Biology subjects

Panda, A.

Publications and source records attributed to Panda, A..

At least 19 recordsLinked to original sources

bioRxiv2026

A CTCF-LDHB axis converts nuclear lactate availability into an H3K18 acylation switch that directs alternative splicing in hypoxic breast cancer

Lactate accumulating in hypoxic tumours lactylates histones, coupling metabolic state to chromatin. Why it differs between tumours of comparable glycolytic rate has remained unresolved. Here we show that nuclear, rather than total intracellular, lactate availability determines histone H3K18 lactylation in breast cancer, and that CCCTC-binding factor (CTCF) and lactate dehydrogenase B (LDHB) jointly set it. CTCF sustains glycolytic gene expression under hypoxia and drives LDHB in triple-negative breast cancer (TNBC), whereas a CTCF-ER complex represses LDHB in non-TNBC. LDHB consumes lactate favouring H3K18 acetylation; where LDHB is low, CTCF-dependent MCT1 delivers lactate into the nucleus and sustains lactylation. At a CTCF site downstream of TACC3 exon 3, an invariant polymerase II pause couples kinetic and adaptor control of splicing, with the mark deciding the outcome: H3K18la recruits SMARCA4 and hnRNPA1 to skip the exon, generating an isoform that drives EMT, whereas H3K18ac recruits TRIM33 and SRSF10 to include it, generating one that confers stemness. Inhibiting LDHB restores exon skipping and suppresses tumour growth in vivo. Nuclear lactate availability therefore acts as a metabolic switch that converts hypoxic stress into subtype-specific splicing decisions and identifies LDHB as a tractable target in TNBC.

cancer biology↗

bioRxiv2026

Controlling membrane tension by dynamic DNA nanorings

Membrane tension, defined as the energy cost to expand the membrane surface area, is a fundamental mechanical property of the lipid bilayer and an important modulator of various cellular processes. Liposomes provide model systems to study protein-mediated membrane dynamics, where membrane tension can be controlled by osmotic pressure and micropipette aspiration. However, it is challenging to individually control membrane tension of nanometer-sized liposomes, such as small unilamellar vesicles (SUVs), that are widely used for modeling subcellular membrane structures and drug delivery. To bridge this technological gap, we present reconfigurable DNA origami rings for dynamically controlling membrane tension of sub-100 nm liposomes. The DNA nanorings template the formation of uniformly sized SUVs and undergo trigger-responsive dilation and contraction, thus applying controlled and reversible mechanical stress to the SUV membranes. Electron microscopy analyses show deformed liposomes with ~2.5% expanded membrane area following ring dilation. The corresponding increase in membrane tension opens a mechanosensitive ion channel MscL with gating tension of ~10 mN/m. Selectively manipulating a mixture of SUV populations enables timed release of their distinct molecular cargos, either concurrently or one at a time. Furthermore, vesicles with expanded membranes are more conducive to SNARE-mediated fusion. The nanomechanical device thus provides a programmable platform for engineering the mechanics of synthetic nano-vesicles and studying membrane tension modulated processes at the molecular level.

biophysics↗

bioRxiv2026

Remodelling of chromatin architecture and super-enhancer landscape in lamin A/C depleted HGSOC

Lamins are nuclear intermediate filament proteins that maintain nuclear architecture through interactions with the chromatin. The A- and B-type lamins tether the genome at the peripheral lamina underlying the inner nuclear membrane in the form of heterochromatic lamina-associated domains (LADs). However, LADs associated with A-type lamins are confined not only to lamina but also to the nuclear core, thereby pointing to their distinct and multifarious roles in chromatin organisation and regulation. Previous studies involving lamin B1 depletion depicted the detachment of LADs from the nuclear periphery, accompanied by alteration of chromatin distribution while preserving the topologically associating domains (TADs) in structurally intact form. In this piece of work, we have shown, for the first time in HGSOC, the effects of lamin A/C knockdown on chromatin organisation, which was characterised by significant detethering of gene-poor chromatin from the periphery along with active (A) to inactive (B) compartment switching. This was associated with a rewiring of oncogenic super-enhancer elements corroborated by the differential gene expression profile. Overall analysis tipped the scale in favour of reduced cellular proliferation upon lamin A/C knockdown. This finding was strengthened by the observed proliferative potential of spheroids ex vivo and tumours in a mouse xenograft model.

