mechanistic / dynamical model

The paper shows how peptide backbones enhance pairwise interactions in dilute phases but weaken them in dense phases, enabling percolation in peptide-based mimics of protein condensates.

This study identifies meningeal regulatory T cells (mTregs) expressing enkephalin that modulate mechanical pain sensitivity in female mice via a sex hormone-dependent opioid receptor mechanism.

This study develops a mechanistic model to explain electrotaxis by showing how charged membrane receptors polarize and control actomyosin dynamics across cell types.

This study uses molecular dynamics simulations to show that specific THz frequencies enhance conductance of Kv1.2 and Nav1.5 ion channels by affecting ion motion in selectivity filters.

This study uses molecular dynamics simulations to show that the V72I mutation in Hsp60 disrupts allosteric communication, rigidifying its complexes and impairing function.

This paper uses molecular dynamics simulations to study temperature effects on conformational stability and order of unliganded adenine riboswitch conformations, finding that apoA is more stable at 293K and 303K but less stable at 323K.

This study uses molecular dynamics simulations to show how calcium ions influence the formation of hetero- and homotrimers of type I collagen, explaining the conditions under which homotrimers form.

This study investigates KCNJ2 mutations linked to ventricular arrhythmia using computational modeling and functional analysis, revealing mutation-specific structural perturbations and their impact on channel stability.

This study identifies how the A82V mutation in Ebola virus GP enhances membrane fusion through conformational changes, using simulations and experiments.

This study evaluates the binding affinity and cell viability effects of natural compounds and cilengitide on HR-NB cells, finding Olax CHA shows superior antiproliferative effects and potential synergism with cilengitide.

This study uses molecular dynamics simulations to uncover the molecular mechanisms of ligand activation in the D2 dopamine receptor and identifies differences in activation mechanisms between dopamine and adrenergic receptors.

This study shows SWEET family transporters in plants act as water-conducting carrier proteins through multiple mechanisms, validated by simulations and experiments.

This study identifies five amino acid residues in mammalian melanopsins responsible for the specific interaction with the antagonist AA92593.

This study elucidates how the Cdc20MIM induces Mad2 conformational conversion by transiently exposing a binding site and facilitating structural changes.

This study uses MD simulations to analyze the membrane partitioning of nifedipine before its binding to Cav1.1, showing drug-membrane interactions occur faster than overall binding.

This study uses molecular dynamics simulations to show that iron-bound mycobactin flip-flops across mycobacterial membranes more slowly than generic lipids, with lipid composition affecting mobility.

This paper uses molecular dynamics simulations to show that base flipping in Tc3a transposase reshapes DNA structure during recognition, challenging existing models of transposon activity.

This paper characterizes the structure and dynamics of HSPB1 oligomers using biophysical and computational methods, revealing conformational heterogeneity and domain-specific interactions.

This study investigates how DNA loop extrusion interacts with protein-DNA condensation, showing that loop extrusion enhances condensation dynamics and leads to domain formation similar to TADs.

This study shows SNX9 selectively binds PI(3,4)P2 lipids through a non-canonical interface, protecting them from hydrolysis during membrane remodeling.

The paper identifies a conserved arginine residue critical for maintaining interface integrity in septin protofilaments across species using molecular dynamics simulations and experimental validation.

This study links molecular properties of LCDs to condensate microstructure and macroscopic material properties using simulations and graph analysis.

This study identifies functional determinants in chicken ANP32A that enable species-specific support of avian influenza virus polymerase.

This study shows that the swing motion of lysine side chains in AapA1 toxin enhances water transport through transmembrane pores formed by the protein.

This paper develops a validated mechanistic framework to predict brain interstitial transport in vivo using mathematical modeling, imaging, and biomechanical testing, demonstrating its application in sheep brains.

This study shows that oxysterol accumulation in aged cells disrupts CXCR4 signaling by altering G-protein coupling specificity.

The paper identifies potential inhibitors of TOP3B using molecular dynamics and docking, showing that bemcentinib and its analogs inhibit TOP3B relaxation activity.

This study shows AMPK is necessary for Treg cell adaptation to metabolic stress in tumors and lung injury but not for baseline immune homeostasis.

This paper challenges the conventional view of HIFs as mediators of hypoxic stress, proposing instead that HIFs prevent hypoxia by regulating electron transport and redefining the Warburg effect as a homeostatic response to metabolic demand.

This study uses a Lotka-Volterra model to analyze tumor-host dynamics under constant and periodic perturbations, showing that periodic treatment can control aggressive tumors by shifting the system to a non-chaotic attractor.