SWISS-MODEL: homology modelling of protein structures and complexes

The gene characteristics and adaptive evolution of the tumor necrosis factor superfamily (TNFSF) in miiuy croaker, Miichthysmiiuy

The tumor necrosis factor superfamily (TNFSF) is crucial in regulating immune responses, with its members mediating various biological functions through key signaling pathways. However, the gene characteristics of this family and their comparative and evolutionary analysis across species remain limited. In this study, 12 TNFSF genes were identified in the genome-wide of miiuy croaker. Analyses were conducted on evolutionary relationships, conserved motifs, gene duplication, and selection pressure. Conserved motif analyses revealed that the C-terminal motifs of vertebrate TNFSF proteins were more conserved than the N-terminus. Sequence alignment and conservation analysis identified an unrecognized helix structure within the TNF homology domain, which exhibited structural conservation among vertebrates. Synteny and selection pressure analyses indicated that the TNFSF in miiuy croaker exhibited tandem and segmental duplication events. Evolutionary selection pressures may contributed to the functional differentiation of this family. These findings could enhance the understanding of TNFSF gene characteristics and evolutionary relationships, and provide new insights for studying immune-related TNFSF genes.

HDAC11 Inhibition as a Potential Therapeutic Strategy for AML: Target Identification, Lead Discovery, Antitumor Potency, and Mechanism Investigation

Herein, we identified that HDAC11 is involved in the pathogenesis of AML and is a potential therapeutic target for AML. Considering the scarcity of HDAC11 inhibitors, structurally novel HDAC11 inhibitors were developed, identifying A9 as the most potent one, which phenocopied the apoptosis induction, cell cycle arrest, and differentiation promotion effects of HDAC11 knockdown in AML cells. Moreover, A9 not only promoted iron uptake by upregulating TF and TFRC but also promoted iron release by upregulating HMOX1, which cooperatively led to iron homeostasis disruption and the consequent ferroptosis in AML cells. Mechanism investigation indicated that A9-induced HMOX1 upregulation was due to the activation of the p62-Keap1-Nrf2 pathway. Notably, the combination of A9 with chemotherapy drugs synergistically reduced AML cell viability in vitro. The robust in vivo anti-AML efficacy of A9, alone and combined with cytarabine, was also validated. Collectively, our study revealed pharmacological inhibition of HDAC11 as a potential therapeutic strategy for AML.

Functional and Mechanistic Insights into the Fatty-Acid CoA Ligase FadK in Escherichia coli

BACKGROUND

Escherichia coli (E. coli) is a common opportunistic bacterial pathogen in both human and animal populations. Fatty acids serve as the central carbon and energy source, a process mediated by fatty acid-coenzyme A (CoA) ligases encoded by fad genes such as FadK. However, the function and the mechanism of FadK remain unclear.

METHODS

The three-dimensional structure of FadK was modeled using AlphaFold2. After expression and purification, monomeric FadK was successfully isolated. The enzymatic activity was assayed, and real-time quantitative polymerase chain reaction (RT-qPCR) was performed to quantify FadK expression levels.

RESULTS

In enzymatic assays of fatty acid CoA ligase activity, caprylic acid was found to be the optimal substrate for FadK. We determined the optimal catalytic conditions for FadK, which include a pH of 7.4, ATP concentration of 0.6 mM, CoA concentration of 0.8 mM, and Mg2+ concentration of 0.8 mM at 37 °C. Notably, the activity of FadK showed a decrease with increasing concentrations of dodecyl-AMP, which was further confirmed by the RT-qPCR results.

CONCLUSIONS

Our findings will serve as a fundamental framework for the development of innovative therapeutics that target E. coli infections.

A facultative plasminogen-independent thrombolytic enzyme from Sipunculus nudus

Current thrombolytic therapies primarily function by converting plasminogen into plasmin, a process dependent on the fibrin-activator complex. This dependence, coupled with the substantial molecular size of plasmin, constrains its effectiveness in degrading D-dimer and restricts its diffusion within thrombi. Here, we introduce a small facultative plasminogen-independent thrombolytic enzyme, snFPITE, isolated from Sipunculus nudus. Compared to traditional thrombolytic agents, snFPITE does not require plasminogen for thrombolysis, although its presence enhances lytic activity. This enzyme fully degrades cross-linked fibrin without leaving residual nondegradable D-dimer and generates a smaller fibrinolytic-active agent from plasminogen. A series of male rats and mice models further confirm that snFPITE is a safety injectable thrombolytic agent. Mechanistically, snFPITE activates plasminogen and degrades fibrin(ogen) in a multisite cleavage manner. snFPITE is inhibited by plasminogen activator inhibitor 1 and α2-antiplasmin via a competitive inhibition. We further identify 28 snFPITE candidate sequences, of which 10 are confirmed as functional genes.

Integrating ensemble machine learning and multi-omics approaches to identify Dp44mT as a novel anti-Candida albicans agent targeting cellular iron homeostasis

Introduction

Candidiasis, mainly caused by Candida albicans, poses a serious threat to human health. The escalating drug resistance in C. albicans and the limited antifungal options highlight the critical need for novel therapeutic strategies.

Methods

We evaluated 12 machine learning models on a self-constructed dataset with known anti-C. albicans activity. Based on their performance, the optimal model was selected to screen our separate in-house compound library with unknown anti-C. albicans activity for potential antifungal agents. The anti-C. albicans activity of the selected compounds was confirmed through in vitro drug susceptibility assays, hyphal growth assays, and biofilm formation assays. Through transcriptomics, proteomics, iron rescue experiments, CTC staining, JC-1 staining, DAPI staining, molecular docking, and molecular dynamics simulations, we elucidated the mechanism underlying the anti-C. albicans activity of the compound.

Result

Among the evaluated machine learning models, the best predictive model was an ensemble learning model constructed from Random Forests and Categorical Boosting using soft voting. It predicts that Dp44mT exhibits potent anti-C. albicans activity. The in vitro tests further verified this finding that Dp44mT can inhibit planktonic growth, hyphal formation, and biofilm formation of C. albicans. Mechanistically, Dp44mT exerts antifungal activity by disrupting cellular iron homeostasis, leading to a collapse of mitochondrial membrane potential and ultimately causing apoptosis.

Conclusion

This study presents a practical approach for predicting the antifungal activity of com-pounds using machine learning models and provides new insights into the development of antifungal compounds by disrupting iron homeostasis in C. albicans.

Enhanced chemotaxis and degradation of nonylphenol in Pseudoxanthomonas mexicana via CRISPR-mediated receptor modification

In this study, a novel nonylphenol (NP)-degrading bacterium, Pseudoxanthomonas mexicana CH, was isolated from wastewater treatment plant effluent. Phylogenetic analysis showed its close relationship to P. mexicana AMX 26BT. The strain displayed chemotaxis toward NP, with Mcp24 as the key chemoreceptor. The Mcp24 deletion mutant (CH- 1) had weaker chemotaxis and NP degradation (over 30% lower in solution and 8% lower in sludge than the wild type). In vitro, Mcp15's C-terminal pentapeptide DWQEF was methylated by CheR. Using CRISPR, this pentapeptide was added to Mcp24 to create CH- 2. CH- 2 showed better NP chemotaxis (17% higher in plate assays and 39% higher in capillary assays) and higher NP degradation rates (23.5% and 24.2% higher in solution and sludge, respectively). These findings demonstrate that NP acts as a bacterial chemoattractant, with Mcp24 as the receptor. Enhancing Mcp24's C-terminal pentapeptide improves chemotaxis and degradation efficiency, representing a significant advancement in bioremediation by strengthening bacterial responses to pollutants.

Lysine source for ε-poly-l-lysine biosynthesis depends on diaminopimelate pathway during its production in Streptomyces albulus

Streptomyces albulus NBRC14147 produces the polycationic homopoly(amino acid) ε-poly-l-lysine (ε-PL). Due to its antimicrobial properties, nontoxicity to humans, biodegradability, and permeability, there is a high demand for ε-PL. As ε-PL is produced by l-lysine polymerization, elucidating the source of l-lysine for ε-PL production is crucial for enhancing its yield. In actinobacteria, l-lysine is produced by diaminopimelate (DAP) pathway. In this study, 2,6-pyridine-dicarboxylate (PDC) was identified as the inhibitor of DapB, a DAP pathway enzyme, by comparing the structure of DapB from Mycobacterium tuberculosis with the model structure of DapB from S. albulus. We also found that adding PDC inhibited the growth of S. albulus. More importantly, PDC additions during the initial stages of the ε-PL production phase led to the accumulation of amino acids generated from pyruvate and l-aspartic 4-semialdehyde, while the ε-PL production was terminated. These findings suggest that de novo biosynthesized nascent l-lysine from the DAP pathway contributes to ε-PL production.