cancer biology↗

bioRxiv2026

K9HeartCircDB: A circRNA Atlas of Tachypacing-Induced Canine Dilated Cardiomyopathy

Cardiovascular disease (CVD) remains a leading cause of death worldwide. Dilated cardiomyopathy (DCM), a major cause of heart failure (HF), exhibits ventricular dilation, impaired systolic/diastolic function, arrythmias, and adverse cardiac remodeling. While genetic causes of DCM have been extensively studied, non-genetic and acquired forms of DCM-like HF are less well characterized, especially with respect to non-coding RNA regulation. Circular RNAs (circRNAs) are stable, covalently closed non-coding RNAs that regulate cellular function via sequestering miRNAs, RNA-binding proteins, or translation. Their role in canine HF that recapitulates features of non-genetic DCM remains largely unexplored. To address this, we developed K9HeartCircDB (https://www.k9heartcircdb.com/), a publicly accessible database that catalogs circRNAs expressed in canine left ventricular (LV) tissues under tachypacing-induced HF, a model of non-genetic DCM-like disease, and healthy control conditions. The online interface enables users to query and explore circRNAs based on exon composition, predicted miRNA binding sites, protein-coding potential, siRNA targets, and primer design for experimental validation. By providing an integrated and user-friendly platform for canine heart circRNA exploration, K9HeartCircDB offers a valuable resource to facilitate mechanistic and advance translational studies on non-genetic DCM-like disease.

Systems Biology↗

bioRxiv2026

A Multi-Epitope Vaccine Design for Human Pasteurellosis using Outer Membrane β-barrel Proteins of Pasteurella multocida

Pasteurella multocida is a facultative anaerobic, Gram-negative coccobacillus that causes pasteurellosis in companion animals, livestock, and poultry and poses a significant zoonotic risk to humans through bite wounds, scratches, licking, and transfer of bodily fluids. Although vaccines are available for livestock and poultry, no vaccine is currently licensed for human use. In this study, we systematically identified and characterized 29 outer membrane {beta}-barrel (OMBB) proteins in P. multocida Past9 proteome and classified them into functional categories, including TonB-dependent receptors, porins, autotransporters, adhesins, and efflux pumps. B-cell, cytotoxic T-lymphocyte (CTL), and helper T-lymphocyte (HTL) epitopes were predicted from the identified proteins and screened based on antigenicity, non-allergenicity, and non-toxicity. Epitopes conserved across eight human-infecting P. multocida strains and located within the extracellular loop (ECL) region were incorporated into a multi-epitope vaccine (MEV) construct. The designed MEV was predicted to be antigenic, non-allergenic, and soluble. Its tertiary structural model was iteratively refined and validated. Molecular docking with human toll-like receptors 4/2 (TLR4/TLR2) predicted stable interactions, further supported by 100 ns molecular dynamics simulations. Immune simulation of the MEV construct predicted a strong simulated immune response. Furthermore, codon optimization and in silico cloning supported the feasibility of recombinant MEV expression in E. coli. The construct was benchmarked against OmpH, a well-known antigenic protein and exhibited broadly comparable predicted immune responses and receptor-binding energetics. This study proposes a designed MEV candidate against human pasteurellosis and highlights OMBB proteins as potential immunogenic targets for vaccine development.

bioinformatics↗

bioRxiv2026

Design of a Multi-epitope Vaccine Against Human Glanders Targeting Outer Membrane β-barrel Proteins of Burkholderia mallei

