mechanistic / dynamical model

This study investigates how the orientation of single amino acids affects current blockades during translocation through graphene nanopores using molecular dynamics simulations.

The paper uses molecular dynamics simulations to study how ligation patterns affect the mechanical properties of DNA crystals.

This study shows that ionic liquids affect enzyme activity and enantioselectivity in carboligation reactions, with specific IL cations altering selectivity patterns.

This study uses molecular dynamics simulations to investigate ABCB4 transport mechanisms, revealing membrane-dependent dynamics and dual translocation pathways for phosphatidylcholine.

This study uses molecular dynamics simulations to analyze the transport mechanism of Ala-Ala through PepTSo, revealing conformational changes and free energy barriers influenced by substrate binding.

This paper proposes a lever hypothesis for Synaptotagmin-1 action in neurotransmitter release, suggesting it pulls SNARE complexes to facilitate membrane fusion.

This study characterizes IDE conformational dynamics using cryo-EM and MD simulations, identifying key residues and mechanisms that modulate enzyme activity.

This study investigates how local and long-range mechanical stresses contribute to cephalic furrow formation in Drosophila embryos using computational models and experimental analysis.

This study identifies a kappa casein-derived peptide, MP31, as a potential inhibitor of GSK-3β, showing stable binding and structural stabilization of the enzyme, suggesting therapeutic potential for Alzheimer's disease.

The paper uses molecular dynamics simulations to evaluate and rank the performance of single fluorescent protein-based calcium biosensors based on water distribution and hydrogen bond changes.

The paper analyzes the evolutionary dynamics of RuBisCO, showing how the small subunit influenced the enzyme's conformational flexibility and response to atmospheric changes.

This study investigates how equivalent gating-charge mutations in voltage-gated sodium channels lead to different functional outcomes through structural and electrophysiological analysis.

This study uses molecular dynamics simulations to show that RNA order determines its interaction with zwitterionic lipid bilayers, explaining experimental observations about RNA affinity for gel-phase membranes.

This paper introduces a mechanistic model to optimize antibiotic combinations by incorporating drug mechanisms and testing synergy in Escherichia coli.

The paper presents a mechanistic model of mountain pine beetle population dynamics, showing how climate change can shift parameters to eliminate endemic equilibria and trigger outbreaks.

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.