biophysical modeling

Ether lipid remodeling during neuronal differentiation prevents ferroptosis

This study shows that ether lipid remodeling during neuronal differentiation prevents ferroptosis by balancing pro- and anti-ferroptotic effects through vinyl ether bonds.

Molecular basis of mitogen-activated protein kinase ERK2 activation by its upstream kinase MEK1

The paper determines cryo-EM structures of MEK1 activating ERK2, elucidating specificity and activation mechanisms in the MAPK pathway.

Self-organized tiling generates tissue-scale hyperuniformity during development

This study shows that growth-repulsion feedback in branched cells leads to hyperuniform tissue patterning and efficient tiling during development.

Molecular insights into protein disulfide isomerase antagonism by punicalagin

This paper shows punicalagin inhibits both oxidase and reductase activities of PDI through noncovalent, allosteric binding at the N-terminal domain and identifies PDI as a high-confidence target of galloylated polyphenols.

Differences in substrate engagement and Retinoblastoma protein (RB) binding of human KDM5A and KDM5B

This study compares the demethylase activity, nucleosome engagement, and RB binding of KDM5A and KDM5B, revealing differences in their interactions and enzymatic behavior.

Structural Genomic Variation and Its Potential Role In Deer Speciation

The paper investigates structural variants in two deer species to understand their role in speciation and divergence, finding species-specific deletions and insertions linked to reproductive and sensory functions.

A comparative investigation of the mannose binding interface in DC-SIGN and MRC1 carbohydrate recognition domains with all-atom molecular dynamics simulations

This study uses molecular dynamics simulations to compare mannose binding in DC-SIGN and MRC1 CRDs, revealing differences in binding modes and affinity.

Geometric optics organizes organelle interactions and positioning

The paper shows that microtubule asters in C. elegans use a cellular analog of geometric optics to position pronuclei during cell division, with surface-anchored motors and dynamic terminator curves governing this process.

Convergent evolution of parrotfish beaks enables stress redistribution during high-force feeding

This study uses biomechanical modeling to show that parrotfish beaks evolved to manage stress during feeding, with fused dentition reducing stress accumulation compared to discrete teeth.

Distinct virus-derived circular RNA molecule influences host response during SARS-CoV-2 infection

The paper identifies a novel SARS-CoV-2-derived circular RNA, circ7b8N, which modulates host gene expression and is detectable in clinical samples, suggesting a role in host-pathogen interactions.

Ceramides disrupt hexokinase HKI-VDAC complex assembly and modulate VDAC tilting

This study shows ceramides disrupt VDAC-HKI complex assembly by modulating VDAC tilt and membrane thinning, revealing a mechanism for ceramide-induced apoptosis.

Ligify 2.0: A web server for predicted small molecule biosensors

Ligify 2.0 predicts small molecule interactions with transcription factors and provides a web interface for visualization and biosensor design.

PPM1B utilizes a trinuclear metal architecture for phosphatase activity

This study identifies a trinuclear metal center in PPM1B that facilitates phosphate hydrolysis through direct substrate coordination and water protonation, revealing a novel catalytic mechanism.

The segregase CDC48 integrates blue light and hormonal cues to regulate photomorphogenesis in Arabidopsis

This study shows CDC48A integrates blue light and gibberellin signaling through protein homeostasis to regulate photomorphogenesis in Arabidopsis.

Study of Protein-Protein Interactions in Septin Assembly: Multiple amphipathic helix domains cooperate in binding to the lipid membrane

This study uses molecular dynamics simulations to show how amphipathic helix domains cooperate in binding to lipid membranes, stabilizing septin structures.

The structural mechanism of eukaryotic fluoride channel activation and inhibition by monovalent cations

This study investigates how sodium and lithium regulate the fluoride exporter FEX, revealing structural and functional differences in their effects on channel activity and fluoride tolerance in yeast.

Structural basis of the protein kinase PKN1 HR1 domain oligomerization and differential regulation by RhoA and Rac1

This study investigates the structural roles of PKN1 HR1 domains in oligomerization and their differential regulation by RhoA and Rac1.

Structural and biochemical insights reveal substrate-modulated nuclease activity of ComEC during DNA processing

This study characterizes the nuclease activity of full-length ComEC during DNA processing, showing how ComEA modulates this activity to ensure fidelity in natural transformation.

Longitudinal Multi-Organ Transcriptomic Atlas of Salt-Induced Hypertension

This study creates a longitudinal transcriptomic atlas of salt-induced hypertension in rats, identifying shared and organ-specific transcriptional changes and candidate therapeutics.

The tRNA dihydrouridine synthase DusA has a distinct mechanism in optimizing tRNAs for translation

This study investigates the role of DusA in tRNA modification and translation, finding it selectively enhances specific tRNA charging and translation at certain codons.

Molecular Basis of Mitochondrial Complex I Disruption by m.14484T>C-Induced Leber Hereditary Optic Neuropathy

This study identifies how the m.14484T>C mutation in ND6 subunit of complex I disrupts quinone binding and proton pumping, leading to LHON through altered hydrogen bond networks and redox chemistry.

ZBP1's Inability to Convert Unmodified RNAs to the Z-form Underlies a Balanced Mechanism of RNA Recognition with ADAR1

This study shows ZBP1 cannot convert unmodified dsRNA to Z-conformation, unlike ADAR1, revealing a competitive mechanism between these proteins in immune responses.

Biochemical Functions of the Membrane-Binding Domain of CARMIL

This study investigates the biochemical functions of the MB domain of CARMIL, showing it targets proteins to membranes, activates CP, and enhances actin assembly.

Integrin loss and tissue mechanics trigger progressive disruption of simple epithelial

This study investigates how integrin loss and tissue mechanics disrupt simple epithelial architecture in Drosophila, revealing mechanisms of epithelial breakdown and their relevance to disease.

GpoA Glutathione Peroxidase Links Oxidative Stress Response, Antibiotic Persistence, and Virulence in Streptococcus pneumoniae

This study identifies GpoA as a glutathione peroxidase in S. pneumoniae that contributes to oxidative stress resistance, antibiotic persistence, and virulence.

A Biophysical Model of Human Colonic Motor Pattern Generation in Health and Disease

This paper develops a biophysical model of human colonic motor patterns that reproduces healthy and disease states, showing how parameters affect motility.

Phosphoregulated SMCR8-FIP200 interaction connects the ALS/FTD-linked C9orf72 complex to autophagy initiation and mitochondrial quality control

Recombinant measles virus equipped with BNiP3, a pro-apoptotic gene, targets β-catenin pathway in triple negative breast cancer cells

This paper investigates how a recombinant measles virus with BNiP3 reduces β-catenin expression and downstream targets, inhibiting migration in triple-negative breast cancer cells.

Glycosylation-Modulated Conformational Diversity in Neurotrophin Receptors

The paper uses molecular dynamics simulations to study how glycosylation affects the structure, flexibility, and neurotrophin binding of p75, TrkA, and TrkB receptors.

Histone diversity in the archaeal domain of life

The paper surveys histone diversity in archaea using bioinformatics and simulations, identifying five histone types and their genomic strategies.