mechanistic / dynamical model

The paper uses machine learning-augmented MD simulations to study ZTP riboswitch ligand interactions, finding that ligand on-rates, not binding affinity, determine activation potency.

The paper investigates how cardiolipin interacts with membrane proteins to stabilize them, using a model protein and simulations to identify key factors.

This study identifies the structural and sequence basis of epistatic interactions driving drug resistance in HIV by combining sequence models and molecular dynamics simulations.

This paper develops an evolutionary model of immune signaling to show that downstream negative feedback loops evolve more robustly than upstream ones due to stronger selective pressures.

This study shows that LMNA deficiency in SCLC increases R-loop accumulation, leading to genomic instability and poor patient survival.

This study identifies the autoinhibition mechanism of KaiC priming phosphorylation and shows how KaiA relieves this inhibition by altering R385 interactions.

This study identifies a pre-active intermediate in GPCR activation and shows how dimer interactions influence signaling efficacy and functional diversity.

This paper demonstrates that a reversible kink instability in nematodes enhances jumping performance and proposes a bio-inspired model for soft robots.

This study uses molecular dynamics simulations to analyze how DNA sequences affect the structural stability and binding affinity of the ZTA transcription factor and DNA complex, identifying ZRE 3 as the most stable and affinity-rich sequence.

The paper shows that endoplasmic reticulum (ER) morphology changes with edge curvature in epithelial gaps, supporting different migration modes through focal adhesion orientation.

This study develops a poroelastic framework to model hydromechanical signaling in plants, showing pressure changes and mass flow can transmit signals locally and systemically.

This study identifies two binding sites of the PET tracer MODAG-005 on lipidic α-synuclein fibrils, with the cavity site being more stable and selectively occupied under certain conditions.

This study uses molecular dynamics and PCA to analyze coordinated movements in tyrosinase subdomains, showing mutations disrupt stability by disrupting helix coordination.

This paper designs a high-affinity nanobody against SARS-CoV-2 spike protein using CDR-grafting combined with molecular simulation and machine learning.

The paper studies how actin dynamics and tension affect endothelial cell mechanics under pressure, showing strain-stiffening and actin-driven reorientation.

The paper develops a mathematical model of mammalian outer hair cell hair bundles with three rows of stereocilia, showing it predicts mechanical creep and MET current adaptation in response to stimuli.

This study investigates how environmental factors like pH and ionic strength affect the conformational and amyloidogenic properties of DPF3a using biophysical and molecular dynamics methods.

This study uses molecular dynamics simulations and machine learning to analyze how mutations affect Smlt1473's binding to substrates, identifying key residues involved in substrate interaction.

This study investigates how ApoA-I interacts with lipid membranes to induce shape remodeling and lipid phase separation in GUVs, revealing key steps in lipoprotein assembly.

This study shows that tension in the neck linker of kinesin-1 suppresses premature binding of the detached head, explaining coordinated stepping through allosteric regulation.

This study uses molecular dynamics simulations to analyze the heterogeneous behavior of condensates formed by four master transcription factors in embryonic stem cells, revealing distinct roles for each factor in condensate formation.

This study investigates how ICA-105574, an HERG activator, shortens cardiac repolarization in severe LQT2 mutations through molecular mechanisms.

This study analyzes IspH homologs in Bacillus and other bacteria to improve terpenoid production through computational and molecular dynamics methods.

This study uses molecular dynamics simulations to show that CHS concentration affects mGluR2's structural stability and conformational dynamics in micelle and bilayer environments.

This study uses molecular dynamics simulations to investigate how cholesterol affects planar and curved lipid bilayers, revealing geometry-dependent structural and dynamic changes.

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.