Structural Motifs Research Articles

Influence of network structure on spreading dynamics via tie range

Abstract There are various phenomena of malicious information spreading in the real society, which cause many negative impacts on the society. In order to better control the spreading, it is crucial to reveal the influence of network structure on network spreading. Motifs, as fundamental structures within a network, play a significant role in spreading. Therefore, it is of interest to investigate the influence of the structural characteristics of basic network motifs on spreading dynamics. Considering the edges of the basic network motifs in an undirected network correspond to different tie ranges, two edge removal strategies are proposed, short ties priority removal strategy and long ties priority removal strategy. The tie range represents the second shortest path length between two connected nodes. The study focuses on analyzing how the proposed strategies impact network spreading and network structure, as well as examining the influence of network structure on network spreading. Our findings indicate that the long ties priority removal strategy is most effective in controlling network spreading, especially in terms of spread range and spread velocity. In terms of network structure, the clustering coefficient and the diameter of network also have an effect on the network spreading, and the triangular structure as an important motif structure effectively inhibits the spreading.

Physico-chemical features and functional relevance of tomato rhomboid proteases

In plants, regulated intramembrane proteolysis (RIP) is crucial for proper growth, development, and stress management. Rhomboid proteases (RPs) residing in the membrane play a vital role in orchestrating RIP. Although RPs can be found in most sequenced genomes, tomato rhomboids (SlRPs) have not yet been studied. Using alternative and comprehensive strategies, we found ten SlRPs encoded in the tomato genome. These SlRPs possess signature motifs and transmembrane domains, showing structural similarity to other members of the RP family. Also, SlRPs are genetically related to other known RPs of the Solanaceae family. Seven of the SlRPs retain serine-histidine catalytic dyads, making them proteolytically active, while three iRhoms lack the dyad and other structural motifs. Although SlRPs could have functional redundancy, their distribution and expression pattern indicate tissue specificity and responsiveness to specific external stimuli. The presence of development and stress-response-related cis-elements in the promoters of SlRPs supports this view. Furthermore, our strategically designed substrate-reporter assay shows that SlRPs have proteolytic activity similar to that of known RPs. This study provides a detailed understanding of all SlRPs and their physico-chemical features, shedding light on their involvement in physiological processes.

Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures.

The previously introduced workflow to achieve an energetically and structurally optimized description of frontier bonds in quantum mechanical/molecular mechanics (QM/MM)-type applications was extended into the regime of computational material sciences at the example of a layered carbon model systems. Optimized QM/MM link bond parameters at HSEsol/6-311G(d,p) and self-consistent density functional tight binding (SCC-DFTB) were derived for graphitic systems, enabling detailed investigation of specific structure motifs occurring in graphene-derived structures quantum-chemical calculations. Exemplary molecular dynamics (MD) simulations in the isochoric-isothermic (NVT) ensemble were carried out to study the intercalation of lithium and the properties of the Stone-Thrower-Wales defect. The diffusivity of lithium as well as hydrogen and proton adsorption on a defective graphene surface served as additional example. The results of the QM/MM MD simulations provide detailed insight into the applicability of the employed link-bond strategy when studying intercalation and adsorption properties of graphitic materials.

Exploring structures of small anionic nickel-ethanol clusters with infrared spectroscopy.

Small anionic nickel clusters with ethanol are investigated with a combination of mass-selective infrared photodissociation spectroscopy in a molecular beam and density functional theory simulations at the BLYP/6-311g(d,p) and TPSSh/def2-TZVPP level. In this context, the O-H stretching vibration of the ethanol is analyzed to obtain information about the structural motif, the geometry of the metal core, and the spin state of the clusters. For the [Ni2(EtOH)]- and [Ni3(EtOH)]- clusters, we assign quartet states of motifs with a hydrogen bond from the ethanol to the linear nickel core. The aggregation of a further ethanol molecule, yielding the [Ni3(EtOH)2]- cluster, results in the formation of a cooperative hydrogen bond network between the nickel core and the two ethanol molecules.