Burkholderia mallei, a facultative intracellular Gram-negative pathogen, is the causative agent of glanders that primarily affects solipeds and is sporadically transmitted to humans. Current interventions mainly rely on antibiotics; however, increasing antimicrobial resistance and the lack of a licensed vaccine further complicate disease management. Surface exposed outer membrane {beta}-barrel (OMBB) proteins serve as excellent targets for vaccine development. In the present study, a consensus-based computational framework was employed on the B. mallei turkey2 proteome that identified 59 OMBB proteins - including porins, TonB receptors, autotransporters, and efflux components. These OMBB proteins were leveraged to predict B- and T-cell epitopes which were manually curated, and mapped onto the corresponding protein models to identify surface-exposed epitopes with direct accessibility to the host immune cells. These epitopes were linked together to construct a multi-epitope vaccine (MEV) that was predicted to be antigenic, and soluble upon overexpression. The tertiary structure of the MEV was generated which was used for molecular docking with TLR4 and TLR2. Molecular dynamics simulation and flexibility analysis confirmed the structural stability of the MEV-TLR4/TLR2 complexes. In-silico immune simulation showed the capability of MEV to induce a strong immune response. Codon optimization and in-silico cloning were performed to evaluate its efficient expression in the E. coli host. The findings suggest that surface exposed OMBB proteins can serve as promising antigenic candidates for designing an MEV construct.

bioinformatics↗

bioRxiv2026

Deciphering the Molecular Structure of the Type III Secretion System in Chlamydia trachomatis for Structure-Based Therapeutic Targeting

Chlamydia trachomatis is an obligate intracellular pathogen that causes sexually transmitted infections and trachoma. Its persistent forms show reduced antibiotic susceptibility, creating a need for new antivirulence strategies. The C. trachomatis injectisome or type III Secretion System (T3SS) injects effector proteins into host cells, yet the molecular structure of the complete apparatus is unknown. Here, we identify and validate all 13 T3SS constituent proteins using TXSSScan and reverse-BLAST analysis, and model and assemble them into the complete T3SS apparatus using an integrated computational pipeline. Template-based modeling revealed a conserved architecture despite low sequence identity (18-46%), and the assemblies were validated stereochemically and energetically against homolog controls. Targeting the oligomerization interface of the CdsN ATPase through structure-based virtual screening of the e-Drug3D and IMPPAT libraries, followed by ADMET filtering, including predicted membrane permeability for intracellular targeting, identified three repurposable FDA-approved candidates: M Roflumilast, Elacestrant, and Tecovirimat. MM-GBSA calculations and molecular dynamics simulations confirmed stable complexes with two adjacent CdsN monomers. Elacestrant showed the most favorable binding free energy. These results provide the first molecular-level map of the C. trachomatis T3SS and a rational basis for antivirulence drug repurposing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/723290v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@6893c8org.highwire.dtl.DTLVardef@1be5eddorg.highwire.dtl.DTLVardef@1462b25org.highwire.dtl.DTLVardef@1baadab_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Structural Characterization of the Type IV Secretion System in Brucella melitensis for Virtual Screening-Based Therapeutic Targeting

