Molybdenum-dependent formate dehydrogenases (Mo-FDHs) reversibly catalyze the interconversion of CO and formate, and therefore may be utilized for the development of innovative energy storage and CO utilization concepts. Mo-FDHs contain a highly conserved lysine residue in the vicinity of a catalytically active molybdenum (Mo) cofactor and an electron-transferring [4Fe-4S] cluster. In order to elucidate the function of the conserved lysine, we substituted the residue Lys44 of Escherichia coli formate dehydrogenase H (EcFDH-H) with structurally and chemically diverse amino acids. Enzyme kinetic analysis of the purified EcFDH-H variants revealed the Lys-to-Arg substitution as the only amino acid exchange that retained formate oxidation catalytic activity, amounting to 7.1% of the wild-type level. Ultraviolet-visible (UV-Vis) spectroscopic analysis indicated that >90% of the [4Fe-4S] cluster was lost in the case of EcFDH-H variants -K44E and -K44M, whereas the cluster occupancy of the K44R variant decreased by merely 4.5%. Furthermore, the K44R substitution resulted in a slight decrease in its melting temperature and a significant formate affinity decrease, apparent as a 32-fold K value increase. Consistent with these findings, molecular dynamics simulations predicted an increase in the backbone and cofactor mobility as a result of the K44R substitution. These results are consistent with the conserved lysine being essential for stabilizing the catalytically active structures in EcFDH-H and may support engineering efforts on Mo-FDHs to design more efficient biocatalysts for CO reduction.

Cystic fibrosis (CF) is a genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, leading to chronic, unresolved inflammation of the airways due to uncontrolled recruitment of polymorphonuclear leukocytes (PMNs). Evidence indicates that CFTR loss-of-function, in addition to promoting a pro-inflammatory phenotype, is associated with an increased risk of developing cancer, suggesting that CFTR can exert tumor-suppressor functions. Three-dimensional (3D) in vitro culture models, such as the CF lung airway-on-a-chip, can be suitable for studying PMN recruitment, as well as events of cancerogenesis, that is epithelial cell invasion and migration, in CF. To gather insight into the pathobiology of CFTR loss-of-function, we generated CFTR-knockout (KO) clones of the 16HBE14o- human bronchial cell line by CRISPR/Cas9 gene editing, and performed a comparative proteomic analysis of these clones with their wild-type (WT) counterparts. Systematic signaling pathway analysis of CFTR-KO clones revealed modulation of inflammation, PMN recruitment, epithelial cell migration, and epithelial-mesenchymal transition. Using a latest-generation organ-on-a-chip microfluidic platform, we confirmed that CFTR-KO enhanced PMN recruitment and epithelial cell invasion of the endothelial layer. Thus, a dysfunctional CFTR affects multiple pathways in the airway epithelium that ultimately contribute to sustained inflammation and cancerogenesis in CF.

Although phosphodiesterase 4 (PDE4) inhibitors have reached the clinic, their lack of selectivity for PDE4 enzyme isoforms leads to documented side effects. Building in enzyme selectivity has proved difficult because all PDE4 enzymes share highly conserved catalytic domains. The report by Sin et al. describes a novel approach in which a potent PDE4 proteolysis targeting chimera (PROTAC) selectively promotes the degradation of a small subset of PDE4 isoforms (i.e., "short forms") and impacts inflammatory events regulated by these enzymes. This approach offers unparalleled selectivity, potency, and could represent the dawn of a new pharmacology for selective regulation of cyclic AMP (cAMP) signaling.

