Multiple Structures Research Articles

R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.

The recent progress in RNA structure determination methods has resulted in a surge of newly solved RNA 3D structures. However, there is an absence of a user-friendly browser-based tool that can facilitate the comparison and visualization of RNA motifs across multiple 3D structures. We introduce R3DMCS, a web server that allows users to compare selected RNA nucleotides across all 3D structures of a given molecule from a given species, or across all 3D structures mapped to a single Rfam family. Starting from one instance of the motif, R3DMCS retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding sets of nucleotides from other 3D structures. With R3DMCS, one can explore conformational changes of motifs due to 3D structures being solved in different functional states or different experimental conditions. One can also investigate conservation of 3D structure across species, or changes in 3D structure due to changes in sequence. R3DMCS is open-source software and freely available at https://rna.bgsu.edu/correspondence/ and https://github.com/BGSU-RNA/RNA-3D-correspondence . Supplementary data are available at Bioinformatics online.

The multiplicative Lie algebra on general linear groups

Abstract The main aim of this paper is to study an obvious linear representation of a multiplicative Lie algebra. Also, we find some criteria to determine all possible multiplicative Lie algebra structures on a general linear group and we show that the general linear group on a finite field is a Lie simple group.

Distinct types of VHHs in Alpaca

IntroductionVHHs (VH of heavy-chain-only antibodies) represent a unique alternative to Q7 conventional antibodies because of their smaller size, comparable binding affinity and biophysical properties. MethodIn this study, we systematically analyzed VHH NGS sequences from 22 Alpacas and structure data from public database. ResultsVHHs in Alpaca can be grouped into five main types with multiple distinct sequence and structure features. Based on the existence of hallmark residues in FR2 region, VHHs can be classified into two groups: nonclassical VHHs (without hallmark residues) and classical VHHs (with hallmark residues). Based on VHH hallmark residues at 42 position (IMGT numbering, FR2 region) and number of cysteines, we found that Alpaca classical VHHs can be further separated into three main types: F_C2 VHHs with F (phenylalanine) at position 42 and having 2 cysteines within sequences, Y_C2 VHHs with Y (tyrosine) at position 42 and having 2 cysteines, and F_C4 with F at position 42 and having 4 cysteines. Non-classical VHHs can be further separated into 2 types based on germlines mapped: N_V3 for VHHs mapped to V3 germlines and N_V4 for V4 germlines. Based on whether FR2 residues are involved in binding, two kinds of paratopes can be identified. Different types of VHHs showed distinct associations with these two paratopes and displayed significant differences in paratope size, residue usage and other structure features. DiscussionSuch results will have significant implications in VHH discovery, engine e ring, and design for innovative therapeutics.

Comparative evaluation of methods for the prediction of protein-ligand binding sites.

The accurate identification of protein-ligand binding sites is of critical importance in understanding and modulating protein function. Accordingly, ligand binding site prediction has remained a research focus for over three decades with over 50 methods developed and a change of paradigm from geometry-based to machine learning. In this work, we collate 13 ligand binding site predictors, spanning 30years, focusing on the latest machine learning-based methods such as VN-EGNN, IF-SitePred, GrASP, PUResNet, and DeepPocket and compare them to the established P2Rank, PRANK and fpocket and earlier methods like PocketFinder, Ligsite and Surfnet. We benchmark the methods against the human subset of our new curated reference dataset, LIGYSIS. LIGYSIS is a comprehensive protein-ligand complex dataset comprising 30,000 proteins with bound ligands which aggregates biologically relevant unique protein-ligand interfaces across biological units of multiple structures from the same protein. LIGYSIS is an improvement for testing methods over earlier datasets like sc-PDB, PDBbind, binding MOAD, COACH420 and HOLO4K which either include 1:1 protein-ligand complexes or consider asymmetric units. Re-scoring of fpocket predictions by PRANK and DeepPocket display the highest recall (60%) whilst IF-SitePred presents the lowest recall (39%). We demonstrate the detrimental effect that redundant prediction of binding sites has on performance as well as the beneficial impact of stronger pocket scoring schemes, with improvements up to 14% in recall (IF-SitePred) and 30% in precision (Surfnet). Finally, we propose top-N+2 recall as the universal benchmark metric for ligand binding site prediction and urge authors to share not only the source code of their methods, but also of their benchmark.Scientific contributionsThis study conducts the largest benchmark of ligand binding site prediction methods to date, comparing 13 original methods and 15 variants using 10 informative metrics. The LIGYSIS dataset is introduced, which aggregates biologically relevant protein-ligand interfaces across multiple structures of the same protein. The study highlights the detrimental effect of redundant binding site prediction and demonstrates significant improvement in recall and precision through stronger scoring schemes. Finally, top-N+2 recall is proposed as a universal benchmark metric for ligand binding site prediction, with a recommendation for open-source sharing of both methods and benchmarks.

