Here, we explored the potential of peptides derived from the catalytic A subunit of Shiga toxin (STxA) to be drug carriers. Using time-resolved biosensor-based assays we examined the interaction between a variety of STxA...Here, we explored the potential of peptides derived from the catalytic A subunit of Shiga toxin (STxA) to be drug carriers. Using time-resolved biosensor-based assays we examined the interaction between a variety of STxA peptides (varying in length and end groups) and the cell receptor binding subunit (STxB). Peptides which bound STxB included the C-terminal α-helix protruding into the interior of STxB and the ß-strands binding to its surface. Specifically, the C-terminal 26-mer resulted in a stable complex in a physiologically relevant pH range for drug delivery. Real-time cell-binding analysis showed that the peptide-STxB complex binds to and is internalized by Gb3-overexpressing cancer cell lines with surface-exposed Gb3 receptors. It highlights STxA-derived peptides as potential as drug carriers.
Altered glycosylation is a hallmark of cancer that shapes immune recognition within the tumor microenvironment. Lectins-glycan-binding proteins-play a dual role in this process: they interpret tumor-associated glycan pat...Altered glycosylation is a hallmark of cancer that shapes immune recognition within the tumor microenvironment. Lectins-glycan-binding proteins-play a dual role in this process: they interpret tumor-associated glycan patterns and can also be exploited as therapeutic tools. In this review, we discuss emerging strategies that harness lectins in cancer immunotherapy. Engineered lectin-based constructs, including antibody-lectin chimeras, lectin-drug conjugates, and glycan-targeting CAR-T cells, enable recognition of tumor-specific glycosylation signatures. At the same time, endogenous lectin pathways such as the galectin-polyLacNAc and sialic acid-Siglec axes function as glyco-immune checkpoints that suppress anti-tumor responses and represent promising therapeutic targets. Understanding how lectins regulate tumor-immune interactions may guide the development of next-generation immunotherapies integrating antigen recognition with glycan sensing.
Cancer progression is regulated by the dynamic matrix code of the tumor microenvironment, which influences cellular behavior and disease development. Importantly, matrix remodeling in three-dimensional cancer models more...Cancer progression is regulated by the dynamic matrix code of the tumor microenvironment, which influences cellular behavior and disease development. Importantly, matrix remodeling in three-dimensional cancer models more accurately reflects in vivo conditions compared to conventional two-dimensional systems. Matrix engineering through bioscaffolds supports physiologically relevant tumor modeling, while matrix-based platforms offer valuable tools for preclinical research and therapeutic development.
The traditional sequence-structure-function paradigm links biological activity to stable three-dimensional structures. However, growing evidence from intrinsically disordered proteins, intrinsically disordered regions, a...The traditional sequence-structure-function paradigm links biological activity to stable three-dimensional structures. However, growing evidence from intrinsically disordered proteins, intrinsically disordered regions, and phase-separating proteins indicates that many proteins function through dynamic conformational ensembles rather than fixed structures alone. These flexible systems adapt to their environments, enabling signal integration, allosteric modulation, and cellular regulation. Biomolecular condensates and dynamic protein assemblies coordinate biochemical activities through reversible, context-responsive interactions. We propose an expanded conceptual model: sequence → dynamics → conformational ensembles → context-dependent behavior. Rather than replacing the classical framework, this perspective serves as a complementary extension within a protein structure-function continuum model. This framework emphasizes conformational flexibility, ensemble redistribution, and cellular context as critical drivers of protein function, regulation, and disease.
The aberrant aggregation of α-synuclein (αS) into insoluble amyloid fibrils is a hallmark of Parkinson's disease. Despite recent advances in characterising the properties of mature αS fibrils, the transient and heterogen...The aberrant aggregation of α-synuclein (αS) into insoluble amyloid fibrils is a hallmark of Parkinson's disease. Despite recent advances in characterising the properties of mature αS fibrils, the transient and heterogeneous intermediates that underlie cellular toxicity remain largely elusive. Here, we review the mechanistic principles of αS aggregation, focussing on liquid-liquid phase separation (LLPS) as a critical intermediate step. We discuss how the structural evolution of αS within the condensed phase governs the subsequent patterns of cellular dysfunction and pathological propagation. This framework supports an emerging state-centric paradigm in therapeutic discovery, where the physical properties of αS condensates are modulated to mitigate the deleterious effects of its misfolding, offering a new sophisticated alternative to classical inhibition strategies.