SprA1 and SprA2 are small hydrophobic peptides that belong to the type I toxin-antitoxin systems expressed by Staphylococcus aureus. Both peptides induce S. aureus death when overexpressed. Although they share 71% of amino acids sequence similarity, SprA2 exhibits stronger hemolytic activity than SprA1. In this study, we investigated the mode of action of these toxins on both prokaryotic-like and eukaryotic-like membranes. We first confirmed that SprA2, like SprA1, is an alpha-helical peptide located at the S. aureus membrane. By overexpressing each toxin, we demonstrated that SprA1 forms stable pores in the S. aureus membrane, evidenced by concomitant membrane depolarization, permeabilization and ATP release leading to growth arrest, whereas SprA2 forms transient pores, causing concomitant membrane depolarization, ATP release, and growth arrest. We showed that the unique cysteine residue present in SprA1 and SprA2 is required for toxicity through disulfide bond formation. Next, we found that both synthetic peptides induce slight leakage in anionic DOPC-DOPG lipid vesicles mimicking prokaryotic membranes, concomitant with lipid vesicles aggregation and/or fusion. Moreover, we observed that SprA1 permeabilizes S. aureus protoplasts, via its ability to form stable pores, whereas SprA2 permeabilizes and lyses them. However, no permeabilization of intact bacteria was detected after the addition of SprA1 and SprA2 in the extracellular medium. Finally, we confirmed that SprA2 has strong activity on zwitterionic DOPC lipid vesicles mimicking eukaryotic membranes, without inducing aggregation. This work highlights the strong selectivity of SprA2 for eukaryotic membranes, suggesting that this toxin may play a role in S. aureus virulence.

NrdR is a bacterial transcriptional repressor consisting of a zinc (Zn)-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two "NrdR boxes" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, in the last of which we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus deoxyadenosine triphosphate (dATP) or equivalent diphosphate combinations. No other combination of adenine nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high-resolution crystal structures of an NrdR. We have also determined cryo-electron microscopy structures of DNA-bound EcoNrdR-ATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATP-cones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that, when loaded with the correct nucleotides, adapt to an optimal promoter-binding conformation.

Parkinson's disease (PD) is a devastating neurodegenerative disorder with a distinct loss of the nigrostriatal dopaminergic pathway. Despite the multiplicity in etiology, alterations that disrupt neuronal integrity can be traced back to defects in fundamental processes that typically run under mitochondrial inputs. Evidence indicates that mitochondrial activities are hierarchically integrated with the energetic performance of these organelles, so that an interesting perspective holds that interventions aimed at improving mitochondrial bioenergetics can potentially mitigate the severity of PD phenotype expression. In this mechanistic framework, approaches that facilitate the mitochondrial anaplerotic use of glutamate (Glut) might counteract the detrimental shift from Glut metabolism, which is typically altered in PD, to excessive Glut transmission that feeds excitotoxicity and the neurodegenerative spiral. In this study, we investigated whether the enhancement of glutamate dehydrogenase (GDH) activity, by using the GDH activator 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH), has neuroprotective potential against PD injury. In both retinoic acid-differentiated SH-SY5Y cells and primary rat mesencephalic neurons challenged with α-synuclein plus rotenone to mimic PD, BCH-dependent GDH activation significantly ameliorated cell viability, improved mitochondrial ATP synthesis and lessened to control levels the cellular redox burden. Strikingly, we collected evidence for the existence of a functional axis connecting GDH activity to a specific intracellular pool of the Excitatory Amino Acid Transporters (EAATs), namely the EAAT3. Overall, our results reveal a novel and non-redundant role of EAAT3 for GDH-dependent protection against PD injury, which may inspire new pharmacological approaches against PD pathology.

A library of known aspartic protease inhibitors was screened to identify compounds that inhibit plasmepsin V from Plasmodium vivax. This screen revealed compounds with an imino-pyrimidinone-fused pyrrolidine (IPF) scaffold that exhibited sub-micromolar inhibitory activity against plasmepsin V. Further screening of IPF analogs against the related aspartic protease plasmepsin X showed inhibitory activity, while a third aspartic protease, plasmepsin IX, was not significantly inhibited. Modifications to the P1 biaryl region of the IPF scaffold differentially modulated inhibition of both plasmepsin V and X. Notably, analogs with potent plasmepsin X inhibitory activity successfully blocked the growth of Plasmodium falciparum in vitro. X-ray structures of IPF analogs in complex with plasmepsin V provided insights into their binding mode and revealed avenues to further improve IPF potency and selectivity between plasmepsin V and X. This understanding of how these compounds interact with the active sites of plasmepsin V and X will serve as a foundation for the future design of dual inhibitors targeting these proteases.