Brucellosis is a globally important zoonotic disease caused by Brucella melitensis, the most virulent and clinically significant species affecting both humans and livestock. Unlike many Gram-negative pathogens, B. melitensis, a facultative intracellular pathogen, lacks conventional virulence factors and instead relies on specialized systems such as the Type IV Secretion System (T4SS) for secretion of effector proteins. In this study, an integrated computational pipeline was implemented to identify, model, and assemble the T4SS components, encoded by virB operon, from the complete B. melitensis proteome. Template-based modeling strategies were employed to generate structures of T4SS subcomplexes, referencing crystallographic data from E. coli T4SS. Structural superposition with E. coli homologs revealed highly conserved architecture despite only 30-50% sequence identity. Stereochemical validation confirmed high model quality and favorable interactions among most VirB protein pairs. Membrane insertion analysis of the membrane-embedded assemblies further corroborated the spatial orientation of the modeled T4SS. Potential of T4SS as a drug target was explored by targeting dimeric interface of VirB11 ATPase to disrupt protein-protein interactions that could disarm the pathogen. Virtual screening of compounds from DrugBank database revealed compounds with docking score [≤] -7.0 kcal/mol that were screened based on ADMET properties, yielding three promising candidates - Ezetimibe (Drug Id: DB00973), Chlordiazepoxide (Drug Id: DB00475), and Alloin (Drug Id: DB15477). MM-GBSA analysis estimated favorable binding free energies for these compounds and molecular dynamics simulation for 200 ns further confirmed the protein-ligand interaction stability. Collectively, these findings provide new insights into the architecture of B. melitensis T4SS and identify three potential drug molecules targeting T4SS. This supports FDA - approved drug repurposing as an effective strategy for anti-virulence therapy against Brucellosis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/706537v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@847c4borg.highwire.dtl.DTLVardef@1fc2551org.highwire.dtl.DTLVardef@f62a7corg.highwire.dtl.DTLVardef@15f3468_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Remote Host Manipulation by Pathogenic Bacterial Extracellular Vesicles

Bacterial extracellular vesicles (BEVs) are known to enhance infection susceptibility in vivo, yet the mechanistic basis for this remote preconditioning of host cells is unknown. Here, we discover an evolutionarily conserved, lipid-driven physical mechanism by which pathogenic bacterial EVs systemically arrest phagosome maturation in bystander host cells. Using live-cell fluorescence lifetime imaging, in vitro reconstitution and micromanipulation, we show that EVs from diverse pathogens - Mycobacterium tuberculosis, Klebsiella pneumoniae, and Staphylococcus aureus - fuse with host plasma, phagosomal, and lysosomal membranes. This fusion increase membrane order and perturbs early phagosomal maturation. Transcriptomic profiling confirms a broad downregulation of phagosome maturation genes while upregulation of lysosomal stress responsive genes. Crucially, in vitro reconstitution shows that EVs, and their purified lipids alone, are sufficient to induce phase separation and increase membrane order, directly inhibiting phago-lysosomal fusion. Our findings establish a paradigm in which pathogens exploit EVs not merely as delivery vehicles, but as tools to remotely rewire host cell membrane mechanics to hijack phagosome maturation and promote infection - a strategy that moves beyond canonical effector-based models of pathogenesis.

cell biology↗

bioRxiv2025

XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans

Dosage compensation of sex chromosomes through X-chromosome inactivation (XCI) is required for mice extra-embryonic tissue growth and embryo development. The species specificity in mechanisms and timing leading to XCI during early embryogenesis, however, left the key question of the interdependence between XCI and human development open. Here, we show that the differentiation of naive human pluripotent stem cells to trophoblast stem cells and extraembryonic mesoderm cells triggers XCI. The inactive X chromosome, however, displays an atypical chromatin state, lacking classical enrichment of heterochromatin markers and DNA methylation. We demonstrate that extraembryonic differentiation and XCI are kinetically and functionally linked. Using loss of function approaches, we prove that XIST is required for human XCI establishment. We also reveal that XCI is key for the survival of human female extraembryonic cells. Our work therefore links XCI to the formation of extraembryonic annexes, with important consequences for human reproductive biology. HIGHLIGHTSO_LINaive hPSCs to EXMCs and TSCs differentiation recapitulates human XCI C_LIO_LIThe Xi has an unusual chromatin status in human extraembryonic cells C_LIO_LIXIST is required for the establishment of human XCI C_LIO_LIXCI supports healthy development of human female extraembryonic cells C_LI

developmental biology↗

bioRxiv2025

Biofuel-driven Adaptable n-type Supramolecular Wires: Mimicking Conducting Microbial Nano-filaments