Stem cell differentiation is central to development and regenerative medicine, but the complex underlying processes hinder our ability to control it experimentally. Computational models can help form hypotheses and gener...Stem cell differentiation is central to development and regenerative medicine, but the complex underlying processes hinder our ability to control it experimentally. Computational models can help form hypotheses and generate predictions. There are many types of computational models available to aid in understanding stem cell differentiation-related processes, but for an experimental biologist, it might be hard to select the modelling approach that matches their research question, and to know what data would be needed to make use of the model. This review is aimed at experimental biologists to introduce various modelling types, relate them to the types of questions these models can help answer and outline the necessary data to gain new insights. The review discusses mechanistic dynamic models, both ordinary differential equation (ODE) and abstract, multiscale models and data-driven deep learning approaches. Each model class is introduced with what the model represents, the insights it can provide, validation strategies and limitations. With this review, we want to make it easier to incorporate modelling within experimental workflows for stem cell differentiation-related research, to aid experimentation and accelerate discovery.
Biological aging is associated with gut microbiome alterations, including depletion of commensals and enrichment of disease-linked pathobionts. However, the extent to which these changes overlap with disease-associated m...Biological aging is associated with gut microbiome alterations, including depletion of commensals and enrichment of disease-linked pathobionts. However, the extent to which these changes overlap with disease-associated microbiome signatures remains unclear. Here, we re-examined 45 454 gut microbiomes (141 studies) to quantify overlap between aging-associated microbiome alterations and six major diseases. Cardiometabolic diseases showed the greatest overlap, followed by colorectal cancer. We identified 15 microbes enriched with aging and depleted in health, of which > 50% belonged to oral-associated Streptococcus, Veillonella and Rothia clades. Review of two population-level cohorts (6029 subjects) revealed reproducible associations between these microbes and seven cardiometabolic disease-linked medications. We further discuss their medication associations and propose strategies to deconfound medication- and disease-associated microbiome signatures in aging studies.
C-terminal Src kinase (Csk) is crucial for the normal function of platelet integrin αIIbβ3 because it inactivates Src kinase. While the molecular mechanism by which cytoplasmic Csk associates with membrane-bound Src is k...C-terminal Src kinase (Csk) is crucial for the normal function of platelet integrin αIIbβ3 because it inactivates Src kinase. While the molecular mechanism by which cytoplasmic Csk associates with membrane-bound Src is known in resting platelets, it remains unknown in activated platelets. Using surface plasmon resonance, a kinase assay, and microscale thermophoresis, we discovered that Csk binds directly to phospho-Tyr747 on the β3 tail via its SH2 domain and that this binding fully activates Csk. Moreover, we found that phospho-Thr753 on the β3 tail prevents Csk from binding. Collectively, our findings provide new insight into the regulation of Csk function in activated platelets, suggesting that Tyr747-phosphorylated β3 recruits Csk near active Src, whereas phospho-Thr753 on β3 inhibits this interaction.
Protein aggregates threaten cellular proteostasis and are linked to aging and disease. In metazoa, aggregate resolution relies on Hsp70-J-domain protein (JDP)-based disaggregases. Previous studies showed human class A an...Protein aggregates threaten cellular proteostasis and are linked to aging and disease. In metazoa, aggregate resolution relies on Hsp70-J-domain protein (JDP)-based disaggregases. Previous studies showed human class A and class B JDP assemblies enhance Hsp70-mediated disaggregation, but the underlying mechanism has remained unclear. Using J-domain mutants that impair Hsp70 binding while preserving mixed-class JDP interaction, we show that synergistic disaggregation is lost when either JDP partner cannot engage Hsp70. Size-resolved disaggregation assays further reveal that mixed-class JDP assemblies influence the processing of distinct luciferase aggregate populations, including aggregate species inefficiently handled by either JDP alone. Our findings support a model in which mixed-class JDP assemblies enhance Hsp70 disaggregation through expanded aggregate-processing capacity and multivalent Hsp70 recruitment by both JDP partners.
