSAR), as a novel microwave remote sensing technique with 3D imaging capability, has been demonstrated to be an valuable tool for accurate inversion of forest structure. At present, the forest vertical structure parameters inversion is almost all concentrated on the forest height estimation. However, the spatial structure of forests is complex, and it is not enough to only use the forest height to express the forest structure. This fails to identify tree canopy, branch layer and underlying vegetation layer, etc., resulting in the partial and inaccurate forest vertical structure information. To solve this problem, this paper constructs 3D structural indices from tomograms, namely Horizontal Structure Index (HS) and Vertical Structure Index (VS). The HS primarily describes canopy density, compensating for the lack of information on the horizontal dimension of forest structure provided by traditional TomoSAR techniques; while VS describes the complexity of canopy distribution in the altitude direction, further enriching information on forest structure vertically. In order to verify their feasibility and validity, HS and VS are extracted using six fully-polarized L-band SAR images covering the Krycklan watershed in Sweden. Moreover, the accuracy is verified by using external high-precision LiDAR data. The results indicate a strong correlation between the structural indices extracted from TomoSAR and those extracted from LiDAR.

A node-based smoothed finite element method (NS-FEM) for free and forced vibration analysis of three-dimensional (3D) structures

A node-based smoothed finite element method (NS-FEM) for free and forced vibration analysis of three-dimensional (3D) structures

EMMAs: Implementation and Assessment of a Suite of Cross-Disciplinary, Case-Based High School Activities to Explore Three-Dimensional Molecular Structure, Noncovalent Interactions, and Molecular Dynamics

EMMAs: Implementation and Assessment of a Suite of Cross-Disciplinary, Case-Based High School Activities to Explore Three-Dimensional Molecular Structure, Noncovalent Interactions, and Molecular Dynamics

AFFORDABLE VIRTUAL REALITY HAPTIC-FEEDBACK SURGICAL SIMULATOR: A PROOF OF CONCEPT

INTRODUCTIONSimulation plays an important role in surgical education and the ability to perfect surgical performance. Simulation can be enhanced by adding various layers of realism to the experience. Haptic feedback enhances the simulation experience by providing tactile responses and virtual reality imagery provides an immersive experience and allows for greater appreciation of three-dimensional structures. In this study, we present a proof-of-concept haptic simulator to replicate key steps of a cervical laminoplasty procedure. The technology uses affordable components and is easily modifiable so that it can be used from novice through to expert level. Custom models can be easily added ensuring the simulator can be used in a wide range of orthopaedic applications from baseline education through to day of surgery pre-operative simulation.METHODWe used the Unity Game Engine, the 3D Systems “Touch” Haptic Feedback Device (HFD), and a Meta Quest VR headset. Our system uses a number of complex algorithms to track the shape and provide haptic feedback of a virtual bone model. This allows for simulation of various tools including a high-speed burr, Kerrison rongeur and intraoperative X-rays.RESULTSOur simulator replicates the tactile sensations of bone-burring tasks. Although we focused on the cervical laminoplasty procedure, the system can load data from CT scans, enabling the simulation of multiple other procedures. The parts cost of our system, $10,000 NZD, is a fraction of the cost of traditional surgical simulators.DISCUSSIONOur simulator reduces financial barriers to accessing orthopaedic simulators. Trainees can perform hands-on practice without compromising patient safety. The immersive nature of VR, combined with realistic haptic feedback, enables trainees to develop the dexterity and three-dimensional understanding of detailed bony work. Further refinements are needed before we can perform validation studies on our system.CONCLUSIONSWe present an affordable surgical simulator capable of simulating bony surgical procedures in a VR environment using haptic feedback technology and consumer-grade components.ACKNOWLEDGEMENTSThis research was made possible by the generosity of the Wishbone Trust.

Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.

Access to the three-dimensional structure of RNA enables an ability to gain a more profound understanding of its biological mechanisms, as well as the ability to design RNA-targeting drugs, which can take advantage of the unique chemical environment imposed by a folded RNA structure. Due to the dynamic and structurally complex properties of RNA, both experimental and traditional computational methods have difficulty in determining RNA's 3D structure. Herein, we introduce TAPERSS (Theoretical Analyses, Prediction, and Evaluation of RNA Structures from Sequence), a physics-based fragment assembly method for predicting 3D RNA structures from sequence. Using a fragment library created using discrete path sampling calculations of RNA dinucleoside monophosphates, TAPERSS can sample the physics-based energy landscapes of any RNA sequence with relatively low computational complexity. We have benchmarked TAPERSS on 21 RNA tetraloops, using a combinatorial algorithm as a proof-of-concept. We show that TAPERSS was successfully able to predict the apo-state structures of all 21 RNA hairpins, with 16 of those structures also having low predicted energies as well. We demonstrate that TAPERSS performs most accurately on GNRA-like tetraloops with mostly stacked loop-nucleotides, while having limited success with more dynamic UNCG and CUYG tetraloops, most likely due to the influence of the RNA force field used to create the fragment library. Moreover, we show that TAPERSS can successfully predict the majority of the experimental non-apo states, highlighting its potential in anticipating biologically significant yet unobserved states. This holds great promise for future applications in drug design and related studies. With discussed improvements and implementation of more efficient sampling algorithms, we believe TAPERSS may serve as a useful tool for a physics-based conformational sampling of large RNA structures.

