mechanistic / dynamical model

The paper uses molecular dynamics simulations to study conformational changes in a nicotinic receptor site induced by agonists, identifying key steps in the low-to-high affinity transition.

This study shows that the {beta}2AR surface facilitates drug membrane permeation, with over 50% of flip-flop events using this pathway, suggesting its importance for drug design.

This study evaluates ipflufenoquin's efficacy against strawberry fungal pathogens and uses AlphaFold2 and Autodock Vina to predict fungicide sensitivity.

This paper examines statistical evidence of mutation enrichment in E. coli and proposes a quantum-mediated signaling framework to explain coordinated adaptive mutation patterns.

This study identifies KIRA6 as a dual inhibitor of LYN and FYN that suppresses IgE-mediated mast cell activation and inflammation.

This study identifies PDA1 as an SH3-binding allosteric modulator that stabilizes Hck conformation, potentially enhancing combination therapy with ATP-site inhibitors.

This study investigates how PUFAs modulate ASIC3 channel activity by preventing phospholipid blockage of the pore using electrophysiology and molecular dynamics simulations.

This study shows that age-dependent miR156-SPL regulation controls extrafloral nectary development in Passiflora species by affecting leaf ontogeny and EFN formation.

This study shows that inhibiting the DNMT/G9a complex targets specific epigenetic vulnerabilities in AML, inducing an IFN response and improving therapeutic outcomes.

This study shows that crops under continuous cultivation evolve less plasticity than those under interrupted cultivation, with higher plasticity not compensating for fitness losses in unpredictable environments.

This study shows that proteasome inhibition reduces HCMV replication by lowering the effective multiplicity of infection, and synergizes with antiviral drugs.

This study shows that SPPL3 in tumor cells affects innate immune responses by modulating nsGSLs, reducing susceptibility to neutrophils, NK cells, and γδ T cells.

This study uses coarse-grained simulations to analyze OMP-phospholipid interactions and water dynamics in E. coli outer membranes.

This study identifies a stable open conformation of human CFTR through simulations, showing it matches experimental Cl- conductance properties and highlights key residues and structural features involved in ion permeation.

The paper uses integrative molecular dynamics simulations to analyze cross-linking mass spectrometry data and reveal mitochondrial protein distributions, including the localization of FAM162A and TMEM126A in cristae.

This paper applies constant-pH MD simulations to study pH-dependent behavior of cationic ionizable lipids in lipid nanoparticles, focusing on their apparent pKa and implications for drug delivery.

This study identifies YhdP as a phospholipid transporter spanning the bacterial cell envelope, using AlphaFold, electron microscopy, and simulations to show its structure and function.

The paper models the risk of antifungal resistance emergence from agricultural fungicide use and its potential impact on human pathogens.

This study investigates how CX3CR1 mediates Tau internalization by microglia and how AZD8797 modulates this interaction through molecular docking and dynamics simulations.

This study uses molecular dynamics and network analysis to investigate the allosteric activation mechanisms of the human TAS2R46 receptor under different conditions.

This study uses high-resolution molecular dynamics simulations to analyze PKM1 and PKM2 structural dynamics, revealing new cryptic pockets for antitumoral drug design.

This study uses molecular dynamics simulations to show how potassium and magnesium ions affect nucleosome binding to mica surfaces, with potassium allowing stable binding with less structural change.

The paper develops a mechanistic model of bacterial promoters to explore how molecular complexity affects evolutionary predictions, finding that simplifying mechanisms does not compromise accuracy.

The paper uses simulations to study the FXR-RXR heterodimer's structure and shows the hinge's role in DNA binding and interdomain allostery.

This study uses molecular modeling and simulations to show that N-linked glycans on Nav channel alpha-subunits may block beta-subunit Ig-domain binding and influence channel clustering.

This study characterizes the RNA-binding properties of a disordered protein, SERF, and shows that binding to RNA causes modest global compaction without inducing structural changes in either molecule.

This paper shows that tetanus toxoid (TT) reduces pancreatic cancer by boosting cytotoxic CD4+ T cells and targeting sialic acids on tumor cells.

This study evaluates five coarse-grained protein models for predicting phase diagrams of hnRNPA1 LCD mutants, finding that only three accurately reproduce experimental data, highlighting the need to balance single-molecule and collective properties.

This study uses molecular dynamics simulations to analyze the behavior of a PDT drug complex in lipid bilayers, showing its internalization and dissociation, supporting its efficacy.