mechanistic / dynamical model

Opposing Roles of Cholesterol and Cholesterol Sulfate in Proton Transfer and Diffusion at Membrane Interfaces

This study shows cholesterol and cholesterol sulfate have opposing effects on proton transfer and diffusion at membrane interfaces, with cholesterol promoting local transfer and inhibiting long-range diffusion, while cholesterol sulfate does the opposite.

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

TRPP Ion Channels Function in the π-Conformation Rather Than the α-Conformation

This study uses molecular dynamics simulations to show that the π-conformation of PKD2 supports ion conduction, challenging the previous model that the α-conformation is the conductive state.

Intrinsic timekeeping in Escherichia coli

This study shows Escherichia coli has an intrinsic timekeeping system that anticipates daily temperature cycles through rhythmic curli plaque formation.

PERTURBATION OF THE AMINO ACID STRESS RESPONSE PATHWAY EXPOSES A METABOLIC VULNERABILITY IN MULTIPLE AGGRESSIVE CANCER SUBTYPES

This study shows that disrupting the amino acid stress response pathway reduces tumor growth in multiple aggressive cancers by targeting chronic metabolic stress adaptation.

Emergence and robustness of 3D complex tissue architectures from simple physical forces

This study builds a 3D mathematical model of adipose tissue showing complex architectures emerge from simple mechanical rules, suggesting mechanical forces drive tissue structure more than genetic programs.

GNG2-MRAS interaction regulates SHOC2-dependent RAF activation and MAPK signaling

This study identifies GNG2 as an inhibitor of the SMP complex by binding MRAS, disrupting its assembly and inhibiting MAPK signaling.

Decoding stress-induced adaptation of cancer cells in spatial confinement by integrating live-cell imaging and mathematical modeling

This study combines live-cell imaging and mathematical modeling to show how cancer cells adapt to stress in spatially confined environments, revealing cooperative and competitive strategies influenced by spatial organization and microenvironment dynamics.

USP18-STAT2 axis enhances hepatic resilience under proteotoxic stress

This study identifies the USP18-STAT2 axis as a critical factor enhancing hepatic resilience under proteotoxic stress by modulating interferon signaling and ISG solubility.

Modeling a Continuum of Drug-induced Persistence during Targeted Cancer Therapy

The paper develops a framework to model drug-induced persistence in cancer therapy, identifying optimal drug concentrations and schedules to reduce persistence-based resistance.

Modulating Transthyretin Fibril Stability with D-Retro-Inverso Peptides

The paper uses molecular dynamics simulations to study how D-Retro-Inverso peptides modulate TTR fibril stability and identifies DRI-K6V as a potential disruptor of TTR fibrils.

Insights on the effect of extracellular acidification on an HCNchannel: a molecular dynamics study

This study uses molecular dynamics simulations to investigate how extracellular acidification affects the structure and function of HCN2 channels by disrupting hydrogen bond networks involving residue E212.

Predicted structure of the 89-kDa invasion-tip protein of Holospora obtusa, an endonuclear symbiont of Paramecium caudatum, suggests a pH-dependent conformational change

The paper predicts the structure of a 89-kDa invasion-tip protein from Holospora obtusa and suggests a pH-dependent conformational change may aid in escaping the host digestive vacuole.

A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9

This study identifies a cryptic divalent metal binding pocket that regulates Cas9's metal-dependent activity through conformational activation and catalytic efficiency.

How the Azadithiolate Ligand Impacts O2-Stability of Group B -Hydrogenase ToHydA

This study investigates how substituting the azadithiolate ligand in ToHydA affects O2-stability by preventing the formation of specific states and altering structural dynamics.

Decoding the Conformational Dynamics and Hyperactivity of Histone H3K36 N-Methyltransferase in Oncogenic Mutations via tICA and Markov State Modeling

This study uses molecular dynamics simulations to show that oncogenic NSD2 mutations enhance catalytic efficiency by reorganizing conformational dynamics rather than destabilizing the enzyme.

Site-specific O-glycans influence lacritin structure and multimerization in tears

This study investigates how site-specific O-glycans on lacritin influence its structure and multimerization, revealing their role in conformational flexibility and crosslinking residue positioning.

Extracellular vesicle-bound bacterial toxin pneumolysin triggers membrane engagement and damage beyond canonical pore formation

This study shows that pneumolysin, a bacterial toxin, can damage target cell membranes through vesicle fusion rather than pore formation.

Psi RNA-specific Binding Promotes HIV-1 Gag Conformational Change Critical for Immature Viral Particle Assembly

This study shows that Psi RNA binding promotes a conformational change in HIV-1 Gag from compact to extended, essential for viral particle assembly, supported by FRET and molecular dynamics simulations.

LC3 forms functional nanocluster on autophagosome

The paper shows LC3B forms nanoclusters on autophagosomes via specific lipid interactions and a unique binding pocket, impacting autophagosome motility.

Asymmetric Hydration and Protonation Switching of Dual Aspartates Drive Flagellar Rotation

This study investigates the rotational mechanism of the bacterial flagellar motor by analyzing protonation dynamics and structural asymmetry in CjMotAB using cryo-EM and computational methods.

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

This study shows that maleic acid enhances BCG vaccination to induce CD4+CD8+ T cells that sterilize Mtb infection in mice.

Whole genome duplication through mitotic slippage causes nuclear instability

The paper investigates how different routes to whole-genome duplication (WGD) affect nuclear stability, finding that mitotic slippage uniquely causes nuclear instability.

Impact of intercalators on the properties of DNA analyzed by molecular dynamics simulations

This study uses MD simulations to analyze how DNA intercalators affect DNA conformation, revealing distinct intercalation patterns and their impact on mechanical properties.

RNA demethylase FTO uses conserved aromatic residues to recognize the mRNA 5' cap and promote efficient m6Am demethylation

This study identifies conserved aromatic residues in FTO that recognize the mRNA 5' cap and enhance m6Am demethylation, providing structural insights into FTO's selectivity for m6Am over m6A.

Molecular rewiring and compensatory mechanisms sustain DNA recognition in mutant ZTA transcription factor: insights from molecular dynamics simulations

This study uses molecular dynamics simulations to analyze how mutations in ZTA transcription factor affect DNA recognition by rewiring interaction networks and compensatory mechanisms.

Ether linkages in phospholipids provide modular control of membrane mechanics

The paper shows that ether linkages in phospholipids modulate membrane mechanics and topology through distinct physical mechanisms, explaining their evolutionary conservation and biological roles.

Distinct Tubulin C-Terminal Tails Control the Efficiency of a Microtubule Severing Machine

This study investigates how different tubulin CTT isotypes influence katanin structure and dynamics, revealing that inhibitory CTTs enhance pore narrowing and flexibility, while non-inhibitory CTTs disrupt coordination.

Molecular Dynamics-Guided All-Atom Reconstruction of Cryo-ET Maps Reveals Mechanisms of Histone Tail-Mediated Chromatin Compaction

This study uses molecular dynamics and cryo-ET to show histone tails drive chromatin compaction through specific interactions, revealing their role in both structural organization and nucleosome communication.

Geothermal gradients restructure metabolism in hot spring microbial communities

This study investigates how geothermal stress reorganizes microbial metabolism in hot spring communities using integrated genomic and metabolic modeling approaches.