mechanistic / dynamical model

This study identifies HSD11B1 as a direct target of magnesium isoglycyrrhizinate, revealing its therapeutic mechanism in alcohol-associated liver disease through the HSD11B1-SREBP2-IDI1 signaling axis.

This study investigates how phosphorylation affects the structure and function of motif A in SIRT1, showing that phosphomimetic mutation at Ser27 enhances SIRT1 activity and induces structural ordering of the disordered region.

This study identifies lupeol from tamarind as a potent inhibitor of HCV entry by disrupting the E2-CD81 interaction, validated through experimental and computational methods.

The paper shows epithelial monolayers converge to the same final size and density after release from confinement, regardless of initial conditions, through mechanical pressure signaling.

This study investigates the formation of the earliest structure during protein folding on the ribosome and identifies sub-ensembles that may facilitate co-translational folding.

This study shows that deleting ferritin heavy chain in medulloblastoma cells limits tumor growth by promoting iron-dependent stress and sensitizing cells to iron toxicity.

This study identifies a direct interaction between SARS-CoV-2 M protein and sphingolipids that regulates its conformational dynamics and virus assembly.

This study uses molecular modeling and simulations to clarify how IRE1 detects unfolded proteins, revealing binding pockets and interactions that stabilize oligomers and prevent larger complex formation.

This paper investigates the mechanisms of ADC-immunotherapy combinations, finding that ADC-induced autophagy upregulates TNFR and M6PR, driving antitumor effects through TNF and granzyme B pathways.

This study uses HS-AFM to visualize coiled coil dynamics in MR complexes, revealing power-law scaling and long relaxation times due to internal friction.

The paper uses molecular dynamics simulations to analyze ion conduction in the ELIC channel, showing that a lateral fenestration is critical for cation selectivity and conductance.

This study uses all-atom simulations to examine how varying concentrations of lipomannan and lipoarabinomannan affect the structure and dynamics of mycobacterial inner membranes.

This study shows azelaic acid reduces Pseudomonas aeruginosa virulence factors without killing bacteria, with safety and molecular docking support.

This study shows that protein crowders alter RNA electrostatics and dynamics differently than PEG, challenging the use of PEG as a model for intracellular conditions.

This study uses molecular dynamics simulations to show how cholesterol concentration and membrane curvature affect the structure and dynamics of liposomes composed of DOPC and cholesterol.

This study uses molecular dynamics simulations to investigate whether parallel Holliday junctions exist in solution, finding they are thermodynamically metastable but rarely observed.

This study investigates how gain-of-function variants in the Kv7.2 channel's activation gate stabilize a partially open conformation, enabling K+ permeation and linking it to neurodevelopmental disorders.

This paper develops a new methodology to model phosphoinositide signaling dynamics, showing that basal PI(4)P levels determine cell-specific responses to genetic perturbations.

This study uses molecular dynamics simulations with solid-state NMR restraints to analyze Aβ42 dimer structural changes during fibrillation, revealing key motifs and pathway differences with and without membrane interactions.

The paper introduces a new Forest Stress Index (ISF) based on hydraulic modeling to better link climatic anomalies to tree mortality risk, showing stronger emphasis on extreme drought years compared to existing indices.

This study uses molecular dynamics simulations and theoretical models to analyze the shape and budding propensity of lipid droplets, finding that their shape resembles a spherical cap and is influenced by membrane properties.

This study uses molecular dynamics simulations to investigate how PIP2/3 and Rnd1 affect Plexin-B1 GAP activity on Rap1b GTPase, revealing lipid-dependent structural and functional changes.

The paper uses metadynamics simulations to design improved ligands for human peroxiredoxin 5 by modifying a single heavy atom in an initial hit.

This study shows the segment-capture model of SMC complexes can explain obstacle bypassing and loop extrusion, and proposes experiments to test the model.

This study shows that integrin-mediated mechanotransduction through supramolecular ligand clustering limits mitochondrial respiratory capacity, thereby suppressing cancer cell motility and tumor growth.

This study shows SARS-CoV-2 M protein conformations induce distinct membrane curvatures, matching virion regions and enabling spatial segregation through curvature-mediated interactions.

The paper identifies two new mutations in PfFNT conferring resistance to MMV007839 and shows how these mutations destabilize inhibitor binding.

This study shows that lateral interactions between FtsZ protofilaments override nucleotide state in determining filament curvature, with implications for Z-ring assembly and constriction.

This study investigates how simulation cell size affects nucleic acid dynamics by comparing different solvent-buffer distances in molecular dynamics simulations.