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This study presents an enhanced protein design algorithm that aims to emulate natural heterogeneity of protein sequences. Initial analysis revealed that natural proteins exhibit a permutation composition lower than the theoretical maximum, suggesting a selective utilization of the 20-letter amino acid alphabet. By not constraining the amino acid composition of the protein sequence but instead allowing random reshuffling of the composition, the resulting design algorithm generates sequences that maintain lower permutation compositions in equilibrium, aligning closely with natural proteins. Folding free energy computations demonstrated that the designed sequences refold to their native structures with high precision, except for proteins with large disordered regions. In addition, direct coupling analysis showed a strong correlation between predicted and actual protein contacts, with accuracy exceeding 82% for a large number of top pairs (> 4 L). The algorithm also resolved biases in previous designs, ensuring a more accurate representation of protein interactions. Overall, it not only mimics the natural heterogeneity of proteins but also ensures correct folding, marking a significant advancement in protein design and engineering. [ABSTRACT FROM AUTHOR]

The three-dimensional organization of chromatin is influenced by chromatin-binding proteins through both specific and non-specific interactions. However, the roles of chromatin sequence and the interactions between binding proteins in shaping chromatin structure remain elusive. By employing a simple polymer-based model of chromatin that explicitly considers sequence-dependent protein binding and protein–protein interactions, we elucidate a mechanism for chromatin organization. We find that tuning protein–protein interactions and protein concentration is sufficient to either promote or inhibit chromatin compartmentalization. Moreover, chromatin sequence and protein–protein attraction strongly affect the structural and dynamic exponents that describe the spatiotemporal organization of chromatin. Strikingly, our model's predictions for the exponents governing chromatin structure and dynamics successfully capture experimental observations, in sharp contrast to previous chromatin models. Overall, our findings have the potential to reinterpret data obtained from various chromosome conformation capture technologies, laying the groundwork for advancing our understanding of chromatin organization. [ABSTRACT FROM AUTHOR]

mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map across the mRNA life cycle in human cells by immunopurification-mass spectrometry (IP-MS) of ∼100 endogenous RBPs with and without RNase, augmented by size exclusion chromatography-mass spectrometry (SEC-MS). We identify 8,742 known and 20,802 unreported interactions between 1,125 proteins and determine that 73% of the IP-MS-identified interactions are RNA regulated. Our interactome links many proteins, some with unknown functions, to specific mRNA life-cycle stages, with nearly half associated with multiple stages. We demonstrate the value of this resource by characterizing the splicing and export functions of enhancer of rudimentary homolog (ERH), and by showing that small nuclear ribonucleoprotein U5 subunit 200 (SNRNP200) interacts with stress granule proteins and binds cytoplasmic RNA differently during stress.

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable. [ABSTRACT FROM AUTHOR]

Protein-protein interactions (PPIs) are at the heart of the molecular landscape permeating life. Proteomics studies can explore this protein interaction landscape using mass spectrometry (MS). Thanks to their high sensitivity, mass spectrometers can easily identify thousands of proteins within a single sample, but that same sensitivity generates tangled spiderwebs of data that hide biologically relevant findings. So, what does a researcher do when she finds herself walking into spiderwebs? In a field focused on discovery, MS data require rigor in their analysis, experimental validation, or a combination of both. In this Review, we provide a brief primer on MS-based experimental methods to identify PPIs. We discuss approaches to analyze the resulting data and remove the proteomic background. We consider the advantages between comprehensive and targeted studies. We also discuss how scoring might be improved through AI-based protein structure information. Women have been essential to the development of proteomics, so we will specifically highlight work by women that has made this field thrive in recent years.

The protein phosphatase 5 (PP5) is normally recruited to its substrates by the molecular chaperones, heat shock protein 70 (Hsp70) and heat shock protein 90 (Hsp90). This interaction requires the tetratricopeptide repeat (TPR) domain of PP5, which binds to an EEVD motif at the extreme C termini of cytosolic Hsp70 and Hsp90 isoforms. In addition to bringing PP5 into proximity with chaperone-bound substrates, this interaction also relieves autoinhibition in PP5s catalytic domain, promoting its phosphatase activity. To better understand the molecular determinants of this process, we screened a large, pentapeptide library for binding to PP5. This screen identified the amino acid preferences at each position, which we validated by showing that the optimal sequences bind 4- to 7-fold tighter than the natural EEVD motifs and stimulate PP5s enzymatic activity. The enhanced affinity for PP5s TPR domain was confirmed using a protein-adaptive differential scanning fluorimetry assay. Using this increased knowledge of structure-activity relationships, we re-examined affinity proteomics results to look for potential EEVD-like motifs in the C termini of known PP5-binding partners. This search identified elongator acetyltransferase complex subunit 1 (IKBKAP) as a putative partner, and indeed, we found that its C-terminal sequence, LSLLD, binds directly to PP5s TPR domain in vitro. Consistent with this idea, mutation of elongator acetyltransferase complex subunit 1s terminal aspartate was sufficient to interrupt the interaction with PP5 in vitro and in cells. Together, these findings reveal the sequence preferences of PP5s TPR domain and expand the scope of PP5s functions to include chaperone-independent complexes.

The intriguing network of antibody–antigen (Ab–Ag) interactions is highly governed by environmental perturbations and the nature of biomolecular interaction. Protein–protein interactions (PPIs) have potential applications in developing protein-adsorption-based sensors and nano-scale materials. Therefore, characterizing PPIs in the presence of a nanomaterial at the molecular level becomes imperative. The present work involves the investigation of antiferritin–ferritin (Ab–Ag) protein interactions under the influence of tungsten disulfide quantum dots (WS2 QDs). Isothermal calorimetry and contact angle measurements validated the strong influence of WS2 QDs on Ab–Ag interactions. The interfacial signatures of nano–bio-interactions were evaluated using sum frequency generation vibration spectroscopy (SFG-VS) at the air–water interface. Our SFG results reveal a variation in the tilt angle of methyl groups by ∼12° ± 2° for the Ab–Ag system in the presence of WS2 QDs. The results illustrated an enhanced ordering of water molecules in the presence of QDs, which underpins the active role of interfacial water molecules during nano–bio-interactions. We have also witnessed a differential impact of QDs on Ab–Ag by raising the concentration of the Ab–Ag combination, which showcased an increased inter-molecular interaction among the Ab and Ag molecules and a minimal influence on the methyl tilt angle. These findings suggest the formation of stronger and ordered Ab–Ag complexes upon introducing WS2 QDs in the aqueous medium and signify the potentiality of WS2 QDs relevant to protein-based sensing assays. [ABSTRACT FROM AUTHOR]

In biological studies in vitro and in vivo, techniques involving Förster resonance energy transfer (FRET) and FRET quantification use the interaction of CyPet-SUMO1 and its E2 ligase, YPet-Ubc9, to determine the dissociation constant (KD). Dipole-dipole resonance interactions, where energy transfers from an excited donor to an acceptor chromophore, allow the detection of molecular interactions to elucidate protein interactions in many regulatory cascades spanning signal transduction, medical diagnostics, and optical imaging. This study was aimed to explore how protein-protein interactions are affected by the crowded environment typically found within cells using FRET signals. An in vitro assay using a 96-well plate was conducted using varying concentrations of bovine serum albumin (BSA) to simulate crowded conditions and determine their effect on KD values. FRET measurements were conducted in a solution phase to mimic the protein interaction affinity in living cells. In contrast, other KD measurement methods such as radio-labeled ligand binding assay, surface plasmon resonance (SPR), or isothermal titration calorimetry (ITC) require extensive preparation or orientation on solid surfaces, making them less representative for such assessments. Emission wavelengths from CyPet-SUMO1 (414 nm to 475 nm) and YPet-Ubc9 (475 nm to 530 nm) were obtained to determine fluorescence signals along with KD. A comparison between protein interactions in crowded and uncrowded settings was made with varying KD value results. This investigation provides insights into protein interactions and cellular crowding, with potential implications for pharmaceuticals, bioseparations processes, and drug discovery targeting protein-protein interactions.

Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination-independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence are not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and mapped a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein-folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology. Data are available via ProteomeXchange with the identifier PXD044275.

