mechanistic / dynamical model

This study compares HIV-1 gp120 subtypes A and B, showing subtype A induces more severe pulmonary arterial hypertension through enhanced furin activity and different CD4 and nAChR interactions.

This study identifies reactive cysteine residues in NLRP3 and shows how their oxidation by ROS affects NLRP3 conformation and inflammasome activation.

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

This study identifies the USP18-STAT2 axis as a critical factor enhancing hepatic resilience under proteotoxic stress by modulating interferon signaling and ISG solubility.

This study investigates how site-specific O-glycans on lacritin influence its structure and multimerization, revealing their role in conformational flexibility and crosslinking residue positioning.

This study shows that pneumolysin, a bacterial toxin, can damage target cell membranes through vesicle fusion rather than pore formation.

This study shows that maleic acid enhances BCG vaccination to induce CD4+CD8+ T cells that sterilize Mtb infection in mice.

This study identifies SAA1-TLR4 signaling as a tumor-derived pathway driving muscle wasting in pancreatic cancer, showing that targeting this pathway can preserve muscle mass and improve survival without affecting tumor growth.

This study evaluates catechins as inhibitors of Dengue virus NS3 helicase using biochemical assays and computational simulations, identifying EGCG and ECG as potent inhibitors with low Ki values.

This study identifies Atg1-mediated phosphorylation of Atg2 as a mechanism to activate lipid transfer during autophagosome biogenesis.

The paper models SARS-CoV-2 replication dynamics in human cells, identifies key bottlenecks, and evaluates antiviral drug effects using mathematical modeling and experimental data.

This study investigates the evolutionary and mechanistic diversity of bacterial NDH-2s, revealing lineage-specific catalytic mechanisms and their implications for drug development.

This study shows that inhibiting KDM5A/B enhances antitumor innate immune responses and induces KSHV lytic reactivation in KSHV-positive B-cell lymphomas.

The paper investigates how condensate material properties affect exopher cargo selection in neurons, finding that gel-like condensates are more efficiently recruited than liquid-like ones.

This study shows HMCES-DPC formation increases DNA template flexibility, enabling slippage and mutagenic bypass of AP sites during replication.

The paper shows that cytoplasm in early embryos behaves as a locally switchable active material, enabling long-range transport of components during cleavage.

The paper defines the MxA-Thogotovirus nucleoprotein interface using structural modeling and experimental validation, revealing key residues involved in restriction and escape.

This study investigates how PTMs modulate peptide translocation through graphene nanopores using molecular dynamics, finding that acetylation and phosphorylation significantly alter dwell-time statistics and current blockade.

This study identifies a stress-lipid kinase axis in NEPC driven by PIKfyve, revealing a synthetic vulnerability between PIKfyve and FASN that can be exploited for therapeutic targeting.

The paper shows that backbone hydrogen bonding determines condensate material states, as demonstrated by experiments with tetrapeptides and simulations.

This study identifies an O-GlcNAc modification on PKM2 that promotes PDAC progression through the ARNT-CDC27-AKT pathway by enhancing aerobic glycolysis.

This study shows that deleting ferritin heavy chain in medulloblastoma cells limits tumor growth by promoting iron-dependent stress and sensitizing cells to iron toxicity.

This paper investigates the mechanisms of ADC-immunotherapy combinations, finding that ADC-induced autophagy upregulates TNFR and M6PR, driving antitumor effects through TNF and granzyme B pathways.

This study shows azelaic acid reduces Pseudomonas aeruginosa virulence factors without killing bacteria, with safety and molecular docking support.

This paper develops a new methodology to model phosphoinositide signaling dynamics, showing that basal PI(4)P levels determine cell-specific responses to genetic perturbations.

This study shows that integrin-mediated mechanotransduction through supramolecular ligand clustering limits mitochondrial respiratory capacity, thereby suppressing cancer cell motility and tumor growth.

The paper investigates how competing factors in biomolecular condensates modulate the rate of poly(A) RNA deadenylation by CNOT7, revealing concentration-dependent increases and diffusion-related decreases in enzymatic efficiency.

This study identifies ATP13A3-antizyme regulation as a mechanism for adaptive polyamine uptake in cancer, showing that targeting ATP13A3 with AMXT 1501 can block this response.

This study compares structural variations in BRCA1/BARD1 orthologs across species to show how a structural loop affects ubiquitylation site selection and chromatin regulation.

This paper identifies putative glucose transporters in Trichuris spp and shows phloretin may inhibit glucose uptake, suggesting a new target for anthelminthic drug discovery.