Recent progress of artificial cells in structure design, functionality and the prospects in food biotechnology

Artificial cells have bridged the gap between non-living systems and biological cells. In recent years, artificial cells designed to simulate cellular structure and function have garnered significant attention. These artificial cells demonstrate vast potential for advancements in various biomedical areas, including simulating cell structure and function, creating innovative biosensors, facilitating bioactives transport, enabling micro and nanoreactors, and improving the targeted therapy for chronic foodborne diseases. In the interdisciplinary field of artificial cell construction, based on their constituent components, these systems can be categorized into lipid/polymer vesicles, coacervate, colloidosome, and metal-organic framework (MOF) artificial cells. They are anticipated to significantly enhance advancements in food science, particularly in cellular structure optimization, precise nutrition delivery, targeted nutrient release, and rapid detection methods. Consequently, this paper will comprehensively cover the historical background, fabrication techniques, and structural characteristics of artificial cells. From a functional design perspective, this review examines the growth and division mechanisms, energy production processes, encapsulation and reaction vessels, carriers, and information exchange systems of artificial cells. Ultimately, it provides a comprehensive evaluation of the safety of artificial cells from both biological and environmental viewpoints, to introduce and expand the application scenarios of this innovative biotechnology in food science.

Bias in, bias out - AlphaFold-Multimer and the structural complexity of protein interfaces

A structural understanding of protein-protein interactions is a key component of many facets of applied molecular biology research. AlphaFold-Multimer (AF-MM) provided a breakthrough in the ability to predict protein-protein interface structure. However, the available training data for this model and the resulting benchmarking and validation efforts show a bias toward interactions between more ordered regions of proteins. Here we highlight some of the successes and limitations of AF-MM and discuss available methods and future directions to enable balanced prediction of all interface types.

Toward deep learning sequence-structure co-generation for protein design

Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majority of today's models focus on generating either sequences or structures, emerging co-generation methods promise more accurate and controllable protein design, ideally achieved by modeling both modalities simultaneously. Here we review recent advances in deep generative models for protein design, with a particular focus on sequence-structure co-generation methods. We describe the key methodological and evaluation principles underlying these methods, highlight recent advances from the literature, and discuss opportunities for continued development of sequence-structure co-generation approaches.

Deep learning for RNA structure prediction

Predicting RNA structures from sequences with computational approaches is of vital importance in RNA biology considering the high costs of experimental determination. AI methods have revolutionized this field in recent years, enabling RNA structure prediction with increasingly higher accuracy and efficiency. With an increase in the number of models proposed for this task, this review presents a timely summary of the applications of AI, particularly deep learning, in RNA structure prediction, highlighting their methodology advances as well as the challenges and opportunities for further work in this field.

Cortico-striatal gamma oscillations are modulated by dopamine D3 receptors in dyskinetic rats

JOURNAL/nrgr/04.03/01300535-202504000-00031/figure1/v/2024-07-06T104127Z/r/image-tiff Long-term levodopa administration can lead to the development of levodopa-induced dyskinesia. Gamma oscillations are a widely recognized hallmark of abnormal neural electrical activity in levodopa-induced dyskinesia. Currently, studies have reported increased oscillation power in cases of levodopa-induced dyskinesia. However, little is known about how the other electrophysiological parameters of gamma oscillations are altered in levodopa-induced dyskinesia. Furthermore, the role of the dopamine D3 receptor, which is implicated in levodopa-induced dyskinesia, in movement disorder-related changes in neural oscillations is unclear. We found that the cortico-striatal functional connectivity of beta oscillations was enhanced in a model of Parkinson's disease. Furthermore, levodopa application enhanced cortical gamma oscillations in cortico-striatal projections and cortical gamma aperiodic components, as well as bidirectional primary motor cortex (M1) ↔ dorsolateral striatum gamma flow. Administration of PD128907 (a selective dopamine D3 receptor agonist) induced dyskinesia and excessive gamma oscillations with a bidirectional M1 ↔ dorsolateral striatum flow. However, administration of PG01037 (a selective dopamine D3 receptor antagonist) attenuated dyskinesia, suppressed gamma oscillations and cortical gamma aperiodic components, and decreased gamma causality in the M1 → dorsolateral striatum direction. These findings suggest that the dopamine D3 receptor plays a role in dyskinesia-related oscillatory activity, and that it has potential as a therapeutic target for levodopa-induced dyskinesia.

Computational exploration of the self-aggregation mechanisms of phenol-soluble modulins β1 and β2 in Staphylococcus aureus biofilms

The formation of functional bacterial amyloids by phenol-soluble modulins (PSMs) in Staphylococcus aureus is a critical component of biofilm-associated infections, providing robust protective barriers against antimicrobial agents and immune defenses. Clarifying the molecular mechanisms of PSM self-assembly within the biofilm matrix is essential for developing strategies to disrupt biofilm integrity and combat biofilm-related infections. In this study, we analyzed the self-assembly dynamics of PSM-β1 and PSM-β2 by examining their folding and dimerization through long-timescale atomistic discrete molecular dynamics simulations. Our findings revealed that both peptides primarily adopt helical structures as monomers but shift to β-sheets upon dimerization. Monomeric state, PSM-β1 exhibited frequent transitions between helical and β-sheet forms, while PSM-β2 largely retained a helical structure. Upon dimerization, both peptides showed pronounced β-sheet formation around conserved C-terminal residues 21-44. Residues 21-33, largely unstructured as monomers, demonstrated strong tendencies for β-sheet formation and intermolecular interactions, underscoring their central role in the self-assembly of both peptides. Additionally, the PSM-β1 N-terminus formed β-sheets only when interacting with the C-terminus, whereas the PSM-β2 N-terminus remained helical and uninvolved in β-sheet formation. These distinct aggregation behaviors likely contribute to biofilm dynamics, with C-terminal regions facilitating biofilm formation and N-terminal regions influencing stability. Targeting residues 21-33 in PSM-β1 and PSM-β2 offers a promising therapeutic approach for disrupting biofilm integrity. This study advances our understanding of PSM-β1 and PSM-β2 self-assembly and presents new targets for drug design against biofilm-associated diseases.

Unraveling the diversity of protein-carbohydrate interfaces: Insights from a multi-scale study

Protein-carbohydrate interactions play a crucial role in numerous fundamental biological processes. Thus, description and comparison of the carbohydrate binding site (CBS) architecture is of great importance for understanding of the underlying biological mechanisms. However, traditional approaches for carbohydrate-binding protein analysis and annotation rely primarily on the sequence-based methods applied to specific protein classes. The recently released DIONYSUS database aims to fill this gap by providing tools for CBS comparison at different levels: both in terms of protein properties and classification, as well as in terms of atomistic CBS organization. In the current study, we explore DIONYSUS content using a combination of the suggested approaches in order to evaluate the diversity of the currently resolved non-covalent protein-carbohydrate interfaces at different scales. Notably, our analysis reveals evolutionary convergence of CBS in proteins with distinct folds and coming from organisms across different kingdoms of life. Furthermore, we demonstrate that a CBS structure based approach has the potential to facilitate functional annotation for the proteins with missing information in the existing databases. In particular, it provides reliable information for numerous carbohydrate-binding proteins from rapidly evolving organisms, whose analysis is particularly challenging for classical sequence-based methods.