PWOs repress gene transcription by regulating chromatin structures in Arabidopsis.

PWWP-DOMAIN INTERACTOR OF POLYCOMBS (PWO) family proteins play a vital role in regulating plant development. However, the molecular mechanisms of how PWOs regulate chromatin structure is elusive. Our data show that the PWO1 binding sites are enriched with positive modifications but exclusive with H3K27me3. Moreover, PWO1 binds to the H3K27me3-enriched compartment domain (H3K27me3-CD) boundary regions, and functions to maintain the boundary strength. Meanwhile, we found that PWOs and Polycomb repressive complex 2 (PRC2) function parallelly in maintaining H3K27me3-CDs' structure. Loss of either PWOs or PRC2 leads to H3K27me3-CD strength reduction, B to A compartment switching as well as the H3K27me3-CD relocating away from the nuclear periphery. Additionally, PWOs and lamin-like proteins collaborate to regulate multiple chromatin structures to repress gene transcription within H3K27me3-CDs. We conclude that PWOs maintain H3K27me3-CDs' repressive state and regulate their spatial position in the nucleus.

Low-cost Biochar from Parthenium Hysterophorus for Efficient Cr⁶⁺ Removal: A Sustainable Wastewater Treatment Solution

Aims: This study explores the development of innovative, cost-effective methods for removing Cr6+ from wastewater, focusing on biochar derived from Parthenium hysterophorus shoots. The biochar was prepared using a conventional slow-pyrolysis process and evaluated for its potential to treat Cr⁶⁺ in aqueous solutions. Study Design: Batch adsorption experiments are carried out in the study. Place and Duration of Study: The study was conducted in the Department of Environmental Science, G B Pant University of Agriculture & Technology, between Feb 2024 and July 2024. Methodology: Parthenium hysterophorus shoots were collected, reagents were purchased from HiMedia, and Cr⁶⁺ solutions were prepared and adjusted using NaOH and HCl. Shoots were washed, sun-dried, ground into powder and pyrolysed at 350°C for 180 minutes. Biochar yield was calculated, pH, proximal parameters (moisture, volatile matter, ash, fixed carbon) and ultimate analysis were measured, chemical functional groups by FTIR and morphology by XRD using Bruker D8 Advance was done. Cr⁶⁺ removal was studied using biochar adsorbent under varying pH, initial Cr6+ concentration, adsorbent dose and contact time, adsorption capacity (q) and removal percentage were then calculated. Results: Characterization techniques such as Fourier Transform Infrared (FTIR) spectroscopy and X-Ray Diffraction (XRD) confirmed the presence of multiple functional groups and crystalline structures, which contribute to its adsorption efficiency. Batch adsorption experiments were conducted to investigate the influence of prepared biochar dosage, initial Cr⁶⁺ concentration, pH and contact time. The optimal removal efficiency of 72.77% was achieved under conditions of pH 10, a biochar dose of 1 g/L, an initial Cr⁶⁺ concentration of 30 mg/L and a contact time of 72 hours. Conclusion: Although challenges remain in optimizing production and functionalization, this research highlights the potential of biochar for sustainable water treatment. Addressing production costs and practical challenges will further enhance its applicability, contributing to environmental sustainability efforts.