Wildtype Escherichia coli cells cannot grow on L-1,2-propanediol, as the fucAO operon within the fucose (fuc) regulon is thought to be silent in the absence of L-fucose. Little information is available concerning the transcriptional regulation of this operon. Here, we first confirm that fucAO operon expression is highly inducible by fucose and is primarily attributable to the upstream operon promoter, while the fucO promoter within the 3'-end of fucA is weak and uninducible. Using 5'RACE, we identify the actual transcriptional start site (TSS) of the main fucAO operon promoter, refuting the originally proposed TSS. Several lines of evidence are provided showing that the fucAO locus is within a transcriptionally repressed region on the chromosome. Operon activation is dependent on FucR and Crp but not SrsR. Two Crp-cAMP binding sites previously found in the regulatory region are validated, where the upstream site plays a more critical role than the downstream site in operon activation. Furthermore, two FucR binding sites are identified, where the downstream site near the first Crp site is more important than the upstream site. Operon transcription relies on Crp-cAMP to a greater degree than on FucR. Our data strongly suggest that FucR mainly functions to facilitate the binding of Crp to its upstream site, which in turn activates the fucAO promoter by efficiently recruiting RNA polymerase.

Polyphenols have widely accepted health benefits which are limited by their low uptake, low bioavailability, and rapid degradation in the gut. While milk proteins are excellent carriers for polyphenols, the specific interactions of the polyphenols with the milk proteins, need to be understood to facilitate the utilization of these delivery systems in food and pharmaceutical applications. We have evaluated the relevance of different factors affecting milk protein-polyphenol interactions and the subsequent impact on the bioavailability and health promoting aspects of polyphenols. Hydrophobic forces are the primary binding forces of polyphenols to milk proteins. The significant factors affecting the interactions and binding affinity are the molecular weight and the hydrophobicity of the polyphenols. The interaction of polyphenols with milk proteins improved the antioxidant activity in comparison to milk proteins, while conflicting results exists for comparisons with polyphenols. In-vitro and cell line studies demonstrated enhanced bioavailability of polyphenols in the presence of milk proteins as well as higher anti-cancer and anti-allergy benefits. Overall, this work will pave the way for better understanding of polyphenol interactions with milk proteins and enable the tailoring of complexes through sustainable green processes, enabling higher bioavailability and health promoting effects of the polyphenols in food and pharmaceutical applications. [ABSTRACT FROM AUTHOR]

Summary: Plant MADS‐box proteins are vital for abiotic stress tolerance, yet their mechanisms for responding to drought remain poorly understood.Here, we investigated the drought tolerance mechanism of a MADS‐box protein (BpMADS11) from birch (Betula platyphylla) using immunoprecipitation, Western blotting, yeast two‐hybrid, yeast one‐hybrid, ChIP, RNA‐seq, and dual‐luciferase assays to explore post‐translational modifications, protein interactions, and gene regulation.Birch plants overexpressing BpMADS11 exhibited enhanced drought tolerance, while knockout lines displayed reduced tolerance. Under drought conditions, BpMADS11 interacts with protein phosphatase 2C22 (BpPP2C22), which dephosphorylates BpMADS11. Birch plants that overexpress BpMADS11 and lack BpPP2C22 show significantly reduced drought tolerance compared with those that only overexpress BpMADS11. BpMADS11 regulates the expression of BpERF61 by binding to CArG‐box in its promoter. The dephosphorylated BpMADS11 exhibits increased DNA binding ability and increased expression of BpERF61. Like BpMADS11, birch plants overexpressing BpERF61 show improved drought tolerance, while those with BpERF61 knockout exhibit decreased tolerance. BpERF61 binds to specific DNA motifs including 'CACGTG' (G‐box), 'GGGCCCC', and 'TTGGAT' to regulate the genes related to drought stress.Collectively, BpMADS11 undergoes dephosphorylation through its interaction with BpPP2C22, prompting the expression of BpERF61. Subsequently, BpERF61 regulates downstream genes by binding to specific DNA motifs, thereby enhancing drought tolerance. [ABSTRACT FROM AUTHOR]

This study aimed to explore the impact of novel method in improving the functionality and nutritional value of lentil-quinoa protein complexes. The method involved manipulating protein interactions through pH shifting and the addition of trehalose, ultimately enhancing water solubility, digestibility, and the functionality. Fluorescence, ultraviolet, and Fourier-transform spectroscopic techniques were applied to characterize the structural and molecular properties of the trehalose-conjugated lentil-quinoa protein complexes at various concentrations. After trehalose conjugation, statistically significant alterations (p < 0.05) in the tertiary and secondary protein structures and protein conformation were observed with trehalose-conjugated lentil-quinoa protein complexes at a trehalose concentration of 5% (w/w). The water solubility and digestibility of the latter conjugate-derived lentil and quinoa complex increased from 75.1 to 80% and 75 to 80.3%, respectively. Modifications in surface properties after conjugation involved significant (p < 0.05) changes in surface charge and hydrophobicity. Overall, combining the protein complexes with trehalose enhanced the digestibility and solubility of the protein complexes and improved their physical properties. The study highlights the potential of this approach to develop more sustainable and efficient plant-based protein sources for various food and nutritional applications in the food industry. [ABSTRACT FROM AUTHOR]

Background: Glioma-induced refractory epilepsy can be alleviated through conventional exercise, providing a potential therapeutic approach to manage this condition. This study aims to investigate the underlying mechanisms. Methods: Bioinformatics methodologies were employed to scrutinize gene expression data from public repositories such as GEO, with a specific focus on mobility-related genes in epilepsy. Through differential and enrichment analyses, differentially expressed genes (DEGs) were identified, while protein-protein interaction networks elucidated pivotal hub genes. Results: Our analysis revealed 32 DEGs, comprising 23 upregulated and 9 downregulated genes. Enrichment analysis underscored significant alterations in immune pathways in epilepsy. Two central hub genes, haptoglobin (HP) and prostaglandin-endoperoxide synthase 2 (PTGS2), were found to be modulated by Arginase 1 (ARG1) and Chemokine (C-X-C motif) ligand 8 (CXCL8). GSVA analysis associated elevated PTGS2 expression with metabolic pathways, while increased HP expression was correlated with angiogenesis and inflammation. Subsequent experiments validated HP's role in tumor cell proliferation, emphasizing its potential as a therapeutic target. Conclusion: This study highlights the crucial involvement of HP and PTGS2 genes in the etiology of epilepsy, linked to discrepancies in the immune system. These findings offer fresh perspectives on the management of epilepsy, emphasizing the neuroprotective possibilities of targeting specific gene pathway. [ABSTRACT FROM AUTHOR]

Self-assembly and molecular spectroscopy are widely used in protein research. However, studies underreported the interaction of rice glutelin (RG) and egg white protein (EWP) under pH-cycle treatments, which had differences between initial and final environment. Herein, the possible interaction mechanism of RG-EWP self-assembly behavior was demonstrated by spectroscopy or other characterization methods under different conditions and proportions. Fourier transform infrared, circular dichroism, intrinsic fluorescence, and UV absorption spectroscopic methods showed changes in the secondary and tertiary structures of RG or RG-EWP. Results also revealed the degree of protein folding and exposure status of aromatic amino acid residues. The nonignorable surface hydrophobic and electrostatic interactions were observed by ζ-potentials and surface hydrophobicity. The electrophoretic analysis showed increased 48 kDa subunits. The high solubility (over 92%) of RG-EWP was discovered as potential functionality at total ratio of 90% and 50% RG. This study improved the asymmetric pH-cycle theoretical mechanism and widened RG-EWP application. [ABSTRACT FROM AUTHOR]

Objective: The improvement of carcass traits is essential for the Hanwoo industry because of the Hanwoo grade determination system, and genome-wide association study (GWAS) analysis is an instrumental tool for identifying the genetic factors that impact these traits. While GWAS analysis utilizing family data offers advantages in minimizing genetic bias, research on family-based GWAS in Hanwoo is currently lacking. Methods: This study classified Group A using both parental and offspring genetic information, and Group B based solely on offspring genetic information, to compare GWAS analysis results of Hanwoo carcass traits. Results: A total of 16 significant single nucleotide polymorphism (SNP) markers were identified in Group A, comprising 7 for carcass weight (CWT), 3 for back fat thickness (BFT), and 6 for marbling score (MS). In Group B, 7 significant SNP markers were identified, including 3 for CWT, 1 for eye muscle area, 1 for BFT, and 2 for MS. Functional annotation analysis revealed only one common function related to carcass traits between the groups, while protein-protein interaction analysis indicated more gene interactions in Group A. The reliability of estimated values for common SNP markers identified between the groups was higher in Group A. Conclusion: GWAS analysis utilizing parental genetic information holds greater potential for application, owing to its higher reliability of estimated values and the ability to explore numerous candidate genes. [ABSTRACT FROM AUTHOR]