Concise synthesis of 2,4-bis(fluoroalkyl)quinoline derivatives from arylamines

Quinolines and their derivatives bearing fluorine-containing substituents are essential structural motifs found in numerous bioactive compounds and advanced functional materials. Therefore, there is an urgent need to develop new synthetic methods for fluoroalkylated quinoline derivatives. In this study, we present a facile and efficient approach to access fluoroalkylated quinoline derivatives by using Eaton's reagent as a cost-effective, and commercially available reagent. This Combes cyclization reaction demonstrated compatibility with various arylamines bearing diverse functional groups, resulting in the synthesis of 2,4-bis(trifluoromethyl)quinolines and 2,4-bis(difluoromethyl)quinolines in moderate to high yields. Furthermore, this reaction can be conveniently carried out in a solvent-free one-pot protocol.

Glass-sulfur composite cathodes: A new strategy for improving the performance of lithium-sulfur batteries

In this study, we investigated the potential of glass-sulfur composites to improve lithium–sulfur battery (LSB) performance. Glass-sulfur composites were prepared by the precipitation method, and the effect of varying carbon black content was studied. The results showed that glass addition improved the battery performance due to the high ion-conductivity of its structural motif. The 75 % glass variant demonstrated the best results, in both the low carbon and high carbon cases. The cyclic voltammetry (CV) and electrical impedance spectroscopy (EIS) measurements showed that glass-sulfur composites had lower resistivity than pure sulfur, which was beneficial for battery performance. The XANES analysis revealed that the incorporated glass interacted with and modified the properties of sulfur, leading to a higher proportion of sulfur in the -1 oxidation state (S−1). This suggests that the high proportion of S−1 phase benefitted battery capacity. Overall, glass-sulfur composites prepared using the precipitation method and incorporating a high content of carbon show promise as a novel and improved cathode material for LSBs.

Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA.

The single-stranded RNA genome of SARS-CoV-2 is highly structured. Numerous helical stem-loop structures interrupted by mismatch motifs are present in the functionally important 5'- and 3'-UTRs. These mismatches modulate local helical geometries and feature unusual arrays of hydrogen bonding donor and acceptor groups. However, their conformational and dynamical properties cannot be directly inferred from chemical probing and are difficult to predict theoretically. A mismatch motif (SL1-motif) consisting of three consecutive U•U base pairs is located in stem-loop 1 of the 3'-UTR. We combined NMR-spectroscopy and MD-simulations to investigate its structure and dynamics. All three U•U base pairs feature two direct hydrogen bonds and are as stable as Watson-Crick A:U base pairs. Plasmodium falciparum 25S rRNA contains a triple U•U mismatch motif (Pf-motif) differing from SL1-motif only with respect to the orientation of the two closing base pairs. Interestingly, while the geometry of the outer two U•U mismatches was identical in both motifs the preferred orientation of the central U•U mismatch was different. MD simulations and potassium ion titrations revealed that the potassium ion-binding mode to the major groove is connected to the different preferred geometries of the central base pair in the two motifs.

Exploring dopant‐enhanced ionic conductivity of AgCl‐doped Li7P3S11 solid electrolytes: Integrating synchrotron Rietveld analysis, DFT, and ANN‐based molecular dynamics approaches