Phase transitions of ice VIII-VII-X: A potential energy landscape perspective

Water ice, an archetypal molecular system, exhibits a complex phase diagram characterized by numerous phase transitions under varying pressure-temperature conditions. However, it remains a significant challenge to theoretical modeling of these transitions owing to the high dimensionality in representing the potential energy landscapes (PEL) of ice crystalline phases. In an attempt to deeply understand the mechanisms of phase transitions between ice VII, VIII, and X, a graph-based stationary-point network was employed to simplify the representation of the PEL and locally constructed the PEL of ice at different pressures by our developed high-index saddle dynamic scheme. The stationary-point networks at 40 and 80 GPa indicate a pronounced flattened PEL of ice over a wide range of pressure (up to at least 80 GPa), where multiple structures (i.e., local minima) are energetically degenerate with phase VIII and separated by low-energy barriers (∼10 meV/atom at 40 GPa). These features indicate the disordered VII phase is more favorable at finite temperatures, in agreement with previous experimental observations. Additionally, we demonstrated that the PEL topology undergoes a fundamental alteration at higher pressures, with a single funnel emerging at 120 GPa, facilitating the crystallization of phase X. This work serves as a proof of concept for using the stationary-point network to explicitly represent the PEL, highlighting their potential in elucidating complex phase transitions. Published by the American Physical Society 2024

Distribution and diversity of classical deacylases in bacteria

Classical Zn2+-dependent deac(et)ylases play fundamental regulatory roles in life and are well characterized in eukaryotes regarding their structures, substrates and physiological roles. In bacteria, however, classical deacylases are less well understood. We construct a Generalized Profile (GP) and identify thousands of uncharacterized classical deacylases in bacteria, which are grouped into five clusters. Systematic structural and functional characterization of representative enzymes from each cluster reveal high functional diversity, including polyamine deacylases and protein deacylases with various acyl-chain type preferences. These data are supported by multiple crystal structures of enzymes from different clusters. Through this extensive analysis, we define the structural requirements of substrate selectivity, and discovered bacterial de-d-/l-lactylases and long-chain deacylases. Importantly, bacterial deacylases are inhibited by archetypal HDAC inhibitors, as supported by co-crystal structures with the inhibitors SAHA and TSA, and setting the ground for drug repurposing strategies to fight bacterial infections. Thus, we provide a systematic structure-function analysis of classical deacylases in bacteria and reveal the basis of substrate specificity, acyl-chain preference and inhibition.

A multiple physical crosslinked cellulose-based bioplastics with robust mechanical and thermal stability.

The widespread use of traditional petroleum-based plastics has created an environmental crisis and health hazard, so there is an urgent need for bioplastics with excellent performance. However, fabricating of robust mechanical properties and heat resistance bioplastics in an efficient way has remained an enormous challenge. Herein, we proposed a strategy for the synergistic preparation of high-performance bioplastics with multiple physical crosslinking network structures via noncovalent and coordination bonds. In this strategy, carboxylated cellulose nanofibers (CNFs) and the polyphenol structures of tannic acid (TA) interacted noncovalently to create network structures; the bioplastic immersed in Ca2+ solution formed ionic crosslinked networks and TA-Ca coordination bonds. The synergistic effect of multiple network structures composed of hydrogen and coordination bonds made cellulose-based bioplastics have dense structures and robust tensile strength (114.2 MPa), while bioplastics had the characteristics of high transparency and superior thermal stability. Furthermore, the laminated composites formed by the bioplastic and PVA could support 1000 g easily, which allowed it to be used as weighing application. Thus, the proposed multiple physical crosslinking strategy provides a method for developing cellulose-based bioplastics with excellent performance, which offers a new approach for the subsequent development of sustainable green materials.

Construction of myofibrillar protein-based pickering emulsion for grass carp (Ctenopharyngodon idellus) based on interfacial self-assembly of spice aldehyde molecules: Mechanism and application of imine reaction-stabilized emulsion.