We report the biofuel-driven self-assembly of a benzimidazole-pyridine platinum (II) complex into supramolecular nanowires. Phosphate promotes Pt{middle dot}{middle dot}{middle dot}Pt metallophilic stacking, whereas the pristine complex forms nanosheets dominated by {pi}-{pi} interactions. By varying phosphate denticity (adenosine/guanosine mono-, di-, and triphosphates), we tune the extent of Pt{middle dot}{middle dot}{middle dot}Pt interactions and the resulting electrical conductance of the nanowires, measured on graphene using a custom EGaIn setup. Triphosphate-templated nanowires exhibit nearly four orders of magnitude higher conductance than non-templated nanosheets. Thermopower measurements reveal a negative Seebeck coefficient, indicating LUMO-mediated electron transport and rare n-type behavior in these supramolecular assemblies. Temperature-dependent measurements show a transition from tunneling (non-templated nanosheets) to thermally activated hopping (triphosphate templated nanowires). The system is recyclable, apyrase hydrolysis disrupts the nanowires, and re-addition of phosphate restores assembly, enabling reversible conductance switching over multiple cycles. This study demonstrates a fuel-responsive, adaptive supramolecular electronic material, highlighting how controlled Pt{middle dot}{middle dot}{middle dot}Pt interactions can be exploited to program charge transport in soft, bioinspired electronic systems.

bioengineering↗

bioRxiv2025

LFA-1 Interaction with GBP-130 on Plasmodium falciparum-infected Red Blood Cells mediates NK Cell Activation and Parasite Control

Natural Killer (NK) cells contribute to early immunity against Plasmodium falciparum by recognizing and eliminating infected red blood cells (iRBCs), a process mediated in part by the integrin LFA-1. However, the cognate parasite ligand for LFA-1 has remained unknown. Here, we identify Glycophorin Binding Protein-130 (PfGBP-130) as a surface-expressed ligand on iRBCs that binds the I-domain of LFA-1 (LFA-1 I). Using an LFA-1 I-Fc fusion protein, we demonstrate stage-specific binding to iRBCs, and LC-MS/MS analysis of immunopreciptates of I-Fc bound to iRBC revealed PfGBP-130 as a high-confidence interactor. Recombinant PfGBP-130 binds NK and THP-1 cells in an LFA-1-dependent manner. Co-culture assays show that PfGBP-130 promotes NK cell activation, degranulation, and facilitates contact-dependent killing of iRBCs. Neutralizing antibodies against PfGBP-130 significantly impair these responses. Our findings establish PfGBP-130 as the LFA-1 ligand on iRBCs, providing new insight into NK cell-mediated immunity in malaria and identifying a potential target for host-directed interventions.

immunology↗

bioRxiv2025

Identification and Characterization of Outer Membrane Proteins and Membrane Spanning Protein Complexes in Brucella melitensis

Brucellosis (Malta fever) is a zoonotic disease that affects both humans and animals, including cattle, sheep, and goats. Brucella melitensis is the most virulent and clinically significant species in humans. It is a Gram-negative bacterium with three groups of outer membrane proteins (OMPs): minor OMPs (Group 1), and major OMPs (Groups 2 and 3). OMPs with {beta}-barrel architecture play important roles in nutrient transport, efflux, adhesion, and membrane biogenesis. Despite their importance, the structure, function, and interaction dynamics of several B. melitensis {beta}-barrel OMPs and associated protein complexes remain mostly unexplored. In this study, we conducted a comprehensive in silico analysis to characterize known outer membrane {beta}-barrel (OMBB) proteins and identify novel OMBBs in B. melitensis 16M. Proteins were modelled using five computational tools: AlphaFold 3, ESMFold, SWISS-MODEL, RoseTTAFold, and TrRosetta. Outer-membrane insertion of the novel OMBBs was confirmed using PPM 3.0, Protein GRAVY, DREAMM, and MemProtMD_Insane. Putative functions were predicted using structure- and sequence-based annotations. Sequence variation across 46 B. melitensis strains were identified and mapped onto the structural models. OMBB-associated protein complexes - the RND (Resistance-Nodulation-Division) efflux pumps, the lipopolysaccharide transport (Lpt) complex, and the {beta}-barrel assembly machinery (BAM) complex - were modelled, and protein-protein interactions (PPIs) were analyzed to confirm thermodynamically stable assemblies. This study presents a robust in silico strategy for exploring OMP architecture and provides valuable structural insights to support the development of diagnostics, targeted therapeutics, and vaccines against B. melitensis.