The gut microbiome changes systematically with age and associates with age-related morbidity and mortality, establishing it as a candidate biomarker and intervention target for ageing. Realising this potential requires m...The gut microbiome changes systematically with age and associates with age-related morbidity and mortality, establishing it as a candidate biomarker and intervention target for ageing. Realising this potential requires methodological rigour, as distinguishing genuine biological signals from methodological artefacts remains challenging given variable findings across cohorts. This review provides an integrated framework for human microbiome-ageing research, organised around five methodological challenges that will collectively strengthen causal inference. We examine how age-associated factors can correlate with chronological age and may confound the microbiome-age associations, while selection biases shape old-age cohorts towards healthier profiles. We address within-host temporal dynamics and between-individual heterogeneity that require appropriate sampling to distinguish age-related signatures from transient states, and validation strategies that separate ageing from batch effects in predictive models. Mendelian randomisation provides causal leverage when triangulated with longitudinal and interventional evidence. Throughout, we examine how design choices determine the limits of analytical inference. The review concludes with a practical checklist, equipping researchers to strengthen reproducibility, improve generalisability and advance microbiome-based metrics towards validated indicators of biological ageing.
It is important to understand how the fascinating diversity of modern enzymes has manifested itself since the onset of life. A powerful approach to address this question is the computational and experimental retracing of...It is important to understand how the fascinating diversity of modern enzymes has manifested itself since the onset of life. A powerful approach to address this question is the computational and experimental retracing of evolutionary processes by protein engineering techniques such as rational design, directed evolution, and ancestral sequence reconstruction. In this review, we show that these methods were used to elucidate how first enzymes have emerged from ligand-binding protein scaffolds, how the enormous variety of enzymes with similar catalytic mechanisms but different substrate specificities have emerged, and how natural selection has driven the formation of oligomeric enzyme complexes from their monomeric ancestors. A further important aspect of enzyme evolution is the adaptation of catalytic activity and thermostability to changing environmental conditions on geological timescales. We will present work in which the interdependence of these enzymatic properties was analyzed and reproduced. Finally, we will discuss case studies that show how the rapid evolution of new enzymatic functions has allowed for the degradation of anthropogenic substances that have only recently been released into the environment.
Inositol pyrophosphates (PP-InsP) are high energy signaling molecules that play important roles in eukaryotes. They are synthesized from inositol polyphosphates by kinases that add a diphosphate (β phosphate) at one or m...Inositol pyrophosphates (PP-InsP) are high energy signaling molecules that play important roles in eukaryotes. They are synthesized from inositol polyphosphates by kinases that add a diphosphate (β phosphate) at one or more positions on the myo-inositol ring. The focus of this review is on the phosphatases specific for the β phosphate. These enzymes are members of three different families of phosphohydrolases: the histidine acid phosphatase family that is specific for β phosphate on 1C, the cysteine phosphatase family that is specific for the diphosphate on 5C, and the Nudix family that is promiscuous both in terms of the position of the diphosphate on PP-InsPs and recognition of a range of molecules with phosphoanhydride linkages. These three families of phosphatases share overlapping PP-InsP substrates, and as a community of enzymes they have a combined influence on PP-InsP pools, impacting cellular processes and phenotypes. Each phosphatase family is discussed from biochemical perspectives (enzyme structure, substrate preferences, kinetic properties), distribution across eukaryotes (evolutionary, phylogenetic), and the similarities and differences in the affected cellular processes across fungi, animals, and plants.
The rules of prokaryotic cell design remain elusive. Here, a theory is presented for interpreting growth rate, overflow metabolism, respiration efficiency, and maintenance energy flux based on cell dimensions, membrane p...The rules of prokaryotic cell design remain elusive. Here, a theory is presented for interpreting growth rate, overflow metabolism, respiration efficiency, and maintenance energy flux based on cell dimensions, membrane protein crowding, and metabolism. The theory employs biophysical properties and systems analysis to successfully interpret phenotypes of Escherichia coli K-12 strains MG1655 and NCM3722. These strains are genetically similar but differ in surface area-to-volume (SA : V) ratios (~ 30%), growth rate on glucose (~ 40%), and overflow-inducing growth rates (~ 80%). Six predictions were tested and validated using experimental phenomics, proteomics, and mutant data. Analyses did not require assumptions regarding cytosolic macromolecular crowding, highlighting the distinct properties of the theory. Cell geometry and membrane protein crowding are significant biophysical constraints of cell biology.