Salt-Resistant and Ethanol-Resistant Monoamine Oxidases: New Sight for yobN Mining from Bacillus and Biogenic Amine Degradation Mechanism in Fermented Food

Amine oxidases have strong capabilities for the degradation of biogenic amines (BAs) in fermented foods. However, their application is limited by substrate specificity, and high concentrations of ethanol and salt can hinder their effectiveness. This study presents a novel approach utilizing comparative genomics, protein clustering analysis, and full homology modeling to identify three amine oxidases: KCYOBN from the salt-resistant Bacillus subtilis, and LYYOBN1 and LYYOBN2 from the ethanol-resistant Bacillus cereus. These enzymes are highly similar in structure and exhibit broad substrate specificities. KCYOBN maintains over 84% relative activity at 20% (w/v) NaCl, while LYYOBN1 and LYYOBN2 retain over 32 and 21% relative activity at 25% vol ethanol. Variations in key residues are one of the reasons for the differences in tolerance. In fermented foods, KCYOBN degraded 45.97% of the total BAs in cooking wine and 38.33% in fish sauce. LYYOBN1 achieved the highest degradation rate of 32.93% in huangjiu. LYYOBN2 exhibited degradation rates of 30.00% in soy sauce and 35.14% in wine with no significant impact on flavor compounds. The significance of this work lies in the identification of the novel salt-resistant KCYOBN and ethanol-resistant LYYOBN1 and LYYOBN2 through this new method, which can simultaneously degrade multiple BAs and have a broad application potential.

Structural Insights into Kainate Receptor Desensitization

Kainate receptors (KARs), along with AMPA and NMDA receptors, belong to the ionotropic glutamate receptor (iGluR) family and play critical roles in mediating excitatory neurotransmission throughout the central nervous system. KARs also regulate neurotransmitter release and modulate neuronal excitability and plasticity. Receptor desensitization plays a critical role in modulating the strength of synaptic transmission and synaptic plasticity. While KARs share overall structural similarity with AMPA receptors, the desensitized state of KARs differs strikingly from that of other iGluRs. Despite extensive studies on KARs, a fundamental question remains unsolved: why do KARs require large conformational changes upon desensitization, unlike other iGluRs? To address this, we present cryo-electron microscopy structures of GluK2 with double cysteine mutations in non-desensitized, shallow-desensitized and deep-desensitized conformations. In the shallow-desensitized conformation, two cysteine crosslinks stabilize the receptors in a conformation that resembles the desensitized state of AMPA receptors. However, unlike the tightly closed pore observed in the deep-desensitized KAR and desensitized AMPAR conformations, the channel pore in the shallow-desensitized state remains incompletely closed. Patch-clamp recordings and fluctuation analysis suggest that this state remains ion-permeable, indicating that the lateral rotational movement of KAR ligand-binding domains (LBDs) is critical for complete channel closure and stabilization of the receptor in desensitization states. Together with the multiple conformations representing different degree of desensitization, our results define the unique mechanism and conformational dynamics of KAR desensitization.

Highlights

We present cryo-EM structures of GluK2 kainate receptors with engineered cysteine crosslinks at the inter-dimer interface, which restrict subunit lateral rotation and attenuate receptor desensitization.The structure of GluK2 double cysteine mutant in complex with the allosteric potentiator BPAM344 and glutamate represents a non-desensitized state, highlighting the critical conformational changes required for ion channel gating.The glutamate-bound GluK2 mutant adopts multiple conformations, representing both shallow- and deep-desensitized states. Electrophysiological recordings indicate that the GluK2 kainate receptor mutant recovers from desensitization more rapidly, resembling AMPA receptors. Our structural and functional data suggest that shallow-desensitized KARs remain conductive, implying that the large lateral LBD rotation during KAR desensitization is essential for complete channel closure, distinguishing KARs from other iGluRs.

A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein

The Coronavirus Immunotherapeutic Consortium (CoVIC) conducted side-by-side comparisons of over 400 anti-SARS-CoV-2 spike therapeutic antibody candidates contributed by large and small companies as well as academic groups on multiple continents. Nine reference labs analyzed antibody features, including in vivo protection in a mouse model of infection, spike protein affinity, high-resolution epitope binning, ACE-2 binding blockage, structures, and neutralization of pseudovirus and authentic virus infection, to build a publicly accessible dataset in the database CoVIC-DB. High-throughput, high-resolution binning of CoVIC antibodies defines a broad and predictive landscape of antibody epitopes on the SARS-CoV-2 spike protein and identifies features associated with durable potency against multiple SARS-CoV-2 variants of concern and high in vivo efficacy. Results of the CoVIC studies provide a guide for selecting effective and durable antibody therapeutics and for immunogen design as well as providing a framework for rapid response to future viral disease outbreaks.

The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection

The obligate intracellular pathogen Chlamydia trachomatis replicates in a specialized membrane-bound compartment where it repositions host organelles during infection to acquire nutrients and evade host surveillance. We describe a bacterial effector, Dre1, that binds specifically to dynactin associated with host microtubule organizing centers without globally impeding dynactin function. Dre1 is required to reposition the centrosome, mitotic spindle, Golgi apparatus, and primary cilia around the inclusion and contributes to pathogen fitness in cell-based and mouse models of infection. We utilized Dre1 to affinity purify the megadalton dynactin protein complex and determined the first cryoelectron microscopy (cryo-EM) structure of human dynactin. Our results suggest that Dre1 binds to the pointed end of dynactin and uncovers the first bacterial effector that modulates dynactin function. Our work highlights how a pathogen employs a single effector to evoke targeted, large-scale changes in host cell organization that facilitate pathogen growth without inhibiting host viability.

Genome-wide identification of the nuclear redox protein gene family revealed its potential role in drought stress tolerance in rice

Introduction

Thioredoxins (TRX) are redox-active proteins critical for plant stress adaptation. As a TRX family member, nucleoredoxin (NRX) maintains drought-induced redox homeostasis, yet its genome-wide characterization in rice remains uninvestigated.

Methods

Using HMMER3.0 (E-value <1e-5) and TBtools, we identified OsNRX genes across three rice varieties (Minghui63, Nipponbare, 9311). Conserved domains were verified by SMART/CDD, while promoter cis-elements were systematically predicted with PlantCARE. Tissue-specific expression patterns were analyzed using RiceXPro data, and drought responses were quantified via qRT-PCR in drought-tolerant (Jiangnong Zao 1B) versus sensitive (TAISEN GLUTINOUS YU 1157) varieties under PEG6000 stress.

Results

Ten OsNRX genes were classified into three subfamilies (NRX1/NRX2/NRX3) exhibiting conserved domain architectures. Promoter analysis identified abundant stress-responsive elements (ABRE, MBS) and phytohormone signals (ABA/JA/SA). Tissue-specific expression profiles revealed NRX1a dominance in roots/hulls, versus NRX1b/NRX2 enrichment in endosperm. Drought stress triggered rapid OsNRX upregulation (20-53-fold within 3-6h), with tolerant varieties showing earlier NRX2 activation than sensitive counterparts.

Discussion

OsNRX genes exhibit dynamic drought-responsive regulation, while their spatiotemporal expression in glumes, embryos, and endosperm suggests potential dual roles in stress adaptation and grain development. These results provide molecular targets for improving drought resilience in rice breeding.

A Comprehensive Analysis of the Alternative Splicing Co-Factor U2AF65B Gene Family Reveals Its Role in Stress Responses and Root Development

U2AF65, a 65 kDa splicing co-factor, promotes spliceosome assembly. Although its role in alternative splicing (AS) is known, the function of U2AF65B (the large subunit of U2AF65) remains unclear. Therefore, we systematically identified and analyzed the U2AF65B gene family across 36 plant species, revealing 103 putative members with conserved structures and functions. Phylogenetic analysis divided the genes into two clades and five subgroups, indicating evolutionary divergence. Gene structure and conserved motif analyses showed that most U2AF65B genes have complex structures and shared similar motifs. Homology modeling and amino acid conservation analyses revealed significant conservation in U2AF65B amino acid sequences, particularly in Groups D and E. Cis-acting element analysis indicated that U2AF65B genes respond to various stimuli, supported by expression analysis under different stress conditions. Subcellular localization predictions indicated that U2AF65B proteins primarily localize in the nucleus and the cytoplasm. Alternative splicing (AS) profile analysis showed that the AS frequency likely varies between species. Functional analysis of the AtU2AF65B mutant in Arabidopsis revealed that AtU2AF65B function loss enhances root elongation and attenuates ABA-dependent germination suppression, indicating negatively regulated seedling growth and development. These findings provide insights into the evolutionary history, molecular mechanisms, and functional roles of the U2AF65B gene family in plants.