bioinformatics↗

bioRxiv2025

Enhanced Formulation of Precision Probiotics through Active Machine Learning

The human gut microbiome is crucial to health, with dysbiosis increasingly linked to disease. Precision probiotics offer a promising approach to restoring microbial balance, but ensuring probiotic viability through gastrointestinal transit remains a challenge. This study applies an advanced active machine learning (ML) approach to predict how excipients affect the growth of Lactobacillus plantarum, a commonly used probiotic. State-of-the-art experiments were carried out to complement the ML study. Starting with five known excipient- probiotic interactions, we apply active ML over three rounds to predict the effects of 116 excipients, iteratively refining model certainty and accuracy. Five ML models--Neural Networks, Gradient Boosting, Logistic Regression, Random Forest, and Support Vector Machines--were trained and evaluated, with the final model achieving certainty levels close to 90%. Unlike previous methods, which retrained new models per iteration, our approach continuously optimized a single model, enhancing prediction stability and reducing error. These results highlight the potential of active ML to support accurate excipient selection in probiotic formulations.

bioinformatics↗

bioRxiv2025

Design of a Multi-Epitope Vaccine using β-barrel Outer Membrane Proteins Identified in Chlamydia trachomatis

Chlamydia trachomatis is an obligate intracellular Gram-negative pathogen responsible for causing sexually transmitted infections (STIs) and trachoma. Current interventions, including screening and antibiotics, are limited due to the widespread nature of asymptomatic infections, and the absence of licensed vaccine exacerbates the challenge. In this study, we predicted outer membrane {beta}-barrel (OMBB) proteins and designed a multi-epitope vaccine (MEV) construct using identified proteins. We employed a consensus-based computational framework on the C. trachomatis D/UW-3/CX proteome and identified 17 OMBB proteins, including well-known Pmp family members and MOMP. Eight OMBB proteins were computationally characterized, which showed significant structural homology with known outer membrane proteins from other bacteria. Sequence-based annotation tools were used to determine their putative functions. B-cell and T-cell epitopes were predicted from the selected proteins. The MEV construct was designed using four cytotoxic T lymphocyte (CTL) epitopes and 29 helper T lymphocyte (HTL) epitopes predicted from six OMBB proteins, which were conserved across 106 C. trachomatis serovars. The vaccine was supplemented at the N-terminus with Cholera enterotoxin subunit B and PADRE sequence to enhance its immunogenicity. The MEV construct of 780 amino acids was antigenic, non-allergenic, non-toxic, and soluble. Secondary structure analysis revealed 95% random coils. The 3D structural model of MEV was generated and validated, confirming its structural reliability. Molecular docking between MEV and Toll-like receptor 4 (TLR4) revealed strong and stable binding interactions, supporting its potential to elicit a strong immune response. This study highlights OMBB proteins as promising immunogenic targets and presents a computationally designed MEV candidate for C. trachomatis infection.

bioinformatics↗

bioRxiv2025

Identification and Characterization of Novel Outer Membrane Proteins of Brachyspira pilosicoli