Background The AQP4-AS1/miR-4476-ALOX15 regulatory axis was discovered in previous studies. We aimed to investigate the regulatory mechanism of the ferroptosis-related regulator ALOX15 by AQP4-AS1 and miR-4476 in lung adenocarcinoma (LUAD) and find new targets for clinical treatment. Methods After bioinformatics analysis, we contained one ferroptosis-related gene (FRG), namely ALOX15. MicroRNAs (miRNAs) and long noncoding RNAs were predicted by miRWalk. Furthermore, we constructed overexpressed LUAD cell lines. Real-time quantitative polymerase chain reaction and western blot were used to determine the expression of mRNA and protein, respectively. Cell Counting Kit-8 (CCK-8) and EdU assay were used to detect the cell proliferation. Double luciferase assay was used to detect the binding relationship between AQP4-AS1 and miR-4464. Results ALOX15 was the most significantly downregulated FRG compared with normal tissues. Furthermore, protein-protein interaction network analysis indicated that the AQP4-AS1-miR-4476-ALOX15 regulatory axis might be involved in the occurrence and development of LUAD and there might be direct interaction between AQP4-AS1 and miR-4476, and miR-4476 and ALOX15. Furthermore, AQP4-AS1 and ALOX15 were significantly downregulated in the LUAD tissue and cell lines, whereas miR-4476 showed the opposite results (p < 0.001). AQP4-AS1 overexpression improved the ALOX15 expression in LUAD cell lines. CCK-8 and EdU assay revealed that overexpression of AQP4-AS1 and ALOX15 inhibited the LUAD cell proliferation. Double luciferase assay results indicated that there was a combination between AQP4-AS1 and miRNA-4476. In addition, we found that overexpressed AQP4-AS1 activates the ferroptosis in LUAD cell lines. Conclusions AQP4-AS1 can regulate the expression of ALOX15 through competitive binding with miR-4476, further activate ferroptosis and inhibit the proliferation of LUAD cells. [ABSTRACT FROM AUTHOR]

Background: The coronavirus disease 2019 (COVID-19) pandemic has brought a heavy burden to the world, interestingly, it shares many clinical symptoms with systemic lupus erythematosus (SLE). It is unclear whether there is a similar pathological process between COVID-9 and SLE. In addition, we don't know how to treat SLE patients with COVID-19. In this study, we analyse the potential similar pathogenesis between SLE and COVID-19 and explore their possible drug regimens using bioinformatics and systems biology approaches. Methods: The common differentially expressed genes (DEGS) were extracted from the COVID-19 datasets and the SLE datasets for functional enrichment, pathway analysis and candidate drug analysis. Result: Based on the two transcriptome datasets between COVID-19 and SLE, 325 common DEGS were selected. hub genes were identified by protein-protein interaction (PPI) analysis. Few found a variety of similar functional changes between COVID-19 and SLE, which may be related to the pathogenesis of COVID-19. Besides, we explored the related regulatory networks. Then, through drug target matching, we found many candidate drugs for patients with COVID-19 only or COVID-19 combined with SLE. Conclusion: COVID-19 and SLE patients share many common hub genes, related pathways and regulatory networks. Based on these common targets, we found many potential drugs that could be used in treating patient with COVID-19 OR COVID-19 combined with SLE. [ABSTRACT FROM AUTHOR]

BACKGROUND: The widespread evolution of pesticide resistance poses a significant challenge to current agriculture, necessitating the discovery of molecules with new modes of action. Despite extensive efforts, no major molecules with new modes of action have been commercialized for decades. Most pesticides function by binding to specific pockets on target enzymes, enabling a single target site mutation to confer resistance. An alternative approach is the disruption of protein–protein interactions (PPI), which require complementary mutations on both interacting partners for resistance to occur. Thus, our aim is the discovery and design of small‐molecule inhibitors that target the interface of the PPI complex of O‐acetylserine sulfhydrylase (OASS) and serine acetyltransferase (SAT), key obligatory interacting plant enzymes involved in the biosynthesis of the amino acid cysteine. RESULTS: By employing in silico filtering techniques on a virtual library of 30 million small molecules, we identified initial hits capable of binding OASS and interfering with its interaction with a peptide derived from SAT with a half‐maximal inhibitory concentration (IC50) of 34 μm. Subsequently, we conducted molecular chemical optimizations, generating an early lead molecule (PJ4) with an IC50 value of 4 μm. PJ4 successfully inhibited the germination of Arabidopsis thaliana seedlings and inhibited clover growth in a pre‐emergence application at an effective concentration of 4.6 kg ha−1. CONCLUSION: These new compounds described herein can serve as promising leads for further optimization as herbicides with a new mode‐of‐action. This technology can be used for discovering new modes of action chemicals inhibiting all pest groups. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Main conclusion: CeOLE6, a tuber-specific gene in tigernut, encodes a diverged SH oleosin that functions in oil accumulation via homo and heteromultimerization. Tigernut (Cyperus esculentus L.) is a rare example accumulating high levels of triacylglycerols (TAGs) in underground tubers; however, the mechanism underlying is poorly understood. Given essential roles of oleosins (OLEs) in oil accumulation, in this study, structural and functional analyses were conducted for CeOLE6, an oleosin gene preferentially expressed in tigernut tubers. Phylogenetic analysis revealed that CeOLE6 encodes a diverged oleosin in Clade SH, which also includes CeOLE4 and -5. Further synteny analysis and sequence comparison indicated that CeOLE6 is more likely to be a whole-genome duplication (WGD) repeat of CeOLE4, which underwent rapid evolution and deletion of the typical C-terminal insertion for SHs. Nevertheless, CeOLE6 retains the capacity of oligomerization and oil accumulation, because (i) CeOLE6 could not only interact with itself but also with CeOLE2 and -5, two tuber-dominant members belonging to Clades SL and SH, respectively, and (ii) overexpressing CeOLE6 in tobacco leaves could significantly enhance the TAG content. Though CeWRI1 exhibits a similar expression pattern as CeOLE6 during tuber development, both CeWRI1 and -3 could not activate the CeOLE6 promoter, implying that they are not transcription factors contributing tuber-specific activation of CeOLE6. These findings not only provide insights into CeOLE genes in tuber oil accumulation, but also lay a foundation for further genetic improvement in tigernut and other species. [ABSTRACT FROM AUTHOR]

Objective: This research investigates the potential anti-tumour effects of bromelain, an aqueous extract from pineapple stems and fruits, on nasopharyngeal cancer (NPC). While bromelain is known for its medicinal properties in various cancers, its impact on NPC remains unexplored. Results: Using in silico methods, we studied the predicted interactions between bromelain and key proteins involved in NPC oncogenesis, specifically β-catenin, PIK3CA, mTOR, EGFR, and BCL2. Molecular docking strategies were performed using a myriad of computational tools. A 3D model of bromelain was constructed using SWISS-MODEL, followed by molecular docking simulations performed with ClusPro. The binding affinities of the docked complexes were evaluated using HawkDock, and the interactions were analysed with LigPlot+. The docking scores indicated potential spontaneous interactions, with binding affinities based on being − 103.89 kcal/mol (PIK3CA), -73.16 kcal/mol (EGFR), -71.18 kcal/mol (mTOR), -65.22 kcal/mol (β-catenin), and − 57.48 kcal/mol (BCL2). LigPlot + analysis revealed the presence of hydrogen bonds, hydrophobic interactions, and salt bridges, indicating stable predicted interactions. Conclusion: Our findings suggest that bromelain can target key proteins involved in NPC oncogenesis, with the strongest affinity towards PIK3CA. This suggests a hypothetical insight into bromelain's anticancer effects on NPC through the modulation of the PI3K/Akt signaling pathway. [ABSTRACT FROM AUTHOR]