Design, synthesis, structural characterization, cytotoxicity and computational studies of Usnic acid derivative as potential anti-breast cancer agent against MCF7 and T47D cell lines

Development of novel inhibitors is necessary to counteract the rising prevalence of breast cancer (BC) in women in recent years, as evidenced by the side-effect profiles of a few clinically approved inhibitors. In this study, the usnic acid derivative (UA1) was synthesized due to the effectiveness of usnic acid (UA) against BC cell line. Furthermore, the structure of synthesized compound was determined using FT-IR, 1H NMR, 13C NMR, HSQC, and HMBC spectroscopic techniques. The anticancer potential of UA1 was assessed using the MTT assay on two different cell lines of BC including MCF7 and T47D. To ascertain the binding affinity and stability of the docking complex, further procedures included the in silico molecular docking, molecular dynamic simulation, principal component analysis, and binding free energy experiments. The cytotoxicity results show that the UA1 exhibits strong antitumor activities and comparable effects against BC cell lines with the IC50 values of 9.21 µM for MCF7 cell and 14.8 µM for T47D cell, respectively, where the positive control cisplatin showed the IC50 values of 8.95 µM for MCF7 cell and 10.9 µM for T47D cell. Additionally, the molecular docking results of UA1 showed that it interacts strongly into the active site of target protein. Molecular dynamics simulation results also revealed that the docking complex was formed stability with the RMSD and RMSF values of 0.50 nm and 0.19 nm, respectively. According to the PCA analysis, the target protein displays good conformational space behaviour when bound with UA1. Furthermore, the UA1 showed the free binding energy value of -18.52 kcal/mol with the target protein, which indicating that UA1 may prevent BC.

Unraveling the mechanisms underlying the fluorescent probe detection of microcystin-LR and its binding with CT-DNA

Cyanobacteria blooms are concerning due to algal toxins like microcystin-leucine arginine (MC-LR). Despite progress in detecting MC-LR and understanding its toxic effects, including calf thymus DNA (CT-DNA) damage, the mechanisms for fluorescent probe detection of MC-LR and its binding to CT-DNA are poorly understood. In this study, we designed three fluorescent probes for MC-LR detection. Probe 1, with an acidic recognition site, is effective but influenced by solution pH. Probe 2, featuring a benzene ring structure, shows stable detection regardless of pH. Probe 3 offers the best performance, combining a long-chain and benzene ring structure. This suggests that combining these structures is beneficial for MC-LR probe design. Using Probe 3, we observed a strong interaction between MC-LR and CT-DNA. UV absorption spectroscopy, circular dichroism (CD) spectra, and molecular docking techniques provided the first evidence of MC-LR binding to CT-DNA through intercalation, with a binding saturation value of 8.33, significantly impacting CT-DNA structure. This study introduces a novel strategy for designing fluorescent probes for MC-LR detection, along with new insights into the interactions between MC-LR and CT-DNA.

ClsC protein encoded by a stress-responsive operon in Escherichia coli functions as a trans-acting activator of RNase III

RNase III, an endoribonuclease that cleaves double-stranded RNAs (dsRNAs), significantly impacts Escherichia coli (E. coli) adaptation by regulating global RNA gene expression. YmdB from E. coli was characterized as a trans-acting regulator of RNase III. However, no protein encoded in E. coli has been characterized as an activator of RNase III. This study reports the discovery of ClsC protein, a phospholipase D (PLD) superfamily enzyme previously known as the third cardiolipin synthase (Cls) and a biofilm inhibitor in E. coli, as a novel RNase III activator. Overexpression of clsC in vivo stimulated the cleavage of RNase III-targeted lacZ fusions and antagonized the inhibition of RNase III by YmdB. Additional in vitro cleavage assays of RNase III-targeted RNAs using RNase III and ClsC confirmed this activity. Moreover, we identified multiple RNAs targeted by RNase III that are regulated dependently on cellular ClsC levels. Mechanistic investigations revealed that ClsC interacts with RNase III. Moreover, the isoleucine residue at the 466th position from the N-terminus of ClsC was identified as crucial for ClsC function. This study is the first to demonstrate that the ymdAB-clsC operon serves as an unexpected source for RNase III regulation in E. coli.

Spectroscopic and in silico data indicate that phenolic acids interact with aldose reductase with different degrees of affinity at a single binding site

Our previous studies demonstrated that the enzyme aldose reductase (AR) is activated by its interaction with tubulin, a mechanism which can lead to the emergence of secondary diseases in diabetic patients. We also found that different compounds derived from phenolic acid (CAFs) can prevent this interaction and thus AR activation. Here, we used spectroscopic and bioinformatic techniques to explore the interaction between AR and three CAFs: 3-nitrotyrosine (NTyr), Tyrosine (Tyr), and vanillic acid (Van). The results revealed that the CAFs alter the UV-Vis absorption spectrum of AR and significantly quenchAR fluorescence. These changes suggest the formation of stable AR-CAF complexes. Moreover, a single binding site for the CAFs was identified in AR, to which a single molecule of NTyr and at least two molecules of Tyr or Van appear to bind. NTyr showed the most affinity for interacting with the enzyme, followed by Tyr and Van. Binding occurs through a thermodynamically favorable and exothermic process. It involves van der Waals interactions and the creation of hydrogen bonds between the phenol substituent in the CAFs and the side residues in AR. Molecular docking calculations confirmed NTyr as the compound with the most affinity and revealed the multiple interactions that contribute to this affinity. These findings enhance our understanding of the molecular mechanisms through which different CAFs bind to AR and inhibit its interaction with tubulin. As such, they could pave the way for the design of novel adjunctive treatments that complement conventional antihyperglycemic therapies and mitigate complications associated with diabetes mellitus.

Virtual screening of polyherbal compounds for AKT1 and HSPB1 inhibition in breast cancer apoptosis pathway

Breast cancer is still a worldwide health issue, demanding the development of tailored, low-toxicity medicines. This study looks at the ability of a polyherbal formulation containing Ziziphus mauritiana, Nigella sativa, Phyllanthus niruri, Curcuma longa, and Annona muricata to inhibit the AKT1 and HSPB1 proteins that are involved in cancer growth. Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) found 23 bioactive chemicals, including 4-Coumaric acid, isovanillic acid, and confertin, exhibiting drug-like properties, membrane permeability, and anticancer bioactivity. Molecular docking demonstrated that these drugs have stable interactions with AKT1, whereas HSPB1 has modest stability. Based on molecular dynamics simulations, the most attractive possibilities were 4-coumaric acid and isovanillic acid, which had consistent binding stability and good energy profiles. Confertin has a lower interaction stability than the other compounds. These findings show that polyherbal substances successfully target essential apoptosis pathways in breast cancer. This work uses a combination of drug-likeness, bioactivity predictions, and computational analytics to identify new bioactive chemicals that might serve as the foundation for alternative breast cancer therapy. Future studies should confirm these findings by doing in vitro and in vivo trials to assess clinical applications. This novel approach emphasizes the potential of natural products in overcoming the limits of traditional cancer therapies, presenting a possible route for generating low-toxicity therapeutic alternatives.

Amyloid capture and aggregation inhibition by human serum albumin

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder characterized by amyloid-beta (Aβ) aggregation, primarily involving the peptides Aβ40 and Aβ42. Human serum albumin (HSA) has emerged as a potential therapeutic agent due to its ability to bind Aβ, inhibit aggregation, and promote disaggregation. This study quantitatively examined the interactions of HSA with both monomeric and aggregated forms of Aβ40 and Aβ42 using fluorescence techniques, including bulk steady-state fluorescence, fluorescence anisotropy, time-resolved fluorescence, and Fluorescence Correlation Spectroscopy (FCS). The binding constants determined from these methods were 4.45 × 104 M-1 for Aβ42 and 1.8 × 104M-1 for Aβ40, indicating strong but differential affinities. FCS demonstrated that HSA effectively dissociates Aβ aggregates, shifting the equilibrium toward monomeric states, with the disaggregation capacity positively correlated with HSA concentration. These findings support HSA's utility in therapies like plasma exchange to reduce the cerebral Aβ burden, providing critical insights into its mechanistic role and therapeutic potential.