Regulated cell death (RCD), the form of cell death that can be genetically controlled by multiple signaling pathways, plays an important role in organogenesis, tissue remodeling, and maintenance of organism homeostasis and is closely associated with various human diseases. Transforming growth factor-beta-activated kinase 1 (TAK1) is a member of the serine/threonine protein kinase family, which can respond to different internal and external stimuli and participate in inflammatory and immune responses. Emerging evidence suggests that TAK1 is an important regulator at the crossroad of multiple RCD pathways, including apoptosis, necroptosis, pyroptosis, and PANoptosis. The regulation of TAK1 affects disease progression through multiple signaling pathways, and therapeutic strategies targeting TAK1 have been proposed for inflammatory diseases, central nervous system diseases, and cancers. In this review, we provide an overview of the downstream signaling pathways regulated by TAK1 and its binding proteins. Their critical regulatory roles in different forms of cell death are also summarized. In addition, we discuss the potential of targeting TAK1 in the treatment of human diseases, with a specific focus on neurological disorders and cancer.

Lactate dehydrogenase A is a key enzyme in energy metabolism, with significant roles in cancer progression. Huang et al. identified LDHAα, a novel LDHA isoform derived from an alternative transcript initiated at AUG198, producing a protein 3 kDa larger than canonical LDHA. LDHAα exhibits enhanced glycolytic activity and promotes glucose uptake, lactate production, and tumor growth more effectively than LDHA. Regulated by c-MYC and FOXM1, LDHAα is mainly cytoplasmic and serves as a potential cancer biomarker and therapeutic target. These findings highlight LDHAα's unique role in cancer metabolism and its potential for advancing targeted cancer therapies.

Proteases rely on their active sites for substrate specificity, but these sites have inherent limitations that impact enzymatic efficiency and regulation. Exosites and cofactors help overcome these constraints by enhancing the protease's substrate interactions, specificity, and inhibition. Recent research by Gangemi et al. highlights the role of exosites in regulating the inhibition of the protease neutrophil elastase by the serpin alpha-1-antitrypsin. Understanding these mechanisms is crucial for developing therapeutic applications. Advances in computational analysis provide new insights into exosite function, complementing traditional structural studies and expanding potential biotechnological applications of protease inhibitors.

Dysregulation of Transient Receptor Potential Canonical 6 (TRPC6) channel is associated with pathologies in which cell contraction is relevant. Therefore, understanding the molecular mechanisms underlying the regulation of actin cytoskeletal function by TRPC6 is important. Here, we observed that TRPC6 upregulates the activity of RhoA GTPase, affecting the organization and polymerization of the actin cytoskeleton and focal adhesion dynamics. Moreover, TRPC6 activity promoted cell contraction and migration. Using mass spectrometry, we identified Rhotekin-1 (RTKN-1), an effector of RhoA, as a new TRPC6-interacting protein. In addition, RTKN-1 expression prevented the effects of TRPC6 on cell contraction, migration, and spreading. Moreover, calcium imaging, TRPC6-jGCaMP8f recordings, and patch clamp assays showed that RTKN-1 acts as a negative regulator of TRPC6 activity by reducing the abundance of TRPC6 in the plasma membrane through a mechanism that depends on RhoA activation. In this context, we found that RTKN-1 expression increased the endocytosis of TRPC6 in the early endosome compartment. In summary, these results suggest RTKN-1 as a new interactor and regulator of TRPC6 activity through a novel mechanism involving the modulation of TRPC6 trafficking.

