mechanistic / dynamical model

This paper computationally designs peptide inhibitors targeting α-Synuclein monomers, fibrils, and liquid condensates using multiscale modeling to reduce aggregation and modulate conformational dynamics.

This study identifies FGFR1 as a key driver of TMZ resistance in GBM through metabolic rewiring and cell cycle regulation, showing that FGFR1 inhibition restores TMZ sensitivity in preclinical models.

The paper investigates the microbiota of date palm sap using culturomics and metagenomics, identifying 250 bacteria and nine fungi, including previously unreported species.

The paper identifies a cryptic pocket in mTOR oncogenic variants through molecular dynamics simulations and suggests designing PI3K-like inhibitors to target this pocket for therapeutic benefit.

This study identifies FLK and HOS5 as KH-domain proteins that repress FLC and stress-responsive genes, coordinating flowering and stress responses in Arabidopsis.

The paper reports the cryo-EM structure of full sACE dimer and uses MD simulations to study its conformational dynamics and domain-specific behavior.

This study uses molecular dynamics simulations and Markov state modeling to predict an open state of GABAA receptors, showing chloride ion conductance and desensitization mechanisms.

The paper engineers a brighter and more photostable variant of avGFP by modifying chromophore interactions, resulting in improved fluorescence and resistance to photobleaching.

This study uses molecular dynamics simulations to explore the folding pathways of an RNA G-quadruplex, revealing multi-pathway mechanisms and highlighting challenges in simulating non-canonical RNA structures.

The paper models cell alignment with collagen fibrils using a hybrid model showing mechanosensitive focal adhesions drive ECM-dependent cell elongation.

This study identifies an arginine switch mechanism that drives the stepwise activation of β-arrestin through conformational changes induced by GPCR interactions.

This paper develops a first-principles geometric model to study motor-driven centrosomal aster dynamics, showing how cell shape and motor number affect aster stability and revealing new nonlinear phenomena.

The paper shows that IFN-gamma-insensitive tumours can still be controlled by immune responses, with IFN-gamma driving myeloid cell remodelling that enhances anti-tumour immunity.

The paper presents cryo-EM structures and molecular dynamics simulations of human XPR1, revealing a channel-like mechanism for phosphate transport and linking mutations to disease.

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 identifies how SARS-CoV-2 evolves to counteract host interferon signaling through interactions with autophagy pathways.