Carbohydrate-active enzyme-catalyzed stereoselective glycosylation of complex natural product glycosides

Natural products and their derivatives are precious resources with extensive applications in various industrial fields. Enzymatic glycosylation is an efficient approach for chemical structure diversification and biological activity alternation of natural products. Herein, we reported a stereoselective glycosylation of complex natural product glycosides catalyzed by two carbohydrate-active enzymes (CAZys). ASP OleD, a mutant of glycosyltransferase OleD from Streptomyces antibioticus, catalyzed an explicit β-1,x-linkage glycosylation of the OH group of the glycosyl moiety of the representative plant-derived complex natural product glycosides, protodioscin (1) and epimedin C (2), producing two complex glycoside derivatives. The glycoside hydrolase Δ27ThCGT, a truncated cyclodextrin glucanotransferase from Thermoanaerobacter sp., exhibited a definite α-1,x-linkage glycosylation of the OH group of the glycosyl moiety of the glycosides 1, 2, and astragaloside IV (3), generating four complex glycoside derivatives. The chemical structures and absolute configurations of these enzymatic glycosylation products were determined by analysis of their HRMS and NMR data. The present study expands the enzymatic glycosylation diversification of complex glycosides catalyzed by the CAZys.

Conversion of Human Multidrug Transporter P-glycoprotein (ABCB1) from Drug Efflux to Uptake Pump: Evidence for a Switch Region Modulating the Direction of Substrate Transport

The multidrug transporter P-glycoprotein (P-gp), is pivotal in exporting various chemically dissimilar amphipathic compounds including anti-cancer drugs, thus causing multidrug resistance during cancer treatment. P-gp is composed of two transmembrane domains (TMDs), each containing six homologous transmembrane helices (TMHs). Among these helices, TMH 6 and 12 align oppositely, lining a drug-binding pocket in the transmembrane region which acts as a pathway for drug efflux. Previously, we demonstrated that specific mutations within TMH 6 and 12 resulted in loss of substrate efflux and altered the transport direction from efflux to uptake for some substrates. This suggested the presence of a regulatory switch that governs the direction of transport. In this study, we sought to elucidate the mechanism of switch region modulation of the uptake function by engineering several mutants via substituting specific residues in TMH 6 and 12. We discovered that the alanine substitution of four residues (V974, L975, V977, and F978) within the upper region of TMH 12, along with three residues (V334, F336, and F343) within TMH 6, was sufficient to convert P-gp from an efflux to an uptake pump. Additional mutagenesis of the residues in the middle region of TMH 12 revealed that the uptake function, like efflux, is reversible. Further studies, including molecular dynamics simulations, revealed that the switch region appears to act during the substrate translocation step. We propose that the switch region in TMH 6 and 12, which modulates the direction of transport by P-gp, provides a novel approach to selectively target P-gp-expressing cancer cells.

Role of ygaD in mediating polymyxin B resistance in Bacillus subtilis via efflux mechanisms

OBJECTIVE

The aim of this study is to analyze the resistance function and mechanism of the putative ATP-binding cassette (ABC) transporter YgaD against polymyxin B in Bacillus subtilis.

METHODS

The interaction between the YgaD protein and the antimicrobial peptide polymyxin B was initially assessed using molecular docking and molecular dynamics simulation. Subsequently, resistance assays and intracellular polymyxin B content measurements were conducted on Bacillus subtilis with a knockout of the ygaD gene and on Escherichia coli with heterologous expression of the ygaD gene to validate the resistance function mediated by the YgaD protein and deduce its potential resistance mechanism.

RESULTS

The results demonstrated that the YgaD protein could form stable complexes with polymyxin B and facilitated its efflux from bacterial cells, thereby reducing its intracellular accumulation and conferring resistance to polymyxin B.

CONCLUSION

Our study revealed that YgaD regulates polymyxin B resistance in Bacillus subtilis through an efflux mechanism. These findings contribute to the understanding of microbial resistance mechanisms against antimicrobial peptides and provide a theoretical basis for the future design and development of antimicrobial drugs.

Predicting the structure-altering mechanisms of disease variants

Missense variants can affect the severity of disease, choice of treatment, and treatment outcomes. While the number of known variants has been increasing at a rapid pace, available evidence of their clinical effect has been lagging behind, constituting a challenge for clinicians and researchers. Multiplexed assays of variant effects (MAVEs) are important to close the gap; nonetheless, computational predictions of pathogenicity are still often the only available data for scoring variants. Such methods are not designed to provide a mechanistic explanation for the effect of amino acid substitutions. To this purpose, we propose structure-based frameworks as ensemble methodologies, with each method tailored to predict a different aspect among those exerted by amino acid substitutions to link predicted pathogenicity to mechanistic indicators. We review available frameworks, as well as advancements in underlying structure-based methods that predict variant effects on several protein features, such as protein stability, biomolecular interactions, allostery, post-translational modifications, and more.

Identification of potential inhibitors targeting yellow fever virus helicase through ligand and structure-based computational studies

Yellow fever is a flavivirus having plus-sensed RNA which encodes a single polyprotein. Host proteases cut this polyprotein into seven nonstructural proteins including a vital NS3 protein. The present study aims to identify the most effective inhibitor against the helicase (NS3) using different advanced ligand and structure-based computational studies. A set of 300 ligands was selected against helicase by chemical structural similarity model, which are similar to S-adenosyl-l-cysteine using infiniSee. This tool screens billions of compounds through a similarity search from in-built chemical spaces (CHEMriya, Galaxi, KnowledgeSpace and REALSpace). The pharmacophore was designed from ligands in the library that showed same features. According to the sequence of ligands, six compounds (29, 87, 99, 116, 148, and 208) were taken for pharmacophore designing against helicase protein. Subsequently, compounds from the library which showed the best pharmacophore shared-features were docked using FlexX functionality of SeeSAR and their optibrium properties were analyzed. Afterward, their ADME was improved by replacing the unfavorable fragments, which resulted in the generation of new compounds. The selected best compounds (301, 302, 303 and 304) were docked using SeeSAR and their pharmacokinetics and toxicological properties were evaluated using SwissADME. The optimal inhibitor for yellow fever helicase was 2-amino-N-(4-(dimethylamino)thiazol-2-yl)-4-methyloxazole-5-carboxamide (302), which exhibits promising potential for drug development.

Targeting CDK6 in hormone receptor-positive breast cancer: inhibitor discovery for precision oncology through dynamics study

CDK6 is a critical protein involved in the regulation of the cell cycle, playing an important role in the progression from the G1 to S phase. In breast cancer, dysregulation of this protein is involved in tumour development and progression, particularly in hormone receptor-positive (HR+) breast cancers. The upregulation of CDK6 have been observed in a subset of breast cancers, leading to uncontrolled progression of the cell cycle and increased proliferation of cells. The purpose of this abstract is to provide an outline of CDK6's role. In breast cancer and the therapeutic strategies targeting CDK6 using specific selected inhibitors. To discover viable therapeutic candidates after competitive inhibition of CDK6 with a small molecular drug complex, high throughput screening and docking studies were used. Further, we carried the compounds based on ADMET properties and prediction of activity spectra for substances analysis. Finally, two different compounds were selected to carry out MD simulations. CDK6-IMPHY002642 and CDK6-IMPHY005260 are the two compounds that were identified. Overall, our results suggest that the CDK6-IMPHY002642 and CDK6-IMPHY005260 complex was relatively stable during the simulation. The compounds that have been found can also be further examined as potential therapeutic possibilities. The combined findings suggest that CDK6, together with their genetic changes, can be investigated in therapeutic interventions for precision oncology, leveraging early diagnostics and target-driven therapy.

Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells

High mutation and replication rates of HIV-1 result in the continuous generation of variants, allowing it to adapt to changing host environments. Mutations often have deleterious effects, but variants carrying them are rapidly purged. Surprisingly, a particular variant incapable of entering host cells was found to be rescued by host antibodies targeting HIV-1. Understanding the molecular mechanism of this rescue is important to develop and improve antibody-based therapies. To unravel the underlying mechanisms, we performed fully atomistic molecular dynamics simulations of the HIV-1 gp41 trimer responsible for viral entry into host cells, its entry-deficient variant, and its complex with the rescuing antibody. We find that the Q563R mutation, which the entry-deficient variant carries, prevents the native conformation of the gp41 6-helix bundle required for entry and stabilizes an alternative conformation instead. This is the consequence of substantial changes in the secondary structure and interactions between the domains of gp41. Binding of the antibody F240 to gp41 reverses these changes and re-establishes the native conformation, resulting in rescue. To test the generality of this mechanism, we performed simulations with the entry-deficient L565A variant and antibody 3D6. We find that 3D6 binding was able to reverse structural and interaction changes introduced by the mutation and restore the native gp41 conformation. Viral variants may not only escape antibodies but be aided by them in their survival, potentially compromising antibody-based therapies, including vaccination and passive immunization. Our simulation framework could serve as a tool to assess the likelihood of such resistance against specific antibodies.