AbstractThe effectiveness of dual‐doping as a method of improving the conductivity of sulfide solid electrolytes (SEs) is not in doubt; however, the atomic‐level mechanisms underpinning these enhancements remain elusive. In this study, we investigate the atomic mechanisms associated with the high ionic conductivity of the Li7P3S11 (LPS) SE and its response to Ag/Cl dual dopants. Synthesis and electrochemical characterizations show that the 0.2 M AgCl‐doped LPS (Li6.8P3Ag0.1S10.9Cl0.1) exhibited an over 80% improvement in ionic conductivity compared with the undoped LPS. The atomic‐level structures responsible for the enhanced conductivity were generated by a set of experiment and simulation techniques: synchrotron X‐ray diffractometry, Rietveld refinement, density functional theory, and artificial neural network‐based molecular dynamics simulations. This thorough characterization highlights the role of dual dopants in altering the structure and ionic conductivity. We found that the PS4 and P2S7 structural motifs of LPS undergo transformation into various PSx substructures. These changes in the substructures, in conjunction with the paddle‐wheel effect, enable rapid Li migration. The dopant atoms serve to enhance the flexibility of PS4–P2S7 polyhedral frameworks, consequently enhancing the ionic conductivity. Our study elucidates a clear structure–conductivity relationship for the dual‐doped LPS, providing a fundamental guideline for the development of sulfide SEs with superior conductivity.

Grain boundary junction disclinations in nanoparticles

Grain boundary junction (GBJ) disclinations are ubiquitous at the nanoscale in icosahedra and decahedra. These structural motifs consist of several tetrahedra sharing a twin grain boundary. According to the coincident site lattice (CSL) theory this twin grain boundary is referred to as Σ3<110>{111} grain boundary. In the present work, GBJ disclinations involving a low energy grain boundary Σ11<110>{113} are reported. Σ3−Σ3−Σ11 triple junction disclination is energetically preferred at the nanoscale as opposed to the ideal (without any misorientation mismatch) Σ3−Σ3−Σ9 triple junction. Molecular dynamics simulations are employed to study the disclinations in three dynamical processes key for nanoparticle synthesis − growth, coalescence, and solidification; across three metal systems Ag, Cu, and Pt which cover a range of stacking fault energies. Results indicate that Pt has a higher preference for disclinations while they are almost non-existent in Cu and to a lesser degree in Ag. Several types of disclinations have been identified and catalogued. Gaussian images (used as a proxy for simulating scanning transmission electron microscopy high angle annular dark field images) reveal that some of the disclinations induce artifacts which makes it non-trivial to identify them even when they are present in experimental particles. A key characteristic of the GBJ disclinations is the rapid change in misorientation angle around Σ11 grain boundary with distance away from the disclination. In this scenario, there is a need to reassess the methodology currently in use for identification of grain boundary type at the nanoscale.

Patterning and folding of intestinal villi by active mesenchymal dewetting

Tissue folds are structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, finger-like protrusions that enable nutrient absorption. However, the molecular and mechanical processes driving villus morphogenesis remain unclear. Here, we identify an active mechanical mechanism that simultaneously patterns and folds the intestinal epithelium to initiate villus formation. At the cellular level, we find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. This symmetry-breaking process requires altered cell and extracellular matrix interactions that are enabled by matrix metalloproteinase-mediated tissue fluidization. Computational models, together with invitro and invivo experiments, revealed that these cellular features manifest at the tissue level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active dewetting of a thin liquid film.

Stabilization of 2D Raft Structures of Au Nanoclusters with up to 60 Atoms by a Carbon Support

Herein, the stabilization of 2D single‐atom high gold rafts containing up to ≈60 Au atoms on amorphous carbon, fabricated by sputtering of atoms and imaged by aberration‐corrected scanning transmission electron microscopy, is demonstrated. These rafts deviate from the established cluster transition from 2D to 3D Au structural motifs in free clusters, which occurs in the region of 10–14 atoms. The experimental findings by performing explicit ab initio calculations of Aun (n = 3–147) clusters on graphene are supported and the role of cluster–surface interactions in the stabilization of the 2D single‐atom high Au cluster rafts on graphene is revealed. The transition from equilibrium 2D–3D structures is delayed to n = 19, while metastable 2D single‐atom high rafts compete with 3D structures up to about n = 60 atoms. The catalytic activity of supported nanoclusters depends strongly on their structure (and carbon‐based supports are used for a number of reactions); therefore these results are relevant to the catalytic performance of nanocluster‐based catalysts.