Role of estrogen signaling in fibroblastic reticular cellsfor innate and adaptive immune responses in antigen-induced arthritis.

Women are more prone to develop rheumatoid arthritis, with peak incidence occurring around menopause. Estrogen has major effects on the immune system and is protective against arthritis. We have previously shown that treatment with estrogen inhibits inflammation and joint destruction in murine models of arthritis, although the mechanisms involved remain unclear. Fibroblastic reticular cells (FRCs) are specialized stromal cells that generate the three-dimensional structure of lymph nodes (LNs). FRCs are vital for coordinating immune responses from within LNs and are characterized by the expression of the chemokine CCL19, which attracts immune cells. The aim of this study was to determine whether the influence of estrogen on innate and adaptive immune cells in arthritis is mediated by estrogen signaling in FRCs. Conditional knockout mice lacking estrogen receptor α (ERα) in CCL19-expressing cells (Ccl19-CreERαfl/fl) were generated and tested. Ccl19-CreERαfl/fl mice and littermate controls were ovariectomized, treated with vehicle or estradiol and subjected to the 28-day-long antigen-induced arthritis model to enable analyses of differentiated T- and B-cell populations and innate cells in LNs by flow cytometry. The results reveal that while the response to estradiol treatment in numbers of FRCs per LN is significantly reduced in mice lacking ERα in FRCs, estrogen does not inhibit joint inflammation or markedly affect immune responses in this arthritis model. Thus, this study validates the Ccl19-CreERαfl/fl strain for studying estrogen signaling in FRCs within inflammatory diseases, although the chosen arthritis model is deemed unsuitable for addressing this question.

Ultrastructural 3D Microscopy for Biomedicine: Principles, Applications, and Perspectives.

Modern biomedical research often requires a three-dimensional microscopic analysis of the ultrastructure of biological objects and materials. Conceptual technical and methodological solutions for three-dimensional structure reconstruction are needed to improve the conventional optical, electron, and probe microscopy methods, which to begin with allow one to obtain two-dimensional images and data. This review discusses the principles and potential applications of such techniques as serial section transmission electron microscopy; techniques based on scanning electron microscopy (SEM) (array tomography, focused ion beam SEM, and serial block-face SEM). 3D analysis techniques based on modern super-resolution optical microscopy methods are described (stochastic optical reconstruction microscopy and stimulated emission depletion microscopy), as well as ultrastructural 3D microscopy methods based on scanning probe microscopy and the feasibility of combining them with optical techniques. A comparative analysis of the advantages and shortcomings of the discussed approaches is performed.

Studies on interactions of ruthenium(II) polypyridyl complexes [Ru(bpy)2(btip)]2+ and [Ru(dmb)2(btip)]2+ with double-stranded RNA poly(A)·poly(U) under molecular crowding conditions

Ruthenium(II) polypyridyl complexes have emerged as excellent nucleic acid binders based on the easy-to-construct three-dimensional structures and rich photophysical and photochemical properties. However, most studies are usually performed under dilute conditions, which might be disturbed by the crowding environment of cells. Herein, two ruthenium(II) polypyridyl complexes, [Ru(bpy)2(btip)]2+ (Ru1, bpy = 2,2′-bipyridine, btip = 2-benzo[b]thien-2-yl-1H-imidazo[4,5-f]-[1,10]phenanthroline) and [Ru(dmb)2(btip)]2+ (Ru2, dmb = 4,4′-dimethyl-2,2′-bipyridine) have been synthesized and characterized. Interactions of the two complexes with double-stranded RNA poly(A)·poly(U) in dilute solution and molecular crowding environment have been studied by spectroscopic techniques and viscosity measurements, respectively. Spectral titration and viscosity experiments show that both Ru1 and Ru2 combine with poly(A)·poly(U) through an intercalative mode in both environments, and the binding affinity in crowding environment is significantly lower than that in dilute solution, but still comparatively high. Moreover, thermal denaturation experiments show that the abilities of Ru1 and Ru2 to poly(A)·poly(U) are significantly reduced under crowding condition, which are attributed to the reduced binding affinity of the complexes to poly(A)·poly(U) in crowding environment.