Recognition of human telomeric G-quadruplex DNA by 1,5-disubstituted diethyl-amido anthraquinone derivative in different ion environments causing thermal stabilization and apoptosis

Ligand binding to G-quadruplex (G4) structures at human telomeric DNA ends promotes thermal stabilization, disrupting the interaction of the telomerase enzyme, which is found active in 80-85% of cancers and serves as a molecular marker. Anthraquinone compounds are well-known G-quadruplex (G4) binders that inhibit telomerase and induce apoptosis in cancer cells. Our current investigation is based on 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, a derivative of anthraquinone and its binding characterization with two different human telomeric DNA structures, wHTel26 and HTel22, in the effect of K+ and Na+ by using an array of biophysical, calorimetry, molecular docking and cell viability assay techniques. Binding constants (Kb) in the range of ∼105-107 M-1 and stoichiometries of 1:1, 2:1 & 4:1 were obtained from the absorbance, fluorescence, and circular dichroism study. Remarkable hypochromism (55, 97%) and ∼17 nm shift in absorbance, fluorescence quenching (95, 97%), the unaltered value of fluorescence lifetime, restoration of Circular Dichroism bands, absence of ICD band, indicated the external groove binding/binding somewhere at loops. This is also evident in molecular docking results, the ligand binds to groove forming base (G4, G5, G24, T25) and in the vicinity to TTA loop (G14, G15, T17) bases of wHTel26 and HTel22, respectively. Thermal stabilization induced by ligand was found greater in Na+ ion (27.5 °C) than (19.1 °C) in K+ ion. Ligand caused cell toxicity in MCF-7 cancer cell lines with an IC50 value of ∼8.4 µM. The above findings suggest the ligand, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione could be a potent anticancer drug candidate and has great therapeutic implications.Binding of disubstituted amido anthraquinone derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione to human telomere HTel22 antiparallel conformation induced thermal stabilization.

Improving protein-ligand docking results using the Semiempirical quantum mechanics: testing on the PDBbind 2016 core set

Molecular docking techniques are routinely employed for predicting ligand binding conformations and affinities in the in silico phase of the drug design and development process. In this study, a reliable semiempirical quantum mechanics (SQM) method, PM7, was employed for geometry optimization of top-ranked poses obtained from two widely used docking programs, AutoDock4 and AutoDock Vina. The PDBbind core set (version 2016), which contains high-quality crystal protein - ligand complexes with their corresponding experimental binding affinities, was used as an initial dataset in this research. It was shown that docking pose optimization improves the accuracy of pose predictions and is very useful for the refinement of docked complexes via removing clashes between ligands and proteins. It was also demonstrated that AutoDock Vina achieves a higher sampling power than AutoDock4 in generating accurate ligand poses (RMSD ≤ 2.0 Å), while AutoDock4 exhibits a better ranking power than AutoDock Vina. Finally, a new protocol based on a combination of the results obtained from the two docking programs was proposed for structure-based virtual screening studies, which benefits from the robust sampling abilities of AutoDock Vina and the reliable ranking performance of AutoDock4.

In-silico screening to identify phytochemical inhibitor for hP2X7: A crucial inflammatory cell death mediator in Parkinson's disease

The second most prevalent neurological disease among the elderly is Parkinson's disease, where neuroinflammation plays a significant role in its pathology. Purinergic signaling mediated by P2X7 plays a significant role in neuroinflammation and pyroptotic cell death pathways through mediators like NLRP3, Caspase-1, and Caspase-3, instigating pyroptotic cell death. No synthetic agent advanced in late-stage clinical trials due to their inefficacy and toxicity. Hence, in this study, we aimed to identify a phytoconstituent inhibitor against the hP2X7 receptor to ameliorate the inflammatory processes involved. To achieve this aim, we performed homology modeling of the receptor and screened phytoconstituents from a library of over 3500 commercially available phytoconstituents. Molecular docking through the Maestro program of the Schrödinger suite was performed considering evaluation parameters like docking score, docking pose and spatial arrangement, and MMGBSA binding free energy. Predictive pharmacokinetic and toxicity profiling was done using tools like QikProp, ADMETLab 2.0, SwissADME, and Protox-II. Molecular dynamic simulation was performed using Schrödinger's Desmond tool for the top 10 phytoconstituents. The complex stability was evaluated based on the ligand- and protein-RMSD, protein-ligand contact stability over a simulation period of 100 ns, protein RMSF, and ligand properties like RMSF, radius of gyration, intramolecular hydrogen bonding, and SASA. Based on the studies' results, silychristin, silybin, rosmarinic acid, nordihydroguaiaretic acid, and aurantiamide were shortlisted as the top 5 phytoconstituents against hP2X7. Further in-vitro and in-vivo studies would offer better clarity on the mechanism of action of these agents specifically related to pyroptotic cell death in various disease models.

Human genetic variants in SLC39A8 impact uptake and steady-state metal levels within the cell

The human SLC39A8 (hSLC39A8) gene encodes a plasma membrane protein SLC39A8 (ZIP8) that mediates the specific uptake of the metals Cd2+, Mn2+, Zn2+, Fe2+, Co2+, and Se4+ Pathogenic variants within hSLC39A8 are associated with congenital disorder of glycosylation type 2 (CDG type II) or Leigh-like syndrome. However, numerous mutations of uncertain significance are also linked to different conditions or benign traits. Our study characterized 21 hSLC39A8 variants and measured their impact on protein localization and intracellular levels of Cd2+, Zn2+, and Mn2+ We identified four variants that disrupt protein expression, five variants with high retention in the endoplasmic reticulum, and 12 variants with localization to the plasma membrane. From the 12 variants with plasma membrane localization, we identified three with complete loss of detectable ion uptake by the cell and five with differential uptake between metal ions. Further in silico analysis on protein stability identified variants that may affect the stability of homodimer interfaces. This study elucidates the variety of effects of hSLC39A8 variants on ZIP8 and on diseases involving disrupted metal ion homeostasis.

Assessment of PRMT6-dependent alternative splicing in pluripotent and differentiating NT2/D1 cells

Protein arginine methyltransferase 6 (PRMT6) is a well-characterized epigenetic regulator that methylates histone H3 at arginine 2 (H3R2me2a) in both promoter and enhancer regions, thereby modulating transcriptional initiation. We report here that PRMT6 also regulates gene expression at the post-transcriptional level in the neural pluripotent state and during neuronal differentiation of NT2/D1 cells. PRMT6 knockout causes widespread alternative splicing changes in NT2/D1 cells, most frequently cassette exon alterations. Most of the PRMT6-dependent splicing targets are not transcriptionally affected by the enzyme and regulated in an H3R2me2a-independent manner. However, for a small subset of splicing events, the PRMT6-mediated deposition of H3R2me2a overlaps with the splice site, suggesting a potential dual function in both transcriptional and co-/post-transcriptional regulation. The splicing targets of PRMT6 include ribosomal proteins, splicing factors, and chromatin-modifying enzymes such as PRMT4, DNMT3B, and ASH2L, some of which are associated with differentiation decisions. Taken together, our results in NT2/D1 cells show that PRMT6 exerts predominantly H3R2me2a-independent functions in RNA splicing, which may contribute to pluripotency and neuronal identity.