Identification of a conserved cryptic epitope with cross-immunoreactivity in outer membrane protein K (OmpK) from Vibrio species

Outer membrane protein K (OmpK) has been proven to be an ideal vaccine candidate for broad-spectrum cross-prevention against Vibriosis. However, due to the extensive biological and genetic diversity of Vibrio species, current OmpK subunit vaccines can only target different strains of the same bacterial species or closely related species and have difficulty providing promising cross-immunoprotection against more diverse Vibrio infections. In recent years, the development of epitope-focused vaccines has been described as the latest stage in the development of vaccine formulations, providing new ideas for the development of broad-spectrum Vibrio vaccines. Interestingly, a cryptic epitope (K7) was identified in OmpK from Vibrio species, which is itself immunogenic but is not involved in the immune response to intact OmpK. Epitope K7 is a 15-residue hairpin structure in OmpK predicted to contain a 6-residue extracellular turn region. Interestingly, unlike other highly variable extracellular long loops, epitope K7 is the only conserved extracellular short turn in OmpK, with a similarity of 33 % to 93 %. K7 homologous peptides stimulated the production of specific antibodies, confirming their high immunogenicity. Cross-immunoreactivity between K7 homologous and K7-induced antibodies was evaluated by peptide-based ELISA, western blot, and cell-based ELISA. Flow cytometry and immunofluorescence assay further confirmed that the native epitope K7 in OmpK is surface-exposed and therefore an extracellular target that binds to antibodies. Moreover, an antibody-dependent and complement-mediated serum bactericidal assay suggested that epitope K7-induced antibodies have vibriocidal activity. In conclusion, we identified a conserved cryptic epitope with cross-immunoreactivity in OmpK from Vibrio species. Our results suggest that epitope K7 could be an ideal candidate for the design of epitope-focused vaccines against diverse Vibrio infections.

Cell-Free Reaction System for ATP Regeneration from d-Fructose

Adenosine triphosphate (ATP)-dependent in vitro bioprocesses, such as cell-free protein synthesis and the production of phosphorylated fine chemicals, are of considerable industrial significance. However, their implementation is mainly hindered by the high cost of ATP. We propose and demonstrate the feasibility of a cell-free ATP regeneration system based on the in situ generation of the high-energy compound acetyl phosphate from low-cost d-fructose and inorganic phosphate substrates. The enzyme cascade chains d-fructose phosphoketolase, d-erythrose isomerase, d-erythrulose phosphoketolase, and glycolaldehyde phosphoketolase activities theoretically enabling production of 3 mol ATP per mol of d-fructose. Through a semirational engineering approach and the screening of nine single-mutation libraries, we optimized the phosphoketolase (PKT) from Bifidobacterium adolescentis, identifying the improved variant Bad.F6Pkt H548N. This mutant exhibited a 5.6-fold increase in d-fructose activity, a 2.2-fold increase in d-erythrulose activity, and a 1.3-fold increase in glycolaldehyde activity compared to the wild-type enzyme. The Bad.F6Pkt H548N mutant was initially implemented in a cell-free reaction system together with an acetate kinase from Geobacillus stearothermophilus and a glycerol kinase from Cellulomonas sp. for the production of glycerol-3 phosphate from ADP and glycerol. We demonstrated the feasibility of ATP regeneration from 25 mM d-fructose with a stoichiometry of 1 mol of ATP per mol of C6 ketose. Subsequently, the reaction system was enhanced by incorporating d-erythrose isomerase activity provided by a l-rhamnose isomerase from Pseudomonas stutzeri. In the complete system, the ATP yield increased to 2.53 mol molfructose-1 with a maximum productivity of 7.2 mM h-1.

Expanding catalytic versatility of modular polyketide synthases for alcohol biosynthesis

Modular polyketide synthases biosynthesize structurally diverse natural products by a set of catalytic domains that operate in an assembly line fashion. Although extensive research has focused on the rational reprogramming of modular polyketide synthases, little has been attempted to introduce noncanonical catalytic reactions on the assembly line. Here, we demonstrate the insertion of a thioester reductase domain, which can generate a terminal alcohol group instead of the canonical carboxylic acid, onto the assembly line polyketide synthases. We show that the didomain insertion of the acyl carrier protein and thioester reductase pair is generally effective for engineering of various polyketide synthase pathways. As a proof of concept, stereoselective and stereodivergent bioproduction of non-natural diols, namely, 1,3-butanediols and 2-methyl-1,3-butanediols, is achieved by harnessing the modularity of polyketide synthases. Our study expands the catalytic versatility of modular polyketide synthases and paves the way toward biosynthesis of designer alcohols.

How to Tell an N from an O: Controlling the Chemoselectivity of Methyltransferases

S-Adenosyl-l-methionine (SAM)-dependent methyltransferases (MTs) are important enzymes in numerous biological pathways. They share a common S N 2 mechanism but act on different nucleophilic substrates in vivo. Therefore, MTs have a specific chemoselectivity to transfer CH3 onto the correct atom type and substrate. Caffeate O-MT from Prunus persica (PpCaOMT) and anthranilate N-MT from Ruta graveolens (RgANMT) share a high similarity regarding their amino acid sequence (>74%). Nevertheless, the physiological substrates (caffeate vs anthranilate) and attacking nucleophiles (hydroxyl vs amino group) are strikingly different. We demonstrate that the differing chemoselectivity is governed by different conformational states of the two enzymes. O-Methylation catalyzed by CaOMTs requires a "closed" conformation, whereas ANMTs perform N-methylation in an "open" state. We rationally designed seven variants for both PpCaOMT and RgANMT, which changed their original nucleophile preference to different extents, up to a full inversion. Interestingly, the generated O-selective ANMT variant catalyzes O-methylation considerably faster than wildtype CaOMT. Molecular dynamics (MD) simulations and hydrogen/deuterium exchange mass spectrometry (HDX-MS) experiments showed that the mutations induced changes in the conformational dynamics of the enzyme variants and by modulating the open/closed transitions impact the corresponding chemoselectivity. Our data show that the selectivity of the methyl transfer reaction is not solely governed by the key residues directly involved in the methyl transfer but is rather synergistically modulated by the conformational dynamics of the enzyme and reaction conditions.

The Identification and Characterization of a Novel Alginate Lyase from Mesonia hitae R32 Exhibiting High Thermal Stability and Potent Antioxidant Oligosaccharide Production

Alginate lyases are of great importance in biotechnological and industrial processes, yet research on these enzymes from Mesonia genus bacteria is still limited. In this study, a novel PL6 family alginate lyase, MhAly6, was cloned and characterized from the deep-sea bacterium Mesonia hitae R32. The enzyme, composed of 797 amino acids, contains both PL6 and GH28 catalytic domains. A phylogenetic analysis revealed its classification into subfamily 1 of the PL6 family. MhAly6 showed optimal activity at 45 °C and pH 9.0, retaining over 50% activity after 210 min of incubation at 40 °C, highlighting its remarkable thermal stability. The enzyme exhibited degradation activity toward sodium alginate, Poly M, and Poly G, with the highest affinity for its natural substrate, sodium alginate, producing alginate oligosaccharides (AOSs) with degrees of polymerization (DP) ranging from 2 to 7. Molecular docking identified conserved catalytic sites (Lys241/Arg262) and Ca2+ binding sites (Asn202/Glu234/Glu236), while the linker and GH28 domain played an auxiliary role in substrate binding. Antioxidant assays revealed that the MhAly6-derived AOSs showed potent radical-scavenging activity, achieving 80.64% and 95.39% inhibition rates against DPPH and ABTS radicals, respectively. This work not only expands our understanding of alginate lyases from the Mesonia genus but also highlights their biotechnological potential for producing functional AOSs with antioxidant properties, opening new avenues for their applications in food and pharmaceuticals.

A new set of mutations in the second transmembrane helix of the Cox2p-W56R substantially improves its allotopic expression in Saccharomyces cerevisiae

The dual genetic control of mitochondrial respiratory function, combined with the high mutation rate of the mitochondrial genome (mtDNA), makes mitochondrial diseases among the most frequent genetic diseases in humans (1 in 5,000 in adults). With no effective treatments available, gene therapy approaches have been proposed. Notably, several studies have demonstrated the potential for nuclear expression of a healthy copy of a dysfunctional mitochondrial gene, referred to as allotopic expression, to help recover respiratory function. However, allotopic expression conditions require significant optimization. We harnessed engineering biology tools to improve the allotopic expression of the COX2-W56R gene in the budding yeast Saccharomyces cerevisiae. Through conducting random mutagenesis and screening of the impact of vector copy number, promoter, and mitochondrial targeting sequence, we substantially increased the mitochondrial incorporation of the allotopic protein and significantly increased recovery of mitochondrial respiration. Moreover, CN-PAGE analyses revealed that our optimized allotopic protein does not impact cytochrome c oxidase assembly, or the biogenesis of respiratory chain supercomplexes. Importantly, the most beneficial amino acid substitutions found in the second transmembrane helix (L93S and I102K) are conserved residues in the corresponding positions of human MT-CO2 (L73 and L75), and we propose that mirroring these changes could potentially help improve allotopic Cox2p expression in human cells. To conclude, this study demonstrates the effectiveness of using engineering biology approaches to optimise allotopic expression of mitochondrial genes in the baker's yeast.

