mechanistic / dynamical model

This paper develops a computational model to simulate mechanical stretching of cultured cells on a flexible membrane and connects it to chromatin deformation.

This study identifies the USP18-STAT2 axis as a critical factor enhancing hepatic resilience under proteotoxic stress by modulating interferon signaling and ISG solubility.

The paper develops a framework to model drug-induced persistence in cancer therapy, identifying optimal drug concentrations and schedules to reduce persistence-based resistance.

The paper uses molecular dynamics simulations to study how D-Retro-Inverso peptides modulate TTR fibril stability and identifies DRI-K6V as a potential disruptor of TTR fibrils.

This study uses molecular dynamics simulations to investigate how extracellular acidification affects the structure and function of HCN2 channels by disrupting hydrogen bond networks involving residue E212.

This study identifies a cryptic divalent metal binding pocket that regulates Cas9's metal-dependent activity through conformational activation and catalytic efficiency.

This study uses molecular dynamics simulations to show that oncogenic NSD2 mutations enhance catalytic efficiency by reorganizing conformational dynamics rather than destabilizing the enzyme.

This study investigates how site-specific O-glycans on lacritin influence its structure and multimerization, revealing their role in conformational flexibility and crosslinking residue positioning.

This study shows that pneumolysin, a bacterial toxin, can damage target cell membranes through vesicle fusion rather than pore formation.

This study shows that Psi RNA binding promotes a conformational change in HIV-1 Gag from compact to extended, essential for viral particle assembly, supported by FRET and molecular dynamics simulations.

The paper shows LC3B forms nanoclusters on autophagosomes via specific lipid interactions and a unique binding pocket, impacting autophagosome motility.

This study investigates the rotational mechanism of the bacterial flagellar motor by analyzing protonation dynamics and structural asymmetry in CjMotAB using cryo-EM and computational methods.

The paper investigates how different routes to whole-genome duplication (WGD) affect nuclear stability, finding that mitotic slippage uniquely causes nuclear instability.

This study uses MD simulations to analyze how DNA intercalators affect DNA conformation, revealing distinct intercalation patterns and their impact on mechanical properties.

This study identifies conserved aromatic residues in FTO that recognize the mRNA 5' cap and enhance m6Am demethylation, providing structural insights into FTO's selectivity for m6Am over m6A.

This study uses molecular dynamics simulations to analyze how mutations in ZTA transcription factor affect DNA recognition by rewiring interaction networks and compensatory mechanisms.

This study investigates how different tubulin CTT isotypes influence katanin structure and dynamics, revealing that inhibitory CTTs enhance pore narrowing and flexibility, while non-inhibitory CTTs disrupt coordination.

This study uses molecular dynamics and cryo-ET to show histone tails drive chromatin compaction through specific interactions, revealing their role in both structural organization and nucleosome communication.

This study identifies salvianolic acids as natural senolytics that enhance lifespan and healthspan in aged mice by targeting senescent cells through redox modulation and inducing apoptosis and ferroptosis.

The paper presents a computational model of tumor invasion, identifying four invasion phenotypes and showing that multimodal invasion is most common under specific mechanical conditions.

This paper uses molecular dynamics simulations to show that hydrophobic mismatch between transmembrane proteins and lipid membranes leads to lipid sorting based on tail unsaturation.

This study uses molecular dynamics to analyze how plant aquaporins selectively transport reactive oxygen and nitrogen species, identifying factors that influence permeability.

MARTINI 2.2 simulations show lateral tension changes the free energies of membrane bending and thickness deformations through a projected-area term (γΔΔA), while leaving lipid mixing, residence and exchange essentially unchanged.

This study proposes a viscosity-mediated signal amplification model to explain left-right symmetry breaking in the mouse node by integrating mechanosensing and chemosensing.

The paper shows epithelial convergent extension can be viewed as a self-tuning process, with local feedback rules better reproducing experimental features than global optimization methods.

The paper develops a mechanistic replicator model to link vaginal microbiota composition to Nugent scores and predict bacterial vaginosis with high accuracy.

This study uses molecular dynamics simulations to show how phosphorylation of alpha or beta-tubulin alters microtubule structure and affects GTP hydrolysis and dynamic instability.

This study demonstrates lipid-coated quantum dots with tunable surface charge that enhance membrane interactions and labeling density in HEK293 cells, supported by molecular dynamics simulations.

This study investigates the mechanism of Na+-dependent HCO3- transport by NBCn2 using structure prediction and simulations, revealing sequential ion binding and conformational changes.

The paper presents a mechanistic framework explaining the facilitation-to-competition transition in plant interactions along rainfall gradients, showing it depends on resource availability and woody density.