biophysical modeling

Redox Control of S-sulfocysteine Formation in Adenosine Phosphosulfate Reductase

This study investigates how the redox state of an iron-sulfur cluster in APSR from Pseudomonas aeruginosa influences catalytic activity and substrate binding through molecular simulations.

Cell division timing shapes the morphology and size of nascent multicellular organisms

The paper identifies cell division timing as a key factor influencing multicellular morphology and size in snowflake yeast, showing that asynchronous division leads to smaller clusters due to increased mechanical stress.

A widespread NADase domain links bacterial immunity with human TEP1

The paper identifies a conserved NADase domain, NIR, in bacterial immunity and eukaryotic proteins like human TEP1, linking bacterial defense mechanisms to eukaryotic functions.

The virulence and motility of Pseudomonas syringae pv. Actinidiae mediated by a temperature sensor HktS-HktR

This study identifies HktS-HktR as a temperature sensor in Psa that regulates virulence and motility by controlling T3SS expression and bacterial movement.

Protein-driven colloid-osmotic pressure controls nuclear size, organization, and function

The paper shows that protein-driven osmotic pressure regulates nuclear size and function, affecting chromatin organization and gene expression in yeast, human, and fly cells.

P. aeruginosa liquid-based pathogenesis triggers HLH-30-dependent metabolic rewiring in C. elegans

This study shows that P. aeruginosa liquid-based pathogenesis induces metabolic changes in C. elegans, involving lipid droplet depletion and HLH-30-dependent rewiring.

Structural basis for P-TEFb association with BRD4

This study identifies the structural basis of BRD4 interaction with P-TEFb and shows how BRD4 and AFF4 regulate P-TEFb activity through distinct mechanisms.

Functional Impact of Nth-like DNA glycosylase on Mitochondrial Dynamics

This study shows that NTHL1 loss increases mtDNA copy number and mitochondrial function, enhancing cellular resilience to oxidative stress through stress response pathways.

Bacterial Stimulation Remodels Macrophage Extracellular Vesicle Lipids and Reveals iNOS as an Inflammatory Cargo

This study shows bacterial stimulation changes macrophage-derived extracellular vesicle lipid composition and identifies iNOS as an active inflammatory cargo in these vesicles.

The nuclear actin cytoskeleton supports DNA double-strand break repair via VCP-mediated extraction of the KU70/80 complex from damaged chromatin

This study identifies Myo6's role in DSB repair by interacting with KU70/80 and VCP, facilitated by F-actin, to extract the KU70/80 complex from chromatin.

Lenacapavir allosterically remodels the HIV-1 capsid

This study shows lenacapavir remodels HIV-1 capsid structure by altering non-covalent interactions and material properties, leading to capsid rupture and impaired viral replication.

Molecular basis of nick ligation in the nucleosome by DNA Ligase IIIα

This study investigates how DNA Ligase IIIα ligates nicks in nucleosomes using biochemical assays, molecular dynamics, and cryo-EM, revealing position-dependent efficiency and structural constraints.

SLFN11 Enhances Cisplatin Sensitivity in Pediatric Cancer via Activation of Stress-Response and Suppression of Survival Pathways

This study shows SLFN11 enhances cisplatin sensitivity in pediatric cancers by modulating stress-response and survival pathways through epigenetic regulation and functional assays.

Structures of LolB bound to LolA or lipoprotein resolve the final steps of bacterial lipoprotein trafficking

This study presents structures of LolB bound to LolA or lipoprotein, revealing the mechanism of bacterial lipoprotein trafficking at the outer membrane.

Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition

This study reveals how LEAFY transcription factors evolved DNA-binding specificity through structural changes in dimerization mechanisms during the water-to-land transition.

Local mechanical heterogeneity drives epidermal cell delamination

This study identifies local mechanical heterogeneity as the driver of epidermal cell delamination through force balance changes and actomyosin remodeling in keratinocytes.

The Conformation of the Complementary Strand and the Deformation of the DNA Groove upon DDB2 Binding Justifies the Different Repair Rates for Cyclobutane Pyrimidine Dimers.

This study shows that DDB2 binding causes different DNA deformations depending on the cyclobutane pyrimidine dimer type, which explains the varying repair rates observed in human cells.

Rapid Bacterial Identification through Biophysical Surface Topography Features

This study identifies bacterial genera using 3D surface topography features with 97% accuracy, showing taxonomic information persists at the population morphology level.

Disease mutations in the PWWP domain of DNMT3A affect chromatin recruitment through multiple mechanisms

This study examines how mutations in the PWWP domain of DNMT3A affect chromatin recruitment through different mechanisms, leading to distinct disease phenotypes.

Structural and biochemical analysis of the IBV nsp15 endoribonuclease reveals the necessity of peripheral site residues for activity

This study analyzes IBV nsp15 endoribonuclease structure and function, showing peripheral residues are critical for RNA cleavage and revealing species-specific RNA engagement mechanisms.

β-strand complementation within tip initiation complexes licenses assembly of diverse type IV filaments

This paper identifies a β-strand complementation mechanism used by PilC/PilY1 proteins to license type IV filament assembly across diverse systems.

Small serine recombinases are markers for antiphage defense system discovery

The paper develops a bioinformatic pipeline using small serine recombinases to identify antiphage defense systems in bacterial genomes and metagenomes, finding they are genetically linked to these systems.

Structural and mechanistic analyses reveal collaborative regulation of HSF1 by the Hsp70-Hsp90 chaperone systems

This study reveals how HSF1 is regulated by Hsp70 and Hsp90 chaperones through structural and mechanistic analyses, showing Hsp90's role in maintaining HSF1 in a pre-activated state.

Copine-6 integrates calcium, phosphoinositide and Rab11 signals to coordinate glutamate receptor recycling

This study identifies Copine-6 as a protein that links calcium, phosphoinositide, and Rab11 signals to regulate glutamate receptor recycling in neurons.

Multiheme selenoenzyme essential for elemental sulfur respiration

This study identifies a multiheme selenoenzyme essential for elemental sulfur respiration in bacteria, revealing its unique catalytic mechanism involving selenium and heme.

Mechanism and regulation of the Bim1 interaction withthe outer kinetochore Ndc80 complex in S. cerevisiae

This study identifies a conserved interaction between Bim1 and the Ndc80 complex in S. cerevisiae, showing it enhances microtubule attachment strength and is regulated by phosphorylation.

Single-dye, transfection-free FLIM multiplexing via bioorthogonal chemistry

The paper demonstrates a method to multiplex FLIM using small molecule probes modified with bioorthogonal chemistry to achieve distinct fluorescent lifetimes without transfection.

Avs2 drives non-canonical tetrameric assembly of trypsin-like domain for anti-phage defense

The paper elucidates the molecular mechanism of the Avs2-trypsin-MBL system, revealing how phage terminase recognition triggers tetramerization and activation of the system for anti-phage defense.

Discovery of a novel UV-absorbing mycosporine-like amino acid in Vertebrata lanosa using an expanded combinatorial structure database incorporating non-proteinogenic amino acids and organic solutes

The paper expands a combinatorial MAA database and uses it to identify a novel MAA in Vertebrata lanosa.

Interactions of outer membrane lipoproteins P. aeruginosa PA3214 and E. coli PqiC with their MCE protein binding partners, PA3213 and PqiB

The paper reports cryo-EM structures of P. aeruginosa PA3214 and E. coli PqiC lipoproteins interacting with their MCE protein partners, revealing their assembly and functional interactions.