Loose Anagen Hair Associated with Wooly Hair Caused by a Heterozygous, Intronic KRT71 Variant

BACKGROUND

Loose anagen hair syndrome is a recently described genetic form of non-scarring alopecia that occurs in children and is due to poorly anchored hair shafts during the anagen phase. It can occur alone or in association with hair pathology or complex systemic phenotypes.

METHODS

We report a mother and daughter with loose anagen hair syndrome that is associated with wooly hair, although it shows variable expressivity. We studied the family using genomic sequencing and identified an intronic variant in their KRT71 that segregates in an autosomal dominant pattern and is suspected to affect splicing in the tail domain of this hair follicle keratin. We studied this variant with a minigene experimental approach.

RESULTS

We provide experimental evidence that the identified intronic variant affects splicing in the tail domain, which is critical to the biomechanical properties of the keratin intermediate filaments. We demonstrate that it affects splicing by adding 12 bases to the mature transcript and consequently four amino acids to the peptide.

CONCLUSION

We suspect that this variant is responsible for the poorly anchored and finely curled hair in the mother and daughter, which leads to a proposed diagnosis of autosomal dominant wooly hair, as well as loose anagen hair syndrome. We thus expand the variant spectrum of KRT71 and its associated phenotypes to include both disorders.

Structural and Energetic Insights into SARS-CoV-2 Evolution: Analysis of hACE2-RBD Binding in Wild-Type, Delta, and Omicron Subvariants

The evolution of SARS-CoV-2, particularly the emergence of Omicron variants, has raised questions regarding changes in its binding affinity to the human angiotensin-converting enzyme 2 receptor (hACE2). Understanding the impact of mutations on the interaction between the receptor-binding domain (RBD) of the spike protein and hACE2 is critical for evaluating viral transmissibility, immune evasion, and the efficacy of therapeutic strategies. Here, we used molecular dynamics (MD) simulations and binding energy calculations to investigate the structural and energetic differences between the hACE2- RBD complexes of wild-type (WT), Delta, and Omicron subvariants. Our results indicate that the Delta and the first Omicron variants showed the highest and the second-highest binding energy among the variants studied. Furthermore, while Omicron variants exhibit increased structural stability and altered electrostatic potential at the hACE2-RBD interface when compared to the ancestral WT, their binding strength to hACE2 does not consistently increase with viral evolution. Moreover, newer Omicron subvariants like JN.1 exhibit a bimodal conformational strategy, alternating between a high-affinity state for hACE2 and a low-affinity state, which could potentially facilitate immune evasion. These findings suggest that, in addition to enhanced hACE2 binding affinity, other factors, such as immune evasion and structural adaptability, shape SARS-CoV-2 evolution.

Protein Engineering and Dual-Module Optimization for Efficient NMN Production in E. coli

Nicotinamide mononucleotide (NMN) has received widespread attention as a supplement of NAD+ in cells. In this study, a dual-module reaction system was constructed to synthesize NR using uridine and nicotinamide, and further to efficiently synthesize NMN. First, module 1 was constructed, which catalyzed the synthesis of NMN from NR using an efficient NRK and ATP regeneration system. Then module 2 was constructed by introducing pyrimidine nucleoside phosphorylase (PyNP) to synthesize NMN from uridine and NAM under the synergistic catalysis of NRK. Based on the fact that NRK has both phosphorylation and group transfer functions in the dual-module system, the mutant KlmNRKM4 with nearly 4-fold increased stability was obtained through predicted structure and evolutionary conservation analysis. At the same time, the pncC, deoD, ushA, nadR and deoB genes encoding endogenous degradative enzymes in Escherichia coli affect substrate and intermediate conversion were knocked out. Finally, by optimizing the reaction conditions of the dual-module recombination system, a high NMN conversion rate of 81.1% was achieved using 300 mM uridine and nicotinamide as substrates. This study provides a novel and efficient pathway for the biosynthesis of NMN.

Structural dynamics of the dengue virus non-structural 5 (NS5) interactions with promoter stem-loop A (SLA)

The dengue virus (DENV) NS5 protein, essential for viral RNA synthesis, is an attractive antiviral drug target. DENV NS5 interacts with the stem-loop A (SLA) promoter at the 5'-untranslated region of the viral genome to initiate negative-strand synthesis. However, the conformational dynamics of this interaction remains unclear. Our study explores the structural dynamics of DENV serotype 2 NS5 (DENV2 NS5) in complex with SLA, employing surface plasmon resonance (SPR), hydrogen-deuterium exchange mass spectrometry (HDX-MS), computational modeling, and cryoEM. Our findings reveal that DENV2 NS5 binds SLA in a closed conformation, with interdomain cooperation between its methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, critical for the interaction. SLA binding induces conformational changes in both domains, highlighting NS5's multifunctional role in viral replication. Our cryoEM results visualizes the DENV2 NS5-SLA complex, confirming a conserved SLA binding across DENV serotypes and provides key insights for antiviral strategies targeting NS5's conformational states.

The physics-AI dialogue in drug design

A long path has led from the determination of the first protein structure in 1960 to the recent breakthroughs in protein science. Protein structure prediction and design methodologies based on machine learning (ML) have been recognized with the 2024 Nobel prize in Chemistry, but they would not have been possible without previous work and the input of many domain scientists. Challenges remain in the application of ML tools for the prediction of structural ensembles and their usage within the software pipelines for structure determination by crystallography or cryogenic electron microscopy. In the drug discovery workflow, ML techniques are being used in diverse areas such as scoring of docked poses, or the generation of molecular descriptors. As the ML techniques become more widespread, novel applications emerge which can profit from the large amounts of data available. Nevertheless, it is essential to balance the potential advantages against the environmental costs of ML deployment to decide if and when it is best to apply it. For hit to lead optimization ML tools can efficiently interpolate between compounds in large chemical series but free energy calculations by molecular dynamics simulations seem to be superior for designing novel derivatives. Importantly, the potential complementarity and/or synergism of physics-based methods (e.g., force field-based simulation models) and data-hungry ML techniques is growing strongly. Current ML methods have evolved from decades of research. It is now necessary for biologists, physicists, and computer scientists to fully understand advantages and limitations of ML techniques to ensure that the complementarity of physics-based methods and ML tools can be fully exploited for drug design.

Investigating the neuroprotective effects of strawberry extract against diesel soot-induced motor dysfunction in Drosophila: an in-vivo and in-silico study

Environmental pollutants including diesel soot, have been known to contribute to neurological disorders. Previous studies highlight the neuroprotective effects of strawberry-derived compounds. This work explores the impacts of diesel soot and strawberry extract in movement-related disorders. In-silico analysis assessed compounds from HPLC/GCMS in the literature of soot and strawberry extract for ADME properties and blood-brain barrier permeability, selecting six compounds and four motor function-related proteins (SOD1, TARDBP, FUS, MAPT) with D. melanogaster orthologs. Homology modeling generated protein structures, molecular docking assessed binding affinities. MLSD examined combined interactions, with RMSD validating accuracy. Docking scores matched neuroprotective controls (quercetin, resveratrol), while differed for negative control (formaldehyde). Phenanthrene and anthocyanin strongly bound to FUS (- 7.60 ± 0.26 kcal/mol, - 7.1 ± 0.26 kcal/mol) and cocoon (- 6.5 ± 0.39 kcal/mol, - 7.23 ± 0.45 kcal/mol). MLSD yielded - 3.00 ± 0.24 kcal/mol and - 3.12 ± 0.11 kcal/mol respectively. In-vivo assays in D. melanogaster exhibited soot impaired movement (p = 0.0006), while strawberry improved it (p = 0.0003) with partial recovery in combined exposure (p = 0.0003). Strawberry enhanced cold stress recovery (p = 0.0048), climbing (p < 0.0001), and vortex recovery (p = 0.0003). One-way ANOVA confirmed significant effects on crawling in males (F (9,20) = 37.67, p < 0.0001, η 2  = 0.53) and female flies (F (9,20) = 70.10, p < 0.0001), with normality confirmed by Shapiro-Wilk test (p > 0.05). Toxicant exposure accelerated mortality, while strawberry improved thermotolerance. Combined exposure provided partial protection with minor sex differences. Findings highlight strawberries' neuroprotective role in counteracting diesel soot toxicity, even under combined exposure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00344-2.

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair

MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.

