Disordered N‐termini enhance the thermostability of SGNH‐hydrolase family polyesterases

The nucleoside proton symporter (NHS) family proteins are part of the major facilitator superfamily and are responsible for transporting nucleosides from the extracellular environment into the cell. Structural and biochemical analysis of NupG, a prototypical NHS member, have pinpointed the critical residues involved in substrate binding. However, the proton-coupled mechanism diving substrate translocation in NHS proteins has remained elusive. In previous research, we identified Asp323 in NupG as a potential protonation site. In this study, using X-ray crystallography, molecular dynamics simulations, and biochemical assays, we discovered that the deprotonation of Asp323 in NupG, or the equivalent Asp315 in YegT, (another NHS family member) triggers a local conformational change in the TM10 region of NHS transporters. Notably, this protonation site is part of a novel motif (GXXXD) located in the middle of the TM10 transmembrane helix in NHS proteins. Further biochemical studies suggest that this local conformational change in the GXXXD motif plays a role in coordinating substrate release, ultimately facilitating substrate translocation. Our findings provide valuable insights into the molecular mechanism of nucleoside transport and expand the understanding of the diverse transport mechanisms within the major facilitator superfamily.

Iron modified biochar derived from diverse feedstock: Enhancing denitrification and mechanistic insights into the detoxification and removal of Cu2+ and Pb2.

Cancer continues to represent a major global health challenge, accounting for millions of deaths annually despite substantial advances in diagnostics and therapeutic interventions. Conventional cancer treatment modalities, including chemotherapy, radiotherapy, targeted therapy, and immunotherapy, are often limited by high toxicity, treatment resistance, and economic burden. In this context, drug repurposing has emerged as an effective strategy to accelerate the discovery of novel anticancer agents by utilizing existing drugs with established safety profiles. Among these, anti-parasitic drugs have gained significant attention due to their pleiotropic biological activities, affordability, and widespread clinical use. A growing body of evidence suggests that several anti parasitic agents exhibit potent anticancer properties through diverse mechanisms such as apoptosis induction, autophagy modulation, inhibition of oncogenic signaling pathways, anti-angiogenic effects, and immune system regulation. This comprehensive review critically examines the therapeutic potential of antiparasitic drugs in cancer treatment, focusing on molecular mechanisms, preclinical and clinical evidence, advantages, limitations, and future research directions. The review highlights the promise of repositioning anti-parasitic drugs as cost-effective and innovative components of modern oncology. Downloads PDF Published 2025-12-15 Issue Vol. 1 No. 02 (2025): Volume 01 , Issue 02 Mar 2025 Section Articles

Cadmium (Cd), a pervasive and highly phytotoxic metal pollutant, poses severe threats to agricultural productivity, ecosystem stability, and human health through its entry into the food chain. Plants have evolved intricate defense mechanisms, among which the strategic manipulation of nutrient elements emerges as a critical physiological and biochemical strategy for mitigating Cd stress. This comprehensive review delves deeply into the multifaceted roles of essential macronutrient elements (nitrogen, phosphorus, potassium, calcium, magnesium, sulfur), essential micronutrient elements (zinc, iron, manganese, copper) and non-essential beneficial elements (silicon, selenium) in modulating plant responses to Cd toxicity. We meticulously dissect the physiological, biochemical, and molecular underpinnings of how these nutrients influence Cd bioavailability in the rhizosphere, Cd uptake and translocation pathways, sequestration and compartmentalization within plant tissues, and the activation of antioxidant defense systems. Nutrient elements exert their influence through diverse mechanisms: competing with Cd for root uptake transporters, promoting the synthesis of complexes that reduce Cd mobility, stabilizing cell walls and plasma membranes to restrict apoplastic flow and symplastic influx, modulating redox homeostasis by enhancing antioxidant enzyme activities and non-enzymatic antioxidant pools, regulating signal transduction pathways, and influencing gene expression profiles related to metal transport, chelation, and detoxification. The complex interactions between nutrients themselves further shape the plant’s capacity to withstand Cd stress. Recent advances elucidating nutrient-mediated epigenetic regulation, microRNA involvement, and the role of nutrient-sensing signaling hubs in Cd responses are critically evaluated. Furthermore, we synthesize the practical implications of nutrient management strategies, including optimized fertilization regimes, selection of nutrient-efficient genotypes, and utilization of nutrient-enriched amendments, for enhancing phytoremediation efficiency and developing low-Cd-accumulating crops, thereby contributing to safer food production and environmental restoration in Cd-contaminated soils. The intricate interplay between plant nutritional status and Cd stress resilience underscores the necessity for a holistic, nutrient-centric approach in managing Cd toxicity in agroecosystems.

