Search Results (477)

Reversible protein phosphorylation is an important regulatory mechanism in cellular signalling and disease, regulated by the opposing actions of kinases and phosphatases. Modern computer methods predict kinase–substrate or phosphatase–substrate interactions in isolation and lack specificity for biological conditions, neglecting triadic regulation. We present SPINET-KSP, a multi-modal LLM–Graph foundation model engineered for the prediction of kinase–substrate–phosphatase (KSP) triads with contextual awareness. SPINET-KSP integrates high-confidence interactomes (SIGNOR, BioGRID, STRING), structural contacts obtained from AlphaFold3, ESM-3 sequence embeddings, and a 512-dimensional cell-state manifold with 1612 quantitative phosphoproteomic conditions. A heterogeneous KSP graph is examined utilising a cross-attention Graphormer with Reversible Triad Attention to mimic kinase–phosphatase antagonism. SPINET-KSP, pre-trained on 3.41 million validated phospho-sites utilising masked phosphorylation modelling and contrastive cell-state learning, achieves an AUROC of 0.852 for kinase-family classification (sensitivity 0.821, specificity 0.834, MCC 0.655) and a Pearson correlation coefficient of 0.712 for phospho-occupancy prediction. In distinct 2025 mass spectrometry datasets, it identifies 72% of acknowledged cancer-resistance triads within the top 10 rankings and uncovers 247 supplementary triads validated using orthogonal proteomics. SPINET-KSP is the first foundational model for simulating context-dependent reversible phosphorylation, enabling the targeting of dysregulated kinase-phosphatase pathways in diseases. Full article

The huge number of possible permutations of genes, proteins and small molecules make the random emergence of cellular networks problematic. How, therefore, do interactomes come into existence? What selects for their stability and functionality? I hypothesize that interactomes originate from molecularly complementary modules (MCMs) that are selected for stability and retain their interactivity when mixed and matched with other such modules to create novel molecules and complexes displaying emergent properties not present in the individual components of the network. Because evolution can only proceed by working upon existing variants, and these variants emerge from selection of MCMs, the resulting systems must exhibit the characteristics of pleiofunctional, epistatic interactomes (PEIs). The resulting systems should display “molecular paleontology”, providing clues as to the historical process by which these MCMs were incorporated into the system. The MCM mechanism of PEI evolution is illustrated here by two case studies. The first concerns the prebiotic emergence of the glutathione–ascorbate anti-oxidant system and its later incorporation into regulation of glucose transport and catecholamine receptor activity. The second concerns the MCM evolution of the ribosome as, perhaps, the first PEI, and its role as a module for the later construction of the first cellular genomes. Full article

Protein complexes, assembled by scaffold proteins, act as molecular machines driving development. The mechanosensitive adapter protein Zyxin is a key example, integrating actin cytoskeleton dynamics with gene expression. However, the developmental regulation of its interactions and post-translational modifications remains poorly understood. Here, we characterize the dynamic Zyxin interactome across three early developmental stages of Xenopus laevis (from gastrulation to neurulation) using co-immunoprecipitation coupled with quantitative mass spectrometry (DDA and DIA). We identify stage-specific changes in Zyxin’s association with core focal adhesion components, transcriptional regulators and kinases. Furthermore, we uncover developmentally regulated phosphorylation events on isoforms, suggesting dynamic post-translational control of its interactions. Our work provides a comprehensive resource that positions Zyxin as a central orchestrator of cell adhesion, survival, and gene regulatory programs during morphogenesis. These findings underscore the role of Zyxin as a multifaceted regulatory hub, with important implications for understanding tissue homeostasis and related pathologies. Full article