Lipopolysaccharides (LPS) are a key component in the defensive barrier of the outer membrane (OM) of Gram-negative bacteria; they are a major drug target and bacteriophage access point. Biomimetic platforms presenting LP...Lipopolysaccharides (LPS) are a key component in the defensive barrier of the outer membrane (OM) of Gram-negative bacteria; they are a major drug target and bacteriophage access point. Biomimetic platforms presenting LPS are therefore important to study OM biophysics of pathogens and initial bacteriophage infection steps. Herein, we present robust protocols for the preparation of LPS-containing supported lipid bilayers (SLBs) incorporating either Salmonella LPS or OM vesicles (OMVs). We characterized SLBs using quartz crystal microbalance with dissipation (QCM-D) and fluorescence microscopy. We probed their interactions with O-antigen specific Salmonella phages and their tailspike receptor binding proteins. Altogether, this work provides a roadmap to create versatile LPS-based platforms that facilitate studies of interactions between phages and Gram-negative bacterial membranes.
CT10 regulator of kinase (CRK) and CRK-Like (CRKL) are important Src homology 2 (SH2)- and SH3-domain containing signaling adaptors, which drive cell adhesion, motility, differentiation, and proliferation. Their genetica...CT10 regulator of kinase (CRK) and CRK-Like (CRKL) are important Src homology 2 (SH2)- and SH3-domain containing signaling adaptors, which drive cell adhesion, motility, differentiation, and proliferation. Their genetically defined and overlapping roles include facilitating proper development of the vertebrate central nervous system. All four members of the SH2-domain containing (SH) protein family are enriched in YXXP motifs, which when the initial tyrosine is phosphorylated form the preferred binding motif of CRK family SH2 domains. We show that ABL kinase drives tyrosine phosphorylation of SH protein YXXP motifs and induces their direct binding to the SH2 domains of CRK family adaptors. The implications of the interactions between CRK/CRKL and SH proteins include signal attenuation and relocation of CRK adaptor signaling.
Inositol phosphates (IPs) and phosphoinositide lipids (PIPs) are regulatory molecules critical for a wide array of functions in eukaryotic cells. Membrane PIPs have clear functions in transient recruitment of signaling p...Inositol phosphates (IPs) and phosphoinositide lipids (PIPs) are regulatory molecules critical for a wide array of functions in eukaryotic cells. Membrane PIPs have clear functions in transient recruitment of signaling proteins to membranes, and IPs have been found locked in the core of proteins as structural cofactors. However, several recent studies have suggested IPs and PIPs can mediate protein-protein interactions at the interface between proteins, functioning as natural molecular glues. Here, we present recent structural biology describing how IPs and PIPs mediate these regulatory responses at protein interfaces. In addition, we describe protein-protein interactions mediated by IPs and PIPs, for which evidence supporting a natural molecular glue role is unclear or awaits further high-resolution structural analyses. Together, we put forth that PIPs and IPs have a historically under-appreciated role at protein-protein interfaces, requiring a more systematic, structural approach to elucidate.
The intestinal epithelium is maintained by stem cells that balance self-renewal and differentiation to sustain homeostasis and enable regeneration after injury. Recent advances-including organoid culture, genome editing,...The intestinal epithelium is maintained by stem cells that balance self-renewal and differentiation to sustain homeostasis and enable regeneration after injury. Recent advances-including organoid culture, genome editing, orthotopic xenotransplantation, and somatic mutation-based analysis-have created new opportunities to investigate intestinal stem cell (ISC) dynamics in humans. These studies have revealed striking species-specific differences: whereas mouse LGR5 ISCs divide daily and are chemo-sensitive, human colonic LGR5 stem cells are predominantly slow-cycling and chemo-resistant. Consistent with this reduced cycling, human ISCs accumulate somatic mutations more slowly than those of mice. Across mammals, ISC proliferation rates inversely correlate with lifespan, a relationship thought to minimize mutation accumulation and reduce cancer risk, in line with Peto's paradox. Regenerative responses in both mice and humans can involve fetal-like reprogramming driven by YAP and other signaling pathways, yet the extent of species differences in intestinal regenerative capacity remains unclear. This review synthesizes current insights into ISC kinetics, injury responses, and evolutionary adaptations, highlighting the need for human-focused studies to bridge translational gaps and guide regenerative medicine strategies.