Zonal free element method for free and forced vibration analysis of two- and three-dimensional structures

This paper presents a new numerical method called the zonal free element method (ZFREM) for the free and forced vibration analysis of elastodynamic problems. In this approach, a complex computational domain is divided into some simple zones and generates a series of regularly arranged nodes in each zone, which can improve the accuracy during the analysis of complex models. The distinguishing feature of the ZFREM is that an independent isoparametric element is formed by only one freely chosen surrounding node at each configuration node. In this method, the mass term exists only in the internal nodes, which can accelerate the assembly of the final system equations. Building upon this foundation, the present study developed the Krylov reduced dimensional iterative method, which approximates the solution of the equation system by constructing a lower-dimensional subspace. This approach avoids the complex equation transformations involved in traditional algorithms for solving eigenvalue problems, thereby further enhancing computational efficiency. Moreover, to tackle damped vibration problems encountered in engineering applications, the proposed method is further extended to solve the non-linear forced vibration problems. The accuracy and effectiveness of the method are verified by numerical examples of free and forced vibration problems.

Western US intraplate deformation controlled by the complex lithospheric structure

The western United States is one of Earth’s most tectonically active regions, characterized by extensive crustal deformation through intraplate earthquakes and geodetic motion. Such intracontinental deformation is usually ascribed to plate boundary forces, lithospheric body forces, and/or viscous drag from mantle flow. However, their relative importance in driving crustal deformation remains controversial due to inconsistent assumptions on crustal and mantle structures in prior estimations. Here, we utilize a fully dynamic three-dimensional modeling framework with data assimilation to simultaneously compute lithospheric and convective mantle dynamics within the western United States. This approach allows for quantitative estimations of crustal deformation while accounting for the realistic three-dimensional lithospheric structure. Our results show the critical role of the complex lithospheric structure in governing intraplate deformation. Particularly, the interaction between the asthenospheric flow and lithospheric thickness step along the eastern boundary of the Basin and Range represents a key driving mechanism for localized crustal deformation and seismicity.

Numerical investigation of fluid flow behavior in steel cord with lattice Boltzmann methodology: The impacts of microstructure and loading force.

Steel cord materials were found to have internal porous microstructures and complex fluid flow properties. However, current studies have rarely reported the transport behavior of steel cord materials from a microscopic viewpoint. The computed tomography (CT) scanning technology and lattice Boltzmann method (LBM) were used in this study to reconstruct and compare the real three-dimensional (3D) pore structures and fluid flow in the original and tensile (by loading 800 N force) steel cord samples. The pore-scale LBM results showed that fluid velocities increased as displacement differential pressure increased in both the original and tensile steel cord samples, but with two different critical values of 3.3273 Pa and 2.6122 Pa, respectively. The original steel cord sample had higher maximal and average seepage velocities at the 1/2 sections of 3D construction images than the tensile steel cord sample. These phenomena should be attributed to the fact that when the original steel cord sample was stretched, its porosity decreased, pore radius increased, flow channel connectivity improved, and thus flow velocity increased. Moreover, when the internal porosity of tensile steel cord sample was increased by 1 time, lead the maximum velocity to increase by 1.52 times, and the average velocity was increased by 1.66 times. Furthermore, when the density range was determined to be 0-38, the pore phase showed the best consistency with the segmentation area. Depending on the Zou-He Boundary and Regularized Boundary, the relative error of simulated average velocities was only 0.2602 percent.

Comprehensive analysis of two hotspot codons in the TUBB4B gene and associated phenotypes

Our purpose was to elucidate the genotype and ophthalmological and audiological phenotype in TUBB4B-associated inherited retinal dystrophy (IRD) and sensorineural hearing loss (SNHL), and to model the effects of all possible amino acid substitutions at the hotspot codons Arg390 and Arg391. Six patients from five families with heterozygous missense variants in TUBB4B were included in this observational study. Ophthalmological testing included best-corrected visual acuity, fundus examination, optical coherence tomography, fundus autofluorescence imaging, and full-field electroretinography (ERG). Audiological examination included pure-tone and speech audiometry in adult patients and auditory brainstem response testing in a child. Genetic testing was performed by disease gene panel analysis based on genome sequencing. The molecular consequences of the substitutions of residues 390 and 391 on TUBB4B and its interaction with α-tubulin were predicted in silico on its three-dimensional structure obtained by homology modelling. Two independent patients had amino acid exchanges at position 391 (p.(Arg391His) or p.(Arg391Cys)) of the TUBB4B protein. Both had a distinct IRD phenotype with peripheral round yellowish lesions with pigmented spots and mild or moderate SNHL, respectively. Yet the phenotype was milder with a sectorial pattern of bone spicules in one patient, likely due to a genetically confirmed mosaicism for p.(Arg391His). Three patients were heterozygous for an amino acid exchange at position 390 (p.(Arg390Gln) or p.(Arg390Trp)) and presented with another distinct retinal phenotype with well demarcated pericentral retinitis pigmentosa. All showed SNHL ranging from mild to severe. One additional patient showed a variant distinct from codon 390 or 391 (p.(Tyr310His)), and presented with congenital profound hearing loss and reduced responses in ERG. Variants at codon positions 390 and 391 were predicted to decrease the structural stability of TUBB4B and its complex with α-tubulin, as well as the complex affinity. In conclusion, the twofold larger reduction in heterodimer affinity exhibited by Arg391 substitutions suggested an association with the more severe retinal phenotype, compared to the substitution at Arg390.