Background: The role of neurons in central post-stroke pain (CPSP) following thalamic hemorrhage remains unclear. This study aimed to identify key genes associated with post-thalamic hemorrhage pain and to explore their functions in neurons. Single-nucleus RNA sequencing (snRNA-seq) data from a mouse model was used for this analysis. Methods: First, snRNA-seq data were analyzed to identify cell types associated with CPSP induced by thalamic hemorrhage. Differentially expressed genes (DEGs) in neurons were then screened between control and model groups, followed by the construction of a protein-protein interaction (PPI) network for the DEGs. CytoNCA was used to assess node connectivity in the PPI network, and the top 5 key genes were identified. Subsequently, transcription factor (TF)-mRNA and miRNA-mRNA networks were constructed, and small-molecule drugs potentially targeting these key genes were predicted. Finally, the expression differences of key genes in neurons were compared between the model and control groups. Results: A total of 13 cell clusters were identified, categorized into 8 cell types: T cells, endothelial cells, monocytes, neural progenitor cells (NPCs), microglia, astrocytes, neurons, and oligodendrocytes. A total of 228 DEGs were detected in neurons when comparing the model group with the control group. The PPI network of the DEGs consisted of 126 nodes and 209 edges, identifying the top 5 key genes: Dlgap1, Cacna1c, Gria2, Hsp90ab1, and Gapdh. The miRNA-mRNA network included 68 miRNA-mRNA pairs, 62 miRNAs, and 5 mRNAs, while the TF-mRNA network consisted of 66 TF-mRNA pairs, 56 TFs, and 5 mRNAs. Drug prediction identified 110 small-molecule drugs (e.g., purpurogallin, nifedipine, and novobiocin) potentially targeting these key genes. Additionally, Cacna1c were significantly upregulated in model mice. Conclusion: This study identified the role of key genes in thalamic hemorrhage-induced CPSP through snRNA-seq, providing a scientific basis for further exploration of the molecular mechanisms underlying CPSP. Key points: • Question: The role of neuronal genes in the development of CPSP following thalamic hemorrhage remains unclear. • Findings: Our snRNA-seq analysis identified five key genes (Gapdh, Cacna1c, Gria2, Dlgap1, and Hsp90ab1) involved in the neuronal response to CPSP induced by thalamic hemorrhage. • Meaning: This study provides a foundational framework for exploring neuron-specific mechanisms underlying CPSP, offering potential targets for therapeutic intervention. [ABSTRACT FROM AUTHOR]

Chlamydomonas reinhardtii , a unicellular green alga, is a prominent model for green biotechnology and for studying organelles' function and biogenesis, such as chloroplasts and cilia. However, the stable expression of foreign genes from the nuclear genome in C. reinhardtii faces several limitations, including low expression levels and significant differences between clones due to genome position effects, epigenetic silencing, and time-consuming procedures. We developed a robust transient expression system in C. reinhardtii to overcome these limitations. We demonstrated efficient entry of in vitro-transcribed mRNA into wall-less cells and enzymatically dewalled wild-type cells via electroporation. The endogenous or exogenous elements can facilitate efficient transient expression of mRNA in C. reinhardtii , including the 5' UTR of PsaD and the well-characterized Kozak sequence derived from the Chromochloris zofingiensis. In the optimized system, mRNA expression was detectable in 120 h with a peak around 4 h after transformation. Fluorescently tagged proteins were successfully transiently expressed, enabling organelle labeling and real-time determination of protein sub-cellular localization. Remarkably, transiently expressed IFT46 compensated for the ift46–1 mutant phenotype, indicating the correct protein folding and function of IFT46 within the cells. Additionally, we demonstrated the feasibility of our system for studying protein-protein interactions in living cells using bimolecular fluorescence complementation. In summary, the established transient expression system provides a powerful tool for investigating protein localization, function, and interactions in C. reinhardtii within a relatively short timeframe, which will significantly facilitate the study of gene function, genome structure, and green biomanufacturing in C. reinhardtii and potentially in other algae. • Successful establishment of an RNA-based transient expression system in Chlamydomonas. • Function of 5' UTR on gene expression occurs at the post-transcriptional level in Chlamydomonas. • Analysis of the localization, function, and interactions of proteins can be completed within one week. [ABSTRACT FROM AUTHOR]

Background: Indole-3-acetic acid (IAA), an indole analog produced by intestinal microorganisms metabolizing tryptophan, has anti-inflammatory and antioxidant properties and thus has potential applications in ovarian protection, although the exact mechanism is unknown. The present study preliminarily investigated the pharmacological mechanism of IAA in alleviating diminished ovarian reserve (DOR) by network pharmacology and molecular docking. Methods: Relevant target proteins of IAA were searched in SwissTargetPrediction, PharmMapper, TargetNet, BATMAN-TCM, and SuperPred databases. The potential targets of DOR were obtained from GeneCards, DisGenet, OMIM, and Drugbank databases. Both common targets were then imported into the String website to construct a PPI network, and these targets were analyzed for GO and KEGG enrichment. Finally, we utilized molecular docking to validate the possible binding conformations between IAA and the candidate targets. We used in vitro experiments to preliminarily investigate the effects of IAA on DOR. Results: We obtained 88 potential targets for IAA and DOR interaction. We received 16 pivotal targets by constructed protein interaction screening. KEGG enrichment analysis mainly included the AGE-RAGE signaling pathway, IL-17 signaling pathway, Chemical carcinogenesis—reactive oxygen species in diabetic complications, etc. GO functional analysis showed that IAA treatment of DOR may involve biological processes such as response to external stimuli, hypoxia, gene expression, and regulation of enzyme activity. Molecular docking and in vitro experiments further revealed the potential effects of IAA on MMP2, TNF-α, AKT1, HSP90AA1, and NF-κ B. Conclusion: We preliminarily revealed the potential protective effects of IAA against DOR through multiple targets and pathways, which provides a new research strategy for the molecular mechanism of IAA to alleviate DOR in the future. However, further studies need to demonstrate whether IAA can be used as a compound to prevent and treat DOR. [ABSTRACT FROM AUTHOR]

Background: Infectious uveitis is a significant cause of visual impairment worldwide, caused by diverse pathogens such as viruses, bacteria, fungi, and parasites. Understanding its prevalence, etiology, pathogenesis, molecular mechanism, and clinical manifestations is essential for effective diagnosis and management. Methods: A systematic literature search was conducted using PubMed, Google Scholar, Web of Science, Scopus, and Embase, focusing on studies published in the last fifteen years from 2009 to 2023. Keywords included "uveitis," "infectious uveitis," "viral uveitis," and others. Rigorous inclusion and exclusion criteria were applied, and data were synthesized thematically. Gene symbols related to infectious uveitis were analyzed using protein-protein interaction (PPI) networks and pathway analyses to uncover molecular mechanisms associated with infectious uveitis. Results: The search from different databases yielded 97 eligible studies. The review identified a significant rise in publications on infectious uveitis, particularly viral uveitis, over the past fifteen years. Infectious uveitis prevalence varies geographically, with high rates in developing regions due to systemic infections and limited diagnostic resources. Etiologies include viruses (39%), bacteria (17%), and other pathogens, substantially impacting adults aged 20–50 years. Pathogenesis involves complex interactions between infectious agents and the ocular immune response, with key roles for cytokines and chemokines. The PPI network highlighted IFNG, IL6, TNF, and CD4 as central nodes. Enriched pathways included cytokine-cytokine receptor interaction and JAK-STAT signaling. Clinical manifestations range from anterior to posterior uveitis, with systemic symptoms often accompanying ocular signs. Diagnostic strategies encompass clinical evaluation, laboratory tests, and imaging, while management involves targeted antimicrobial therapy and anti-inflammatory agents. Conclusion: This review underscores the complexity of infectious uveitis, driven by diverse pathogens and influenced by various geographical and systemic factors. Molecular insights from PPI networks and pathway analyses provide a deeper understanding of its pathogenesis. Effective management requires comprehensive diagnostic approaches and targeted therapeutic strategies. [ABSTRACT FROM AUTHOR]