The purpose of this research is to investigate multiple structural spice aldehydes (cinnamaldehyde (CA), citronellal (CN), and melonal (MA)) interact with myofibrillar protein in grass carp (GCMP) and the effects of interfacial interactions on stability properties of Pickering emulsion. It was demonstrated that the functional characteristics of interfacial protein might be greatly improved by the complexation of spice aldehydes with protein particles at the water-oil interface. The fluorescence quenching and molecular docking results revealed that the binding mode of spice aldehyde is primarily dominated by hydrophobic interactions, yet there are hydrogen bonding interactions exist in special structure. When comparing multiple structure aldehyde, CA has a greater binding affinity than CN and MA, as well as the most binding sites at different temperatures. Among them, the interaction of CA and GCMP is enhanced by forming hydrogen bonds through π-bonds owing to its special aromatic ring structure. The O/W structure was further stabilized by the formation of conjugated and unconjugated imines of interfacial protein with spice aldehydes. This work provides a theoretical basis for the interaction and development of protein particles with spice aldehyde in Pickering emulsion stabilization and novel ideas for the application of low value aquatic protein for high quality.

Application of the Nirmala Index in Nanotechnology: Optimizing Molecular Structures for Advanced Nanomaterials

Abstract Chemical graph theory has played a key role in advancing our understanding of molecular structure by producing degree-based topological indices that forecast crucial physical and chemical properties. In this paper we attempt to investigate this recently defined Nirmala index as an invariant from different topological angles and applications on multiple molecular graph structures such as triangular, double, and alternate quadrilateral snake structures. This index offers a more profound comprehension of the connections between molecular structures and attributes. The next generation of ground breaking developments in nanotechnology, where the creation of devices and functional nanomaterials hinges on molecular interaction at the nanoscale, may also be greatly influenced by this index. These indices have potential applications in drug delivery systems and in molecular structure optimization related to nanotechnological fields like nanophotonics and nanoelectronics. Consequently, the Nirmala index will pave the way for the development of more sophisticated tools for the production of high-performing nanoscale materials.

Characterization results of MAPS digital prototypes for the ALICE ITS3

The three innermost layers of the ALICE Inner Tracking System (ITS2) will be replaced by a truly cylindrical tracker, the ITS3, to be ready for LHC Run 4 (2029-2032). The ITS3 will be composed of three layers, each made by two self-supporting, ultra-thin (≤50μm) flexible Monolithic Active Pixel silicon Sensors (MAPS) of large area (O(10 × 26 cm2)). The final sensor will be realized using the 65 nm CMOS imaging process and stitching technology. Multiple small-scale test structures were included in the first production run (Multiple Layer Reticle 1 - MLR1) to validate the 65 nm CMOS imaging technology. First large-scale stitched MAPS were included in the second production run (Engineering Run 1 - ER1). The pixel cell performance has been qualified on the MLR1 Digital Pixel Test Structures (DPTS) in laboratory and with in-beam measurements. The large-area (1.4 × 25.9 cm2) ER1 MOnolithic Stitched Sensor (MOSS) prototype has been used to prove the stitching principle and evaluate the detection efficiency and spatial resolution. This contribution will give an overview of the most recent results of the digital prototype tests.

A Quasi-Floating Channel-Based SPICE Model for Improving the Modeling Accuracy of SiC MOSFETs With Multiple Device Structures

A Quasi-Floating Channel-Based SPICE Model for Improving the Modeling Accuracy of SiC MOSFETs With Multiple Device Structures

A kidney-specific fasting-mimicking diet induces podocyte reprogramming and restores renal function in glomerulopathy.

Cycles of a fasting-mimicking diet (FMD) promote regeneration and reduce damage in the pancreases, blood, guts, and nervous systems of mice, but their effect on kidney disease is unknown. In addition, a FMD has not been tested in rats. Here, we show that cycles of a newly developed low-salt FMD (LS-FMD) restored normal proteinuria and nephron structure and function in rats with puromycin-induced nephrosis compared with that in animals with renal damage that did not receive the dietary intervention. LS-FMD induced modulation of a nephrogenic gene program, resembling renal developmental processes in multiple kidney structures. LS-FMD also activated podocyte-lineage reprogramming pathways and promoted a quiescent state in mature podocytes in the rat kidney damage model. In a pilot clinical study in patients with chronic kidney disease, FMD cycles of 5 days each month for 3 months promoted renoprotection, including reduction of proteinuria and improved endothelial function, compared with that in patients who did not receive the FMD cycles. These results show that FMD cycles, which promote the reprogramming of multiple renal cell types and lead to glomerular damage reversal in rats, should be tested further for the treatment of progressive kidney diseases.