Targeting SufC ATPase in Staphylococcus aureus AR465: Insights from an in silico and molecular docking approach

Staphylococcus aureus AR465 (S. aureus AR465) is a deadly pathogen that often inherits multidrug resistance, where the antibiotics become ineffective against it. The iron‑sulfur (FeS) cluster assembly pathway has the potential to serve as a new drug target, allowing for the modification of these molecules to be susceptible to oxidative conditions. Our study focuses on the preliminary stage of the FeS pathway inhibition by inhibiting the SufC protein, unlike previous studies that targeted the final stage. SufC has an Adenosine triphosphate (ATP) binding site. The main goal of this study is to inhibit the SufBCD complex of S. aureus AR465 to bind with other subunits to form an FeS cluster. The Sulfur Utilization Factor (SUF) system plays a massive role in the survival of this pathogen by producing electron carrier proteins which possess FeS cofactors. The SufC protein from the SufBCD system was chosen as the main target for the potential inhibitor molecules. SufC is an ATP-binding cassette (ABC) that transfers an FeS cluster to SufA, which then transports it to an apoprotein involved in electron transport processes. In this research, several drugs were selected which can block this particular stage of the FeS cluster formation pathway. The idea was to competitively inhibit the binding of ATP with the help of inhibitors so that it cannot bind to the desired site of SufC. Eventually, the inhibitor molecule blocks the transfer of the FeS cluster to a newly synthesized apo-protein and kills the pathogen.

Competitive Affinity-Based Protein Profiling Reveals Potential Antifungal Targets of 1,2,3-Triazole Hydrazide in Fusarium graminearum

In previous research, 1,2,3-triazole hydrazide NAU-6ad exhibited remarkable broad-spectrum antifungal activity. However, the specific targets of NAU-6ad remained unknown. Initially, we excluded three targets─succinate dehydrogenase, laccase, and ergosterol synthase─commonly associated with hydrazide derivatives mentioned in the literature. Subsequently, we developed two types of photoprobes: one incorporating diazirine (DA) and the other phenyl tetrazole (TZ), both featuring terminal alkynes for bioorthogonal reactions. Using these two sets of probes, a total of 52 potential targets were identified through competitive affinity-based proteome profiling. Notably, Ndufs6 and I1RC94 were consistently identified by both sets. The overexpression or knockout of Ndufs6, a subunit of complex I, led to significant changes in sensitivity to NAU-6ad in F. graminearum. Similarly, the knockout of other subunits of complex I, specifically Ndufs2, Ndufv1, and Ndufa9, altered the sensitivity of F. graminearum to NAU-6ad, indicating that NAU-6ad might act upon complex I. Further validation was provided by enzyme activity tests, ATP content assays, pyruvate addition assays, and molecular docking, collectively reinforcing the hypothesis that NAU-6ad might function as a complex I inhibitor.

Identification of a novel chromosome-encoded fosfomycin resistance gene fosC3 in Aeromonas caviae

Background

Owing to the rapid emerging of multidrug-, even pandrug-resistant pathogens, and lack of new antibiotics, the older antibiotic, fosfomycin, has been reused in recent years in the clinical practice, especially for treatment of uropathogen infections. With the increased use of fosfomycin, bacterial resistance to it has also increased drastically. Elucidating the resistance mechanism to the antimicrobial has become an urgent task.

Methods

The putative fosfomycin resistance gene fosC3 was cloned, and minimal inhibitory concentrations were determined by the agar dilution method. Enzyme kinetic parameters were measured by high-performance liquid chromatography. Bioinformatics analysis was applied to understand the evolutionary characteristics of FosC3.

Results

The A. caviae strain DW0021 exhibited high level resistance to several antimicrobials including kanamycin, streptomycin, chloramphenicol, florfenicol, tetracycline, and especially higher to fosfomycin (> 1,024 μg/mL), while genome annotation indicated that no function-characterized resistance gene was associated with fosfomycin resistance. A novel functional gene designated fosC3 responsible for fosfomycin resistance was identified in the chromosome of A. caviae DW0021. Among the function-characterized proteins, FosC3 shared the highest amino acid similarity of 58.65% with FosC2. No mobile genetic element (MGE) was found surrounding the fosC3 gene. The recombinant pMD19-fosC3/DH5α displayed a MIC value of 32 μg/mL to fosfomycin, which revealed a 128-fold increase of MIC value to fosfomycin compared to the control pMD19/E. coli DH5α (0.25 μg/mL). FosC3 was phylogenetically close to FosC2 and exhibited a k cat and K m of 82,442 ± 1,475 s-1, 70.99 ± 4.31 μM, respectively, and a catalytic efficiency of (1.2 ± 0.3) × 103 μM-1·s-1.

Conclusion

In this work, a novel functional fosfomycin thiol transferase, FosC3, which shared the highest protein sequence similarity with FosC2, was identified in A. caviae. The fosfomycin inactivation enzyme FosC3 could effectively inactivate fosfomycin by chemical modification. It is implied that such mechanism facilitates A. caviae to respond to fosfomycin exposure, thereby enhancing survival. However, fosC3 was not related with any MGE, which differs from many other fosfomycin thiol transferase genes. As a result, fosC3 is not expected to be transmitted to other species through horizontal gene transfer mechanism. Our findings will contribute to the resistance mechanism of the common pathogenic A. caviae.

Diverse toxins exhibit a common binding mode to the nicotinic acetylcholine receptors

Nicotinic acetylcholine receptors (nAChRs) are critical ligand-gated ion channels in the human nervous system. They are targets for various neurotoxins produced by algae, plants, and animals. While many structures of nAChRs bound by neurotoxins have been published, the binding mechanism of toxins to the nAChRs remains unclear. In this work, we have performed extensive Gaussian accelerated molecular dynamics simulations on several Aplysia californica nAChRs in complex with α-conotoxins, strychnine, and pinnatoxins, as well as human nAChRs in complex with α-bungarotoxin and α-conotoxin, to determine the binding and dissociation pathways of the toxins to the nAChRs and the associated effects. We uncovered two common binding and dissociation pathways shared by toxins and nAChRs. In the first binding pathway, the toxins diffused from the bulk solvent to bind a region near the extracellular pore before moving downwards along the nAChRs to the nAChR orthosteric pocket. The second binding pathway involved a direct diffusion of the toxins from the bulk solvent into the nAChR orthosteric pocket. The dissociation pathways were the reverse of the observed binding pathways. Notably, we determined that the electrostatically bipolar interactions between the nAChR orthosteric pocket and toxins provided an explanation for the common binding mode shared by diverse toxins.

MGAT1-Guided complex N-Glycans on CD73 regulate immune evasion in triple-negative breast cancer

Despite the widespread application of immunotherapy, treating immune-cold tumors remains a significant challenge in cancer therapy. Using multiomic spatial analyses and experimental validation, we identify MGAT1, a glycosyltransferase, as a pivotal factor governing tumor immune response. Overexpression of MGAT1 leads to immune evasion due to aberrant elevation of CD73 membrane translocation, which suppresses CD8+ T cell function, especially in immune-cold triple-negative breast cancer (TNBC). Mechanistically, addition of N-acetylglucosamine to CD73 by MGAT1 enables the CD73 dimerization necessary for CD73 loading onto VAMP3, ensuring membrane fusion. We further show that THBS1 is an upstream etiological factor orchestrating the MGAT1-CD73-VAMP3-adenosine axis in suppressing CD8+ T cell antitumor activity. Spatial transcriptomic profiling reveals spatially resolved features of interacting malignant and immune cells pertaining to expression levels of MGAT1 and CD73. In preclinical models of TNBC, W-GTF01, an inhibitor specifically blocked the MGAT1-catalyzed CD73 glycosylation, sensitizing refractory tumors to anti-PD-L1 therapy via restoring capacity to elicit a CD8+ IFNγ-producing T cell response. Collectively, our findings uncover a strategy for targeting the immunosuppressive molecule CD73 by inhibiting MGAT1.

Molecular Mechanisms Underlying the Impacts of Available-Iron Levels on the Accumulation and Translocation of 6:2 Chlorinated Polyfluoroalkyl Ether Sulfonate in Soybean (Glycine max L. Merrill)

Soil available-iron (Fe) is crucial for various physiological properties and processes in plants, particularly those related to the accumulation and translocation of per- and polyfluoroalkyl substances (PFAS). However, the mechanisms underlying the impact of available-Fe levels on PFAS accumulation and translocation in plants remain unclear. In this study, we investigated the impacts of available-Fe levels on the accumulation of an emerging PFAS, 6:2 chlorinated polyfluoroalkyl ether sulfonate (6:2 Cl-PFESA), in soybean, a typical dicot, through hydroponic experiments. Interestingly, Fe deficiency significantly enhanced soybean root volume, surface area, root tip count, and lipid content, thus favoring 6:2 Cl-PFESA adsorption on the root epidermis. However, its absorption and translocation to aboveground tissues were markedly suppressed due to significantly reduced transpiration rate and soluble protein content induced by Fe deficiency. Conversely, although excessive available-Fe also inhibited transpiration, it notably increased root membrane permeability and soluble protein content in aboveground tissues, thus greatly facilitating the absorption and translocation of 6:2 Cl-PFESA within soybeans. These findings demonstrate that appropriate Fe application in agricultural soils is essential to promote the growth of dicot crops and mitigate the potential ecological risks associated with the accumulation of 6:2 Cl-PFESA in the aboveground tissues of soybeans.