Photocatalytic [3+2] Cycloaddition of Alkyl/aryl Iodides and Internal Alkynes by Merging Halogen and Hydrogen Atom Transfer

Comprehensive SummaryA visible light photocatalytic [3+2] cycloaddition of alkynes with readily accessible organic iodides as the C3 synthon is developed herein. By merging halogen atom transfer (XAT) and hydrogen atom transfer (HAT), alkyl/aryl iodides serve as a formal diradical precursor and add across C‐C triple bonds to deliver a number of functionalized cyclopentanes in moderate to high yields with exceptional regio‐ and diastereoselectivity. A reductive radical‐polar crossover mechanism, involving the cascade XAT, radical addition, 1,5‐HAT, polar effect‐promoted 5‐endo annulation, single electron transfer (SET) reduction, and protonation, may account for this unprecedented dehalogenative [3+2] cycloaddition. This work not only expands the repertoire of the traditional RATC methodology, but also provides a robust platform for the expedient assembly of cyclopentanes, a valuable structural motif in the realms of medicinal chemistry and material sciences.

The SUN-family protein Sad1 mediates heterochromatin spatial organization through interaction with histone H2A-H2B

Heterochromatin is generally associated with the nuclear periphery, but how the spatial organization of heterochromatin is regulated to ensure epigenetic silencing remains unclear. Here we found that Sad1, an inner nuclear membrane SUN-family protein in fission yeast, interacts with histone H2A-H2B but not H3-H4. We solved the crystal structure of the histone binding motif (HBM) of Sad1 in complex with H2A-H2B, revealing the intimate contacts between Sad1HBM and H2A-H2B. Structure-based mutagenesis studies revealed that the H2A-H2B-binding activity of Sad1 is required for the dynamic distribution of Sad1 throughout the nuclear envelope (NE). The Sad1-H2A-H2B complex mediates tethering telomeres and the mating-type locus to the NE. This complex is also important for heterochromatin silencing. Mechanistically, H2A-H2B enhances the interaction between Sad1 and HDACs, including Clr3 and Sir2, to maintain epigenetic identity of heterochromatin. Interestingly, our results suggest that Sad1 exhibits the histone-enhanced liquid-liquid phase separation property, which helps recruit heterochromatin factors to the NE. Our results uncover an unexpected role of SUN-family proteins in heterochromatin regulation and suggest a nucleosome-independent role of H2A-H2B in regulating Sad1’s functionality.

A comprehensive study on the intermolecular interactions and energy frameworks exist in crystal structures of Form-I, Form-II and Form-III polymorphs of Ethyl maltol

The present study serves as a comprehensive investigation into the molecular crystal structures of three polymorphic forms of ethyl maltol. Crystal structures of the polymorphs grown via slow evaporation and quench cooling crystallization processes were determined through single crystal X-ray diffraction (SCXRD) analysis. Through the utilization of SCXRD data CIF file as an input, we explored the nature and strength of intermolecular interactions, atom pair close contacts, interaction types, 2D fingerprint plots, surface characteristics and percentage of voids present within each polymorph of ethyl maltol. The comparative analysis involves the application of advanced methods, such as Hirshfeld surface analysis and 3D-energy frameworks using Crystal Explorer 17.5. In a supramolecular organization, intermolecular interaction between the carbonyl and hydroxyl groups is a collective structural motif employed among the three polymorphs. However the three polymorphs share common structural features, but the conformations within the crystal packing of each form are different from each other. Shape Index and Curvedness surfaces reveal π stacking interactions with varying properties on differing sides of the molecular moieties between the polymorph. Fingerprint analysis emphasizes that (H…H) is the predominant interaction whereas (O…H) and (H…O) interactions contribute more towards the generation of H-bond interactions in the structure of ethyl maltol polymorphs. The crystal structures of all the three ethyl maltol polymorphs stabilized by various intermolecular contacts within the Hirshfeld surface area was comparable. The interaction energy and the 3D-energy frameworks offer a visualization of the crystal packing topology, enhancing our understanding of the three-dimensional arrangement of molecules and their structural stability. The resulting overall average total energy values for Form-I, Form-II and Form-III polymorphs of ethyl maltol are -56.3 kJ /mol, -74 kJ /mol and -80.45 kJ /mol respectively which reveals that all the three polymorphs show a significant difference in their total energies and reveals further that Form-III polymorph of ethyl maltol is the most stable one while Form-I is the least stable and Form-II is metastable relatively. Moreover, the dispersion energy framework is predominant over the electrostatic energy framework. The void analysis reveals the percentage of volume occupied by the voids present in the unit cell of Form-I, Form-II, and Form-III polymorphs of ethyl maltol are found to be 7.20%, 6.55 %, and 9.43% respectively.