Over the past decade, research on urolithins has expanded significantly due to their role as mediators between polyphenol-rich diets and human health. Understanding the relationships between ellagitannin intake, gut microbiota composition, and urolithin production is essential for evaluating their biological effects and nutraceutical potential. The primary objective of this review is to critically summarise current knowledge on urolithins, bioactive metabolites derived from ellagitannins in plant-based foods, with a focus on their biosynthesis, bioavailability, protein interactions, and potential therapeutic applications. A comprehensive literature search was conducted using PubMed, Scopus, and Google Scholar to identify studies on urolithin biosynthesis, absorption, transport mechanisms, protein binding, and incorporation into extracellular vesicles. Relevant articles were critically analysed to synthesise current evidence and highlight emerging concepts. Key findings indicate that after absorption, urolithins bind to serum albumin, which facilitates their transport to target tissues, exerting anti-inflammatory and antioxidant actions. Recent evidence also shows that urolithins can be packaged into extracellular vesicles, suggesting novel mechanisms for intracellular transport and potential therapeutic applications. This review highlights gaps in current knowledge and proposes directions for future research to optimise their therapeutic potential. Full article

Marine flora is a significant source of bioactive metabolites. These compounds have been demonstrated to have outstanding bioactivity and biocompatibility, enabling their use in various therapeutic applications. Therefore, examining the biological potential of marine natural compounds remains important, with particular emphasis on their interaction profiles to identify the macromolecular partners they can modulate. This study focused on the interactome profiling of the marine alkaloid caulerpin (CAU), isolated from the alga Caulerpa cylindracea. Along with the discovery of its antitumor properties, this metabolite has garnered attention for its potential therapeutic applications, including modulation of MAO-B and PPARs involved in inflammatory responses, as well as the discovery of its antitumor properties. Two complementary MS-based proteomic approaches were used to identify CAU target proteins in cancer cells: DARTS, which enabled proteome-wide screening to identify proteins interacting with the compound, and t-LIP-MRM-MS, which pinpointed the target protein regions involved in ligand binding. RUVB-like 1 (RUVBL1), a protein that regulates the essential mechanism of carcinogenesis, including chromatin remodeling, DNA repair, and transcriptional control, was discovered as an intriguing CAU target. These results were corroborated via in silico and biological investigations that elucidated CAU role in the regulation of RUVBL1 activity, highlighting its promising therapeutic relevance. Full article

Recent advances in sequencing technologies have highlighted long non-coding RNAs (lncRNAs) as key regulators that perform essential biological functions without encoding proteins. Despite growing interest, the molecular mechanisms of most lncRNAs remain poorly understood, with only a few characterized in detail. A promising strategy to elucidate these mechanisms is to explore their structure–function relationships. Such studies require advanced biophysical and biochemical methods due to the large size and structural complexity of lncRNAs. Equally important is the analysis of lncRNA interactomes, which reveal how lncRNAs engage RNA-binding proteins and other biomolecules to drive conformational and functional changes underlying diverse biological pathways. Ultimately, integrative approaches combining structural and interactome analyses will yield deeper insight into lncRNA function and uncover new therapeutic opportunities. This review highlights recent advances in elucidating lncRNA structure–function relationships by integrating biophysical, biochemical, and sequencing-based approaches to overcome challenges of size and heterogeneity, identify functional binding partners, and inform therapeutic target development. Full article

N6-methyladenosine (m⁶A) constitutes the most prevalent nucleotide modification within eukaryotic messenger RNA (mRNA). Variations in m⁶A levels are associated with numerous human diseases and health conditions, including various forms of cancer, diabetes, neurological disorders, male infertility, and obesity. Nevertheless, the molecular mechanisms underpinning the recognition of m⁶A by different ‘reader’ proteins remain incompletely elucidated. In this study, we used phage display to identify key sequence features that methyl readers recognize in m⁶A. This study shows that m⁶A modifications affect the mRNA interactome. A peptide motif recognizing m⁶A in DRACH sequences suggests a common recognition mechanism, though proteins may use different methods to detect m⁶A in less accessible areas. The sequence of the hnRNP A1 RRM domain that aligns with the newly discovered m⁶A-binding peptide, m1p1, is crucial for the binding of m⁶A-modified RNAs, indicating a strong link between the m1p1 sequence and m⁶A recognition, which is key for recognizing m⁶A-modified, unstructured RNAs. Gaining a comprehensive understanding of the evolutionary influence of m⁶A on its reader proteins may facilitate the identification of additional m⁶A readers. These signature peptides could enhance theranostic approaches across cancers, enabling more targeted therapies. Full article