A sustainable lignin-clay nano-absorbent for highly efficient methylene blue removal

Water pollution caused by toxic dyes such as methylene blue (MB) has become a bottleneck for recycling or reusing enormous industrial wastewater. Designing a green and cost-effective bio-absorbent for the highly efficient removal of MB from wastewater is crucial but remains a great challenge. In this study, abundant, inexpensive, and environmentally benign lignin and bentonite were used as starting materials, and quaternary and amphiphilic lignin as a network macromolecule was designed to be inserted into the galleries of the stacked bentonite clay to prepare lignin-bentonite nanohybrids. The specific surface area of the modified nano-absorbent was significantly increased to 45.60 m2/g and owned a type II-like isothermal mechanism. The absorbent showed a maximum removal of MB of 99.7 % at neutral pH and room temperature with a maximum adsorption capacity of 822.22 mg/g, demonstrating the potential of an excellent adsorbent. The MB adsorption process fits well with both Langmuir and Freundlich isotherm models, the adsorption mechanism includes strong electrostatic attraction between absorbent and MB, and physical adsorption in a complicated monolayer and multiple macroporous structures. This study leverages the economic and environmental benefits of lignin and bentonite clay to prepare a cost-effective bio-absorbent for efficient removal of MB from aqueous solutions.

On the suitability of rigorous coupled-wave analysis for fast optical force simulations

Abstract Optical force responses underpin nanophotonic actuator design, which requires a large number of force simulations to optimize structures. Commonly used computation methods, such as the finite-difference time-domain (FDTD) method, and finite element methods (FEM), are resource intensive and require large amounts of calculation time when multiple structures need to be
compared during optimization. This research demonstrates that performing optical force calculations on 2D-periodic structures using the rigorous coupled-wave analysis (RCWA) method is typically on the order of 10 times faster than other approaches and with sufficient accuracy to suit optical design purposes. Moreover, this speed increase is available on consumer grade laptops, avoiding the need for a high performance computing resource.

Asymmetric fluctuation of overlapping dinucleosome studied by cryoelectron microscopy and small-angle X-ray scattering.

Nucleosome remodelers modify the local structure of chromatin to release the region from nucleosome-mediated transcriptional suppression. Overlapping dinucleosomes (OLDNs) are nucleoprotein complexes formed around transcription start sites as a result of remodeling, and they consist of two nucleosome moieties: a histone octamer wrapped by DNA (octasome) and a histone hexamer wrapped by DNA (hexasome). While OLDN formation alters chromatin accessibility to proteins, the structural mechanism behind this process is poorly understood. Thus, this study investigated the characteristics of structural fluctuations in OLDNs. First, multiple structures of the OLDN were visualized through cryoelectron microscopy (cryoEM), providing an overview of the tilting motion of the hexasome relative to the octasome at the near-atomistic resolution. Second, small-angle X-ray scattering (SAXS) revealed the presence of OLDN conformations with a larger radius of gyration than cryoEM structures. A more complete description of OLDN fluctuation was proposed by SAXS-based ensemble modeling, which included possible transient structures. The ensemble model supported the tilting motion of the OLDN outlined by the cryoEM models, further suggesting the presence of more diverse conformations. The amplitude of the relative tilting motion of the hexasome was larger, and the nanoscale fluctuation in distance between the octasome and hexasome was also proposed. The cryoEM models were found to be mapped in the energetically stable region of the conformational distribution of the ensemble. Exhaustive complex modeling using all conformations that appeared in the structural ensemble suggested that conformational and motional asymmetries of the OLDN result in asymmetries in the accessibility of OLDN-binding proteins.

