Search Results (782)

Valine-glutamine motif proteins (VQ), plant-specific transcriptional co-regulators harboring the conserved FxxhVQxhTG motif, play pivotal roles in coordinating plant stress adaptation through dynamic interactions with WRKY transcription factors (WRKY), mitogen-activated protein kinases (MAPKs) cascades, and hormone signaling pathways. Evolutionary analyses reveal the characteristics of their evolutionary protection and ancient origin, with lineage-specific expansion via genome duplication events. Structurally, compact genes lacking introns and the presence of intrinsic disordered regions (IDRs) facilitate rapid stress responses and versatile protein interactions. Functionally, VQ proteins orchestrate abiotic stress tolerance (e.g., drought, salinity, temperature extremes) by modulating reactive oxygen species (ROS) homeostasis, osmotic balance, and abscisic acid/salicylic acid (ABA/SA)-mediated signaling. Concurrently, they enhance biotic stress resistance via pathogen-responsive WRKY-VQ modules that regulate defense gene expression and hormone crosstalk. Despite advances, challenges persist in deciphering post-translational modifications, tissue-specific functions, and cross-stress integration mechanisms. Harnessing CRISPR-based editing and multi-omics approaches will accelerate the exploitation of VQ genes for developing climate-resilient crops. This review synthesizes the molecular architecture, evolutionary dynamics, and multifunctional regulatory networks of VQ proteins, providing a roadmap for their utilization in sustainable agriculture. Full article

Intrinsically disordered proteins (IDPs), such as the Alzheimer’s-associated tau protein, pose challenges for conventional drug discovery. This study applied the Informational Spectrum Method for Small Molecules (ISM-SM), a computational technique utilizing electron–ion interaction potentials (EIIPs), to identify potential tau modulators. Characteristic interaction frequencies derived from known ligands and conserved mammalian tau sequences were used to screen DrugBank and the COCONUT natural product database. The screening identified approved drugs previously reported to indirectly influence tau pathology or Alzheimer’s disease pathways, alongside natural products including Bryostatin-14, which is known to modulate kinases involved in tau phosphorylation. These findings suggest that ISM-SM can serve as an in silico tool to identify candidate small molecules, including repurposed drugs and natural products, with potential relevance to tau function and pathology, complementing other IDP drug discovery strategies. Full article

Ataxin-2 (Atx2) is a general RNA-binding protein involved in processes such as RNA processing and metabolism in cells. Atx2 is also a polyglutamine (polyQ) tract-containing protein; its abnormal expansion can lead to protein aggregation associated with neurodegenerative diseases. Previous studies have shown that the C-terminal intrinsically disordered regions (c-IDRs) of Atx2 participate in its condensation and aggregation processes. To elucidate the role of polyQ expansion in biomolecular condensation and aggregation, we studied the N-terminal fragments of Atx2 (namely, Atx2-N317 and Atx2-N81) that preserve a polyQ tract and compared their molecular behaviors in cells to those of the full-length Atx2. We found that the molecular mobility of the N-terminal fragments decreases with the increasing length of polyQ, indicating that polyQ expansion promotes a gradual phase transition to an irreversible and insoluble state. Moreover, the molecular state and mobility of Atx2-N317 are not distinct from those of Atx2-N81, regardless of the presence of other domains, demonstrating that the polyQ tract is a direct and sufficient element for protein condensation and aggregation, while the Like Sm (LSm) and LSm-associated (LSmAD) domains and their interactions with RNA are not necessary for these processes. This result is also validated through the in vitro investigation of Atx2-N81 with different polyQ expansions. This study reveals that polyQ expansion controls the biomolecular condensation and aggregation of the N-terminal fragments of Atx2 and is thus thought to modulate the dynamic behaviors of the full-length protein as well, which is implicated in the pathological accumulation of Atx2 in cells. Full article

