biophysical modeling

The paper investigates how MDA5 CARDs assemble and interact with LGP2 through one-dimensional movement along dsRNA to regulate immune response.

This study models GPR174 bound to an antagonist and compares its dynamics to LysoPS, revealing distinct ligand-specific mechanisms and potential for immunotherapeutic antagonists.

This paper identifies and characterizes pellemicin, a spirotetronate with antiviral activity against influenza A and B viruses by inhibiting clathrin-mediated endocytosis.

This study investigates the RNA-binding mechanism of ProQ using molecular dynamics simulations, revealing electrostatic interactions and structural changes upon raiZ RNA binding.

This study identifies the diversity and prevalence of amino acid decarboxylase enzymes in the human gut microbiome, highlighting key genera and enzymes involved in metabolite production.

This study uses a coarse-grained model to show DNA length and flexibility influence protein-DNA condensate structure and protein dynamics, revealing multiphasic organization and differential diffusion modes.

This study identifies how P-cadherin and Desmoglein-2 form strand-swap dimers to facilitate desmosome assembly through structural and functional analyses.

The paper analyzes microbial biosynthetic potential across geothermal environments, finding that tectonic settings influence the diversity and types of biosynthetic gene clusters.

This study identifies PH4EFB as the primary prolyl 4-hydroxylase for collagen IV in Drosophila through bioinformatic, transcriptomic, and biochemical analyses.

This study identifies matrisome signatures in quiescent and activated muscle stem cells using transcriptomic data, linking ECM gene expression to niche function and muscle repair.

This paper shows that phosphorylated EpsW activates exopolysaccharide biosynthesis by promoting EpsZ dimerization in Myxococcus xanthus.

This study investigates how organ-specific extracellular vesicles (sEVs) contribute to metabolic improvements after vertical sleeve gastrectomy (VSG) in adolescents with obesity, finding that liver-derived sEVs correlate with BMI and BCAAs, while adipose-derived sEVs correlate with liver function markers.

The paper identifies conserved stickers in the Canoe IDR that bind F-actin, showing their combinatorial role in junctional localization, mechanosensing, and function during morphogenesis.

This study identifies the mTOR-Z-Phae1 axis as a genetic pathway regulating stress-induced organismal death in Drosophila larvae.

This paper identifies a dual interaction between RSV NS1 and MED25 ACID domain that suppresses antiviral responses by blocking transcription factor access to MED25.

The paper identifies additional tRNA targets of the AriB nuclease in the PARIS system and shows that phage-encoded tRNAs can inhibit this defense.

This study uses an in-silico model to show that interactions between centrosomal microtubules and cellular structures drive early centrosome separation during prophase.

The paper shows that rotational migration in Drosophila egg chambers is initiated by a feedback loop involving Fat2 and tissue geometry, revealing a biophysical mechanism for self-organized collective motion.

This study identifies a pivotal aa-tRNA pivoting mechanism in human translation that enhances fidelity by navigating the constrained ribosomal accommodation corridor.

The paper uses molecular dynamics simulations to study the formation of cross-β sheets in the HIV-associated peptide PAP248-286, identifying key residues and thermodynamic properties of dimerization.

The paper models immune cell migration by integrating nuclear piston, uropod, and microenvironment mechanics to show how they synergize for efficient movement through dense tissues.

This study identifies single-domain AA12 oxidoreductases and free AA8 modules as direct and cooperative electron donors to lytic polysaccharide monooxygenase (LPMO) in cellulolytic fungi.

This study identifies PIF4 as a regulator of H2O2 homeostasis that controls hypocotyl elongation in Arabidopsis seedlings under high temperature.

This study shows the MLLT3 YEATS domain binds both histone marks and the 7SK RNA, influencing hematopoietic lineage commitment and gene expression.

This study develops a biophysical model to show how lipid binding and mutations affect Orf9b's conformational equilibrium and its interaction with Tom70, influencing interferon suppression.

This study investigates how the G256E HCM mutation affects myosin function by altering nucleotide handling, leading to prolonged relaxation and contributing to hypertrophic cardiomyopathy.

This study identifies the IctPQM TRAP transporter as essential for Pseudomonas aeruginosa to utilize itaconate, a host-derived metabolite, by showing its specific binding and structural adaptations.

The paper investigates the mechanical properties of the Izumo1:Juno complex using force spectroscopy and simulations, revealing its mechanostability and how mutations affect it.

This study shows that arabinose nucleotides inhibit SARS-CoV-2 and poliovirus polymerases by causing long pauses due to the 2'-endo conformation of the incorporated nucleotides.

This study shows migrating cells retain a mechanical memory of past morphological states through actin cortex remodeling, aiding navigation in confined spaces.