Y. Miao

Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides

LiGaMD3 improves prediction of binding thermodynamics and kinetics for small molecules and flexible peptides by enhancing sampling efficiency through triple boosts in energy terms.

Structure and function of an intermediate GPCR-G protein complex

The paper resolves the structure of an intermediate GPCR-G protein complex and shows it initiates nucleotide exchange without progressing to the fully activated state, providing insights into GPCR signaling complexity.

Characterization of natural product inhibitors of quorum sensing in Pseudomonas aeruginosa reveals competitive inhibition of RhlR by ortho-vanillin

This study evaluates benzaldehyde derivatives as quorum sensing inhibitors in Pseudomonas aeruginosa, identifying ortho-vanillin as a competitive inhibitor of RhlR.

HCCDB v2.0: Decompose the Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

HCCDB v2.0 integrates bulk, single-cell, and spatial transcriptomic data from HCC samples to enhance meta-analysis and provide new metrics for gene expression patterns.

Spatiotemporal recruitment of the ubiquitin-specific protease USP8 directs endosome maturation

This study identifies USP8's role in endosome maturation by mediating Rab5-to-Rab7 switch through recruitment by Rabex5 and promotion of SAND-1/Mon1 recruitment.

Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists

This study identifies stalk-derived peptides that activate PC1 signaling by binding to specific regions, revealing structural dynamics and potential therapeutic applications for ADPKD.

Potential clinical value and influence of conductivity in conductive cardiac patches for reducing post-MI arrythmia risks

This study evaluates the clinical value of conductive cardiac patches by testing different conductivities and shows that higher conductivity reduces arrhythmia risks in post-MI hearts.

Vitamin D attenuates diabetic myocardial injury via the Erbb4/ferroptosis axis

This study shows vitamin D reduces diabetic myocardial injury by inhibiting the Erbb4/ferroptosis pathway in both in vivo and in vitro models.

Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein

This study investigates ligand dissociation from the SARS-CoV-2 spike glycoprotein using simulations, revealing two unbinding pathways and key residues involved in ligand binding and ACE2 interaction.

RAG1 and RAG2 Non-core Regions Are Implicated in Leukemogenesis and Off-target V(D)J Recombination in BCR-ABL1-driven B-cell Lineage Lym-phoblastic Leukemia

This study shows that non-core RAG regions reduce off-target V(D)J recombination and maintain genomic stability in BCR-ABL1+ B-ALL by improving RAG cleavage accuracy.

Molecular Dynamics Activation of γ-Secretase for Cleavage of Notch1 Substrate

This study uses molecular dynamics simulations and mass spectrometry to model how γ-secretase cleaves Notch1, revealing structural dynamics and substrate interactions.

MolPhase: An Advanced Phase Separation Predictor and an Investigation of Phytobacterial Effector in Plant

MolPhase predicts protein phase separation using physicochemical features and experimental data, showing T3Es undergo homotypic phase separation in vitro and in vivo.

Collective dynamics of formin and microtubule and its crosstalk mediated by FHDC1

This study investigates the collective dynamics of formin and microtubule networks, revealing FHDC1's role in regulating actin wave nucleation and its crosstalk with microtubules.

A dynamic partitioning mechanism polarizes membrane protein distribution

This study identifies a dynamic partitioning mechanism that explains asymmetric membrane protein distribution during signaling events.

Ligand Gaussian accelerated molecular dynamics 2 (LiGaMD2): Improved calculations of ligand binding thermodynamics and kinetics with closed protein pocket

This paper introduces LiGaMD2, a method that improves ligand binding thermodynamics and kinetics calculations by enhancing sampling of closed protein pockets.

Structure of the Wnt-Frizzled-LRP6 initiation complex reveals the basis for co-receptor discrimination

The paper determines the structure of a ternary Wnt-Frizzled-LRP6 complex, revealing how co-receptor discrimination occurs through specific domains.

Bacillus velezensis SQR9 sways the rhizosphere community and its sociality toward cooperation and plant growth promotion

This study shows that B. velezensis SQR9 alters rhizosphere microbial community structure and promotes cooperation among Bacillus species, enhancing plant growth.

Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics

The paper presents cryo-EM structures of the M4 mAChR with ligands and modulators, revealing structural and dynamic insights into allosteric modulation and receptor activation mechanisms.

Vitamin C is an efficient natural product for prevention of SARS-CoV-2 infection by targeting ACE2 in both cell and in vivo mouse models

This paper shows that Vitamin C reduces ACE2 protein levels and blocks SARS-CoV-2 infection in cell and mouse models by inhibiting USP50-ACE2 interaction.

Structural Characterisation of Nanoparticle-Supported Lipid Bilayers by Grazing Incidence X-ray and Neutron Scattering

This study uses grazing incidence X-ray and neutron scattering to analyze the structure of curved and fluid lipid bilayers formed on nanoparticle arrays, revealing curvature effects on lipid packing.

Biofunctional nanodot arrays in living cells uncover synergistic co-condensation of Wnt signalodroplets

The paper develops biofunctional nanodot arrays to study Wnt signalodroplets in live cells, revealing synergistic co-condensation through liquid-liquid phase separation.

Nanotopography modulates intracellular excitable systems through cytoskeleton actuation

The paper shows nanotopography is sensed directly by cytoskeletal networks, with implications for texture sensing and guidance cues in microenvironments.

Spatiotemporal dynamics of membrane surface charge regulates cell polarity and migration

This study shows that surface charge regulation on the plasma membrane integrates signaling networks to control cell polarity and migration through dynamic changes in phospholipid composition.

Super-resolution vibrational imaging using expansion stimulated Raman scattering microscopy

The paper introduces MAGNIFIERS, a technique combining SRS microscopy with expansion microscopy to achieve sub-50 nm resolution and scalable multiplexity for label-free chemical imaging.

Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

This study evaluates the use of the housekeeping gene gyrA as a molecular marker for Bacillus species diversity and ecology, showing improved resolution compared to 16S rRNA.

CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity

CoVac501, a self-adjuvanting peptide vaccine with TLR7 agonists, induces strong neutralizing antibodies and T cell responses in non-human primates against SARS-CoV-2.

Understanding immune-driven brain aging by human brain organoid microphysiological analysis platform

This study develops a human brain organoid microphysiological platform to model immune-driven brain aging by perfusing aged monocytes and observing their effects on organoid tissues.

The Intrinsically Disordered Region of Coronins Fine-tunes Oligomerization and Actin Polymerization

The paper investigates the role of the intrinsically disordered region (IDR) in coronins, showing it fine-tunes oligomerization and actin polymerization through evolutionary conserved patterns.

Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

The paper investigates age-dependent H3K9 acetylation changes in rice flag leaf senescence, finding increased H3K9ac levels correlate with gene expression and identify regulatory networks.

PySOFI: an open source Python package for SOFI

The paper introduces PySOFI, an open-source Python package for SOFI analysis, enabling flexible algorithm inspection, testing, modification, and extension.