biophysical modeling

This study shows that protamines, despite being intrinsically disordered, bind DNA with nucleobase-specific preferences, favoring GC over AT in the major groove and vice versa in the minor groove.

The paper identifies BCAS3 as a novel interactor of WIPI2b that regulates its membrane association through interaction with PtdIns3P.

The paper identifies SEC16A/MAG5 as essential for ABA receptor homeostasis by mediating ER export and trafficking, impacting ABA signaling without affecting ABA levels.

The paper shows that heat stress reverses the growth-promoting thermomorphogenesis pathway in Arabidopsis by suppressing auxin and PIF4 in cotyledons, revealing an active molecular mechanism.

The paper develops a biophysical model of the SCN to explain circadian rhythm splitting under chronic light and shows how E/I balance and chloride cotransporter dynamics drive this behavior.

This study shows lysenin pores induce membrane curvature into rigid dome-like structures, suggesting beta-PFTs alter host cell membranes beyond pore formation.

This study characterizes the conformational dynamics and phosphorylation-dependent changes in the SF3B1 N-terminal domain using a combination of biophysical and computational methods.

The paper updates the Human Neocortical Neurosolver model to include biophysically realistic dynamics in human neurons, enabling better interpretation of EEG/MEG signals.

The paper reconstructs the asperosaponin biosynthesis pathway in Dipsacus asperoides by integrating genomics, transcriptomics, and biochemical analyses, revealing gene family diversification and glycosylation order.

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

The paper introduces topoiesis, a mechanism where diffusion and geometry drive collective morphogenesis and survival in Xenopus embryos under stress.

This study investigates how tau protein regulates motor proteins on microtubules using single-molecule imaging, cryo-EM, and MD simulations, revealing distinct mechanisms for inhibiting kinesin-1 and dynein.

This study identifies anti-phage defense systems in VREfm genomes and finds limited associations between specific systems and phage resistance, with one candidate gene reducing susceptibility.

This study shows that myelin affects hippocampal network function by shaping extracellular space, not only by insulating axons, with demyelination altering diffusion, flow, and synaptic transmission.

This study identifies distinct peripheral elements in senataxin that mediate R-loop unwinding and RNA polymerase II regulation through structural and biochemical analyses.

This study identifies a seesaw configuration of the ODC-OAZ1-AZIN1 axis that determines breast cancer cell sensitivity to polyamine-targeting inhibitors, offering a framework for personalized therapy.

The paper identifies a novel virus lineage, IME1, found in Dehalococcoides-containing cultures, characterized by features similar to filamentous bacterial viruses.

The paper uses a Drosophila connectome and biophysical simulations to show that a reciprocal circuit between T4a motion detectors and vCH cells supports figure-ground discrimination through shunting inhibition.

The paper investigates how the IspG-FldA electron transfer complex functions through conformational selection and redox-dependent destabilization.

This study compares Zyxin and LPP's mechanoaccumulation at tricellular junctions under tension, revealing differences in their LIM domain sensing mechanisms.

The paper identifies a bacterial transcription factor, GloR, that senses glyoxal to enable Pseudomonas aeruginosa lung infection.

The paper develops a bioinformatic pipeline using 23S-5S rRNA sequencing to identify Legionella species in culture-negative PCR-positive samples, successfully assigning species in 60% of cases and revealing high diversity.

BGC Atlas v2 expands the collection of predicted biosynthetic gene clusters to over 16 million, providing taxonomic and environmental context for natural product discovery.

This study shows that ANP32 is a conserved host factor for viral replication in the Articulavirales order, using structural and biochemical analyses of TiLV and its interaction with ANP32.

The paper identifies conserved actin-driven mechanisms in jellyfish oocytes that facilitate meiosis, suggesting ancient origins in metazoans.

This study shows SF1 helicase Rep translocates processively on ssDNA and, unexpectedly, also on dsDNA, with high speed and processivity, challenging existing models of helicase function.

This study uses molecular dynamics simulations to characterize the TRPC6-CAV1 interaction, revealing an acidic patch in TRPC6 and a basic segment in CAV1 that form a cooperative binding interface with favorable binding free energy.

The paper shows that IFNg induces both stemness and differentiation in AML cells, leading to heterogeneous responses that affect leukemia growth and regeneration.

The paper uses simulations to show that lipid-type asymmetry, not phospholipid-number imbalance, is sufficient to reproduce key physical properties of plasma membranes.