The Myotubularin Related Proteins and the Untapped Interaction Potential of Their Disordered C-Terminal Regions

Intrinsically disordered regions (IDRs) of proteins remain understudied with enigmatic sequence features relevant to their functions. Members of the myotubularin-related protein (MTMR) family contain uncharacterized IDRs. After decades of research on their phosphatase activity, recent work on the C-terminal IDRs of MTMR7 revealed new interactions and important new functions beyond the phosphatase function. Here we take a broader look at the C-terminal domains (CTDs) of 14 human MTMRs and use bioinformatic tools and biophysical methods to ask which other functions may be probable in this protein family. The predictions show that the CTDs are disordered and carry short linear motifs (SLiMs) important for targeting of MTMRs to defined subcellular compartments and implicating them in signaling, phase separation, interaction with diverse proteins, including transcription factors and are of relevance for cancer research and neuroscience. We also present experimental methods to study the CTDs and use them to characterize the coiled coil (CC) domains of MTMR7 and MTMR9. We show homo- and hetero-oligomerization with preference for MTMR7-CC to form dimers, while MTMR9-CC forms trimers. We relate the results to sequence features and make predictions for the structural landscape of other MTMRs. Our work gives a broad insight into the so far unrecognized features and SLiMs in MTMR-CTDs, and provides the basis for more in-depth experimental research on this diverse protein family and understudied IDRs in proteins in general.

α/β Hydrolases: Toward Unraveling Entangled Classification

α/β Hydrolase-like enzymes form a large and functionally diverse superfamily of proteins. Despite retaining a conserved structural core consisting of an eight-stranded, central β-sheet flanked with six α-helices, they display a modular architecture allowing them to perform a variety of functions, like esterases, lipases, peptidases, epoxidases, lyases, and others. At the same time, many α/β hydrolase-like families, even enzymatically distinct, share a high degree of sequence similarity. This imposes several problems for their annotation and classification, because available definitions of particular α/β hydrolase-like families overlap significantly, so the unambiguous functional assignment of these superfamily members remains a challenging task. For instance, two large and important peptidase families, namely S9 and S33, blend with lipases, epoxidases, esterases, and other enzymes unrelated to proteolysis, which hinders automatic annotations in high-throughput projects. With the use of thorough sequence and structure analyses, we newly annotate three protein families as α/β hydrolase-like and revise current classifications of the realm of α/β hydrolase-like superfamily. Based on manually curated structural superimpositions and multiple sequence and structure alignments, we comprehensively demonstrate structural conservation and diversity across the whole superfamily. Eventually, after detailed pairwise sequence similarity assessments, we develop a new clustering of the α/β hydrolases and provide a set of family profiles allowing for detailed, reliable, and automatic functional annotations of the superfamily members.

Exosomes secreted from M2-polarized macrophages inhibit osteoclast differentiation via CYLD

OBJECTIVE

Bone resorption mediated by osteoclast differentiation induces the occurrence of bone-related diseases. Macrophages, an origin of osteoclasts, whose M2 type can reduce inflammation-induced bone damage. We aimed to investigate the effect of M2 macrophage-derived exosomes on osteoclast formation and elucidate its underlying mechanism.

MATERIALS AND METHODS

Exosomes were isolated from M2 macrophages (M2-exo) and were used to treat osteoclast-like cells. Osteoclast formation was evaluated using tartrate-resistant acid phosphatase, quantitative real-time polymerase chain reaction (qRT-PCR), and Western blotting. The molecular mechanism of M2-exo function was analyzed by qRT-PCR, phosphor-kinase array analysis, and Western blotting.

RESULTS

M2-exo was internalized by osteoclasts and inhibited osteoclast differentiation in vitro. Moreover, CYLD was highly expressed in M2 macrophages and M2-exo-treated osteoclasts, and knockdown of it abrogated the inhibition of osteoclast differentiation caused by M2-exo. Additionally, CYLD suppressed the phosphorylation of STAT3, and STAT3 activator colivelin reversed the inhibition of osteoclast differentiation induced by CYLD overexpression.

CONCLUSION

M2-exo inhibits osteoclast differentiation via delivering CYLD, which inactivates STAT3 signaling. These findings may provide a novel therapeutic option for bone diseases including periodontitis.

Teaching AI to speak protein

Large Language Models for proteins, namely protein Language Models (pLMs), have begun to provide an important alternative to capturing the information encoded in a protein sequence in computers. Arguably, pLMs have advanced importantly to understanding aspects of the language of life as written in proteins, and through this understanding, they are becoming an increasingly powerful means of advancing protein prediction, e.g., in the prediction of molecular function as expressed by identifying binding residues or variant effects. While benefitting from the same technology, protein structure prediction remains one of the few applications for which only using pLM embeddings from single sequences appears not to improve over or match the state-of-the-art. Fine-tuning foundation pLMs enhances efficiency and accuracy of solutions, in particular in cases with few experimental annotations. pLMs facilitate the integration of computational and experimental biology, of AI and wet-lab, in particular toward a new era of protein design.

Temperature-driven CsgA-enhanced mutant enable distinct self-assembly

Functional coating materials have found extensive applications across various technological fields. However, the effectiveness of these coating depends critically on the choice of an appropriate medium. In this study, we developed an advanced "molecular glue", a CsgA variant known as CsgA-pro, which can serve as a versatile medium for biotherapy. CsgA-pro exhibits a remarkable temperature-driven transition, forming millimeter-scale protein fibers at low temperatures and transitioning to a "molecular glue" state at elevated temperatures. To demonstrate its potential as a "molecular glue", CsgA-pro-GFP was first immobilized onto a gauze surface, which was subsequently treated with chloroauric acid to generate gauze loaded with gold nanoparticles (Au NPs). These Au NPs were shown to possess potent antibacterial properties and to promote migration of L929 and HUVEC cells. When applied to wound healing, the Au NP-loaded gauze significantly accelerated the healing process compared to control groups, highlighting the therapeutic potential of this approach. These findings underscore the promise of CsgA-pro as a multifunctional tool in a wide range of applications, including multi-enzyme biocatalysis and immobilization. We envision that CsgA-pro will have broad applicability across diverse fields, offering substantial contributions to both technological innovations and biomedical advancements.

In silico bioprospecting of receptors for Oligoventin: An antimicrobial peptide isolated from spider eggs of Phoneutria nigriventer

BACKGROUND

Irresponsible and wholesale use of antimicrobial agents is the principal cause of the emergence of strains of resistant microorganisms to traditional drugs. Oligoventin is a neutral peptide isolated from spider eggs of Phoneutria nigriventer, with antimicrobial activity against Gram-positive, Gram-negative, and yeast organisms. However, the molecular target and pathways of antimicrobial activity are still unknown. Thus, the aim of the present study is to prospect receptors associated with the antimicrobial activity of Oligoventin using in silico tools.

METHODS

The PharmMapper and PDB server was used to prospect targets originating from microorganisms. Additionally, the PatchDock server was utilized to perform molecular docking between Oligoventin and the targets. Subsequently, the I-TASSER server was adopted to predict the ligand site. Finally, the docking results and predicted sites were compared with literature sites of each target.

RESULTS

Over 100 potential receptors for oligoventin have been identified. Among these, enoyl-ACP reductase (Idpdb1LXC) and thymidylate synthase ThyX (Idpdb 1O28) from bacteria and N-acetylglucosamine phosphate mutase (Idpdb 2DKD) showed superior interaction with oligoventin, exhibiting colocalization between docked residues and cofactor/active sites. These enzymes play a crucial role in fatty acid and DNA biosynthesis in prokaryotes and in cell wall synthesis in yeast.

CONCLUSION

Therefore, in silico results suggest that Oligoventin can impair fatty acid DNA, cell wall synthesis, thereby reducing microbial proliferation and causing microorganism death.