Long Terminal Repeat (LTR) retrotransposons (LTR-RTEs) comprise up to 90% of some plant genomes and drive genome diversification through their amplification. Novel insertions arise during the final stages of the LTR-RTE life cycle, which depends on both LTR-RTE-encoded proteins and host cellular factors. The LTR-RTE elements require host transcriptional machinery for RNA production, followed by nuclear processing/export, translation, virus-like particle assembly, reverse transcription, and genomic integration. This review addresses the following question: What host proteins promote LTR-RTE transposition in plants? Our analysis of recent literature on host factors and cellular compartments implicated in the retrotransposition cycle reveals the extensive integration of LTR-RTEs into host processes. Nonetheless, the precise mechanisms remain poorly resolved, especially in plants with their rich repertoire of LTR-RTEs. We propose integrating plant mobilomics with transposition reporters, genome editing, synthetic biology, and interactomics to elucidate plant-specific mechanisms. Full article

Background: Climate change, urbanization, and global mobility increase the risk of emerging infectious diseases with pandemic potential. There is a need for rapid methods that can assess their long-term effects on human health. In silico approaches are particularly suited to study processes that may manifest years later, under the assumption that perturbed biomolecular interactions underlie these outcomes. Here we focus on viral oncogenicity—the ability of viruses to increase cancer risk—which accounts for about 15% of global cancer cases. Methods: We characterize viruses through multilayer representations of protein–protein interaction (PPI) networks reconstructed from the human interactome. Statistical analyses of topological features, combined with interpretable machine learning models, are used to distinguish oncogenic from non-oncogenic viruses and to identify proteins with potential central role in these processes. Results: Our analysis reveals clear statistical differences between the network properties of oncogenic and non-oncogenic viruses. Furthermore, the machine learning approach enables classification of virus–host interaction networks and identification of relevant subsets of proteins associated with oncogenesis. Functional enrichment analysis highlights mechanisms related to viral oncogenicity, including chromatin structure and other processes linked to cancer development. Conclusions: This framework enables virus classification and highlights mechanisms underlying viral oncogenicity, providing a foundation for investigating long-term health effects of emerging pathogens. Full article

Porcine reproductive and respiratory syndrome virus (PRRSV) nonstructural protein 9 (NSP9), the viral RNA-dependent RNA polymerase (RdRp), is essential for viral replication but its comprehensive host interactome remains uncharacterized. This study employed co-immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to systematically identify NSP9-associated host proteins. We identified 222 high-confidence host interactors, with Gene Ontology and KEGG pathway analyses revealing significant enrichment in RNA/DNA-binding proteins, ubiquitin-proteasome pathways, metabolic regulators (amino acid/lipid biosynthesis), endoplasmic reticulum processing, and cell cycle components. Protein-protein interaction network analysis further delineated six functional modules involved in RNA processing, vesicular transport, and innate immunity. Crucially, validation studies confirmed direct binding between NSP9 and key candidates (CAPZ1, PSMA3, CDK1, USP48). Functional assessment demonstrated that CDK1 overexpression significantly inhibited PRRSV replication, implicating CDK1 as a host restriction factor. These findings collectively unveil the multifaceted role of NSP9 in subverting host machinery while identifying novel host defense mechanisms and potential targets for antiviral development against PRRSV. Full article

Ischemic stroke remains one of the leading causes of disability and mortality worldwide, and effective therapeutic options are still limited. Therefore, this study aimed to evaluate the neuroprotective effect of the aqueous extract of Bacopa procumbens (B. procumbens) in a murine model of ischemia/reperfusion induced by middle cerebral artery occlusion (MCAO). This widely used model is generated by the transient intraluminal insertion of a nylon filament through the external carotid artery to occlude the middle cerebral artery, allowing controlled induction and subsequent reperfusion. Wistar rats underwent 2 h MCAO, followed by tail vein administration of B. procumbens extract (40 mg/kg) or Edaravone (0.45 mg/kg) before reperfusion. Neurological, histological, and molecular parameters were assessed 48 h later. Additionally, in silico analyses were performed to predict the antioxidant activity of the extract’s major metabolites and to explore Nrf2-related signaling. B. procumbens treatment improved neurological condition, reduced the volume of the infarct lesion, increased the expression and activation of Akt and Nrf2, reduced lipid peroxidation (4-HNE), and downregulated AQP4, the main water channel involved in cerebral edema formation. These molecular effects were associated with enhanced neuronal survival and collectively resulted in significant neuroprotection in the MCAO model. In silico analysis identified key metabolites with high antioxidant potential through free radical scavenging, lipid peroxidation inhibition, and redox enzyme modulation. Nrf2-centered interactome analysis revealed eighty-two proteins linked to ischemia, neuroinflammation, neuronal death regulation, and oxidative stress response. These findings support the therapeutic potential of B. procumbens metabolites as neuroprotective agents against ischemic cerebral injury. Full article