Eukaryotic phosphorylation of serine and threonine residues is a central regulatory mechanism in cell signalling, carried out by more than 500 kinases and a diverse array of phosphatases. Traditionally understood as a two-component system driven by writers (kinases) and erasers (phosphatases), this regulatory network is now appreciated to involve additional proteins that modulate or interpret phosphorylation-dependent changes. Among them, the 14-3-3 protein family has emerged as a prominent example due to its ability to bind phosphorylated serine/threonine motifs—typically located within intrinsically disordered regions—and influence the activity, stability, or localization of its partners. In this review, we discuss the importance, evolution, structure, and dynamics of 14-3-3 proteins, as well as their interactions with small molecules—both natural and designed—that bind to them. We highlight several underexplored aspects of their molecular behaviour, integrate recent discoveries, and emphasize how these insights contribute to a broader understanding of phosphorylation-dependent regulation across eukaryotes. Full article

Background: Abiotic stresses, such as drought, salinity, temperature fluctuations, waterlogging, and heavy metal contamination, have a detrimental impact on plants, leading to reduced global agricultural productivity. The accumulation of cadmium (Cd) and arsenic (As) in agricultural soil, resulting from both natural and anthropogenic activities, poses significant threats to crop production and food safety. Dehydrins, also known as Group II Late Embryogenesis Abundant (LEA) proteins, are intrinsically disordered proteins that play crucial roles in protecting cellular structures during abiotic stress conditions. These proteins are considered promising candidates for enhancing plant tolerance to environmental stresses through their membrane-stabilizing and protective functions. Methods: This study evaluated the tolerance of Arabidopsis transgenic lines expressing a bacterial dehydrin gene (BG757) to Cd and As stresses using various physiological and biochemical parameters. Results: Compared with the wild-type (WT) control, the transgenic line (35S::BG757-1/Col-0) displayed significant increases in root and shoot growth upon exposure to Cd and As. Furthermore, transgenic plants exposed to heavy metal stress exhibited higher concentrations of chlorophyll, total protein, free proline, total flavonoid, and total phenolic content compared to WT plants. Likewise, transgenic plants showed higher 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and retained higher relative water content under stress conditions. Conclusions: Taken together, these findings suggest that bacterial dehydrins confer enhanced tolerance to heavy metal stress in transgenic Arabidopsis plants, highlighting their potential application in developing stress-resilient crops for contaminated environments. Full article

Late Embryogenesis Abundant (LEA) proteins play vital roles in plant responses to abiotic stress and developmental regulation. Pineapple (Ananas comosus L.) is a major tropical fruit crop with high economic value, but its production is often threatened by cold stress, particularly in regions at the northern margin of its cultivation. Despite the recognized importance of LEA proteins in stress adaptation, their genomic landscape and functional characteristics in pineapple remain largely unexplored. In this study, 37 AcLEA genes were identified in the pineapple (Ananas comosus L.) genome and classified into six subfamilies, with LEA_2 being the largest. Most AcLEA proteins were predicted to be hydrophilic, thermally stable, and intrinsically disordered, consistent with typical LEA protein characteristics. Phylogenetic and collinearity analyses revealed species-specific expansion patterns, primarily driven by segmental duplication events. Most duplicated gene pairs shared similar exon–intron structures, motif compositions, and expression profiles, although several displayed signs of functional divergence based on distinct expression patterns, Ka/Ks ratios > 1, and motif differences. Promoter cis-element, transcription factor, and miRNA network predictions indicated that AcLEA genes are widely involved in stress responses as well as growth and development. Expression profiling showed that many AcLEA genes including AcLEA32, AcLEA7, AcLEA9, AcLEA30, AcLEA29, AcLEA33, and AcLEA18 were significantly upregulated under cold stress and declined upon stress removal, indicating a potential role in cold tolerance. Some AcLEA genes, such as AcLEA32 and AcLEA33, showed faster and stronger induction under cold stress in the cold-tolerant cultivar “Comte de Paris” (BL) compared to the sensitive cultivar “Tainong No. 20” (NN), suggesting that differential gene responsiveness may contribute to cultivar-specific cold tolerance. Additionally, most AcLEA genes exhibited distinct spatiotemporal expression patterns across floral organs and fruit at various developmental stages, suggesting their involvement in reproductive development. These findings provide a foundation for future functional studies and highlight candidate genes for improving cold resilience and developmental traits in pineapple through molecular breeding. Full article