Characterization of the second type of tubuliform spidroin (TuSp1 variant 2) elucidates the essential role of cysteine within the repetitive domain in liquid-liquid phase separation-mediated silk formation and the mechanical properties of silk fibers

Orb-weaver spiders utilize morphologically differentiated abdominal glands to produce up to seven types of silks throughout their life cycles. Tubuliform silk is unique as it serves to protect developing embryos and hatchlings. However, our current understanding of the relationship between structure and function of tubuliform silk protein remains limited. Here, we present the full-length gene sequence of the second type of tubuliform spidroin (TuSp1 variant 2) from the orb-weaver spider Leucauge blanda. The L. blanda TuSp1 variant 2 (TuSp1-v2) contains 18 tandemly arrayed repeats, with each repeat having a cysteine residue. We demonstrate that the cysteine in L. blanda TuSp1-v2 repeats can form intermolecular disulfide bond and promote the liquid-liquid phase separation (LLPS) for silk formation. Moreover, the presence of cysteine partially enhances the thermostability of soluble spidroins and the mechanical properties of fibers, as demonstrated by comparative analyses of miniature TuSp1-v2 and its mutants. The integration of mechanical and structural data indicates that the recombinant TuSp1-v2 fiber exhibits high UV-A stability in both its mechanical and structural properties. This study provides new insights into the functions of cysteine in repetitive region and implies promising potentials for development new spidroin-based biomaterials.

A chitin-binding domain-containing gene is essential for shell development in the mollusc Tritia

Mollusc shells are diverse in shape and size. They are created by a shell epithelium which secretes a chitinous periostracum membrane at the growing edge of the shell, and then coordinates biomineral deposition on the underside of this membrane. Although mollusc shells are important for studying the evolution of morphology, the molecular basis of the shell development is poorly understood. In this paper, we investigate genes involved in the shell development of the gastropod mollusc Tritia (previously known as Ilyanassa). We characterize the contributions of the 2d micromere to the shell and other non-shell structures. We identify eight shell-specific genes and five non-shell specific genes by comparing the transcriptomes of wild-type and 2d ablated embryos. Morpholino knockdown of one of the shell-specific genes, ToChitin-binding domain-containing (ToChitin BD), results in shell defects. The chitinous periostracal membranes in ToChitin BD morpholino knockdown embryos lose their well-defined edge and peroxidase gradient.

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Overexpressed CD73 attenuates GSDMD-mediated astrocyte pyroptosis induced by cerebral ischemia-reperfusion injury through the A2B/NF-κB pathway

Ischemic stroke, resulting from the blockage or narrowing of cerebral vessels, causes brain tissue damage due to ischemia and hypoxia. Although reperfusion therapy is essential to restore blood flow, it may also result in reperfusion injury, causing secondary damage through mechanisms like oxidative stress, inflammation, and excitotoxicity. These effects significantly impact astrocytes, neurons, and endothelial cells, aggravating brain injury and disrupting the blood-brain barrier. CD73, an ectoenzyme that regulates adenosine production through ATP hydrolysis, plays a critical role in purinergic signaling and neuroprotection. During ischemic stroke, CD73 expression is dynamically regulated in response to ischemia and inflammation. It catalyzes the conversion of AMP to adenosine, which activates adenosine receptors to exert neuroprotective effects. Targeting the CD73-adenosine pathway presents a potential therapeutic strategy for mitigating ischemic stroke damage. Pyroptosis, a highly inflammatory form of programmed cell death mediated by inflammasomes like NLRP3 and caspases, plays a significant role in cerebral ischemia-reperfusion injury. Astrocytes, the most abundant CNS cells, contribute to both neuroprotection and injury, with pyroptosis exacerbating inflammation and brain damage. Regulating astrocyte pyroptosis is a promising therapeutic target. Our study investigates CD73's role in regulating astrocyte pyroptosis during ischemia-reperfusion injury. Using CD73 knockout mice and overexpression models, along with in vitro oxygen-glucose deprivation/reperfusion experiments, we found that CD73 overexpression reduces GSDMD-mediated astrocyte pyroptosis via the A2B/NF-κB pathway. These findings offer a novel approach to reducing neuroinflammation, protecting astrocytes, and improving outcomes in ischemic stroke.

The roles of intrinsically disordered proteins in neurodegeneration

Neurodegenerative diseases such as Amyotrophic Lateral Sclerosis, Alzheimer's disease, Parkinson's disease, and Huntington's disease share a common pathological hallmark: the accumulation of misfolded proteins, particularly involving intrinsically disordered proteins (IDPs) like TDP-43, FUS, Tau, α-synuclein, and Huntingtin. These proteins undergo pathological aggregation, forming toxic inclusions that disrupt cellular function. The dysregulation of proteostasis mechanisms, including the ubiquitin-proteasome system (UPS), ubiquitin-independent proteasome system (UIPS), autophagy, and molecular chaperones, exacerbates these proteinopathies by failing to clear misfolded proteins effectively. Emerging therapeutic strategies aim to restore proteostasis through proteasome activators, autophagy enhancers, and chaperone-based interventions to prevent the toxic accumulation of IDPs. Additionally, understanding liquid-liquid phase separation (LLPS) and its role in stress granule dynamics offers novel insights into how aberrant phase transitions contribute to neurodegeneration. By targeting the molecular pathways involved in IDP aggregation and proteostasis regulation, and better understanding the specificity of each component, research in this area will pave the way for innovative therapeutic approaches to combat these neurodegenerative diseases. This review discusses the molecular mechanisms underpinning IDP pathology, highlights recent advancements in drug discovery, and explores the potential of targeting proteostasis machinery to develop effective therapies.

Exposure to low concentrations of ethanol alters global gene expression patterns in Vibrio parahaemolyticus

Vibrio parahaemolyticus is a foodborne pathogen commonly associated with seafood worldwide. Ethanol is widely used as a disinfectant and preservative in the food industry. Low concentrations of ethanol can inhibit the growth of V. parahaemolyticus and alter its protein expression profile and stress resistance. However, it remains unknown how ethanol exposure affects the behavior and gene expression of V. parahaemolyticus. In this study, RNA sequencing revealed differential expression of 1020 genes in response to 1.5 % (v/v) ethanol, including biofilm-associated genes, c-di-GMP metabolism-related genes, major virulence genes, putative regulatory genes, and Hsp-like protein encoding genes. Specifically, genes involved in exopolysaccharides, type VI secretion system 1, thermostable direct hemolysin, and type III secretion system 2 were upregulated upon exposure to 1.5 % ethanol. Additionally, the data also suggest a significant decrease in swimming and swarming motility, as well as a notable increase in biofilm formation, under 1.5 % ethanol stress. This study enhances our understanding of how V. parahaemolyticus adapts its behavior and gene expression to low concentrations of ethanol.

RNA structure prediction using deep learning - A comprehensive review

In computational biology, accurate RNA structure prediction offers several benefits, including facilitating a better understanding of RNA functions and RNA-based drug design. Implementing deep learning techniques for RNA structure prediction has led tremendous progress in this field, resulting in significant improvements in prediction accuracy. This comprehensive review aims to provide an overview of the diverse strategies employed in predicting RNA secondary structures, emphasizing deep learning methods. The article categorizes the discussion into three main dimensions: feature extraction methods, existing state-of-the-art learning model architectures, and prediction approaches. We present a comparative analysis of various techniques and models highlighting their strengths and weaknesses. Finally, we identify gaps in the literature, discuss current challenges, and suggest future approaches to enhance model performance and applicability in RNA structure prediction tasks. This review provides a deeper insight into the subject and paves the way for further progress in this dynamic intersection of life sciences and artificial intelligence.