ABSTRACT This study focuses on the synthesis, characterization, and evaluation of NiBIDP and CuBIDP mixed‐ligand complexes. Synthesized with high yields in ethanol‐based solutions, these complexes demonstrate exceptional stability and non‐hygroscopic properties, with melting points exceeding 300°C. Solubility tests reveal compatibility with organic solvents such as acetonitrile, DMF, and DMSO, while being insoluble in water. Characterization through UV‐visible, IR, and mass spectrometry confirms octahedral coordination geometries around Ni(II) and Cu(II) centers. Thermal stability assessments indicate robust properties up to 180°C for NiBIDP and 170°C for CuBIDP. Computational analyses reveal significant electron localization and enhanced electron‐accepting capabilities in CuBIDP, as evidenced by its low LUMO value and high electrophilicity index. Molecular electrostatic potential (MEP) analyses identify nucleophilic sites important for protein interactions, underscoring their potential in catalysis and materials science. Biological evaluations show that although the BI and DP ligands exhibit moderate antimicrobial, anti‐inflammatory, and antioxidant activity, their metal complexes, particularly CuBIDP, demonstrate enhanced efficacy. Molecular docking studies further highlight the improved binding affinities of NiBIDP and CuBIDP with target proteins, suggesting their potential as therapeutic agents in drug discovery. In conclusion, this study provides significant insights into the structural, electronic, and biological properties of NiBIDP and CuBIDP complexes, supporting their development as versatile compounds in biomedical and materials science applications. Key outcomes include enhanced stability and bioactivity of metal complexes compared with their ligands, as well as promising therapeutic potential revealed through molecular docking analyses. [ABSTRACT FROM AUTHOR]

The mitochondrial disulphide relay machinery is essential for the import and oxidative folding of many proteins in the mitochondrial intermembrane space. Its core component, the import receptor MIA40 (also CHCHD4), serves as an oxidoreductase but also as a chaperone holdase, which initially interacts with its substrates non‐covalently before introducing disulphide bonds for folding and retaining proteins in the intermembrane space. Interactome studies have identified diverse substrates of MIA40, among them the intrinsically disordered HCLS1‐associated protein X‐1 (HAX1). Interestingly, this protein does not contain cysteines, raising the question of how and to what end HAX1 can interact with MIA40. Here, we demonstrate that MIA40 non‐covalently interacts with HAX1 independent of its redox‐active cysteines. While HAX1 import is driven by its weak mitochondrial targeting sequence, its subsequent transient interaction with MIA40 stabilizes the protein in the intermembrane space. HAX1 solely depends on the holdase activity of MIA40, and the absence of MIA40 results in the aggregation, degradation and loss of HAX1. Collectively, our study introduces HAX1 as the first endogenous MIA40 substrate without cysteines and demonstrates the diverse functions of this highly conserved oxidoreductase and import receptor. [ABSTRACT FROM AUTHOR]

ARL5 is a member of the ARF family of small GTPases that is recruited to the trans-Golgi network (TGN) by another ARF-family member, ARFRP1, in complex with the transmembrane protein SYS1. ARL5 recruits its effector, the multisubunit tethering complex GARP, to promote SNARE-dependent fusion of endosome-derived retrograde transport carriers with the TGN. To further investigate the function of ARL5, we sought to identify additional effectors. Using proximity biotinylation and protein interaction assays, we found that the armadillo-repeat protein ARMH3 (C10orf76) binds to active, but not inactive, ARL5, and that it is recruited to the TGN in a SYS1-ARFRP1-ARL5-dependent manner. Unlike GARP, ARMH3 is not required for the retrograde transport of various cargo proteins. Instead, ARMH3 functions to activate phosphatidylinositol 4-kinase IIIβ (PI4KB), accounting for the main pool of phosphatidylinositol 4-phosphate (PI4P) at the TGN. This function contributes to recruitment of the oncoprotein GOLPH3 and glycan modifications at the TGN. These studies thus identify the SYS1-ARFRP1-ARL5-ARMH3 axis as a regulator of PI4KB-dependent generation of PI4P at the TGN. GTPases are master regulators at the trans-Golgi network (TGN). Here, authors report that ARMH3 (C10orf76) is an ARL5 effector, and that a SYS1-ARFRP1-ARL5-ARMH3-PI4KB axis promotes PI4P synthesis, GOLPH3 recruitment, and glycan modifications at the TGN. [ABSTRACT FROM AUTHOR]

According to the FAO/WHO guidelines, selection of probiotics requires the assessment of survival under gastrointestinal stress and adhesion to human epithelial cells. These attributes were evaluated on Akkermansia muciniphila ATCC BAA-835 simulating the gastrointestinal transit (GIT) immediately followed by adhesion to human intestinal cell lines (CaCo2, HT-29, and HT-29-MTX) as an alternative approach to in vitro methods performed with fresh cells in each trial. The survival rate after GIT, as determined by plate counts and fluorescent probes, was significantly higher for A. muciniphila (about 8 Log CFU/mL) than for the probiotic Lacticaseibacillus rhamnosus GG ATCC 53103 (about 3 Log CFU/mL). The use of Live/Dead assay highlighted that A. muciniphila forms cell aggregates in the gastric phase as protective mechanism, explaining its high viability in the intestine. The rate of adhesion to human cell lines was always lower for strains tested after simulated GIT than for strains that did not undergo simulated GIT. Akkermansia muciniphila exhibited significantly higher adhesion than Lbs. rhamnosus GG, particularly to the mucus-secreting HT-29-MTX cells across a range of concentrations (2–8 Log CFU/mL). Finally, the bioinformatic analysis of A. muciniphila proteome confirmed the Amuc_1434 as a potential factor in binding to the human MUC2 protein. [ABSTRACT FROM AUTHOR]

Introduction: Polygenic Risk Scores (PRS) are an emerging tool for predicting an individual's genetic risk to a complex trait. Several methods have been proposed to construct and calculate these scores. Here, we develop a biologically driven PRS using the UK BioBank cohort through validated protein interactions (PPI) and network construction for psoriasis, incorporating variants mapped to the interacting genes of 14 psoriasis susceptibility (PSORS) loci, as identified from previous genetic linkage studies. Methods: We constructed the PPI network via the implementation of two major meta-databases of protein interactions, and identified variants mapped to the identified PSORS-interacting genes. We selected only European unrelated participants including individuals with psoriasis and randomly selected healthy controls using an at least 1:4 ratio to maximize statistical power. We next compared our PPI-PRS model to (i) clinical risk models and (ii) conventional PRS calculations through p -value thresholding. Results: Our PPI-PRS model provides comparable results to both clinical risk models and conventional approaches, despite the incorporation of a limited number of variants which have not necessarily reached genome-wide significance (GWS). Exclusion of variants mapped to the HLA-C locus, an established risk locus for psoriasis resulted in highly similar associations compared to our primary model, indicating the contribution of the genetic variability mapped to non-GWS variants in PRS computations. Discussion: Our findings support the implementation of biologically driven approaches in PRS calculations in psoriasis, highlighting their potential clinical utility in risk assessment and treatment management. [ABSTRACT FROM AUTHOR]

Despite SH2 domains, being pivotal in protein interactions linked to various diseases like cancer, we lack specific research tools for intracellular assays. Understanding SH2-mediated interactions and creating effective inhibitors requires tools which target individual protein domains. Affimer reagents exhibit promise, yet their potential against the extensive SH2 domain family remains largely unexplored. Our study aimed to bridge this gap by identifying Affimer reagents that selectively bind to 22 out of 41 SH2 domains. These reagents enabled a medium-throughput screening approach resembling siRNA studies, shedding light on their functionality. Notably, select Affimers demonstrated the ability to curtail the nuclear translocation of pERK, with Grb2 being a prominent target. Further analyses revealed that these Grb2-specific Affimer reagents displayed competitive inhibition with impressive metrics: IC50s ranging from 270.9 nM to 1.22 µM, together with low nanomolar binding affinities. Moreover, they exhibited the ability to pull down endogenous Grb2 from cell lysates, illustrating their efficacy in binding the Grb2 SH2 domain. This comprehensive assessment underscores the potential of Affimer reagents as domain-specific inhibitors. Their viability for medium/high-throughput phenotypic screening presents a promising avenue via which to identify and characterize potential drug targets within the SH2 domain family. [ABSTRACT FROM AUTHOR]