Brachyspira pilosicoli is a pathogenic, Gram-negative, spirochete bacterium that causes intestinal spirochetosis (IS) in birds, pigs, and humans and is distributed worldwide. This anaerobic intestinal bacterium colonizes the large intestine, potentially leading to colitis, diarrhoea, and decreased growth rate. Outer membrane proteins of Gram-negative bacteria play crucial roles in adhesion and host-pathogen interaction, helping the bacteria to evade the host immune system, and enhancing their virulence. However, B. pilosicoli outer membrane proteins are yet to be identified and characterized. Here, we report the computational discovery of 42 outer membrane {beta}-barrel (OMBB) proteins in B. pilosicoli proteome predicted using a consensus-based computational framework. {beta}-barrel architectures of the predicted proteins were confirmed by generating AlphaFold 3-based structural models. Structure-based functional annotation predicted putative functions for the identified OMBB proteins, including BamA homolog involved in folding and membrane insertion of OMPs, LptD homolog involved in transport of lipopolysaccharides into the OM, efflux pumps, transporters, enzymes, diffusion channels, and porins. Sequence variations across nine strains of B. pilosicoli were identified and mapped onto structural models, revealing that many of the variations were present on the surface exposed loop regions of the {beta}-barrel structures. Our in-silico analysis has identified 42 OMBB proteins, including homologs of BamA, LptD, TolC, TonB-dependent receptors, CsgG. Seven of these were identified as hypothetical proteins. Computational characterization of the predicted OMBB proteins offer insights into their potential roles in physiology, virulence, and disease pathogenesis, highlighting their potential for applications in diagnostics, vaccine development, or therapeutic interventions.

bioinformatics↗

bioRxiv2024

Structure and function of the human apoptotic scramblase Xkr4

Phosphatidylserine externalization on the surface of dying cells is a key signal for their recognition and clearance by macrophages and is mediated by members of the X-Kell related (Xkr) protein family. Defective Xkr-mediated scrambling impairs clearance, leading to inflammation. It was proposed that activation of the Xkr4 apoptotic scramblase requires caspase cleavage, followed by dimerization and ligand binding. Here, using a combination of biochemical approaches we show that purified monomeric, full-length human Xkr4 (hXkr4) scrambles lipids. CryoEM imaging shows that hXkr4 adopts a novel conformation, where three conserved acidic residues create an electronegative surface embedded in the membrane. Molecular dynamics simulations show this conformation induces membrane thinning, which could promote scrambling. Thinning is ablated or reduced in conditions where scrambling is abolished or reduced. Our work provides insights into the molecular mechanisms of hXkr4 scrambling and suggests the ability to thin membranes might be a general property of active scramblases.

biophysics↗

bioRxiv2024

Importin alpha inhibitors act against the differentiated stages of apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii

Protozoan parasites of the phylum Apicomplexa, including Plasmodium falciparum and Toxoplasma gondii, cause widespread disease in humans. New drugs and protein targets are required for the treatment of these diseases, particularly therapies targeting multiple stages of the parasite life cycles. Nuclear import, carried out by the transporters importin (IMP) and {beta} subunits, is a valid target for the discovery of lead compounds against these protozoan parasites: small molecules were identified that inhibit interactions between IMP and nuclear localisation signals in vitro and also inhibit the growth of the rapidly-dividing stages of P. falciparum and T. gondii (asexual stages and tachyzoites) in culture. In this report, we add another small molecule (Bay 11-7082) to the panel of inhibitors of IMP and test the ability of these inhibitors to first, inhibit nuclear transport in the rapidly dividing stages and, next, the maturation of differentiated stages of both parasites. We show that GW5074 and CAPE inhibit nuclear transport in the P. falciparum blood stages, while Bay 11-7085 inhibits nuclear transport in T. gondii tachyzoites. Interestingly, CAPE strongly inhibits gametocyte maturation, the sexual stages of P. falciparum, and Bay 11-7085 weakly inhibits bradyzoite differentiation, the latent stages of T. gondii. As differentiation of both these stages is dependent on activation of gene expression, triggered by the nuclear translocation of transcription factors, our work provides a "proof of concept" that targeting nuclear import is a viable strategy for the development of therapeutics against multiple stages of apicomplexan parasites, some of them recalcitrant to existing drugs.

molecular biology↗