biophysical modeling

This paper identifies Aqs1, a phage-encoded protein that inhibits type IV pilus function in multiple Gram-negative bacteria by targeting the PilB ATPase.

This study identifies a mechanism of asynchronous nuclear division in Plasmodium falciparum that enhances proliferation by minimizing resource idling through sequential allocation of a limiting replication resource.

This paper redesigns an Fc-binding peptide to enable multivalent antibody assembly without altering the IgG scaffold, showing enhanced stability and functional utility.

The paper uses molecular dynamics simulations to study the dynamic interactions between Tau protein and tubulin C-terminal tails, revealing sequence-dependent effects and disorder-disorder interplay.

This study identifies structural and mechanistic principles of Atg15 activation and membrane recognition using MD simulations and experimental validation.

This study uses molecular dynamics simulations to show that cholesteryl esters increase lipid droplet rigidity and monolayer organization in liver cancer.

This study develops a multiscale computational model linking TMJ structural changes to nociceptive activation by integrating biomechanics, neural morphology, and electrophysiology.

This study develops a coarse-grained model to investigate how caveolin-1 proteins drive membrane curvature through collective interactions.

This study reports the crystal structure of the THEMIS CABIT1 domain and shows that LCK phosphorylation enables its interaction with SHP1 and protects SHP1 from ROS inhibition.

This study identifies thaxtomin A as a potent cellulose biosynthesis inhibitor with broad-spectrum activity and elucidates its mechanism of action through structural and functional analyses.

This study investigates DAF-12 interactions with transcriptional coactivators in parasitic nematodes using structural and bioinformatic approaches, revealing conserved and nematode-specific mechanisms of coactivator recruitment.

This study identifies BCR-dependent enhancement (BDE) as a mechanism by which DENV infects B cells, showing that BCR-E protein interactions and dynamin-mediated entry are critical for viral replication in these cells.

This study identifies TspA, a biofilm-degrading enzyme from Rhodobacter capsulatus GTA, which enhances gene transfer by clearing biofilms and navigating the extracellular matrix.

This paper identifies two structural elements in HELB essential for its interaction with RPA-coated ssDNA, showing how they facilitate RPA displacement and DNA loop formation.

The paper identifies a new family of dehydrating condensation domain proteins involved in the biosynthesis of azabicyclocarbamates in Pseudomonas aeruginosa.

The paper investigates ZnF-UBP domains in USP DUBs, showing they relieve product inhibition by facilitating Ub release, thereby regulating enzyme activity.

This study identifies VDAC2 as a regulator of BAX activation by stabilizing a primed, membrane-inserted intermediate in the BAX activation pathway.

This study investigates how the terminal Glc-(1-2)- in the LLO donor affects OST catalytic efficiency through molecular dynamics simulations of yeast OST with and without this motif.

This study develops a multiscale cytoskeletal network model to simulate shear rheological properties and their evolutionary mechanisms, revealing how chemo-mechanical coupling and actin filament dynamics influence cellular mechanical responses.

This study identifies substrate biasing in UCHL5 proteoforms, showing N-terminal ubiquitination activates the enzyme toward monoubiquitin substrates and regulates debranching activity.

The paper develops a biophysical model showing how crosslinker binding and filament spacing feedback to self-organize cytoskeletal bundles into specific geometries.

This study shows sonication causes selective fragmentation of intrinsically disordered proteins in proteomics, leading to structural bias and potential misinterpretation of protein size and stability.

This study reveals the structural basis for Rifamycin B's activity against rifampicin-resistant RNA polymerase, showing its unique binding mechanism and potential for drug development.

The paper identifies conserved RNAi effector genes in trematode-vectoring snails, suggesting potential for RNAi-based disease control despite lacking classical systemic and amplification components.

This study identifies new TIME-COMP-like structures containing antibiotic resistance genes in Enterobacteriaceae genomes, highlighting the role of TIMEs in ARG mobilization.

This study defines the structure and mechanism of retron type IX, revealing how its DNA-scaffolded ring assembly mediates antiphage immunity through phage-encoded nuclease-triggered activation.

This study investigates how Anandamide affects microRNA expression in HIV1 TAT-stimulated human astrocytes, identifying miRNAs involved in anti-inflammatory pathways.

This paper identifies CenIR as an essential BlaIR-family regulatory system in C. difficile that lacks a β-lactam-binding domain and is required for viability, with its regulon containing genes involved in peptidoglycan hydrolase and cell envelope maintenance.

This study identifies electrostatic and aromatic residues as key determinants of lipid binding and membrane penetration in synaptotagmin C2 domains through molecular dynamics simulations.