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has already been described for members of the p47^phox-related protein family, individual cases have never been collected and analyzed collectively, which precluded the definition of the binding preferences and targeted discovery of further instances. Here, we apply an integrative approach that includes data collection, curation, bioinformatics analyses and state-of-the-art structure prediction methods to fill these gaps. A search of the human proteome with the sequence signatures of SH3 tandemization and follow-up structure analyses suggest that SH3 tandemization could be specific for this family. We define the optimal binding preference of tandemly arranged SH3 domains as [PAVIL]PPR[PR][^DE][^DE] and propose potential new instances of this SLiM among the family members and their binding partners. Structure predictions suggest the possibility of a novel, reverse binding mode for certain motif instances. In all, our comprehensive analysis of this unique SH3 binding mode enabled the identification of novel, interesting tandem SH3-binding motif candidates with potential therapeutic relevance. Full article

Type-P5 ATPases are the least characterized among the P-type ATPases and this is especially true in the case of the malaria parasite. In this study, Spf1, a subtype-P5A ATPase of yeast, and ATP13A2, a subtype-P5B ATPase of humans, were used as templates to extensively characterize the sequences and structural features of haemosporidian type-P5 ATPases. Malaria parasites have both subtype-P5A and subtype-P5B ATPase genes and the structural features of the proteins recapitulate the known structures of subtype-P5A and subtype-P5B ATPases. Detailed structural analysis detected an additional α-helix in the P-domain of subtype-P5A ATPases, which is not found in subtype-P5B ATPases. This feature may be an additional signature to distinguish subtype-P5A and subtype-P5B ATPases, in addition to the previously described differences in the membrane loops of the N-terminal domain, the arm in the P-domain of subtype-P5A, and substrate differences. A notable difference in the type-P5 ATPases from the malaria parasite, as compared to the templates, is the insertion of multiple variable and low-complexity regions that form intrinsically disorganized loops. These loops may form a shroud-like structure that protects the core ATPase structure and/or participates in low-affinity interprotein interactions. Homology modeling did not provide definitive answers about the substrate specificity of the haemosporidian type-P5 ATPases. However, the haemosporidian subtype-P5A ATPase is likely an ER transmembrane dislocase as are the other subtype-P5A ATPases. In contrast, the subtype-P5B ATPases of the malaria parasite are not likely to be polyamine transporters in lysosomes, as have been described in fungi and metazoans. This suggests that subtype-P5B ATPases have undergone lineage-specific divergence in regard to their function(s). Full article

We report the implementation of replica-averaged molecular dynamics in the UNRES coarse-grained model of polypeptide chains, with application to the restraints determined by nuclear magnetic resonance. The analytical ESCASA algorithm is used to estimate interproton distances from coarse-grained geometry. With synthetic restraints derived from two selected conformations of the L129–L153 loop of the Slr1183 protein from Synechocystis sp. (2KW5), the replica-averaged extension of UNRES retrieved the ensemble of conformations close to the parent structures, with residual content of those not similar to any of them, and comparable populations of both families. Tests with a small putatively multistate protein (PDB: 2LWA) and two proteins with disordered regions (2KW5 and 2KZN, respectively) run in multiplexed temperature replica exchange mode with replica averaging resulted in conformational ensembles that had fewer distance-restraint violations than those deposited in the Protein Data Bank. The ensembles obtained with replica averaging also had fewer distance-restraint violations than those obtained in our previous work, in which time-averaged restraints were implemented. The upgraded UNRES can be used in data-assisted simulations of multistate and intrinsically-disordered proteins and proteins with intrinsically disordered regions. Full article

