J. Duan

Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations

The paper benchmarks free energy perturbation calculations for predicting mutation effects on protein-protein binding affinity and introduces an automated method to improve accuracy.

de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination

This paper presents a method to sequence polyclonal IgG antibodies from human plasma post-SARS-CoV-2 vaccination, generating recombinant antibodies with neutralizing capabilities.

The microbial community of rust layer biofilm was driven by seawater microbial community

The paper analyzes microbial communities in rust layer biofilm and seawater, identifying dominant taxa and their interactions, and provides insights into microbial corrosion mechanisms in marine environments.

Long-term reliable neural decoding based on flexible implantable microelectronics and machine learning for seizure prediction application

This study combines flexible implantable microelectronics with machine learning to achieve reliable long-term neural decoding for seizure prediction in epileptic mice.

Structure of a G protein-coupled receptor with GRK2 and a biased ligand

The paper reports the structure of NTSR1 bound to GRK2, Gq, and a biased ligand, revealing how the ligand enhances GRK2 binding and enables arrestin-biased signaling.

Universal mechanism of hormone and allosteric agonist mediated activation of glycoprotein hormone receptors as revealed by structures of follicle stimulating hormone receptor

The paper reports cryo-EM structures of FSHR in inactive and active states, revealing a conserved activation mechanism and the role of H6157.42 in agonist selectivity.

Noninvasive cancer detection by extracting and integrating multi-modal data from whole-methylome sequencing of plasma cell-free DNA

This paper develops a method to detect cancer noninvasively by integrating methylation, fragmentation, and copy number data from plasma cell-free DNA using machine learning.

Plastid-specific RsmD methyltransferase and ribosome maturation factor RimM are crucial for 16S rRNA maturation and proteostasis

This study identifies chloroplast-specific factors AtRsmD and AtRimM essential for 16S rRNA maturation and chloroplast proteostasis in Arabidopsis thaliana.

Phosphoantigens are Molecular Glues that Promote Butyrophilin 3A1/2A1 Association Leading to Vγ9Vδ2 T Cell Activation

The paper shows phosphoantigens glue BTN3A1 and BTN2A1 together, initiating gamma-delta T cell activation through intracellular signaling.

A survey of Chinese pig farms and human healthcare isolates reveals separate human and animal MRSA populations

This study compares MRSA populations from Chinese pig farms and hospitals, finding distinct human and animal lineages with different genetic features and no evidence of spillover from farms to humans.

Online μSEC2-nRPLC-MS for improved sensitivity of intact protein detection of IEF separated non-human primate cerebrospinal fluid proteins

The paper introduces an online SEC2-nRPLC-MS platform to enhance intact protein detection in complex samples, achieving higher sensitivity and coverage in non-human primate cerebrospinal fluid.

Structural basis for ligand recognition and G protein-coupling promiscuity of the cholecystokinin A receptor

The paper presents cryo-EM structures of CCKAR with different G proteins to elucidate its G protein coupling promiscuity and ligand recognition mechanism.

Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+ T cells in vivo

This study links antigen responsiveness, proviral sequences, integration sites, and TCRβ sequences to show antigen-driven clonal selection maintains HIV-1 persistence in CD4+ T cells.

Antagonistic modules, SIB1 and LSD1, regulate photosynthesis-associated nuclear genes via GOLDEN2-LIKE transcription factors in Arabidopsis

This study shows SIB1 and LSD1 antagonistically regulate GLK1/2 to control PhANGs expression, affecting chloroplast biogenesis and 1O2 homeostasis in Arabidopsis.

Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

The paper reports the crystal structure of SARS-CoV-2 main protease bound to shikonin, revealing conformational changes and binding modes that could inform drug design.

Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation

The paper reports the structure of SARS-CoV-2 main protease in the apo state at physiological pH, revealing its inactive conformation and structural differences from the active state.

Prohibitin protects against cigarette smoke extract-induced cell apoptosis in cultured human pulmonary microvascular endothelial cells

This study shows prohibitin protects human pulmonary microvascular endothelial cells from cigarette smoke extract-induced apoptosis by preserving mitochondrial function and reducing oxidative stress.

High-throughput organoid screening enables engineering of intestinal epithelial composition

This paper develops a high-throughput organoid screening method to identify agents that alter intestinal epithelial composition, finding Xpo1 inhibitors increase Paneth cell abundance.

2D-HELS-AA MS Seq: Direct sequencing of tRNA reveals its different isoforms and multiple dynamic base modifications

The paper introduces 2D-HELS-AA MS Seq to directly sequence tRNA, revealing different isoforms and dynamic base modifications.

PLANT NATRIURETIC PEPTIDE A antagonizes salicylic acid-primed cell death

The paper shows that PNP-A antagonizes SA-mediated cell death in Arabidopsis lsd1 mutants by interacting with a newly identified receptor PNPAR.

Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution

The paper presents the 2.9 angstrom cryo-EM structure of TRPC5, revealing its partially open apo state and structural differences from other TRP channels.

Structure of the mouse TRPC4 ion channel

This study presents the cryo-EM structure of the mouse TRPC4 ion channel, revealing unique features that contribute to its ion selectivity and evolutionary diversity within the TRP family.

PKD2 is an essential ion channel subunit in the primary cilium of the renal collecting duct epithelium

The paper identifies PKD2 as a functional ion channel subunit in primary cilia of renal collecting duct epithelial cells, showing it conducts potassium and sodium but little calcium and is sensitized by high cilioplasmic [Ca2+].