Actin polymerization is often associated with membrane proteins containing capping-protein-interacting (CPI) motifs, such as capping protein, Arp2/3, myosin I linker (CARMIL), CD2AP, and WASHCAP/Fam21. CPI motifs bind directly to actin-capping protein (CP), and this interaction weakens the binding of CP to barbed ends of actin filaments, lessening the ability of CP to functionally cap those ends. The protein V-1/myotrophin binds to the F-actin-binding site on CP and sterically blocks CP from binding barbed ends. CPI-motif proteins also weaken the binding between V-1 and CP, which decreases the inhibitory effects of V-1, thereby freeing CP to cap barbed ends. Here, we address the question of whether CPI-motif proteins on a surface analogous to a membrane lead to net activation or inhibition of actin assembly nucleated by Arp2/3 complex. Using reconstitution with purified components, we discovered that CARMIL at the surface promotes and enhances actin assembly, countering the inhibitory effects of V-1 and thus activating CP. The reconstitution involves the presence of an Arp2/3 activator on the surface, along with Arp2/3 complex, V-1, CP, profilin, and actin monomers in solution, recreating key features of cell physiology. [Display omitted] • Active capping protein (CP) levels determine actin network growth and organization • V-1 inhibits CP and decreases Arp2/3-based actin network growth • Low levels of CARMIL activate CP by displacing V-1, allowing CP to cap barbed ends • Protein interactions may provide fine-tuning for feedback of actin assembly Mooren et al. show that membrane-bound CARMIL activates capping protein (CP) by dissociating CP from V-1, thereby promoting actin polymerization nucleated by Arp2/3. The activity of CP is a critical determinant for polarized and structured growth of the actin network. Interactions among the proteins provide several points of feedback control. [ABSTRACT FROM AUTHOR]

The inhibition of intracellular protein‐protein interactions is challenging, in particular, when involved interfaces lack pronounced cavities. The transcriptional co‐activator protein and oncogene β‐catenin is a prime example of such a challenging target. Despite extensive targeting efforts, available high‐affinity binders comprise only large molecular weight inhibitors. This hampers the further development of therapeutically useful compounds. Herein, we report the design of a considerably smaller peptidomimetic scaffold derived from the α‐helical β‐catenin‐binding motif of Axin. Sequence maturation and bicyclization provided a stitched peptide with an unprecedented crosslink architecture. The binding mode and site were confirmed by a crystal structure. Further derivatization yielded a β‐catenin inhibitor with single‐digit micromolar activity in a cell‐based assay. This study sheds light on how to design helix mimetics with reduced molecular weight thereby improving their biological activity. [ABSTRACT FROM AUTHOR]

The ongoing global threats posed by COVID‐19 pandemic, catalyzed by SARS‐CoV‐2, underscores the pressing need for effective antiviral strategies. The viral non‐structural protein 1 (Nsp1) significantly influences pathogenicity by impeding host protein expression and enhancing viral RNA translation through its interaction with the stem‐loop 1 (SL1) in the 5′ untranslated region (UTR). We have developed a novel dual‐luciferase reporter assay, designed to investigate the critical Nsp1–SL1 interaction, and identified P23E02 as a potential inhibitor. Our investigation, combining molecular docking studies and alanine mutagenesis, has unveiled that P23E02 disrupts Nsp1–40S ribosomal subunit interaction, liberating translational inhibition and empowering host antiviral responses. P23E02 exhibits antiviral efficacy against various sarbecoviruses, making it a promising candidate for combatting COVID‐19 and related diseases. This study underscores the therapeutic potential of targeting the Nsp1/SL1 axis and lays the foundation for innovative antiviral interventions, ultimately fortifying global preparedness against future viral threats. [ABSTRACT FROM AUTHOR]

Drug combinations have emerged as a promising therapeutic approach in cancer treatment, aimed at overcoming drug resistance and improving the efficacy of monotherapy regimens. However, identifying effective drug combinations has traditionally been time-consuming and often dependent on chance discoveries. Therefore, there is an urgent need to explore alternative strategies to support experimental research. In this study, we propose network-based prediction models to identify potential drug combinations for 11 types of cancer. Our approach involves extracting 55,299 associations from literature and constructing human protein interactomes for each cancer type. To predict drug combinations, we measure the proximity of drug-drug relationships within the network and employ a correlation clustering framework to detect functional communities. Finally, we identify 61,754 drug combinations. Furthermore, we analyze the network configurations specific to different cancer types and identify 30 key genes and 21 pathways. The performance of these models is subsequently assessed through in vitro assays, which exhibit a significant level of agreement. These findings represent a valuable contribution to the development of network-based drug combination design strategies, presenting potential solutions to overcome drug resistance and enhance cancer treatment outcomes. [ABSTRACT FROM AUTHOR]

Activities of ATP binding cassette (ABC) proteins are regulated by multiple mechanisms, including protein interactions, phosphorylation, proteolytic processing, and/or oligomerization of the ABC protein itself. Here we present the structure of yeast cadmium factor 1 (Ycf1p) in its mature form following cleavage by Pep4p protease. Ycf1p, a C subfamily ABC protein (ABCC), is homologue of human multidrug resistance protein 1. Remarkably, a portion of cleaved Ycf1p forms a well-ordered dimer, alongside monomeric particles also present in solution. While numerous other ABC proteins have been proposed to dimerize, no high-resolution structures have been reported. Both phosphorylation of the regulatory (R) region and ATPase activity are lower in the Ycf1p dimer compared to the monomer, indicating that dimerization affects Ycf1p function. The interface between Ycf1p protomers features protein-protein interactions and contains bound lipids, suggesting that lipids stabilize the dimer. The Ycf1p dimer structure may inform the dimerization interfaces of other ABCC dimers. Authors present the structure of Ycf1p, a homolog of multidrug resistance protein 1 (MRP1). The monomeric and dimeric Ycf1p species are differentially phosphorylated and possess different ATPase activities indicating that dimerization affects the function of the protein. [ABSTRACT FROM AUTHOR]

Networks have emerged as a natural data structure to represent relations among entities. Proteins interact to carry out cellular functions and protein-Protein interaction network analysis has been employed for understanding the cellular machinery. Advances in genomics technologies enabled the collection of large data that annotate proteins in interaction networks. Integrative analysis of interaction networks with gene expression and annotations enables the discovery of context-specific complexes and improves the identification of functional modules and pathways. Extracting subnetworks whose vertices are connected and have high attribute similarity have applications in diverse domains. We present an enumeration approach for mining sets of connected and cohesive subgraphs, where vertices in the subgraphs have similar attribute profile. Due to the large number of cohesive connected subgraphs and to overcome the overlap among these subgraphs, we propose an algorithm for enumerating a set of representative subgraphs, the set of all closed subgraphs. We propose pruning strategies for efficiently enumerating the search tree without missing any pattern or reporting duplicate subgraphs. On a real protein-protein interaction network with attributes representing the dysregulation profile of genes in multiple cancers, we mine closed cohesive connected subnetworks and show their biological significance. Moreover, we conduct a runtime comparison with existing algorithms to show the efficiency of our proposed algorithm. [ABSTRACT FROM AUTHOR]

This study explores novel ligands that potentially offer superior binding and stability compared to the peptidic molecules currently associated with the ribosomal RNA–protein complex. This study aims to elucidate the molecular mechanisms underlying protein–RNA interactions and their disruptions, identify potential therapeutic targets, and explore novel compounds capable of modulating these interactions for therapeutic benefit. We conducted molecular docking and dynamics simulations using advanced computational tools such as rDock and REINVENT4 to generate novel compounds. ADMET analysis confirmed the chosen compound's advantageous pharmacokinetic attributes and safety profiles. Among the generated compounds, C21, C23, C56, C120, and C195 were identified as the best candidate molecules for inhibiting protein–RNA interactions. These ligands demonstrated superior binding affinity and stability, outperforming the peptidic molecules bound to the reference protein–RNA–peptide complex structure.The ligand molecules were notable for their ability to settle into low–energy states, indicating a strong potential to outperform the peptide bound in the reference protein–RNA–peptide complex structure. These findings highlight the capability of these ligands to serve as more effective therapeutic agents and as superior alternatives to the current peptidic molecules, with implications for developing novel therapeutic strategies targeting protein–RNA interactions. [ABSTRACT FROM AUTHOR]

