mechanistic / dynamical model

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.

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 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 compare ion and water permeability of Cldn10b and Cldn15 paracellular channels, revealing structural determinants of their permeability properties.

This study evaluates force field limitations in constant pH molecular dynamics simulations of a mini-protein, showing significant pKa errors due to force field and water model choices.

This paper introduces AlphaFold-Metainference to predict structural ensembles of disordered proteins using AlphaFold-derived distances in molecular dynamics simulations.

The paper investigates how anchor point selection affects the mechanical stability of an Affibody/PD-L1 complex using multiple experimental and computational methods.

This study investigates how an amyloidogenic peptide binds to DNA, showing its structural interactions and effects on DNA function.

This study shows that NOLC1 suppresses cisplatin chemotherapy and immune checkpoint inhibitor therapy in gastric cancer by inhibiting p53-mediated ferroptosis.

This paper uses molecular dynamics simulations to show that cholesterol stabilizes M2 channel clusters, enhancing membrane curvature and promoting viral budding.

This study uses molecular dynamics simulations to investigate how H3/H4 tetramers are recycled during DNA replication in yeast, revealing pathways and regulatory factors involved in strand-specific recycling.

This study identifies polyphosphate as the 'mystery density' in α-synuclein fibrils by showing it binds to lysine residues, affecting fibril formation and toxicity.

This study uses molecular dynamics to compare Cu2+ and Mg2+ binding to Dickerson DNA, revealing similar binding preferences but distinct binding mechanisms for Cu2+.

This study shows membrane tension drives NINJ1 filament opening, causing cell lysis, and explains why NINJ2 fails to form lesions.

IsRNAcirc predicts circular RNA 3D structures using coarse-grained molecular dynamics, outperforming template-based methods on a validation set.

This study uses molecular dynamics simulations to analyze ligand escape pathways and conformational stability in LIV-binding protein, identifying two distinct pathways and the role of water in the process.

This study resolves a discrepancy in aromatic amino acid sticker strength by showing tyrosine is stronger in condensates due to lower transfer free energy, but this reverses in apolar media.

This study investigates A22's interactions with prokaryotic MreB and eukaryotic actin using computational and experimental methods, revealing strong binding and toxicity to eukaryotic cells.

This study uses molecular dynamics to analyze inhibitor binding to DHFR, showing that reduced activity correlates with multiple-bound states on the protein surface.

This study uses molecular dynamics simulations to investigate how phosphorylation patterns and salt concentration affect RNA Polymerase II CTD clustering behavior.

This paper develops a physical model of the endoplasmic reticulum as an active liquid network to explain its dynamic structure and function.

This study uses statistical coupling analysis and molecular dynamics to show that dynamically coupled residues in DHFR influence evolution and allosteric communication.