Genome-wide identification and examination of the wheat glycosyltransferase family 43 regulation during Fusarium graminearum infection

In Arabidopsis and rice, the glycosyltransferase (GT) 43 family is involved in xylan synthesis. However, there have been limited reports on the study of the TaGT43 family in wheat. In this study, 28 TaGT43 family members were identified in wheat (Triticum aestivum L.) and clustered into three major groups based on the similarity of amino acid sequences. The results of the TaGT43 family's conserved motif and gene structure analyses agree with this result. Collinearity analysis revealed segmental duplications mainly promoted TaGT43 family expansion. cis-Acting element analysis revealed that the TaGT43 genes were involved in the light response, phytohormone response, abiotic/biotic stress response, and growth and development. The TaGT43 family showed a tissue-specific expression pattern, primarily expressed in roots and stems. Besides, the transcriptional and expression levels of multiple TaGT43 genes were upregulated during the infection of F. graminearum. According to metabolomics studies, F. graminearum infection affected the phenylpropanoid biosynthesis pathway in wheat, a critical factor in cell wall construction. Furthermore, GO enrichment analysis indicated that the TaGT43 genes play a significant role in cell wall organization. Based on these results, it may be concluded that the TaGT43 family mediates cell wall organization in response to F. graminearum infection.

Genome-wide characterization of the glutathione S-transferase gene family in Phaseolus vulgaris reveals insight into the roles of their members in responses to multiple abiotic stresses

Glutathione S-transferases (GSTs) are a class of multifunctional enzymatic antioxidants that play a significant role in several aspects of plant physiology, including growth, development, and cellular protection from biotic and abiotic stressors. A total of 59 GST genes were found in Phaseolus vulgaris genome, which were categorized into 11 distinct classes according to their evolutionary connection and the existence of conserved structural domains and motifs. Gene duplication analysis revealed that the evolution of the members of the GST gene family in P. vulgaris was driven by both segmental and tandem duplication events. Analysis of the expression profiles of identified PvGST genes using the available transcriptome data demonstrated notable expression patterns and organ specificity of many genes throughout several developmental stages and under drought or salinity. Subsequent RT-qPCR analysis of several drought-responsive or salinity-responsive candidate genes showed that PvGSTF4 was up-regulated solely by drought, PvGSTU11 was up-regulated only by salinity, and PvGSTU3, PvGSTU12, PvGSTU13, PvGSTU14, PvGSTU16, PvGSTT1, and PvGSTZ2 were up-regulated by both salt and drought. The up-regulated PvGSTs under drought and/or salinity might enable P. vulgaris to adapt to stressful environments. These candidate genes could be explored in genetic engineering programs for development of stress-tolerant P. vulgaris varieties.

Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs).

Helix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.

Characterization of MADS-box gene family and its unique response to drought and nickel stresses with melatonin-mediated tolerance in dragon fruit (Selenicereus undatus L.)