BackgroundAngiogenesis is important in physiological and pathological conditions, as blood vessels provide nutrients and oxygen needed for tissue growth and survival. Therefore, targeting angiogenesis is a prominent strategy in both tissue engineering and cancer treatment. However, not all of the approaches to promote or inhibit angiogenesis lead to successful outcomes. Angiogenesis-based therapies primarily target pro-angiogenic factors such as vascular endothelial growth factor-A (VEGF) or fibroblast growth factor (FGF) in isolation. However, pre-clinical and clinical evidence shows these therapies often have limited effects. To improve therapeutic strategies, including targeting FGF and VEGF in combination, we need a quantitative understanding of the how the promoters combine to stimulate angiogenesis.ResultsIn this study, we trained and validated a detailed mathematical model to quantitatively characterize the crosstalk of FGF and VEGF intracellular signaling. This signaling is initiated by FGF binding to the FGF receptor 1 (FGFR1) and heparan sulfate glycosaminoglycans (HSGAGs) or VEGF binding to VEGF receptor 2 (VEGFR2) to promote downstream signaling. The model focuses on FGF- and VEGF-induced mitogen-activated protein kinase (MAPK) signaling and phosphorylation of extracellular regulated kinase (ERK), which promotes cell proliferation. We apply the model to predict the dynamics of phosphorylated ERK (pERK) in response to the stimulation by FGF and VEGF individually and in combination. The model predicts that FGF and VEGF have differential effects on pERK. Additionally, since VEGFR2 upregulation has been observed in pathological conditions, we apply the model to investigate the effects of VEGFR2 density and trafficking parameters. The model predictions show that these parameters significantly influence the response to VEGF stimulation.ConclusionsThe model agrees with experimental data and is a framework to synthesize and quantitatively explain experimental studies. Ultimately, the model provides mechanistic insight into FGF and VEGF interactions needed to identify potential targets for pro- or anti-angiogenic therapies.

Manganese (Mn) homeostasis in humans is tightly regulated by the transporters ZIP8, ZIP14, and ZnT10, and pathogenic mutations in these proteins cause systemic Mn dysregulation, leading to severe disorders in multiple systems. Here, we performed a systematic survey of naturally occurring missense variants in these transporters. Pathogenicity was assessed with two widely used computational tools, CADD and AlphaMissense (AM), and results were integrated with AlphaFold-predicted structural models. Although the prediction methods showed general agreement, substantial discrepancies were observed, with CADD tending to overpredict deleteriousness and AM failing to identify a portion of confirmed pathogenic variants. Structural mapping revealed that predictions were more accurate for amino acid substitutions in structured and buried residues than for solvent-exposed loops and flexible regions. Mechanistic insights further highlighted variants at functionally important regions as critical. Our study helps prioritize Mn transporter variants for future experimental validation and provides a framework for bridging computational predictions with structure-guided mechanistic studies.

Folding kinetics of recognition loop peptides from a photolyase and cryptochrome-DASH

Antipsychotics-induced metabolic alterations: Recounting the mechanistic insights, therapeutic targets and pharmacological alternatives