Spatial profiling of ANO7 in prostate tissue: links to AR-signalling-associated lipid metabolism and inflammation

Prostate cancer (PrCa) is highly prevalent in the Western world. Currently, however, there are many unmet needs in PrCa care, for example in distinguishing between clinically significant and indolent cases in early phases of the disease. ANO7 is a prostate-specific gene associated with PrCa risk and prognosis, but its exact function in the prostate remains unclear. This study investigates the role of ANO7 in benign prostatic epithelium using spatial transcriptomics by examining differences between ANO7-expressing and non-expressing epithelial regions and their corresponding stromal compartments. A total of 18,676 protein-coding genes were assessed from prostatectomy samples collected from patients with localised prostate cancer. In the collected sample cohort, ANO7 exhibited a distinct, heterogeneous, on-off epithelial expression pattern, enabling an in-depth analysis of ANO7-dependent processes. ANO7-positive epithelium was predominantly enriched with luminal epithelial cells and a specific NK cell subtype, CD56bright. In contrast, ANO7-negative regions were characterised by enrichment of club cells, inflammation, and features of proliferative inflammatory atrophy. Gene-set enrichment analysis revealed that ANO7 expression is associated with androgen receptor (AR) signalling and lipid metabolism. A detailed analysis of differentially expressed genes identified an ANO7- signature, which consisted of genes co-expressed with ANO7 in luminal cells, that demonstrated high consistency in bulk RNA-sequencing (RNA-seq) data. The ANO7-signature was enriched for AR-regulated genes, which highlighted lipid metabolism processes, particularly arachidonic acid metabolism, as a key metabolic feature of the ANO7-positive epithelium. Furthermore, the ANO7-signature demonstrated clinical significance in low-grade PrCa, correlating with a better response to therapy. In summary, these results highlight the potential role of ANO7 in regulating lipid metabolism associated with androgen signalling in benign luminal cells and low-grade cancer, reinforcing the hypothesis that ANO7 functions as a tumour suppressor. © 2025 The Pathological Society of Great Britain and Ireland.

Are protein language models the new universal key?

Protein language models (pLMs) capture some aspects of the grammar of the language of life as written in protein sequences. The so-called pLM embeddings implicitly contain this information. Therefore, embeddings can serve as the exclusive input into downstream supervised methods for protein prediction. Over the last 33 years, evolutionary information extracted through simple averaging for specific protein families from multiple sequence alignments (MSAs) has been the most successful universal key to the success of protein prediction. For many applications, MSA-free pLM-based predictions now have become significantly more accurate. The reason for this is often a combination of two aspects. Firstly, embeddings condense the grammar so efficiently that downstream prediction methods succeed with small models, i.e., they need few free parameters in particular in the era of exploding deep neural networks. Secondly, pLM-based methods provide protein-specific solutions. As additional benefit, once the pLM pre-training is complete, pLM-based solutions tend to consume much fewer resources than MSA-based solutions. In fact, we appeal to the community to rather optimize foundation models than to retrain new ones and to evolve incentives for solutions that require fewer resources even at some loss in accuracy. Although pLMs have not, yet, succeeded to entirely replace the body of solutions developed over three decades, they clearly are rapidly advancing as the universal key for protein prediction.

Benzbromarone improves blood hypercoagulability after TBI by reducing phosphatidylserine externalization through inhibition of TMEM16F expression

AIMS

Traumatic brain injury-induced coagulopathy (TBI-IC) frequently occurs after TBI, exacerbating the severity of TBI and affecting patient prognosis. Benzbromarone (BBR) is commonly used to treat hyperuricemia; however, its protective effects against TBI-IC remain unknown. Therefore, we explored whether BBR could improve TBI.

MATERIALS AND METHODS

C57BL/6 wild-type mice were subjected to fluid percussion injury to mimic TBI, and BBR was administered intraperitoneally 30 min after TBI. Magnetic resonance imaging (MRI) and Evans blue dye extravasation were used to assess the prognosis, tail bleeding time, ELISA, and coagulation tests assess coagulation function. We further explored the potential mechanism by which BBR alleviates hypercoagulation after TBI using flow cytometry.

KEY FINDINGS

The intraperitoneally injected BBR group showed improved survival and neurological severity scores compared to the TBI group. Subsequently, we found that hypercoagulability developed 3 h after TBI and that the administration of BBR improved this hypercoagulability. BBR also reduced the degree of platelet phosphatidylserine (PS) exposure after TBI, platelet activation, and Ca2+ overload, in addition to inhibition of scramblase activity in procoagulant platelets.

SIGNIFICANCE

Our findings indicate that BBR reduces PS externalization by inhibiting TMEM16F expression, thereby improving blood hypercoagulability after TBI.

Hydrodynamic characterization of the FtsZ protein from Escherichia coli demonstrates the presence of linear and lateral trimers

FtsZ is a bacterial protein that plays a crucial role in cytokinesis by forming the Z-ring. This ring acts as a scaffold to recruit other division proteins and guide the synthesis of septal peptidoglycan, which leads to cell constriction. In its native state, the FtsZ protein from Escherichia coli (EcFtsZ) is a multi-oligomer comprising dimers, trimers, tetramers, and hexamers in a dynamic self-association equilibrium depending on its concentration. This study employed classical methods of analytical biochemistry that included native polyacrylamide gel electrophoresis, size-exclusion chromatography, sedimentation through sucrose gradients, and chemical cross-linking with formaldehyde to characterize the EcFtsZ. The dimers, trimers, and tetramers are the most prevalent oligomers of the EcFtsZ protein; however, the trimer has been understudied compared to the dimer. In this study, we characterized uncross-linked trimers by exclusion chromatography and crosslinked trimers by sedimentation. The results of size-exclusion chromatography demonstrated that the uncross-linked trimer of EcFtsZ has a mass of 128.8 kDa and a frictional ratio f/fo of 1.96, which coincides with the theoretical frictional ratio of 1.80 for a linear trimer. The EcFtsZ protein treated with formaldehyde resulted in a polypeptide band of 128 kDa recognized by anti-FtsZ antibodies and a frictional ratio Smax/S20,w equal to 1.95, which agrees with the theoretical calculation of the frictional ratio of a lateral trimer. The protein-protein interaction prediction program (PEPPI) identified a contact site between subunits in the C-terminal linker region of the EcFtsZ protein, which has the potential to interfere with the recognition of the C-terminal linker by the ClpX(P) protease.

Hemoglobin-derived amyloid fibrils: Fibrillization mechanisms and potential applications

Fibrils from food proteins were widely reported but it has not been reported on sus scrofa hemoglobin. Utilizing fibrillization strategies can efficiently utilize hemoglobin and reduce waste. This work explores a new strategy to prepare hemoglobin-derived fibrils by removing the heme group. Hydrophobic interaction was found to be a key factor in promoting the fibrillization process. Heme presence hindered the fibrillization process possibly by restricting the unfolding process due to its high hydrophobicity. The core sequences of fibrils were identified as HBA 30-36, HBA 96-110, HBA 126-139, HBB 15-41, HBB 104-117 and HBB 83-145, which are generally of high hydrophobicity and HSA (Hot spots of aggregation) scores. Fibrils exhibited excellent gel properties, water retention, iron-binding properties, and enhanced positive surface charge. These findings contribute to establishing a fibrillization mechanism of hemoglobin and highlight the possibility of hemoglobin-sourced fibrils in food industry.

Strategies for the design of biomimetic cell-penetrating peptides using AI-driven in silico tools for drug delivery

Cell-penetrating peptides (CPP) have gained rapid attention over the last 25 years; this is attributed to their versatility, customisation, and 'Trojan horse' delivery that evades the immune system. However, the current CPP rational design process is limited, as it requires several rounds of peptide synthesis, prediction and wet-lab validation, which is expensive, time-consuming and requires extensive knowledge in peptide chemistry. Artificial intelligence (AI) has emerged as a promising alternative which can augment the design process, for example by determining physiochemical characteristics, secondary structure, solvent accessibility, disorder and flexibility, as well as predicting in vivo behaviour such as toxicity and peptidase degradation. Other more recent tools utilise supervised machine learning (ML) to predict the penetrative ability of an amino acid sequence. The use of AI in the CPP design process has the potential to reduce development costs and increase the chances of success with respect to delivery. This review provides a survey of in silico tools and AI platforms which can be utilised in the design process, and the key features that should be taken into consideration when designing next generation CPPs.