Robust quantization of circular photogalvanic effect in multiplicative topological semimetals

Nonlinear response signatures are increasingly recognized as useful probes of condensed matter systems, in particular for the characterization of topologically nontrivial states. The circular photogalvanic effect (CPGE) is particularly useful in the study of topological semimetals, as the CPGE tensor quantizes for well-isolated topological degeneracies in strictly linearly dispersing band structures. Here, we study multiplicative Weyl semimetal band structures, and find that the multiplicative structure robustly protects the quantization of the CPGE even in the case of nonlinear dispersion. Computing phase diagrams as a function of Weyl node tilting, we find a variety of quantized values for the CPGE tensor, revealing that the CPGE is also a useful tool in detecting and characterizing the parent topology of multiplicative topological states. Published by the American Physical Society 2024

On the hypercomplex numbers and normed division algebras in all dimensions: A unified multiplication.

Mathematics is the foundational discipline for all sciences, engineering, and technology, and the pursuit of normed division algebras in all finite dimensions represents a paramount mathematical objective. In the quest for a real three-dimensional, normed, associative division algebra, Hamilton discovered quaternions, constituting a non-commutative division algebra of quadruples. Subsequent investigations revealed the existence of only four division algebras over reals, each with dimensions 1, 2, 4, and 8. This study transcends such limitations by introducing generalized hypercomplex numbers extending across all dimensions, serving as extensions of traditional complex numbers. The space formed by these numbers constitutes a non-distributive normed division algebra extendable to all finite dimensions. The derivation of these extensions involves the definitions of two new π-periodic functions and a unified multiplication operation, designated as spherical multiplication, that is fully compatible with the existing multiplication structures. Importantly, these new hypercomplex numbers and their associated algebras are compatible with the existing real and complex number systems, ensuring continuity across dimensionalities. Most importantly, like the addition operation, the proposed multiplication in all dimensions forms an Abelian group while simultaneously preserving the norm. In summary, this study presents a comprehensive generalization of complex numbers and the Euler identity in higher dimensions, shedding light on the geometric properties of vectors within these extended spaces. Finally, we elucidate the practical applications of the proposed methodology as a viable alternative for expressing a quantum state through the multiplication of specified quantum states, thereby offering a potential complement to the established superposition paradigm. Additionally, we explore its utility in point cloud image processing.

Saturation Mobility of 100 cm2 V-1 s-1 in ZnO Thin-Film Transistors through Quantum Confinement by a Nanoscale In2O3 Interlayer Using Spray Pyrolysis.

In this study, we present a comprehensive study on the fabrication and characterization of heterojunction In2O3/ZnO thin-film transistors (TFTs) aimed at exploiting the quantum confinement effect to enhance device performance. By systematically optimizing the thickness of the crystalline In2O3 (c-In2O3) layer to create a narrow quantum well, we observed a significant increase in saturation mobility (μSAT) from 12.76 to 97.37 cm2 V-1 s-1. This enhancement, attributed to quantum confinement, was achieved through the deposition of a 3 nm c-In2O3 semiconductor via spray pyrolysis. Various In2O3 layer thicknesses (2-5 nm) were obtained by adjusting precursor solution concentration, flow rate, and number of spray cycles. Post annealing treatments were employed to reduce the defects at the interface and within the oxide film, enhancing device stability and performance. Transmission electron microscopy (TEM) confirmed the uniformity of the c-In2O3 film thickness, while variations in thickness significantly influenced TFT performance, particularly the turn-on voltage (VGS) due to changes in the carrier concentration. Ultraviolet photoelectron spectroscopy (UPS) and X-ray photoelectron spectroscopy (XPS) supported the formation of a potential well with a two-dimensional electron gas (2DEG). The study of single and multiple superlattice structures of consecutive c-In2O3 and c-ZnO layers provided insights into the effects of multiple quantum wells on the TFT performance. This research presents an advanced approach to TFT optimization, highlighting high reliability, and environmental and bias stabilities. These lead to enhanced mobility and performance uniformity through the precise control of c-In2O3 layer thickness for the quantum confinement effect.