Coronaviruses recognize a variety of receptors using different domains of their envelope-anchored spike protein. How these diverse receptor recognition patterns affect viral entry is unknown. Mouse hepatitis coronavirus (MHV) is the only known coronavirus that uses the N-terminal domain (NTD) of its spike to recognize a protein receptor, CEACAM1a. Here we determined the cryo-EM structure of MHV spike complexed with mouse CEACAM1a. The trimeric spike contains three receptor-binding S1 heads sitting on top of a trimeric membrane-fusion S2 stalk. Three receptor molecules bind to the sides of the spike trimer, where three NTDs are located. Receptor binding induces structural changes in the spike, weakening the interactions between S1 and S2. Using protease sensitivity and negative-stain EM analyses, we further showed that after protease treatment of the spike, receptor binding facilitated the dissociation of S1 from S2, allowing S2 to transition from pre-fusion to post-fusion conformation. Together these results reveal a new role of receptor binding in MHV entry: in addition to its well-characterized role in viral attachment to host cells, receptor binding also induces the conformational change of the spike and hence the fusion of viral and host membranes. Our study provides new mechanistic insight into coronavirus entry and highlights the diverse entry mechanisms used by different viruses.

ATPases are important molecular machines that convert the chemical energies stored in ATP to mechanical actions within the cell. ATPases are among the most abundant proteins with diverse functions involved in almost every cellular pathway. The well characterised ATPases include the various motor proteins responsible for cargo transfers, cell motilities, and muscle contractions; the protein degradation machinery - the proteasome; the ATP synthase, F-ATPase; and the chaperone systems. Other ATPases include DNA helicases and DNA replication complex; proteins responsible for protein/complex disassembly; and certain gene regulators. It is beyond the scope of this review to cover the complete range of ATPases. Instead, we will focus on a few representative ATPases, chosen based on their diverse mechanisms and properties. Furthermore, this review is by no means trying to cover comprehensively the literature for each ATPase nor the historical aspects in each field. We will focus on describing the various techniques being employed to derive the mechanisms and properties of the chosen ATPases. Among them, high and low resolution structural studies combined with biochemical assays seem to be the dominant technical advances adapted to reveal mechanisms for most of the ATPases except the bacterial sigma54 activators, whose mechanism of action is mostly derived from large amount of biochemical studies. A number of them, especially the F-ATPase and motor proteins, have been studied successfully by various single molecule and imaging techniques. We will therefore discuss them in greater details in order to describe the wide range techniques being utilised.

Stem cell balance of proliferation, differentiation and self-renewal, is regulated by the microenvironment in which they reside, termed the stem cell niche (Schofield, 1978). Niche microenvironments provide physical and functional regulatory cues that control fundamental cell intrinsic and extrinsic mechanisms. In adults, the process of haematopoiesis is sustained by a population of haematopoietic stem cells (HSCs) that are found primarily in the bone marrow (BM) (Jagannathan-Bogdan and Zon, 2013). The BM niche also houses populations of mesenchymal stromal and perivascular cells (MSPCs), that are themselves regulated by the niche, and are fundamental cellular constituents in HSC regulation (Pinho and Frenette, 2019). Both HSCs and MSPCs hold enormous clinical potential. HSCs have the ability to reconstitute the entire blood and immune system (Jagannathan-Bogdan and Zon, 2013), whereas MSPCs contain immunosuppression capacity and have the ability to regenerate damaged and diseased tissue (Caplan, 1991; Uccelli et al., 2008). However, there are still important hurdles that must be overcome before the potential of these cells are fully realised. The regenerative capacity of these stem cells is quickly lost upon ex vivo culture, meaning achieving clinically relevant numbers of cells is challenging (Dalby et al., 2018; Zon, 2008). Although BM MSPCs (such as nestin+ MSPCs) contain HSC support activity, their ability to maintain HSCs ex vivo is only modest due to loss of expression of these niche factors in culture (Kunisaki et al., 2013; Nakahara et al., 2019). The absence of sustained self-renewal or maintenance of the stem cell phenotype could be related to the lack of integration of biophysical and biochemical cues required for stem cell regulation, provided by the native BM niche microenvironment in vivo. This has led to a focus on biomaterial and engineering strategies that aim to recapitulate BM niche properties in vitro (Müller et al., 2014). It is envisaged that bioengineered artificial niches will offer protocols for ex vivo expansion and maintenance of HSCs without the need for high risk protocols (e.g. genetic manipulations (Nakahara et al., 2019)), but also platforms on which to study the fundamental mechanisms that control self-renewal in both HSCs and MSPCs in the niche. In this thesis, biomaterial strategies were employed to mimic aspects of the BM niche microenvironment. First retention of HSC support activity in a population of MSPCs was investigated and the metabolic mechanisms that may support this phenotype were probed. The ability of the system to support HSC maintenance in vitro was then assessed. Poly(ethyl acrylate) (PEA) is a polymer that causes spontaneous unfolding of the extracellular matrix protein (ECM) fibronectin (FN). These physiological-like networks expose key binding sites on the FN molecule, which can be harnessed for cell adhesion and growth factor tethering (Cheng et al., 2018; Llopis-hernández et al., 2016). Noting that low-stiffness matrices support nestin expression in MSPCs (Engler et al., 2006), a key niche marker (Kunisaki et al., 2013; Pinho et al., 2013), low-stiffness collagen hydrogels were introduced into the system. We were able to use this system to promote a population of nestin+ MSPCs that express key HSC support factors and were able to maintain a population of HSCs in vitro. The nestin+ MSPCs utilise hypoxic-like metabolic mechanisms in response to low-stiffness, that may be important in retaining this BM niche-like phenotype in long term in vitro culture.