Engineering thermostable fluorescent DNA aptamer for the isothermal amplification of nucleic acids

Isothermal amplification-based nucleic acid detection technologies have become rapid and efficient tools for molecular diagnostics. Sequence-specific monitoring methods are crucial for isothermal amplification, as they help identify the occurrence of extended primer dimers, which can lead to false positive results. Fluorescent aptamers are promising tools for real-time monitoring of isothermal amplification but are inherently limited by thermostability. Here, we report an engineered fluorescent DNA aptamer variant, named thermostable Lettuce (TS-Lettuce), with a 5 °C higher melting temperature and 20 times greater fluorescence at 60 °C, ideal for real-time monitoring of sequence-specific isothermal amplification. Using molecular dynamics simulations for structural analyses, we introduced mutations to wild-type Lettuce to redesign the non-core sequences of the aptamer structure for tightly stabilizing its folding, thereby enhancing thermostability. The TS-Lettuce offers greater versatility and ease of design for coupling with isothermal amplification for all-in-one nucleic acid detection. We demonstrated three applications of TS-Lettuce in isothermal amplification: fluorescent turn-off, fluorescent turn-on, and fluorescent aptamer switch, facilitating the sequence-specific detection of nucleic acids. In addition, the results generated by TS-Lettuce are visible to the naked eye, enhancing the utility of isothermal amplification reactions in resource-constrained areas. The thermostable fluorescent DNA aptamers can be further utilized in more isothermal amplification methods.

A Triple-pose Complex Between an Extended WIP Motif and a C-terminal SH3 Domain Modulates Cortactin Activity

The central domain of WASp-interacting protein (WIP) interacts with the cortactin SH3 domain through a previously undefined binding motif. This interaction affects extracellular matrix (ECM) degradation and the invasive phenotype of cells. Here, using NMR-based methods, we identify the major WIP epitope modulating this binding event as residues 168-183, an unexpectedly long segment uncharacteristic of SH3 peptidic ligands. A scanning mutagenesis analysis showed that peptide binding 'hotspots' are distributed throughout the binding sequence. To uncover the structural basis of WIP-cortactin recognition we utilized edited-filtered NOESY experiments to determine the structure of the intermediate-affinity SH3/peptide complex. Analysis of the NOESY pattern suggests that the peptide sequence dictates three interchanging binding modes, two oppositely oriented canonical poses involving N-terminal interactions, corresponding to class I and class II complexes, and a non-canonical pseudo-class II pose involving C-terminal interactions. The latter pose highlights the importance of the hydrophobic surface adjacent to the canonical binding grooves and accounts for the extended binding motif. Design of mutant peptides with increased affinity based on this multi-conformational complex demonstrates how these structural insights may impact design of improved inhibitors of the WIP-cortactin interaction with potential therapeutic applications.

Bacterial microcompartment architectures as biomaterials for conversion of gaseous substrates

Bacterial microcompartments (BMCs) are protein shells encapsulating multiple enzymes of a metabolic pathway. Interpretations of early experiments on carboxysomes led to the narrative that transport of small gases (CO2, O2) across the shell membrane is restricted. Since then, this notion has been largely contradicted by studies of engineered shells, although these shell constructs lack important proteins present in the native BMCs, altering the synthetic shells' topology, surface and mechanical properties. We discuss here an updated model of gas permeability that informs the design of engineered shells for catalysis on gas substrates and outline how nonshell suprastructures of BMC shell proteins could be used in formulating sustainable biomaterials for hydrogen generation via methane pyrolysis and for other greenhouse gas mitigations.

The role of long non-coding RNAs in cardiovascular diseases: A comprehensive review

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide, posing significant challenges to healthcare systems. Despite advances in medical interventions, the molecular mechanisms underlying CVDs are not yet fully understood. For decades, protein-coding genes have been the focus of CVD research. However, recent advances in genomics have highlighted the importance of long non-coding RNAs (lncRNAs) in cardiovascular health and disease. Changes in lncRNA expression specific to tissues may result from various internal or external factors, leading to tissue damage, organ dysfunction, and disease. In this review, we provide a comprehensive discussion of the regulatory mechanisms underlying lncRNAs and their roles in the pathogenesis and progression of CVDs, such as coronary heart disease, atherosclerosis, heart failure, arrhythmias, cardiomyopathies, and diabetic cardiomyopathy, to explore their potential as therapeutic targets and diagnostic biomarkers.

Regulation of Branchial Anoctamin 1 Expression in Freshwater- and Seawater-Acclimated Japanese Medaka, Oryzias latipes

In euryhaline teleosts, the cystic fibrosis transmembrane conductance regulator (CFTR) in seawater (SW)-type chloride cells facilitates apical Cl- secretion for SW adaptation, while alternative Cl- excretion pathways remain understudied. This study investigates the role of the calcium-activated chloride channel, Anoctamin 1 (ANO1), in the gills of the euryhaline Japanese medaka (Oryzias latipes) under hyperosmolality and cortisol (CORT) influence. Acclimation to artificial SW, NaCl, mannitol, or glucose significantly upregulated ANO1 and CFTR mRNA expression in gills, unlike urea treatment. In situ hybridization revealed ANO1 mRNA in chloride cells co-expressing CFTR and Na+, K+-ATPase under hyperosmotic conditions. ANO1 inhibition elevated plasma Cl- concentration, indicating impaired Cl- excretion. CORT or dexamethasone administration in freshwater (FW) fish significantly increased branchial ANO1 and CFTR mRNA expression, an effect attenuated by the glucocorticoid receptor (GR) antagonist RU486. Hyperosmotic treatment of isolated gill tissues rapidly induced ANO1 mRNA expression independent of CFTR mRNA changes, and this induction was unaffected by RU486. These findings highlight the dual regulation of ANO1 expression via hyperosmolality-induced cellular response and the CORT-GR system. Thus, branchial ANO1 may likely complement CFTR in Cl⁻ excretion, playing a key role in the hyperosmotic adaptation of euryhaline teleosts.

Novel computational and drug design strategies for the inhibition of human T-cell leukemia virus 1-associated lymphoma by Astilbin derivatives

Human T-cell leukemia virus 1 (HTLV-1) associated lymphoma is a devastating malignancy triggered by HTLV-1 infections. We employeda comprehensive drug design and computational strategy in this work to explore the inhibitory activitiesof Astilbin derivatives against HTLV-1-associated lymphoma. We evaluated the stability, binding affinities, and various computational analysis of Astilbin derivatives against target proteins, such as HTLV-1 main protease and HTLV-1 capsid protein. The root mean square deviation (RMSD), root mean square fluctuation, radius of gyration, hydrogen bond analysis, principal component analysis (PCA) and dynamic cross-correlation matrix (DCCM) were applied to characterize these protein-ligand interactions further. Ligand-03 and ligand-04 exhibited notable binding affinity to HTLV-1 capsid protein, while ligand-05 displayed high binding affinity to HTLV-1 protease. MD simulation analysis revealed that ligand-03, bound to HTLV-1 capsid protein, demonstrated enhanced stability with lower RMSD values and fewer conformational changes, suggesting a promising binding orientation. Ligand-04, despite stable binding, exhibited increased structural deviations, making it less suitable. Ligand-05 demonstrated stable binding to HTLV-1 protease throughout the simulation period at 100 nanoseconds. Hydrogen bond analysis indicated that ligand-05 formed persistent hydrogen bonds with significantresidues, contributing to its stability. PCA highlighted ligand-03's more remarkable conformational changes, while DCCM showed ligand-05's distinct dynamics, indicating its different behavior in the complex. Furthermore, binding free energy calculations supported the favorable interactions of ligand-03 and ligand-04 with HTLV-1 capsid protein, while ligand-05 showed weaker interactions with HTLV-1 protease. Molecular electrostatic potential and frontier molecular orbital analyses provided insights into these compounds' charge distribution and stability. In conclusion, this research found Astilbin derivatives as potential inhibitors of HTLV-1-associated lymphoma. Future attempts at drug development will benefit from the steady interaction landscape provided by Ligand-03, Ligand-04 and Ligand-05, which showed the most attractive binding profile with the target protein. These results open up new opportunities for innovative drug development, and more experimental testing should be done between Astilbin derivatives and HTLV-1-associated lymphoma.