Q. Jiang , F. Li , K. Shi , P. Wu , J. An , Y. Yang and C. Xu , "ATF4 Activation by the p38MAPK-eIF4E Axis Mediates Apoptosis and Autophagy Induced by Selenite in Jurkat Cells," FEBS Letters 587, no. 15 (2013): 2420-2429...Q. Jiang , F. Li , K. Shi , P. Wu , J. An , Y. Yang and C. Xu , "ATF4 Activation by the p38MAPK-eIF4E Axis Mediates Apoptosis and Autophagy Induced by Selenite in Jurkat Cells," FEBS Letters 587, no. 15 (2013): 2420-2429, https://doi.org/10.1016/j.febslet.2013.06.011. The above article, published online on 19 June 2013 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors; the journal Editor-in-Chief, Michael Brunner; the Federation of European Biochemical Societies; and John Wiley & Sons Ltd. The retraction has been agreed upon following concerns raised by a third party. An investigation identified several instances in which elements appear to be duplicated across different figures, including between Figures 1B and 3F, 2C and 5F, 5F and 6A, and 3E and 5E. Additional duplications were identified within Figures 1C and 5B. Further duplications were observed involving elements from Figures 1A, 1C, 3E, and 6D of this article and figures published in a later article elsewhere by some of the same authors. The authors acknowledged some of the duplications and indicated that these arose during figure preparation. Due to the time that has elapsed since publication, the original data are no longer available. The editors consider the results and conclusions of this article to be unreliable. The authors did not respond to our notice of retraction.
Proteostasis and the gut microbiota are two major determinants of host health and longevity. Proteostasis ensures proper protein folding and degradation thereby preventing the accumulation of unwanted proteins. Similarly...Proteostasis and the gut microbiota are two major determinants of host health and longevity. Proteostasis ensures proper protein folding and degradation thereby preventing the accumulation of unwanted proteins. Similarly, microbiota contribute to host metabolism, immunity, and protection from pathogens. However, as aging progresses, the proteostasis network declines, and the composition and functionality of gut microbiota are altered, often resulting in dysbiosis. While the impact of the microbiota on various aspects of host physiology is extensively studied, its specific influence on host protein quality control remains relatively underexplored. In this review, we provide an integrated overview of the relationship between microbiota and host proteostasis. Accumulating findings, particularly from C. elegans models, provide substantial support for the concept that microbiota-derived factors (vitamins and RNA) can shape host proteostasis and influence aging-related phenotypes. We discuss emerging evidence showing that microbial communities and their metabolites can either support or impair cellular proteostasis, highlighting their potential as prebiotics or dietary intervention candidates for promoting healthy aging. Understanding the intricate interplay between microbiota and proteostasis opens new avenues for designing microbiota-based strategies for healthy aging.
Gram-negative bacteria produce nonulosonic acids, a family of nine-carbon sugars that mimic host sialic acids and may contribute to bacterial virulence. The nonulosonic acid C8-epimeric 5,7-di-N-acetyllegionaminic acid (...Gram-negative bacteria produce nonulosonic acids, a family of nine-carbon sugars that mimic host sialic acids and may contribute to bacterial virulence. The nonulosonic acid C8-epimeric 5,7-di-N-acetyllegionaminic acid (8-epi-Leg5,7Ac2) is a component of the K-locus 49 (KL49) capsule of hypervirulent Acinetobacter baumannii, and its epimerization is proposed to be mediated by ElaA, ElaB, and ElaC. We identified a KL49 strain that induces lethal sepsis in mice and found deletion of elaA, elaB, or elaC abolished lethality and markedly reduced capsule production. Crystal structures of ElaB, ElaA, and ElaC revealed conserved N-acetyl recognition underlying CMP-Leg5,7Ac2 synthesis and regioselective C8 epimerization. Together, these genetic, structural, and in vivo findings identify ElaABC as potential antivirulence targets in emerging hypervirulent KL49 A. baumannii strains.