T7 RNA polymerase (RNAP), the preferred tool for in vitro transcription (IVT), can generate double-stranded RNA (dsRNA) by-products that elicit immune stress and pose safety concerns. By combining the molecular beacon-based fluorescence-activated droplet sorting (FADS) utilized for random library screening with site-directed mutagenesis aimed at facilitating conformational changes in T7 RNAP, we successfully identified four mutants that exhibit reduced dsRNA content: M1 (V214A), M7 (F162S/A247T), M11 (K180E) and M14 (A70Q). Furthermore, the combinatorial mutant M17 (A70Q/F162S/K180E) exhibited significantly reduced dsRNA production under various conditions. Cellular experiments confirm the application potential of the mutants, displaying mitigated immune stress responses and enhanced protein translation compared to the wild-type protein. We then observed a close correlation between the production of dsRNA and the terminal transferase and RNA-dependent RNAP (RDRP) activities of T7 RNAP. The terminal transferase activity adds several nucleotides to the terminus of RNAs, while the RDRP activity extends the complementary region formed by self-pairing. In summary, we developed a novel approach for engineering T7 RNAP and demonstrated its potential in screening for T7 RNAP variants with reduced dsRNA production or improved product integrity.

In the framework of studies on protometabolism, Schlikker et al. characterized the conversion of pyridoxal to pyridoxamine under conditions mimicking the ones likely existing at the origin of metabolism. These conditions triggered nitrogen incorporation into amino acids in solution before the origins of enzymes. The suggested role for pyridoxal highlights its pivotal function in the transition from inorganic ammonia-dependent amino acid synthesis to organic reactions in aqueous solution and supports the "metabolism first" theory for biological evolution. Insights from the early evolution of natural enzymes can inspire the development of novel biocatalysts for biotechnological applications based on the catalytic versatility of pyridoxal.

Starch-binding domain-containing protein 1 (Stbd1) is a glycogen-binding protein which localizes to the endoplasmic reticulum (ER) membrane and ER-mitochondria contact sites (ERMCs). The protein undergoes N-myristoylation, which is a major determinant of its subcellular targeting. Stbd1 has been implicated in the control of glucose homeostasis, as evidenced by the finding that mice with targeted inactivation of Stbd1 display insulin resistance associated with increased ERMCs in the liver. In the present study, we addressed the effects of increased Stbd1 expression levels on insulin signaling. We show that Stbd1 overexpression enhances cellular sensitivity to insulin and improves insulin resistance in an in vitro hepatocyte cell model. We further demonstrate that increased Stbd1 expression levels are associated with enhanced activation of the AMP-activated protein kinase (AMPK), which is a central regulator of metabolism and an attractive therapeutic target for metabolic disorders related to insulin resistance, such as type 2 diabetes (T2D). The activation of AMPK signaling and the improved cellular response to insulin induced by Stbd1 overexpression occurred independently of N-myristoylation and associated changes in the number of ERMCs, glycogen levels, mitochondrial calcium, mitochondrial morphology, and respiratory function. Collectively, our findings uncover a new level of interaction between Stbd1 and AMPK, with Stbd1 acting as an upstream activator of AMPK signaling. Given that first-line drug treatments for insulin resistance and T2D are known activators of the AMPK pathway, these findings may provide a new perspective for the development of more effective therapeutic strategies.

The minichromosome maintenance protein (MCM) complex and Bloom syndrome helicase (BLM) are crucial components in DNA replication and cell division. MCM, a hexameric helicase that unwinds double-stranded DNA, serves as an important diagnostic and prognostic biomarker for cancer cells and a target for anticancer drug development. BLM, associated with G-quadruplex structures, is another key helicase in maintaining genomic stability. In this study, we investigate the interaction between MCM6 and BLM at the atomic level, as their expression levels are highly correlated in various cancer types, with elevated levels indicating poor prognosis. To elucidate the molecular basis of MCM6/BLM interaction, we employed fluorescence polarization anisotropy analysis, NMR chemical shifts perturbation analysis (CSP), and paramagnetic relaxation enhancement (PRE) experiments. MCM6 binding domain (MBD) C and D exhibit similar binding affinities to MCM6 winged-helix domain (WHD). However, significant CSPs with MBD-D and PRE experiments suggested that MBD-D is closer to MCM6 WHD than MBD-C. Despite both proteins containing numerous negatively charged residues, hydrophobic interactions govern the association between MCM6 WHD and BLM MBD-D. This biophysical characterization of the MCM6/BLM interaction provides new insights into their functional relationship and challenges existing models. Our findings reveal that MCM6 binds BLM at a different site than its other known partner chromatin licensing and DNA replication factor. Understanding these protein-protein interactions at the molecular level may contribute to the development of novel anticancer therapies targeting the MCM6/BLM interaction.

