biophysical modeling

The paper proposes the Texas 2-Step model to explain how YcgR modulates flagellar motor rotation in E. coli by interacting with MotA and FliG through conformational changes.

This study identifies a tyrosination-dependent mechanism that enables dynein-2 to specifically bind the A-tubule of ciliary doublet microtubules, facilitating retrograde IFT.

The paper identifies a biomechanical pathway in beige adipocytes that mediates thermogenic activation through Myh9-FAK signaling, distinct from white adipocytes.

This study reveals that PAC-1, a clinical-stage oncology compound, targets drug-resistant cancers by disrupting iron homeostasis and exploiting MDR1 expression to induce iron depletion.

This study identifies 3-phenylpropionic acid (3-PPA) as a colon-enriched PPAR-γ agonist derived from polyphenol metabolism, which ameliorates colitis in mice and highlights its potential as a microbiota-targeted therapeutic for Crohn's disease.

This study identifies TPM4 as a gene promoting anaplastic thyroid cancer progression through EMT by enhancing cell migration and invasion.

This study uses molecular dynamics simulations to show how CMG helicase translocates directionally and navigates nucleosomes during DNA replication, with contributions from Csm3/Tof1 and RPA.

This paper identifies NmbA as an N-methyltransferase for bacillithiol in Chlorobaculum tepidum, revealing its unique structure and function in N-Me-BSH biosynthesis.

The paper uses steered molecular dynamics to evaluate ligands' ability to modulate fast inactivation of P. americana cockroach Nav channels, identifying PF-05089771 and PIP2 as inhibitors.

The paper demonstrates that local stimulation of cell migration in tissues can drive collective motion through cell-cell adhesion, accelerating healing and growth by 5-fold.

This study uses molecular dynamics simulations to show how H2A and H2B ubiquitination opposingly affect nucleosome stability and assembly kinetics through structural changes.

The paper characterizes a cyanobacterial FeSBCP using bioinformatics, biochemistry, and biophysics, showing efficient binding and repair of 6-4 photolesions.

This study analyzes PTEN-deficient prostate tumors to reveal stromal reprogramming and senescent paracrine communication through transcriptional network analysis and single-cell RNA-Seq.

This study investigates how alpha-actinin stabilizes actin filament structure, preventing cofilin-induced helical shortening and cooperative binding.

The paper shows stress causes bacterial BR-bodies to switch from mRNA decay to storage by changing their physical state and function.

The paper develops a biophysical model to jointly analyze single-cell RNA and protein data, demonstrating its utility with simulated and 10x multiomic data.

This study identifies Enterocin C's mechanism of action by targeting BacA, revealing cooperative peptide interactions leading to cell death and suggesting potential for bioengineering antimicrobials.

The study identifies antiphage defense systems and prophages in Streptococcus mutans clinical isolates using bioinformatics tools, revealing diversity in defense mechanisms and a unique prophage.

This paper shows eIF2B activates mutant KRAS by forming a complex with SOS at the plasma membrane and regulating glycosphingolipid biosynthesis.

The paper measures ERGs in mice to assess contributions of rod, RPE, and Müller glial cells to dark and light-driven changes in sub-retinal space ion concentrations.

This study shows hydrogen sulfide modulates hypoxic responses in Arabidopsis by inhibiting plant cysteine oxidases through persulfidation, affecting gene activation and submergence tolerance.

This study investigates how different regulatory subunits modulate p110α activity and finds no significant differences in lipid kinase activity or conformational changes across subunit variants.

This study identifies a monoclonal antibody that neutralizes HCoV-HKU1 by mimicking sialic acid binding to block receptor engagement.

The paper maps the conformational landscape of TRMT2A RRM using molecular dynamics and identifies a hydrophobic cluster that governs allostery and RNA recognition.

This study investigates how the alarmones ppGpp and pppGpp differentially regulate the nucleosidase PpnN in E. coli, revealing its role in bacterial survival under antibiotic stress and uncovering a conserved catalytic mechanism shared with plant cytokinin signaling proteins.

The paper identifies 15 candidate cytoplasmic retention peptides in human proteins, with 10 having unrelated sequences, and shows that retention sequences are located at specific sites across protein isoforms.

This study characterizes the Bub bacterial ubiquitination-like pathway, revealing its unique biochemical mechanisms and structural similarities to eukaryotic ubiquitination.

This study uses RNA-seq to assess the transcriptional effects of cisplatin and TiO2 nanoparticles in Drosophila, finding synergistic gene suppression and impaired climbing performance in combined exposure.