African swine fever virus (ASFV) causes a highly fatal disease in domestic pigs, resulting in substantial economic losses to the global swine industry. Vaccine development continues to be hindered by limited characterization of viral proteins and their functional redundancies. In this study, we employ combined experimental and computational approaches to characterize the ASFV I73R protein (pI73R), which contains a Z-DNA binding domain and plays a critical role in ASFV virulence and pathogenesis. We demonstrate that pI73R shares significant structural similarity with transcription factors of the forkhead box (FOX) protein family. Overexpression of pI73R results in downregulation of Crooked neck-like protein 1 (CRNKL1), a core spliceosome component, suggesting a potential mechanism by which pI73R modulates host protein synthesis. Using high-resolution mass spectrometry, we map the pI73R interactome and identify the host protein Guanine nucleotide-binding protein subunit beta-1 (GNB1) as a novel direct interactor of pI73R which may facilitate its nuclear transport. Furthermore, we show that pI73R exhibits consistent oligomerization and expression across different ASFV genotypes, highlighting its functional importance. Taken together, these results provide new insights into pI73R function, ASFV–host dynamics, and offer promising directions for antiviral strategy development. Full article

The 26S proteasome is the main proteolytic machinery involved in protein degradation, thereby contributing to the homeostasis and stress response of eukaryotic cells. This macromolecular complex consists of a 20S core particle assembled with one or two 19S regulatory particles. Here, we describe the Plasmodium berghei (Pb) proteasome AAA-ATPase regulatory subunit Rpt3 and demonstrate its binding to the Protein Phosphatase 1 catalytic subunit (PP1c), which is one of the major and essential parasite phosphatases. The PbRpt3 protein enhances the activity of PP1c both in vitro and in a Xenopus oocyte heterologous model. Further investigation of this model suggests that the PbRpt3-PP1c interaction may occur outside of the proteasome, and it reveals that the RVxF motifs of PbRpt3 are involved in its binding and regulatory function. Moreover, the ATP-binding capacity of PbRpt3 may also contribute to its phosphatase regulatory activity. In the parasite, reverse genetic studies suggest an essential role for PbRpt3 during erythrocytic cycle of P. berghei, and an interactome analysis confirmed that PbRpt3 belongs to the 19S regulatory particle of the proteasome and may interact with proteins previously shown to be involved in phospholipid binding. Full article

C-reactive protein (CRP) is a well-known acute phase reactant and putative biomarker for advancing and chronically established inflammation. Its biological activity across its multiple isoforms plays various roles in the initiation, potentiation, and resolution of inflammation. Its molecular signaling within the tissue microenvironment regulates cell–cell communication across cell types (e.g., epithelial cells, endothelial cells, fibroblasts, adipocytes, and immune cells) and affects the development of conditions such as cancer that are subject, at least in part, to inflammatory signaling. Considering the dynamic nature of CRP in modulating disease progression, and the growing evidence of the context-dependent direct molecular activity of CRP on regulating intra- and inter-cellular signaling, it is critical to further understand how this integral molecule alters cell signaling pathways. Although the ability of CRP to directly interact with some extracellular matrix proteins involved with inflammation and disease has been reported as early as the mid-1980s, recent advances in unbiased proteomics have revealed a broader interactome of protein–protein interactions (PPIs) involving CRP. The present study evaluates the CRP PPIs identified to date and explores the potential novel regulatory capacity of CRP on multiple key cellular functions in metabolism and cell–cell signaling, offering an updated framework of the possible biological activities of CRP relevant to tumorigenic processes. Full article