Inadequate binding of metal ions is a major cause of low activity and loss of function in metalloenzymes such as superoxide dismutase (SOD). In this study, we report a previously undescribed metal ion transfer mechanism mediated by the metal ion binding domain (MIBD) of SOD, which significantly improves SOD activity and stability. MIBD is mainly found in the N-terminal domain of SOD from Paenibacillus, which evolves under a metal ion deficient environment. MIBD can capture and transfer Fe to the conserved functional domain of SOD (SODA) via inter- and intramolecular interactions to maintain and enhance enzymatic activity at different ion concentrations. MIBD also exhibits a similar positive effect on the activity and stability of SOD from other species. Moreover, MIBD does not affect the optimum temperature and optimum pH of SOD, but it increases SOD activity to varying degrees compared with SODA at different temperatures and pHs. This unique MIBD also significantly improves the resistance of SOD to protein denaturants and detergents such as Gdn-HCl, Urea, and SDS, and improves physiological stability of SOD in simulated digestive fluids. This naturally evolved mechanism of SOD provides valuable insights into the design of well-performing metalloenzymes.

The pyridoxal-5'-phosphate-dependent enzyme DoeD is a L-2,4-diaminobutyric acid (DABA) transaminase that is part of the degradation pathway of the compatible solute ectoine. Ectoines are used by halophilic organisms to maintain osmotic balance under fluctuating salt concentrations (osmoadaptation). Classified under class III ω-aminotransferases, DoeD utilizes substrates with terminal amines, facilitated by dual substrate recognition involving two binding pockets, the O-pocket and the P-pocket. In this study, we have determined the first crystal structure of DoeD at 1.5 Å and conducted a biochemical and biophysical characterization of the dimeric DABA transaminase from the halophilic bacterium and model organism Chromohalobacter salexigens DSM 3043. Our findings reveal that pyruvate is the preferred co-substrate and that DoeD has a broad pH tolerance, minimal salt requirements, and can utilize a variety of amino donors. The crystal structure and substrate specificity studies of this highly expressed and stable DoeD suggest opportunities for enhancing enzymatic activity through targeted mutagenesis, optimizing it for industrial applications in green chemistry for chiral amine synthesis.

Modulation of enzyme activity by metabolites represents the most efficient and rapid way of controlling metabolism. Investigating enzyme-metabolite interactions can deepen our understanding of metabolic control and aid in identifying enzyme modulators with potential therapeutic applications. These interactions vary in strength, with dissociation constants (K) ranging from strong (nm) to weak (μm-mm). However, weak interactions are often overlooked due to the challenges in studying them. Despite this, weak modulators can reveal unknown binding modes and serve as starting points for compound optimization. In this study, we aimed to identify metabolites that weakly modulate the activity of human glucose-6-phosphate isomerase (GPI) and triosephosphate isomerase (TPI), which are potential therapeutic targets in tumor glycolysis. Through a combination of activity and binding assays, the screening revealed multiple weak inhibitors for the two targets, causing partial attenuation of their activity, with K and K in the low mm range. X-ray crystallography revealed six orthosteric ligands binding to the active sites - four inhibitors of GPI and two of TPI. Our findings underscore the role of weak interactions in enzyme regulation and may provide structural insights that could aid the design of inhibitors targeting human GPI and TPI in cancer intervention.