Molecular dynamics reveal potential effects of novel VHL variants on VHL-Elongin C binding in ccRCC patients from Eastern India

Renal cell carcinoma (RCC) is the one of the most fatal and frequent form of urological malignancy worldwide. The von Hippel-Lindau (VHL) tumour suppressor gene is a critical component of the VHL-Cullin2-ElonginB/C (VCB) complex that regulates the ubiquitin-mediated proteasomal degradation of proteins with mutations consistently associated with the development of clear cell renal cell carcinoma (ccRCC). Despite extensive investigations conducted worldwide, there is a notable lack of data concerning VHL mutations in sporadic ccRCC patients from India. Our study aimed to investigate the sporadic VHL mutations within the tumours of 210 ccRCC patients without a familial history of VHL disease. We extracted genomic DNA from tumour and adjacent normal tissues, PCR amplified and sequenced the VHL gene. In silico tools were used assess the damaging potential of missense variants on pVHL structure and stability. Protein-protein docking and protein flexibility molecular docking simulation study were employed to study the interaction between wild-type and mutated VHL models with Elongin C. Sequence analysis revealed seven novel missense mutations in patient tumour tissues p.(Val170Phe), p.(Arg69Cys), p.(Phe76Leu), p.(Glu173Asp), p.(Leu201Val), p.(His208Leu), p.(Arg205Pro). I-Mutant 2.0 indicated these mutations reduced pVHL stability (ΔΔG < -0.5 kcal/mol). Protein Flexibility-Molecular Dynamic (MD) Simulation study indicated that mutations weaken the interaction of VHL with Elongin C, with V170F showing the most significant reduction in binding quality and stability. In conclusion, this study introduces novel genetic data from an understudied population and highlights the impact of VHL mutations on its interaction with Elongin C. These findings contribute to our understanding of the molecular basis of VHL-related pathologies and may guide future therapeutic strategies targeting these interactions.

Role of glycosylation mutations at the N-terminal domain of SARS-CoV-2 XEC variant in immune evasion, cell-cell fusion, and spike stability

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, producing new variants that drive global coronavirus disease 2019 surges. XEC, a recombinant of KS.1.1 and KP.3.3, contains T22N and F59S mutations in the spike protein's N-terminal domain (NTD). The T22N mutation, similar to the DelS31 mutation in KP.3.1.1, introduces a potential N-linked glycosylation site in XEC. In this study, we examined the neutralizing antibody (nAb) response and mutation effects in sera from bivalent-vaccinated healthcare workers, BA.2.86/JN.1 wave-infected patients, and XBB.1.5 monovalent-vaccinated hamsters, assessing responses to XEC alongside D614G, JN.1, KP.3, and KP.3.1.1. XEC demonstrated significantly reduced neutralization titers across all cohorts, largely due to the F59S mutation. Notably, removal of glycosylation sites in XEC and KP.3.1.1 substantially restored nAb titers. Antigenic cartography analysis revealed XEC to be more antigenically distinct from its common ancestral BA.2.86/JN.1 compared to KP.3.1.1, with the F59S mutation as a determining factor. Similar to KP.3.1.1, XEC showed reduced cell-cell fusion relative to its parental KP.3, a change attributed to the T22N glycosylation. We also observed reduced S1 shedding for XEC and KP.3.1.1, which was reversed by ablation of T22N and DelS31 glycosylation mutations, respectively. Molecular modeling suggests that T22N and F59S mutations of XEC alter hydrophobic interactions with adjacent spike protein residues, impacting both conformational stability and neutralization. Overall, our findings underscore the pivotal role of NTD mutations in shaping SARS-CoV-2 spike biology and immune escape mechanisms.IMPORTANCEThe continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of novel variants with enhanced immune evasion properties, posing challenges for current vaccination strategies. This study identifies key N-terminal domain (NTD) mutations, particularly T22N and F59S in the recent XEC variant, which significantly impacts antigenicity, neutralization, and spike protein stability. The introduction of an N-linked glycosylation site through T22N, along with the antigenic shift driven by F59S, highlights how subtle mutations can drastically alter viral immune recognition. By demonstrating that glycosylation site removal restores neutralization sensitivity, this work provides crucial insights into the molecular mechanisms governing antibody escape. Additionally, the observed effects on spike protein shedding and cell-cell fusion contribute to a broader understanding of variant fitness and transmissibility. These findings emphasize the importance of monitoring NTD mutations in emerging SARS-CoV-2 lineages and support the need for adaptive vaccine designs to counteract ongoing viral evolution.

Identification of novel drug targets and small molecule discovery for MRSA infections

Introduction

The topmost deadliest microorganism, namely, methicillin-resistant Staphylococcus aureus (MRSA), causes dreadful infections like bacteremia, pneumonia, endocarditis, and systemic inflammations. The virulence factors associated with MRSA exhibit multidrug-resistant characteristics, complicating treatment choices. So, the primary objective of this study is to identify the MRSA virulence factors and inhibiting its activity utilizing bioinformatic approaches.

Methods

The screening of novel therapeutic MRSA targets was conducted based on the predictions retrieved from non-homologous, physicochemical analysis, subcellular localization, druggability, and virulence factor examinations. Following that, flavonoid compounds were docked against specific MRSA targets using AutoDock Vina. Further, molecular dynamic simulations and binding free energy calculations were performed using simulation software.

Results

After examining 2,640 virulence factors that presented in MRSA, the heme response regulator R (HssR) was found to be a novel protein that greatly controls the levels of heme in MRSA infections. Subsequently, the binding energy calculations for flavonoid compounds and HssR revealed that the catechin provided -7.9 kcal/mol, which surpassed the standard drug, namely, vancomycin (-5.9 kcal/mol). Further, the results were validated by evaluating molecular dynamic simulation parameters like RMSD, RMSF, ROG, SASA, and PCA. Through analyzing these parameters, catechin provided a more stable, compact nature and less solvent exposure with HssR than vancomycin. Moreover, the predicted binding free energy for HssR-catechin was found to be -23.0 kcal/mol, which was less compared to the HssR-vancomycin (-16.91 kcal/mol) complex. The results suggested that the catechin was able to modulate the activity of the HssR protein effectively.

Conclusion

These potential findings revealed that heme response regulator R as a promising therapeutic target while the flavonoid compound catechin could act as alternative therapeutic inhibitor that target MRSA infections.

Role of Cre Dynamics in Autoinhibition and Priming

Cre recombinase, a powerful tool for genome engineering, associates into an intasome, a tetrameric complex of alternate active and inactive monomers that bring together two loxP sequences, stabilized by key protein-protein and protein-DNA interactions. High-resolution structural information for free Cre is still missing, in contrast to the many structures found for Cre-DNA complexes in the Protein Data Bank, hindering understanding of the initial steps in intasome formation. To approach Cre structure and dynamics, we carried out 100 μs of molecular dynamics simulations of free Cre, starting from five Cre structures from different stages of intasome assembly. In the generated ensemble, the linker connecting the CBD and CAT domains is an intrinsically disordered region (IDR) that promotes different orientations of the two domains. The domains remain folded and interact with each other through short-lived interactions, retaining ∼70% of their surface available for interaction with loxP. The C-terminal Helix N in the CAT domain is also an IDR that interacts with the entire protein, including the active site, transiently forming an autoinhibited complex. The active site can be assembled in the absence of DNA, albeit inefficiently. The CAT domain has a clam-like motion, opening and closing the cavity where helix N docks, establishing protein-protein interactions in the intasome. Helix A in the CBD domain slides over the domain like a windshield wiper, sampling intasome-like conformations, among others. The wide range of intramolecular motion sampled by free Cre suggests that it uses conformational selection, using primed DNA-binding surfaces in both domains while assembling into the intasome.