Dragon fruit (pitaya) is an important tropical crop with medicinal and industrial values. However, severe environmental stress factors affect dragon fruit production and development. The MADS-box gene family performs essential role in the regulation of stress tolerance, reproduction, and fruit ripening in various plants, but relevant studies haven't been conducted on dragon fruit. In this study, the identification and expression analysis of the MADS-box gene family was conducted in response to abiotic stress factors in pitaya seedlings. We identified 67 MADS-box genes distributed across 11 chromosomes of the pitaya genome. All the genes were named from HuMADS-1 to HuMADS-67. The phylogenetic tree of HuMADS-box genes was constructed together with soybean, wheat, and Arabidopsis. Based on the phylogenetic analysis, tree tropology and motif's structure, all the genes were divided into 3 groups as Mα, Mδ, and MIKC. The HuMADS genes showed a conserved intron-exon structure and motif domain organization. The expression patterns of all HuMADS-box genes varied in 15 tissues of pitaya. The analysis of subcellular localization of all proteins predicted that 55.8 % of the total gene members were localized in the nucleus. The syntenic analysis showed 28 collinearity gene pairs, in which 4 gene pairs showed tandem duplication and 24 pairs showed segmental duplication on the chromosomes. Cis-acting element predicted their regulatory roles in plant defense processes. RNA-seq analysis of pitaya seedlings under single and combined stresses of drought and nickel exhibited higher expression of HuMADS-box genes. In addition, several HuMADS genes showed enhanced expression in response to melatonin treatment under drought and nickel stresses, thereby enhancing pitaya seedlingsgrowth and development. To validate the RNA-Seq data, RT-qPCR analysis was performed on 12 HuMADS genes, our results revealed that six of them (HuMADS-14/15/22/62/63/67) play important role in abiotic stress tolerance. Overall, our findings offer key insights for future genetic engineering strategies to develop stress-tolerant pitaya genotypes.

Identification and Functional Verification of the Glycosyltransferase Gene Family Involved in Flavonoid Synthesis in Rubus chingii Hu.

Glycosylation is catalyzed by UDP-glycosyltransferase (UGT) and plays an important role in enriching the diversity of flavonoids. Rubus plants contain a lot of natural flavonoid glycosides, which are important plants with a homology of medicine and food. However, information about the Rubus UGT gene family is very limited. In this study, we carried out genome-wide analysis and identified the 172, 121, 130, 121 UGT genes in R. chingii, R. corchorifolius, R. idaeus, and R. occidentalis, respectively, and divided them into 18 groups. The analysis of the protein motif and gene structure showed that there were structural and functional conservations in the same group, but there were differences among different groups. Gene replication analysis showed that raspberry and dicotyledons had a higher homology. The expansion of the UGTs gene family was mainly driven by tandem replication events, and experienced purified selection during the long evolution of the raspberry. Cis-acting element analysis showed that they were related to plant growth and development, hormone regulation, and stress response. In addition, according to a comprehensive analysis of the co-expression network constructed by transcriptome data and phylogenetic homology, RchUGT169 was identified as a flavonoid glucosyltransferase. Through the transient expression in tobacco, it was verified that RchUGT169 could catalyze the conversion of kaempferol and quercetin to the corresponding flavonoid glycosides. In conclusion, this research enriched the understanding of the diversity of UGTs in Rubus and determined that RcUGT169 can catalyze flavonoids.

The 18F‐Difluoromethyl Group: Challenges, Impact and Outlook

AbstractThe difluoromethyl functionality has proven useful in drug discovery, as it can modulate the properties of bioactive molecules. For PET imaging, this structural motif has been largely underexploited in (pre)clinical radiotracers due to a lack of user‐friendly radiosynthetic routes. This Minireview provides an overview of the challenges facing radiochemists and summarises the efforts made to date to access 18F‐difluoromethyl‐containing radiotracers. Two distinct approaches have prevailed, the first of which relies on 18F‐fluorination. A second approach consists of a 18F‐difluoromethylation process, which uses 18F‐labelled reagents capable of releasing key reactive intermediates such as the [18F]CF2H radical or [18F]difluorocarbene. Finally, we provide an outlook for future directions in the radiosynthesis of [18F]CF2H compounds and their application in tracer radiosynthesis.