Within the intricate landscape of the tumour microenvironment (TME), hypoxia stands out as a pivotal factor profoundly shaping immune cell dynamics. Our study delves into this dynamic interplay, uncovering a cascade of events triggered by hypoxia. We unveil the emergence of protease-activated receptor 2 (PAR2; also known as F2R-like trypsin receptor 1 [F2RL1]) expression in monocyte cell lines (THP1) and peripheral blood mononuclear cells (PBMCs), orchestrated by the active serine protease matriptase (TMPRSS2; also known as transmembrane protease serine 2). Hypoxic conditions set the stage for a dual mechanism: lactate accumulation drives extracellular pH reduction, and facilitates matriptase activation from its latent form. A 10 mm lactate threshold activates matriptase, which in turn activates PAR2, driving monocytes towards M1 macrophage differentiation through the AKT2-NF-κβ axis. This triggers miR155 expression, which suppresses cytokine signaling 1 (SOCS1), a key regulator of M1-M2 polarisation, while NF-κβ enhances proinflammatory responses. Notably, our study reveals a temporal switch in this hypoxia-driven process. After 48 h of hypoxia, lactate levels rise to 25 mm, suppressing matriptase activation and driving a shift towards M2 polarisation. This transition, marked by reduced miR155 expression via AKT2-NFκβ axis inactivation, highlights the dynamic nature of macrophage polarisation. Our findings demonstrate matriptase as a key regulator driving macrophage polarisation towards the M1 phenotype within hypoxic microenvironments. This insight into macrophage behaviour under hypoxia suggests new strategies for immune modulation to counter tumour progression.

N6-methyladenosine (m6A) is a prevalent posttranscriptional mRNA modification involved in the regulation of transcript turnover, translation, and other aspects of RNA fate. The modification is mediated by multicomponent methyltransferase complexes (so-called writers) and is reversed through the action of the m6A-demethylases fat mass and obesity-associated (FTO) and alkB homolog 5 (ALKBH5) (so-called erasers). FTO promotes cell proliferation, colony formation and metastasis in models of triple-negative breast cancer (TNBC). However, little is known about genome-wide or specific downstream regulation by FTO. Here, we examined changes in the genome-wide transcriptome and translatome following FTO knockdown in TNBC cells. Unexpectedly, FTO knockdown had a limited effect on the translatome, while transcriptome analysis revealed that genes related to extracellular matrix (ECM) and epithelial-mesenchymal transition (EMT) are regulated through yet unidentified mechanisms. Differential translation of CEBPB mRNA into the C/EBPβ transcription factor isoform C/EBPβ-LIP is known to act in a pro-oncogenic manner in TNBC cells through regulation of EMT genes. Here we show that FTO is required for efficient C/EBPβ-LIP expression, suggesting that FTO has oncogenic functions through regulation of C/EBPβ-LIP.

C-X-C chemokine receptor type 4 (CXCR4) belongs to the seven-span G protein-coupled receptor family and plays an important role in promoting cancer metastasis. The single-span receptor, low-density lipoprotein receptor-related protein 6 (LRP6) is commonly considered to be a co-receptor of Wnt and plays an indispensable role during animal development. We recently demonstrated that LRP6 directly binds to CXCR4 via its ectodomain and prevents CXCR4-induced breast cancer metastasis. As a result of structural similarity, LRP6 is also categorized within the low-density lipoprotein receptor (LDLR) family that is involved in lipoprotein transport. We therefore explored whether other LDLR family members could interact with CXCR4. Immunoprecipitation and western blotting analysis showed that LDLR and very low-density lipoprotein receptor (VLDLR) physically interacted with CXCR4. Although stromal cell-derived factor 1/CXCR4 signaling was inhibited by LDLR and LRP1, it was promoted by VLDLR, LRP8 and apolipoprotein E, a general agonist of the LDLR family. Furthermore, breast cancer patients with high CXCR4 expression exhibited the worst prognosis only when combined with high levels of VLDLR/LRP8/apolipoprotein E or low expression of LDLR/LRP1, further suggesting distinct positive and negative roles of LDLR family members in regulating CXCR4. Additional members of the LDLR family, SORL1 and LRP2, also showed a negative correlation with CXCR4 in the prognosis of breast cancer patients. The findings of the present study show that the LDLR family can regulate CXCR4, endowing its members with a previously undescribed role, also suggesting their potential as new breast cancer therapeutic targets and prognostic markers.