Aggregates of misfolded α-synuclein proteins are key markers of Parkinson’s disease. The protein α-synuclein (aSyn) is an intrinsically disordered protein (IDP) and therefore lacks a single stable 3D structure, instead sampling multiple conformations in solution. It is primarily located in presynaptic terminals and is thought to help regulate synaptic vesicle trafficking and neurotransmitter release. ASyn proteins have three domains: an N-terminal domain, a hydrophobic non-amyloid-β component (NAC) core implicated in aggregation, and a proline-rich C-terminal domain. Asyn proteins with truncated C-terminal domains are known to be prone to aggregation and suggest that understanding domain–domain interactions in aSyn monomers could help elucidate the role of the flanking domains in modulating protein structure. To this end, we used Gaussian accelerated molecular dynamics (GAMD) to simulate wild-type (WT), N-terminal truncated (ΔN), C-terminal truncated (ΔC), and isolated NAC domain (isoNAC) aSyn protein variants. Using clustering and contact analysis, we found that removal of the N-terminal domain led to increased contacts between NAC and C-terminal domains and the formation of inter-domain β-sheets. Removal of either flanking domain also resulted in increased compactness of every domain. We also found that the contacts between flanking domains in the WT protein result in an electrostatic potential (ESP) that may lead to favorable interactions with anionic lipid membranes. Removal of the C-terminal domain disrupts the ESP in a way that could result in over-stabilized protein–membrane interactions. These results suggest that cooperation between the flanking domains may modulate the protein’s structure in a way that helps maintain elongation and creates an ESP that may aid favorable interactions with the membrane. Full article

Low-complexity domains (LCDs) are protein regions characterized by a simple amino acid composition and low sequence complexity, as they are typically composed of repeats or a limited set of a few amino acids. Historically dismissed as “garbage sequences”, these regions are now acknowledged as critical functional elements. This review systematically explores the structural characteristics, biological functions, pathological roles, and research methodologies associated with LCDs. Structurally, LCDs are marked by intrinsic disorder and conformational dynamics, with their amino acid composition (e.g., G/Y-rich, Q-rich, S/R-rich, P-rich) dictating structural tendencies (e.g., β-sheet formation, phase separation ability). Functionally, LCDs mediate protein–protein interactions, drive liquid–liquid phase separation (LLPS) to form biomolecular condensates, and play roles in signal transduction, transcriptional regulation, cytoskeletal organization, and nuclear pore transportation. Pathologically, LCD dysfunction—such as aberrant phase separation or aggregation—is implicated in neurodegenerative diseases (e.g., ALS, AD), cancer (e.g., Ewing sarcoma), and prion diseases. We also summarize the methodological advances in LCD research, including biochemical (CD, NMR), structural (cryo-EM, HDX-MS), cellular (fluorescence microscopy), and computational (MD simulations, AI prediction) approaches. Finally, we highlight current challenges (e.g., structural heterogeneity, causal ambiguity of phase separation) and future directions (e.g., single-molecule techniques, AI-driven LCD design, targeted therapies). This review provides a comprehensive perspective on LCDs, illuminating their pivotal roles in cellular physiology and disease, and offering insights for future research and therapeutic development. Full article

Alzheimer’s disease is driven by multiple molecular drivers, including the pathological behavior of two intrinsically disordered proteins, amyloid-β (Aβ) and tau, whose aggregation is regulated by sequence-encoded ensembles and liquid–liquid phase separation (LLPS). This review integrates recent advances in biophysics, structural biology, and computational modeling to provide a multiscale perspective on how sequence determinants, post-translational modifications, and protein dynamics regulate the conformational landscapes of Aβ and tau. We discuss sequence-to-ensemble principles, from charge patterning and aromatic binders to familial mutations that reprogram structural ensembles and modulate LLPS. Structural studies, including NMR, SAXS, cryo-EM, and cryo-electron tomography, trace transitions from disordered monomers to fibrils and tissue-level structures. We highlight experimental challenges in LLPS assays, emerging standards for reproducibility, e.g., LLPSDB, PhaSePro, and FUS benchmarks, and computational strategies to refine and condensate modeling. Finally, we explore the therapeutic implications, including condensate-aware medicinal chemistry, ensemble-driven docking, and novel insights from clinical trials of anti-Aβ antibodies. Together, these perspectives underscore a paradigm shift toward environment- and ensemble-aware therapeutic design for Alzheimer’s and related protein condensation disorders. Full article