Transient Expression of Hen Egg White Lysozyme (EWL) in Nicotiana benthamiana Influences Plant Pathogen Infection

Lysozyme is an enzyme that hydrolyzes bacterial cell walls, which is functional for destroying the integrity of bacteria, enhancing the activity of immune cells, participating in immune signal transmission, helping to maintain the micro-ecological balance of the gastrointestinal tract, etc. Egg white lysozyme (EWL), as one of the typical representatives of lysozyme, is the most widely used enzyme in production so far, and is also one of the most complex structures of lysozyme. EWL also helps protect plants from fungal and bacterial diseases. Here, we report the effect of EWL on infections from plant viruses. The EWL gene was cloned and characterized. The EWL protein sequence analysis identified a conserved domain of lysozyme activity and the sharing of a 100% identical EWL protein from the Coturnix japonica lysozyme. Then, the EWL gene was cloned into the plant expression vector pEAQ-HT-DEST3 and transiently expressed in Nicotiana benthamiana (N. benthamiana). We found that EWL expression in N. benthamiana significantly contributed to infections by the turnip mosaic virus (TuMV) but not by the tobacco mosaic virus (TMV). Plants that transiently expressed EWL showed an obvious increase in resistance to Botrytis cinerea (B.cinerea). Our results suggested a new research point for the application of EWL on plant pathogen infections.

Regulatory Interactions between APOBEC3B N- and C-Terminal Domains

APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting our understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared the dynamics of the truncated (A3Bctd) to that of the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD-CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics and potential druggability of fl-A3B, including observations regarding both the active and allosteric sites, which may offer new avenues for therapeutic intervention in cancer.

Understanding the structural basis of ALS mutations associated with resistance to sulfonylurea in wheat

Developing herbicide-tolerant wheat varieties is highly desirable for effective weed management and improved crop yield. The enzyme acetolactate synthase (ALS) is the target enzyme for the sulfonylurea class of herbicides. The structural analysis of mutable sites in ALS is crucial for the generation of herbicide-resistant crops. Previous studies indicated that mutant lines of Triticum aestivum ALS (TaALS) with amino acid substitutions at P174, G631, and G632 residues provided resistance to sulfonylurea herbicide, nicosulfuron. The present study aimed to provide structural insights into mutable residues causing sulfonylurea herbicide resistance to TaALS enzyme through in-silico molecular docking and simulation approaches. The molecular docking analysis suggested a single point mutation at TaALS-P174S, its double mutant conformations (TaALS-G632S/P174S and TaALS-G631D/G632S) and associated triple mutant conformation (TaALS-G631D/G632S/P174S) to have the lowest binding affinity with nicosulfuron than the wild-type conformation of TaALS. Furthermore, the molecular dynamic simulation study confirms the weakest and more stable binding of the triple mutant conformation with nicosulfuron. Our computational study identifies a triple mutant conformation (TaALS-G631D/G632S/P174S) to be more effective in developing sulfonylurea herbicide-resistant wheat crops.

Cyclization of Short Peptides Designed from Late Embryogenesis Abundant Protein to Improve Stability and Functionality

LEA peptides, which are designed based on late embryogenic abundant (LEA) protein sequences, have demonstrated chaperone-like functions, such as improving drought stress tolerance of Escherichia coli (E. coli). Previous studies have focused on the biological functions of linear LEA peptides. However, the function of cyclic LEA peptide still unknown. This study aimed to explore the cyclic LEA peptides' bio function like enhance the drought stress tolerance of E. coli by cyclizing the LEA peptide using SICLOPPS (Split Intein Circular Ligation of Peptides and Proteins). The results indicated that cyclization significantly improved the function and extended the potential applications. At the same time, we found that peptides containing numerous lysine residues exhibited reduced performance, which may be due to the exteins' residues affecting the SICLOPPS efficiency.

Using AlphaFold-Multimer to study novel protein-protein interactions of predation essential hypothetical proteins in Bdellovibrio

Bdellovibrio bacteriovorus is the most studied member of a group of small motile Gram-negative bacteria called Bdellovibrio and Like Organisms (BALOs). B. bacteriovorus can prey on Gram-negative bacteria, including multi-drug resistant pathogens, and has been proposed as an alternative to antibiotics. Although the life cycle of B. bacteriovorus is well characterized, some molecular aspects of B. bacteriovorus-prey interaction are poorly understood. Hypothetical proteins with unestablished functions have been implicated in B. bacteriovorus predation by many studies. Our approach to characterize these proteins employing Alphafold has revealed novel interactions among attack phase-hypothetical proteins, which may be involved in less understood mechanisms of the Bdellovibrio attack phase. Here, we overlapped attack phase genes from B. bacteriovorus transcriptomic data sets and from transposon sequencing data sets to generate a set of proteins that are both expressed at the attack phase and are necessary for predation, which we termed Attack Phase Predation-Essential Proteins (AP-PEP). By applying Markov Cluster Algorithm and AlphaFold-Multimer to analyze the protein network and interaction partners of the AP-PEPs, we predicted high-confidence protein-protein interactions and two structurally similar but unique novel protein complexes formed among proteins of the Bd2209-Bd2212 and Bd2723-Bd2726 operons. Furthermore, we confirmed the interaction between hypothetical proteins Bd0075 and Bd0474 using the Bacteria Adenylate Cyclase Two-Hybrid system. In addition, we confirmed that the C-terminal domain of Bd0075, which contains Tetratricopeptide repeat motifs, participates principally in its interaction with Bd0474. This study revealed previously unknown cooperation among predation essential hypothetical proteins in the attack phase B. bacteriovorus and has paved the way for further work to understand molecular mechanisms of BALO predation processes.

IFIT3 RNA-binding activity promotes influenza A virus infection and translation efficiency

Host cells produce a vast network of antiviral factors in response to viral infection. The interferon-induced proteins with tetratricopeptide repeats (IFITs) are important effectors of a broad-spectrum antiviral response. In contrast to their canonical roles, we previously identified IFIT2 and IFIT3 as pro-viral host factors during influenza A virus (IAV) infection. During IAV infection, IFIT2 binds and enhances translation of AU-rich cellular mRNAs, including many IFN-simulated gene products, establishing a model for its broad antiviral activity. But, IFIT2 also bound viral mRNAs and enhanced their translation resulting in increased viral replication. The ability of IFIT3 to bind RNA and whether this is important for its function was not known. Here we validate direct interactions between IFIT3 and RNA using electromobility shift assays (EMSAs). RNA-binding site identification (RBS-ID) experiments then identified an RNA-binding surface composed of residues conserved in IFIT3 orthologs and IFIT2 paralogs. Mutation of the RNA-binding site reduced the ability IFIT3 to promote IAV gene expression and translation efficiency when compared to wild type IFIT3. The functional units of IFIT2 and IFIT3 are homo- and heterodimers, however the RNA-binding surfaces are located near the dimerization interface. Using co-immunoprecipitation, we showed that mutations to these sites do not affect dimerization. Together, these data establish the link between IFIT3 RNA-binding and its ability to modulate translation of host and viral mRNAs during IAV infection.

Genetic variants and molecular profiling of 46,XY gonadal dysgenesis using whole-exome sequencing

Background

More than 60% of cases of 46,XY gonadal dysgenesis (GD), a condition classified as a disorder of sex development (DSD), remain unexplained, which is due to high genetic and clinical heterogeneity. Whole-exome sequencing (WES) is an efficient primary genetic diagnostic method; specifically, the use of WES in patients with 46,XY GD to explore the underlying genetic variants of the disorder may help us gain a deeper understanding of the pathogenesis and phenotype-genotype correlation of 46,XY GD.

Methods

We performed WES and pedigree studies to investigate the underlying genetic etiology of patients with 46,XY GD (six patients and six familial controls). The variants were confirmed via Sanger sequencing, and detailed functional prediction of the discovered genetic variants was conducted. Furthermore, we performed in-silico protein structural analysis and protein thermodynamic analysis to further explore the pathogenicity of these variants. GATA4 variants in patients with 46,XY GD with/without CHD and patients with cardiac disease alone were also analyzed.

Results

We identified three novel pathogenic variants in GATA4:c.725G>C(p.Cys242Ser), NR5A1:c.370_380del(p.Pro124Glyfs*21), and DHX37:c.2020C>T(p.Arg674Trp), as well as one previously reported MAP3K1:c.1016G>A(p.Arg339Gln) variant. These variant sites are conserved among species and were predicted to be damaging according to functional algorithms and protein analyses. Additionally, 71.4% of the GATA4 amino acid changes in 46,XY GD were located in or close to the N-terminal zinc finger (N-ZF) domain. However, most GATA4 pathogenic variants (31.82%) in patients with isolated cardiac diseases were located in transactivation domain 1 (TAD1), and only 9.09% of the variants were located in the N-ZF domain.

Conclusion

The N-ZF domain may play an exclusive role in the mechanism of GATA4 in the pathogenesis of 46,XY GD; therefore, this domain may be an interesting topic for future investigation. This study enhances our understanding of the genetic etiology and pathogenesis of 46,XY GD, which may aid in the diagnosis and intervention of this disorder.