The hypothalamus is the coordination center of the sheep (Ovis aries) endocrine system and plays an important role in the reproductive processes of sheep. However, the specific mechanism by which the hypothalamus affects sheep reproductive performance remains unclear. In this study, the hypothalamus tissues of high-reproduction small-tailed Han sheep and low-reproduction Wadi sheep were collected, and full-length transcriptome sequencing by Oxford Nanopore Technologies (ONT) was performed to explore the key functional genes associated with sheep fecundity. The differentially expressed genes (DEGs) were screened and enriched using DESeq2 software through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Approximately 41.75 million clean reads were obtained from the hypothalamus tissues of high- and low-reproduction sheep, after quality control, 32,194,872 high-quality full-length sequences and 2,114 DEGs were obtained, including 1,247 upregulated genes and 867 downregulated genes (P adjust < 0.05, |log2FC|>1). Some DEGs were enriched in oocyte meiosis, progesterone-mediated oocyte maturation, estrogen signaling pathway, GnRH signaling pathway and other development-related signaling pathways. The constructed protein-protein interaction (PPI) networks identified the reproduction-related genes, such as GSK3B, PPP2R1B, and PPP2CB. The results of this study will enrich and supplement the genomic information available for small-tailed Han sheep and Wadi sheep, as well as expand the understanding of the molecular mechanisms underlying the regulation of animal reproduction by the hypothalamus, and they also provided reference data for further investigations on the mechanism of high reproduction in sheep. [ABSTRACT FROM AUTHOR]

The identification of individual protein-protein interactions (PPIs) began more than 40 years ago, using protein affinity chromatography and antibody co-immunoprecipitation. As new technologies emerged, analysis of PPIs increased to a genome-wide scale with the introduction of intracellular tagging methods, affinity purification (AP) followed by mass spectrometry (MS), and co-fractionation MS (CF-MS). Now, combining the resulting catalogs of interactions with complementary methods, including crosslinking MS (XL-MS) and cryogenic electron microscopy (cryo-EM), helps distinguish direct interactions from indirect ones within the same or between different protein complexes. These powerful approaches and the promise of artificial intelligence applications like AlphaFold herald a future where PPIs and protein complexes, including energy-driven protein machines, will be understood in exquisite detail, unlocking new insights in the contexts of both basic biology and disease. From identifying individual protein-protein interactions (PPIs) in the 1980s to characterizing whole-cell interactomes more recently, approaches for identifying cellular PPIs have opened the way for understanding how protein complexes and molecular machines operate. These data, coupled with structural and computational techniques, offer functional insights and uncover how interactions are perturbed in pathogenic contexts. [ABSTRACT FROM AUTHOR]

In the rapidly expanding domain of scientific research, tracking and synthesizing information from the rapidly increasing volume of publications pose significant challenges. To address this, we introduce a novel high-throughput pipeline that employs ChatGPT to systematically extract and analyze connectivity information from the full-texts and abstracts of 24,237 and 150,538 research publications concerning Caenorhabditis elegans and Drosophila melanogaster, respectively. This approach has effectively identified 200,219 and 1,194,587 interactions within the C. elegans and Drosophila biomaps, respectively. Utilizing Cytoscape Web, we have developed a searchable online biomaps that link relevant keywords to their corresponding PubMed IDs, thus providing seamless access to an extensive knowledge network encompassing C. elegans and Drosophila. Our work highlights the transformative potential of integrating artificial intelligence with bioinformatics to deepen our understanding of complex biological systems. By revealing the intricate web of relationships among key entities in C. elegans and Drosophila, we offer invaluable insights that promise to propel advancements in genetics, developmental biology, neuroscience, longevity, and beyond. We also provide details and discuss significant nodes within both biomaps, including the insulin/IGF-1 signaling (IIS) and the notch pathways. Our innovative methodology sets a robust foundation for future research aimed at unravelling complex biological networks across diverse organisms. The two databases are available at worm.bio-map.com and drosophila.bio-map.com. [ABSTRACT FROM AUTHOR]

The pathway for synthesis of proline in most forms of life produces a highly unstable intermediate, L- glutamyl 5-phosphate (GP). For nearly 70 y, channeling of this intermediate from the active site of glutamate 5-kinase to the active site of GP reductase has been believed to protect GP from cyclization to a dead-end product. However, the evidence presented in support of this idea is not conclusive. We show that changes in the structures of the kinase or reductase that should preclude a protein-protein interaction do not compromise proline synthesis in Escherichia coli, demonstrating that channeling does not occur. We calculate that the half-life of GP is 320 ms. Although GP is indeed unstable, it should diffuse the length of an E. coli cell in less than 3 ms. Thus, most GP produced by glutamate 5-kinase should encounter the active site of GP reductase before cyclization occurs. [ABSTRACT FROM AUTHOR]

Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a critical threshold. It maintains cell homeostasis by enhancing protein folding, initiating quality control, and activating degradation pathways when damage is irreversible. This response functions as a dynamic signaling network, with proteins as nodes and their interactions as edges. We analyze these protein-protein networks across different organisms to understand their intricate intra-cellular interactions and behaviors. In this work, analyzing twelve organisms, we assess how fundamental measures in network theory can individuate seed proteins and specific pathways across organisms. We employ network robustness to evaluate and compare the strength of the investigated protein-protein interaction networks, and the structural controllability of complex networks to find and compare the sets of driver nodes necessary to control the overall networks. We find that network measures are related to phylogenetics, and advanced network methods can identify main pathways of significance in the complete Unfolded Protein Response mechanism. [ABSTRACT FROM AUTHOR]

Background: High-quality goatskins are valuable byproducts usually produced by indigenous goat breeds with poorer production performance in Asia and Africa. However, the genetic and molecular mechanisms underpinning goatskin's biomechanical properties (e.g., tensile strength) remain elusive. Mechanistic exploration of these traits could greatly aid the genetic improvement and genetic resource conservation of native breeds in these regions. To fulfill this purpose, we collected skin tissues from three goat breeds: Huai goat (HG), a Chinese native variety producing high-quality goatskins; Yudong meat goat (YDMG), a crossbreed of HG and Boer goat; Henan dairy goat (HNDG), a dairy goat breed. Results: Scanning electronic microscopy analysis of skin tissues found that the collagen fiber diameters, collagen fibril diameters, and crimps significantly differed among the three goat breeds; however, collagen fibril diameters are similar in HG and HNDG. A sum of 230, 775, and 86 differentially expressed genes (DEGs) were identified from YDMG versus HNDG, HG versus HNDG, and YDMG versus HG, respectively. Functional enrichment analysis suggested that signaling pathways involved in fatty acid, retinol, steroid metabolisms, and GO items related to the physical properties of the skin (e.g., collagen-containing extracellular matrix) are significantly overrepresented in DEGs identified from meat versus dairy goats. Furthermore, 106 DEGs (e.g., COL1A1, COL1A2, and SPARC) showed specific expression patterns in HG and YDMG versus HNDG. Items about biophysical features of skin (e.g., extracellular matrix organization and ECM proteoglycans) are markedly enriched. Protein-protein interaction analysis suggested that two growth factors (IGF1 and PDGFD) are latent collagen and other ECM protein expression modulators. Conclusion: Ultrastructural analysis of goat skin tissues suggested that collagen fibril diameter is not a major factor affecting goatskin quality. Transcriptomic profiles unveiled core genes and associated biological processes potentially involved in regulating goatskin quality. These discoveries shined new light on deeper understanding the mechanisms of hide-related traits in goat and other livestock. [ABSTRACT FROM AUTHOR]