DNA unwinding and primer synthesis are fundamental processes in genome replication. The human herpes simplex virus type 1 (HSV-1) helicase-primase forms a unique heterotrimeric primosome that is essential for viral DNA unwinding and primer synthesis and represents an ideal drug target. However, its molecular mechanism remains poorly understood. Here we report the cryo-electron microscopic structure of the primosome in complex with single-stranded DNA, ADP and Mg2+ to 3.47 Å resolution, which reveals that the primosome forms an unprecedented architecture in a fully open DNA binding groove between the helicase domains 1A and 2A–2B and that the primase subunit UL52 interacts extensively with the helicase subunit UL5 and accessory protein subunit UL8. Integrating mutagenesis, biochemical assays, structural analysis and 3D variability display analysis, we have identified the active sites of the ATPase, helicase and primase and critical interfaces between UL52, UL5 and UL8. Our work suggests that the primosome unwinds and translocates DNA via bidirectional rotation, and proposes a mechanistic model for DNA-dependent ATPase activation and alternating activity between helicase and primase. Herpesviridae family viruses pose significant threats to human health worldwide, and this trimeric assembly of primosomes is conserved. Our work provides a framework for understanding replication mechanisms across related viruses and for the rational design of broad-spectrum antivirals.

Structural and mechanistic insights into ALS patient derived mutations in D-amino acid oxidase

Curcumin analogs exhibit anti-cancer activity by selectively targeting G-quadruplex forming c-myc promoter sequence

Protein prenylation involves the attachment of a hydrophobic isoprenoid moiety to the C-terminus of proteins. Several small GTPases, including members of the Ras and Rho subfamilies, require prenylation for their normal and pathological functions. Recent work has suggested that SmgGDS proteins regulate the prenylation of small GTPases in vivo. Using RhoA as a representative small GTPase, we directly test this hypothesis using biochemical assays and present a mechanism describing the mode of prenylation regulation. SmgGDS-607 completely inhibits RhoA prenylation catalyzed by protein geranylgeranyltransferase I (GGTase-I) in an in vitro radiolabel incorporation assay. SmgGDS-607 inhibits prenylation by binding to and blocking access to the C-terminal tail of the small GTPase (substrate sequestration mechanism) rather than via inhibition of the prenyltransferase activity. The reactivity of GGTase-I with RhoA is unaffected by addition of nucleotides. In contrast, the affinity of SmgGDS-607 for RhoA varies with the nucleotide bound to RhoA; SmgGDS-607 has a higher affinity for RhoA-GDP compared to RhoA-GTP. Consequently, the prenylation blocking function of SmgGDS-607 is regulated by the bound nucleotide. This work provides mechanistic insight into a novel pathway for the regulation of small GTPase protein prenylation by SmgGDS-607 and demonstrates that peptides are a good mimic for full-length proteins when measuring GGTase-I activity.