Genome-Wide Identification of the Defensin Gene Family in Triticum durum and Assessment of Its Response to Environmental Stresses

Plant defensins (PDFs) are a group of cationic antimicrobial peptides that are distinguished by their unique tertiary structure and play significant roles in physiological metabolism, growth, and stress tolerance. Defensins are key components of plant innate immunity; they can target a wide variety of microorganisms. This study aimed to identify and investigate the role of Triticum durum PDFs (TdPDFs) in response to environmental stresses. Prior to this, in silico analyses of TdPDF genes were conducted to assess their chromosomal locations, conserved motifs, exon-intron distribution, and cis-regulatory elements in the promoter regions. Additionally, bioinformatic analyses were performed to characterize the structure of TdPDF proteins, evaluate their phylogenetic relationships, predict their subcellular localization, and estimate their physicochemical properties. Docking studies were conducted to assess the interactions between TdPDF proteins and the fungal plasma membrane. A total of 28 TdPDF genes were identified in durum wheat based on their conserved domain PF00304 (gamma-thionin). These genes are distributed across all chromosomes of the durum wheat genome, except for chromosomes 4A and 7A. Analysis of the promoters of these genes revealed numerous elements associated with development, hormone responsiveness, and environmental stress. The majority of TdPDF proteins were predicted to be located extracellular. In addition, TdPDF proteins were classified into three clusters based on sequence similarity. Phylogenetic analysis suggested that TdPDF proteins share ancestral similarities with the PDF sequences of other monocotyledonous species. Molecular docking studies revealed that TdPDF proteins interact with fungal plasma membranes, suggesting that they play a critical role in the resistance of plants to pathogen infections. Expression analysis underlined the crucial role of nine TdPDF genes in the defense responses of durum wheat against both pathogenic and environmental stressors. Overall, our findings underscore the potential of TdPDF genes in host-plant resistance and highlight opportunities for their application in crop improvement toward stress tolerance.

MprF from Pseudomonas aeruginosa is a promiscuous lipid scramblase with broad substrate specificity

The multiple peptide resistance factor (MprF) is a bifunctional membrane protein found in many bacteria, including Pseudomonas aeruginosa and Staphylococcus aureus. MprF modifies inner leaflet lipid headgroups through aminoacylation and translocates modified lipid to the outer leaflet. This activity provides increased resistance to antimicrobial agents. MprF presents a promising target in multiresistant pathogens, but structural information is limited and both substrate specificity and energization of MprF-mediated lipid transport are poorly understood. Here, we present the cryo-EM structure of MprF from P. aeruginosa (PaMprF) bound to a synthetic nanobody. PaMprF adopts an "open" conformation with a wide, lipid-exposed groove on the periplasmic side that induces a local membrane deformation in molecular dynamics simulations. Using an in vitro liposome transport assay, we demonstrate that PaMprF translocates a wide range of different lipids without an external energy source. This suggests that PaMprF is the first dedicated lipid scramblase to be characterized in bacteria.

Genome-Wide Identification and Expression Analysis of m6A Methyltransferase Family in Przewalskia tangutica Maxim

N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adaptation to the environment. However, there has been no research regarding m6A RNA methyltransferases (MT-A70) in Przewalskia tangutica Maxim. Here, we performed a comprehensive analysis of the MT-A70 family in Przewalskia tangutica (PtMTs), including gene structures, phylogenetic relationships, conserved motifs, gene location, promoter analysis, GO enrichment analysis, and expression profiles. We identified seven PtMT genes. Phylogeny analysis indicated that the seven PtMT genes could be divided into three groups; two MTA genes, three MTB genes, and two MTC genes, and domains and motifs exhibited similar patterns within the same group. These PtMT genes were found to contain a large number of cis-acting elements associated with plant hormones, light response, and stress response, suggesting their widespread regulatory function. Furthermore, the expression profiling of different tissues was investigated using RNA-seq data, and the expression of seven genes was further validated by qPCR analysis. These results provided valuable information to further elucidate the function of m6A regulatory genes and their epigenetic regulatory mechanisms in Przewalskia tangutica.

Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits

The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ribosome biogenesis between yeast and humans, illustrated by the structural similarities of ribosomal subunit intermediates. By using X-ray crystallography and cryo-EM, the interaction between the human AAA+ ATPase MDN1 and the 60S assembly factor NLE1 is compared with the yeast homologs Rea1 and Rsa4. The MDN1-MIDAS and NLE1-Ubl complex structure at 2.3 Å resolution mirrors the highly conserved interaction patterns observed in yeast. Moreover, human pre-60S intermediates bound to the dominant negative NLE1-E85A mutant revealed at 2.8 Å resolution an architecture that largely matched the equivalent yeast structures. Conformation of rRNA, assembly factors and their interaction networks are highly conserved. Additionally, novel human pre-60S intermediates with a non-rotated 5S RNP and processed ITS2/foot structure but incomplete intersubunit surface were identified to be similar to counterparts observed in yeast. These findings confirm that the MDN1-NLE1-driven transition phase of the 60S assembly is essentially identical, supporting the idea that ribosome biogenesis is a highly conserved process across eukaryotic cells, employing an evolutionary preservation of ribosomal assembly mechanisms.

Decoding SP-D and glycan binding mechanisms using a novel computational workflow

Surfactant protein D (SP-D) plays an important role in the innate immune system by recognizing and binding to glycans on the surface of pathogens, facilitating their clearance. Despite its importance, the detailed binding mechanisms between SP-D and various pathogenic surface glycans remain elusive due to the limited experimentally solved protein-glycan crystal structures. To address this, we developed and validated a computational workflow that integrates induced fit docking, molecular mechanics/generalized Born surface area binding free energy calculations, and binding pose metadynamics simulations to accurately predict stable SP-D-glycan complex structure and binding mechanisms. By utilizing this workflow, we identified primary and secondary binding sites in SP-D critical for glycan recognition and uncovered a calcium chelation mode correlating with high binding affinity. To demonstrate the workflow's utility, we investigated the binding of pilin glycan from Pseudomonas aeruginosa (P. aeruginosa) to SP-A, SP-D, and mannose-binding lectin (MBL). We found that SP-D exhibited the most stable binding with pilin glycan versus SP-A and MBL, highlighting its potential role in the innate immune response against P. aeruginosa infection. These findings deepen our understanding of SP-D's role in the innate immune response and provide a basis for engineering SP-D variants for therapeutic applications. Moreover, our computational workflow can serve as a powerful tool for exploring protein-ligand interactions in diverse, biologically significant systems. It provides a robust framework to guide experimental studies and accelerates the development of novel therapeutics, effectively bridging the gap between computational insights and practical applications.

tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator

In yeast, tRNA modifications that are introduced by the Elongator complex are recognized by zymocin, a fungal tRNase killer toxin that cleaves the anticodon. Based on zymocin resistance conferred by mutations in KTI12, a gene coding for an Elongator interactor, we further examined the yet vaguely defined cellular role of Kti12. Guided by structural similarities between Kti12 and PSTK, a tRNA kinase involved in selenocysteine synthesis, we identified conserved basic residues in the C-terminus of Kti12, which upon site-directed mutagenesis caused progressive loss of tRNA binding in vitro. The inability of Kti12 to bind tRNA led to similar phenotypes caused by Elongator inactivation in vivo. Consistently, tRNA binding deficient kti12 mutants drastically suppressed Elongator dependent tRNA anticodon modifications and reduced the capacity of Kti12 to interact with Elongator. We further could distinguish Elongator unbound pools of Kti12 in a tRNA dependent manner from bound ones. In summary, the C-terminal domain of Kti12 is crucial for tRNA binding and Kti12 recruitment to Elongator, which are both requirements for Elongator function suggesting Kti12 is a tRNA carrier that interacts with Elongator for modification of the tRNA anticodon.

In Silico Targeting and Immunological Profiling of PpiA in Mycobacterium tuberculosis: A Computational Approach

Tuberculosis (TB) remains a leading cause of mortality, with drug resistance highlighting the need for new vaccine targets. Peptidyl-prolyl isomerase A (PpiA), a conserved Mycobacterium tuberculosis (Mtb) protein, plays a role in bacterial stress adaptation and immune evasion, making it a potential target for immunotherapy. This study uses computational methods to assess PpiA's antigenicity, structural integrity, and immunogenic potential. The PpiA sequence was retrieved from NCBI and analyzed for antigenicity and allergenicity using VaxiJen, AllerTOP, and AllergenFP. Physicochemical properties were evaluated using ProtParam, and structural models were generated through PSIPRED and SWISS-MODEL. Structural validation was performed with MolProbity, QMEANDisCo, and ProSA-Web. B-cell epitopes were predicted using BepiPred 2.0 and IEDB, while T-cell epitopes were mapped via IEDB's MHC-I and MHC-II tools. Epitope conservation across Mtb strains was confirmed using ConSurf. Results indicate PpiA is highly antigenic, non-allergenic, and stable, with several immunogenic epitopes identified for both B- and T-cells. This study supports PpiA as a promising immunogenic target for TB vaccine development.