ABSTRACT Wheat is a crucial food crop, yet its production is continually threatened by abiotic stresses, particularly salt stress. Understanding the molecular mechanisms by which wheat responds to salt stress is essential for developing salt‐tolerant varieties. In this study, we investigated the molecular pathway involving the wheat TaDHN7 in response to salt stress. The overexpression of TaDHN7 enhances salt tolerance and reactive oxygen species (ROS) scavenging in wheat, while the knockout of TaDHN7 significantly impairs salt tolerance. Furthermore, we identified that TaWRKY44 promotes the expression of TaDHN7 by binding to the W‐box within the TaDHN7 promoter. Additionally, TaWRKY17 interacts with TaWRKY44, and this interaction enhances the protein stability of TaWRKY44 under salt stress, thereby enhancing its transcriptional regulatory capacity on TaDHN7. This study elucidates the TaWRKY17‐TaWRKY44‐TaDHN7 pathway in response to salt stress in wheat, providing valuable insights for the development of salt‐tolerant wheat cultivars. [ABSTRACT FROM AUTHOR]

Background: Currently, adequate treatment and prognostic prediction means for Hepatocellular Carcinoma (HCC) haven't entered into medical vision. Tanshinone IIA (TanIIA) is a natural product, which can be utilized as a potential treatment of HCC due to its high anti-tumor activity. However, the effect on HCC prognosis, as well as the potential targets and molecular mechanism of TanIIA still remain ambiguous. Herein, we investigated them via network pharmacology, explored TanIIA-related prognostic genes by machine learning methods, and verified using molecular docking and cell experiments. Methods: Potential TanIIA-targeted genes and HCC-related genes were obtained from the corresponding database. The Protein-Protein Interaction (PPI) network and enrichment analyses of the intersection targets were conducted. Furthermore, a TanIIA-related prognostic model was built and verified. We attempted to explore the expression of the TanIIA-related prognostic genes and evaluate its chemotherapeutic sensitivities and the immune infiltrations. Followed by exploration of anti-tumor activity on the human HCC cells Hep3B and HepG2 cell lines in vitro (CCK-8, flow cytometry and transwell assay), the docking molecular was performed. Ultimately, the corresponding protein expressions were determined by western blotting. Results: A total of 64 intersecting targets were collected. Similarly, GO/KEGG enrichment analysis showed that TanIIA can inhibit HCC by affecting multiple pathways, especially the MAPK signaling pathway. A five-gene signature related to TanIIA was constructed on account of Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression model. Among five genes, ALB, ESR1 and SRC tend to be core genes because of probable status as potential targets for sorafenib. Molecular docking results demonstrated the potential for active interaction between the core genes relevant proteins and TanIIA. Studies in vitro had shown that TanIIA regulated the expressions of Bcl-2, Bax and MMP9 in HCC cells, inhibiting their growth, inducing apoptosis and preventing cell invasion. Additionally, we are able to detect an up-regulated trend in the expression of ALB and ESR1, while a down-regulated in the expression of SRC by TanIIA. Conclusion: Regulating the expression of TanIIA-related gene signatures (ALB, SRC and ESR1), and inhibiting the SRC/MAPK/ERK signaling axis might potentially contribute to the TanIIA treatment of HCC. And the three gene signatures could be identified for predicting the prognosis of HCC, which may provide novel biomarkers for HCC treatment. [ABSTRACT FROM AUTHOR]

The present study intended to divulge the potential role of garlic-derived organosulfur compounds (OSCs) in targeting PCSK-9 and averting its interaction with the EGF-A portion of LDL-R via in-vitro and in-silico analysis. Our in-silico screening data showed that 3-(Propylsulfinyl)-L-alanine (PSA), S-Ethyl-L-cysteine (SEC), alliin, and S-Allyl-L-cysteine (SAC) exhibited higher binding energy (−7.05, −7.00, −6.65, and −6.31 Kcal/mol, respectively) against PCSK-9, among other selected OSCs. Further, the protein-protein interaction study of PCSK-9-OSCs-complex with EGF-A demonstrated a similar binding pattern with E-total values ranging from −430.01 to −405.6 Kcal/mol. These results were further validated via in-vitro analysis which showed that SEC, SAC, and diallyl trisulphide (DAT) exhibited the lowest IC50 values of 4.70, 5.26, and 5.29 µg/mL, respectively. In conclusion, the presented data illustrated that SEC, SAC, and DAT were the best inhibitors of PCSK-9 activity and may have the potential to improve the LDL-R function and lower the circulatory LDL-C level. [ABSTRACT FROM AUTHOR]

Skin wound healing is a complex process which involves multiple molecular events and the underlying mechanism is not fully understood. We presented a comparative transcriptomic analysis of skin wound healing in humans and mice to identify shared molecular mechanisms across species. We analyzed transcriptomes from three distinct stages of the healing process and constructed protein-protein interaction networks to elucidate commonalities in the healing process. A substantial number of differentially expressed genes (DEGs) were identified in human transcriptomes, particularly upregulated genes before and after wound injury, and enriched in processes related to extracellular matrix organization and leukocyte migration. Similarly, the mouse transcriptome revealed thousands of DEGs, with shared biological processes and enriched KEGG pathways, highlighting a conserved molecular signature in skin wound healing. A total of 21 common DEGs were found across human comparisons, and 591 in mouse comparisons, with four genes (KRT2, MARCKSL1, MMP1, and TNC) consistently differentially expressed in both species, suggesting critical roles in mammalian skin wound healing. The expression trends of these genes were consistent, indicating their potential as therapeutic targets. The molecular network analysis identified five subnetworks associated with collagen synthesis, immunity, cell-cell adhesion, and extracellular matrix, with hub genes such as COL4A1, TLR7, TJP3, MMP13, and HIF1A exhibited significant expression changes before and after wound injury in humans and mice. In conclusion, our study provided a detailed molecular network for understanding the healing process in humans and mice, revealing conserved mechanisms that could help the development of targeted therapies across species. [ABSTRACT FROM AUTHOR]

Type 2 innate lymphoid cells (ILC2s) have emerged as pivotal regulators in the pathogenesis of diseases, with their roles in inflammation, metabolism, and tissue homeostasis becoming increasingly recognized. This review provides an overview of the current understanding of ILC2s in inflammation and metabolic disorders, including their functional contributions. Moreover, we will discuss how these cells adapt their metabolic processes to support their function and survival and how their metabolic requirements change under different physiological and pathological conditions. Lastly, we will review recent omics studies that have provided insights into the molecular and cellular characteristics of ILC2s. This includes transcriptomic, proteomic, and metabolomic analyses that have elucidated the gene expression profiles, protein interactions, and metabolic networks, respectively, associated with ILC2s. These studies have advanced our understanding of the functional diversity of ILC2s and their involvement in metabolic disease. [ABSTRACT FROM AUTHOR]

Background: Rheumatoid arthritis (RA), a chronic autoimmune condition, is characterized by persistent synovial inflammation, bone degradation, and progressive joint deterioration. Despite considerable research efforts, the precise molecular mechanism underlying RA remains elusive. This investigation aims to elucidate the potential role and molecular mechanism of N6-methyladenosine (m6A) methylation regulators in the pathogenesis of RA. Methods: In this study, we employed bioinformatics tools to elucidate the association between RA and m6A modifications, aiming to identify potential biological markers. We extracted datasets GSE12021, GSE55235, and GSE55457 from the Gene Expression Omnibus (GEO) database for comprehensive analysis. Utilizing differential expression analysis, protein-protein interaction (PPI) analysis, and single-cell sequencing techniques, we identified pivotal hub genes implicated in the pathogenesis of RA. Subsequently, we assessed the correlation between these hub genes and the pathogenesis of RA using Gene Set Enrichment Analysis (GSEA). Both in vivo and in vitro experiments were performed to confirm the expression and functional roles of the identified key hub gene in RA. Results: Differential expression analysis, PPI analysis, and single-cell analysis identified three key hub genes (YTHDC1, YTHDC2, and YTHDF2) associated with RA. GSEA results further revealed that these genes are enriched in pathways associated with inflammatory responses. Subsequent correlation analysis demonstrated a significant negative correlation between YTHDC1 expression and CD8+ T cell levels. Notably, the gene and protein expression levels of YTHDC1 and YTHDF2 were significantly reduced in the synovial tissue of RA patients. Furthermore, silencing YTHDC1 in fibroblast-like synoviocytes (FLSs) significantly inhibited their migration, invasion, proliferation, and induced apoptosis. Conclusion: YTHDC1 may potentially be involved in the pathogenesis of RA through its regulation of migration, invasion, proliferation, and apoptosis in FLSs. [ABSTRACT FROM AUTHOR]