Estrogen-related receptor, a molecular target against lepidoptera pests

Until recently, chemical pesticides were one of the most effective means of controlling agricultural pests; therefore, the search for insecticide targets for agricultural pests has been an ongoing problem. Estrogen-related receptors (ERRs) are transcription factors that regulate cellular metabolism and energy homeostasis in animals. Silkworms are highly sensitive to chemical pesticides, making them ideal models for pesticide screening and evaluation. In this study, we detected ERR expression in key organs involved in pesticide metabolism in silkworms (Bombyx mori), including the fat body and midgut. Using ChIP-seq technology, many estrogen- related response elements were identified in the 2000-bp promoter region upstream of metabolism-related genes, almost all of which were potential ERR target genes. The ERR inhibitor, XCT-790, and the endocrine disruptor, bisphenol A, significantly inhibited expression of the ERR target genes, BmTreh-1, BmTret-1, BmPK, BmPFK, and BmHK, in the fat bodies of silkworms, resulting in pupation difficulties in silkworm larvae that ultimately lead to death. In addition, based on the clarification that the ERR can bind to XCT-790, as observed through biofilm interferometry, its three-dimensional spatial structure was predicted, and using molecular docking techniques, small-molecule compounds with a stronger affinity for the ERR were identified. In summary, utilizing the powerful metabolic regulatory function of ERR in Lepidoptera pests, the developed small molecule inhibitors of ERR can be used for future control of Lepidoptera pests.

Precision three-dimensional imaging of nuclei using recoil-free jets

In this study, we explore the azimuthal angle decorrelation of lepton-jet pairs in e-p and e-A collisions as a means for precision measurements of the three-dimensional structure of bound and free nucleons. Utilizing soft-collinear effective theory, we perform the first-ever resummation of this process in e-p collisions at NNLL accuracy using a recoil-free jet axis. Our results are validated against Pythia simulations. In e-A collisions, we address the complex interplay between three characteristic length scales: the medium length L, the mean free path of the energetic parton in the medium λ, and the hadronization length Lh. We demonstrate that in the thin-dilute limit, where L ≪ Lh and L ~ λ, this process can serve as a robust probe of the three-dimensional structure for bound nucleons. We conclude by offering predictions for future experiments at the Electron-Ion Collider within this limit.

Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles.

A substantial portion of various organisms' proteomes comprises intrinsically disordered proteins (IDPs) that lack a defined three-dimensional structure. These IDPs exhibit a diverse array of conformations, displaying remarkable spatiotemporal heterogeneity and exceptional conformational flexibility. Characterizing the structure or structural ensemble of IDPs presents significant conceptual and methodological challenges owing to the absence of a well-defined native structure. While databases such as the Protein Ensemble Database (PED) provide IDP ensembles obtained through a combination of experimental data and molecular modeling, the absence of reaction coordinates poses challenges in comprehensively understanding pertinent aspects of the system. In this study, we leverage the energy landscape visualization method (JCTC, 6482, 2019) to scrutinize four IDP ensembles sourced from PED. ELViM, a methodology that circumvents the need for a priori reaction coordinates, aids in analyzing the ensembles. The specific IDP ensembles investigated are as follows: two fragments of nucleoporin (NUL: 884-993 and NUS: 1313-1390), yeast sic 1 N-terminal (1-90), and the N-terminal SH3 domain of Drk (1-59). Utilizing ELViM enables the comprehensive validation of ensembles, facilitating the detection of potential inconsistencies in the sampling process. Additionally, it allows for identifying and characterizing the most prevalent conformations within an ensemble. Moreover, ELViM facilitates the comparative analysis of ensembles obtained under diverse conditions, thereby providing a powerful tool for investigating the functional mechanisms of IDPs.