Neuronal membrane capacitance (Cm) has traditionally been viewed as a static biophysical property determined solely by the geometric and dielectric characteristics of the lipid bilayer. Recent discoveries have fundamentally challenged this perspective, revealing that Cm exhibits robust circadian oscillations that profoundly influence neural computation and behavior. These rhythmic fluctuations in membrane capacitance are orchestrated by intrinsic cellular clocks through coordinated regulation of molecular processes including transcriptional control of membrane proteins, lipid metabolism, ion channel trafficking, and glial-mediated extracellular matrix remodeling. The dynamic modulation of Cm directly impacts the membrane time constant (τm = RmCm), thereby altering synaptic integration windows, action potential dynamics, and network synchronization across the 24 h cycle. At the computational level, circadian Cm oscillations enable neurons to shift between temporal summation and coincidence detection modes, optimizing information processing according to behavioral demands throughout the day–night cycle. These biophysical rhythms influence critical aspects of cognition including memory consolidation, attention, working memory, and sensory processing. Disruptions in normal Cm rhythmicity are increasingly implicated in neuropsychiatric and neurodegenerative disorders, including depression, schizophrenia, Alzheimer’s disease, and epilepsy, where altered membrane dynamics compromise neural circuit stability and information transfer. The integration of circadian biophysics with chronomedicine offers promising therapeutic avenues, including chronotherapeutic strategies that target membrane properties, personalized interventions based on individual chronotypes, and environmental modifications that restore healthy biophysical rhythms. This review synthesizes evidence from molecular chronobiology, cellular electrophysiology, and systems neuroscience to establish circadian Cm regulation as a fundamental mechanism linking molecular timekeeping to neural computation and behavior. Full article

The occurrence and impact of cellular senescence on skin aging and hyperpigmentation is an ongoing area of exploration, encompassing both intrinsic and extrinsic stressors. Traditionally, research has focused on melanocyte and fibroblast senescence due to their slower turnover compared to keratinocytes. In this study, we identified the accumulation of p16, a senescence marker, in keratinocytes from biopsies of multiple spot types. We explored their impact using doxorubicin-induced senescent keratinocytes in vitro. Conditioned media from these senescent keratinocytes stimulated melanocyte dendricity, a hallmark of hyperpigmented spots. Transcriptomic analysis of senescent keratinocytes identified two key senescence-induced factors: Insulin-like Growth Factor-Binding Protein 3 (IGFBP3) and Nerve Growth Factor (NGF). IGFBP3 and NGF ligand treatment enhanced melanin synthesis by 33% and 17%, and dendricity by 23% and 14%, respectively, in human melanocyte cultures. These findings suggest that keratinocyte senescence contributes to spot formation by mediating melanocyte activation through IGFBP3 and NGF. Furthermore, we evaluated skincare ingredients such as sucrose dilaurate, glabridin, and niacinamide in neutral and low pH solutions, demonstrating their efficacy in reducing the secretion of these ligands, thereby offering potential cosmetic benefits. This study provides insights into the mechanisms of spot formation and highlights promising strategies for managing pigmentation disorders. Full article

The localization and remodeling of mRNPs is inextricably linked to translational control. In recent years there has been great progress in the field of mRNA translational control due to the characterization of the proteins and small RNAs that compose mRNPs. But our initial assumptions about the physical nature and participation of germ cell granules/condensates in mRNA regulation may have been misguided. These “granules” were found to be non-membrane-bound liquid–liquid phase-separated (LLPS) condensates that form around proteins with intrinsically disordered regions (IDRs) and RNA. Their macrostructures are dynamic as germ cells differentiate into gametes and subsequently join to form embryos. In addition, they segregate translation-repressing RNA-binding proteins (RBPs), selected eIF4 initiation factors, Vasa/GLH-1 and other helicases, several Argonautes and their associated small RNAs, and frequently components of P bodies and stress granules (SGs). Condensate movement, separation, fusion, and dissolution were long conjectured to mediate the translational control of mRNAs residing in contained mRNPs. New high-resolution microscopy and tagging techniques identified order in their organization, showing the segregation of similar mRNAs and the stratification of proteins into distinct mRNPs. Functional transitions from repression to activation seem to corelate with the overt granule dynamics. Yet increasing evidence suggests that the resident mRNPs, and not the macroscopic condensates, exert the bulk of the regulation. Full article