biophysical modeling

This study identifies a hydrophobic groove on vitronectin's HX domain that binds phospholipids and mediates its association with HDL through structural modeling and simulations.

This study analyzes prophages and defense systems in Bifidobacterium genomes to reveal co-evolutionary 'arms race' dynamics between bacteria and phages.

This study identifies a novel mechanism by which caspase-4 and -5 interact with executioner caspases-3 and -7 to enable pyroptosis-apoptosis crosstalk, enhancing inflammatory responses.

This paper develops a biophysical cross-bridge model to predict muscle short-range stiffness during movement, finding that cooperative myofilament activation is essential for accurate predictions.

The paper shows periodic obstacles regulate membrane tension propagation in neurons, enabling localized mechanotransduction by restricting tension spread.

This study proposes a non-canonical lipid-mediated mechanism for eukaryotic membrane formation through molecular dynamics simulations.

This study models chemotaxis in Dictyostelium cells by coupling myosin dynamics with traction forces, showing that a central myosin patch generates step-wise migration and convergent traction patterns.

This paper develops a biophysical model linking electromechanical fields to tissue-level dynamics, showing how slow beats influence cell division and development.

The paper describes the acquisition of mobile genetic elements by Pseudomonas fluorescens through jumbo phage-mediated transduction, revealing new insights into horizontal gene transfer mechanisms.

This study uses metatranscriptomic data to analyze how dietary composition affects gut microbiota function, finding that a fiber-rich diet promotes beneficial metabolic pathways while a low-fiber diet increases harmful protein and mucin degradation.

The paper develops a synthetic BM niche model to test CRISPR-CAR T-cell therapy for AML, showing its efficacy in a human-like environment.

This study identifies how bacterial TIR domains recognize viral capsids to initiate defense by forming complexes that trigger NAD+ depletion.

This study shows that tRNA thiolation defects in humans cause proteostasis and tissue homeostasis issues, but mice with similar defects develop normally.

This paper shows Altiratinib targets PRP4K in Theileria annulata, disrupting RNA processing and inducing apoptosis in infected cells, with efficacy against drug-resistant strains.

This study shows that cooperative and antagonistic interactions between sub-clones in melanoma allow multiple resistance mechanisms to coexist, and identifies GSK-J4 as a potential therapeutic target.

This study uses biophysical methods to characterize lipid nanoparticle properties and predict their transfection efficiency.

This study demonstrates that ATP from photosynthesis in Synechocystis can power biocatalytic reactions, enabling sustainable chemical synthesis using whole-cell biocatalysis.

This study characterizes meiotic axis proteins in the brown alga Ectocarpus, revealing novel domain architecture and thermodynamic properties that suggest alternative HORMA domain regulation mechanisms compared to other eukaryotes.

This study identifies contingency loci in phages that generate genetic diversity through frameshift mutations, enabling bet-hedging against host defenses.

This study identifies torque on the TRP domain as the primary driver of NOMPC channel opening, revealing a twist-to-open mechanism facilitated by AR domain compression-twist coupling.

This study shows Oct4 promotes DNA accessibility by forming clusters that deform chromatin and expose DNA through liquid-like states, enhancing gene activation during reprogramming.

The paper identifies Giardia intestinalis ARF GTPases and their regulators as key components of non-canonical endosomal compartments involved in vesicle formation and membrane fusion.

This study shows that radiation resistance in TNBC enhances metastasis through RNA metabolism changes, specifically via HNRNPL-mediated circRNAs that regulate ITGβ3 expression.

This study investigates how the Staphylococcus aureus SauUSI restriction enzyme recognizes and cleaves methylated DNA through ATP-driven translocation and loop formation.

This study shows that TelN protects hairpin telomeres from Mre11-Rad50 degradation in E. coli by sequence-specific DNA binding and protein-protein interactions, independent of its resolution activity.

This study shows that paralogs H-NS and StpA form distinct condensates with different phase behaviors, enabling bacteria to adjust condensate stability for stress response.

This study shows that adding cysteine residues to FAP improves its photostability by quenching harmful triplet states of the FAD cofactor.

This study identifies dipeptidase 1 as the receptor for PHEV, showing it does not require sialic acid and reveals structural versatility in receptor binding.

This study uses molecular dynamics simulations to analyze how HIF-2 ligands differentially affect the structure, dynamics, and transcriptional activity of the HIF-2/ARNT complex, enabling high-throughput virtual screening.

This study investigates how carbohydrate-active enzymes induce conformational changes in glycans through ring distortions, revealing mechanisms that influence enzyme specificity and inhibitor design.