biophysical modeling

This study challenges the role of resident cardiac macrophages in AV node conduction by showing no evidence of Cx43-mediated coupling and no effect of macrophage depletion on AV electrical activity.

The paper investigates how RNA polymerase I recognizes promoters and selects transcription start sites in yeast, revealing a two-step mechanism and factors influencing TSS selection.

This paper identifies a metal-responsive UMPylation mechanism in Salmonella that enables intracellular biphasic growth and antibiotic tolerance by modulating protein aggregation and translational arrest.

This study identifies the dimerization mechanism of HIV-1 RNA hairpins to extended duplex structures using simulations, revealing intermediates and ion-dependent pathways.

This study uses molecular dynamics simulations to show that VISTA's conformational switching between Up and Down states regulates its immune checkpoint function through CC' loop accessibility.

This paper identifies AnkX as a Legionella effector that posttranslationally modifies IMPDH2, disrupting its filament assembly and altering GTP metabolism in host cells.

This study shows CD28 co-stimulation forms signaling condensates with Lck, which PD-1 modulates by binding and disrupting these structures, leading to engineered CAR T cells with improved antitumor activity.

This study shows human INO80 slides hexasomes as efficiently as nucleosomes and reveals structural mechanisms for topology-driven chromatin remodeling.

This study uses molecular dynamics simulations to compare ion conduction mechanisms in HCN and CNG channels, revealing differences in selectivity filter dynamics that explain their functional divergence.

This study identifies IFNγ-producing intraepithelial CTLs in celiac disease that interact with HLA-E/B on enterocytes, promoting CTL recruitment and epithelial killing.

The paper investigates how electric and mechanical signals interact in cell migration, showing electric fields can override mechanical cues and proposes a platform to predict these interactions.

This study investigates the conformational flexibility of kinesin-1 using biophysical methods, revealing its open structure without cargo and insights into autoinhibition.

The paper identifies small RNA regulatory modules involved in tomato fruit ripening and quality traits through genome-wide bioinformatics analysis.

The paper develops a bond graph model of enterocyte homeostasis, showing how physical laws constrain ion and glucose transport mechanisms to maintain cellular homeostasis.

This study identifies the glycine-arginine-rich motif of 53BP1 as essential for RNA interactions and phase separation during DNA damage response, showing its role in DNA repair.

This study reveals the structural and functional mechanism of Retron-Eco8, a bacterial defense system that uses a holocomplex to cleave phage DNA and inhibit infection.

The paper shows that voluntary running maintains gene expression corrections from AAV gene therapy in mdx mice, indicating physical exercise does not negatively affect therapy outcomes.

This study identifies Ca2+-CaM as a direct activator of INF2, linking calcium signals to actin assembly and mitochondrial fission through an allosteric mechanism.

This study develops a framework for cellular-resolution electrical stimulation of neurons using current steering and biophysical models, demonstrating its effectiveness in targeting retinal ganglion cells.

The paper shows that bacterial chemotaxis allows Escherichia coli to form fronts that escape phage predation without resistance.

This paper identifies a SCCmec-located gene cluster (cst2) that enables MRSA to tolerate polysulfides, giving it a competitive advantage in polysulfide-rich environments.

This study shows that host sphingomyelin and cholesterol act as a lipid chaperone to facilitate the conformational changes of the bacterial toxin Cytolysin A, enabling pore formation.

The paper identifies P2RX5 as a new B-cell surface marker and multi-lineage immunotherapy target, showing its expression in B-cell malignancies and T-cell leukemia, and demonstrating the efficacy of P2RX5-directed therapies.

The paper investigates whether the antisense lncRNA THAP9-AS1 can bind to the product of its sense pair, THAP9, by analyzing G-quadruplex forming sequences and validating their structural importance.

This study identifies the role of 2'-hydroxyl groups in crRNA for Cas9 DNA binding and develops chemically stabilized crRNAs with enhanced nuclease resistance and editing efficiency.

This study characterizes McHemW, a heme-binding radical SAM enzyme in Moraxella catarrhalis, showing it binds heme and contains an active [4Fe-4S] cluster, suggesting a role in heme transport.

This paper identifies two distinct MAP3K pathways activated by beetle toxins that trigger NLRP1 inflammasome activation in human keratinocytes.

The paper identifies a mechanical homeostasis mechanism in podocytes where balance between fluid shear stress and cellular contractility prevents injury, showing that reducing blood pressure can worsen outcomes when contractility is impaired.

This study shows that pore-size dynamics in pyroptosis control cell swelling through GSDMD and Ninj1, with distinct permeability regimes affecting ion selectivity and water filtration.

This study identifies a PrfH subfamily that rescues both damaged and intact ribosomes stalled in translation, revealing dual mechanisms for peptide hydrolysis.