A5083747544- Ubiquitin and proteasome pathways
- Peptidase Inhibition and Analysis
- Advanced Proteomics Techniques and Applications
- Click Chemistry and Applications
- Mass Spectrometry Techniques and Applications
- Hepatitis B Virus Studies
- Hepatitis C virus research
- Fungal and yeast genetics research
- Cancer Research and Treatments
- Heat shock proteins research
- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- Cancer-related Molecular Pathways
- Genetics and Neurodevelopmental Disorders
- Analytical chemistry methods development
- Protease and Inhibitor Mechanisms
- Antimicrobial Peptides and Activities
- Enzyme Structure and Function
- Alzheimer's disease research and treatments
- Autophagy in Disease and Therapy
- Ferroptosis and cancer prognosis
- Protein Degradation and Inhibitors
- interferon and immune responses
- Ginseng Biological Effects and Applications
- Chemical Synthesis and Analysis
Beijing National Laboratory for Molecular Sciences
2022-2025
Peking University
2022-2025
Beijing Proteome Research Center
2019-2023
Chinese Academy of Medical Sciences & Peking Union Medical College
2019-2023
Center for Life Sciences
2023
State Key Laboratory of Proteomics
2019
Nankai University
2015-2018
ShanghaiTech University
2018
Protein modification by ubiquitin and ubiquitin-like proteins (UBLs) regulates numerous biological functions. The UFM1 system, a novel UBL conjugation is implicated in mouse development hematopoiesis. However, its broad functions working mechanisms remain largely elusive. CDK5RAP3, possible ufmylation substrate, essential for epiboly gastrulation zebrafish. Herein, we report critical role of CDK5RAP3 liver hepatic Cdk5rap3 knockout mice displayed prenatal lethality with severe hypoplasia, as...
Itaconate is an important antimicrobial and immunoregulatory metabolite involved in host-pathogen interactions. A key mechanistic action of itaconate through the covalent modification cysteine residues via Michael addition, resulting "itaconation". However, it unclear whether has other regulatory mechanisms. In this work, we discovered a novel type post-translational by promiscuous antibody enrichment data analysis with open-search strategy further confirmed as lysine "itaconylation". We...
Saccharomyces cerevisiae has been intensively studied in responses to different environmental stresses such as heat shock through global omic analysis. However, the S. industrial strains with superior thermotolerance have not explored any proteomic studies for elucidating tolerance mechanism. Recently a new diploid strain was obtained evolutionary engineering of parental strain, and it exhibited even higher resistance prolonged thermal stress. Herein, we performed iTRAQ-based quantitative...
The fundamental importance of the 26S proteasome in health and disease suggests that its function must be finely controlled, yet our knowledge about regulation remains limited. Posttranslational modifications, especially phosphorylation, subunits have been shown to impact through different mechanisms, although vast majority phosphorylation events not studied. Here, we characterized 1 most frequently detected phosphosites, namely Ser361 Rpn1, a base subunit 19S regulatory particle. Using...
Colorectal cancer (CRC) is a major cause of cancer-related death worldwide and an effective screening strategy for diagnosis early-stage CRC highly desired. Although extracellular vesicles (EVs) are expected to become some the most promising tools liquid biopsy early disease diagnosis, existing EV-based proteomics methods practical application in clinical samples limited by technical challenges high-throughput isolation detection EVs. In current study, we have developed simplified efficient...
Data-dependent acquisition (DDA) is widely applied in shotgun proteomics. However, restricted by the scanning speed of mass spectrometry (MS) instruments, it remains challenging for DDA to directly detect peptides with low abundance. Herein, we developed a real-time targeted MS data method, "isoSTAR", which identifies target their unique isotopic signatures during stage full-MS and subjects them MS/MS scans immediately. The method showed dramatic improvement sensitivity identifying abundance...
De novo peptide sequencing for large-scale proteomics remains challenging because of the lack full coverage ion series in tandem mass spectra. We developed a mirror protease trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The spectrum pairs derived from Ac-LysargiNase trypsin treated samples can generate b y series, which provide mutual complementarity each other, allow us to develop novel algorithm, pNovoM, de sequencing. Using pNovoM sequence...
Trypsin specifically cleaves the C-terminus of lysine and arginine residues but often fails to cleave modified lysines, such as ubiquitination, therefore resulting in uncleaved K-ε-GG peptides. Therefore, cleaved ubiquitinated peptide identification was regarded false positives discarded. Interestingly, unexpected cleavage at K48-linked ubiquitin chain has been reported, suggesting latent ability trypsin residues. However, it remains unclear whether other trypsin-cleavable sites are present....
Anemarrhena asphodeloides is an herb widely used to treat symptoms associated with diabetes in traditional Chinese medicine. However, its key components and metabolites have low bioavailability poor host absorption. To clarify the anti-diabetic mechanism of A. extract (AAE), we examined effects AAE rats induced by a high-fat diet streptozotocin. Faeces levels main were significantly higher than plasma, which indicated that gut microbiota might play important roles effect. Microbiological...
Proteomic analysis with data-independent acquisition (DIA) approaches represented by the sequential window of all theoretical fragment ion spectra (SWATH) technique has gained intense interest in recent years because DIA is able to overcome intrinsic weakness conventional data-dependent (DDA) methods and afford higher throughout reproducibility for proteome-wide quantification. Although raw mass spectrometry (MS) data quality data-mining workflow conceivably influence throughput, accuracy...
Protein lipoylation is an evolutionarily conserved post-translational modification from prokaryotes to eukaryotes. Lipoylation implicated with several human diseases, including metabolic disorders, cancer, and Alzheimer's disease. While individual lipoylated proteins have been biochemically studied, a strategy for globally quantifying site-specific resolution in proteomes still lacking. Herein, we developed butyraldehyde–alkynyl probe specifically label enrich lipoylations complexed...
To gain a deep understanding of yeast-cell response to heat stress, multiple laboratory strains have been intensively studied via genome-wide expression analysis for the mechanistic dissection classical heat-shock (HSR). However, robust industrial Saccharomyces cerevisiae hardly explored in global elucidation mechanism thermotolerant (TR) during fermentation. Herein, we employed data-independent acquisition and sequential window all theoretical mass spectra based proteomic workflows...
Hepatitis B Virus (HBV) constitutes a major threat to global public health. Current understanding of HBV-host interaction is yet limited. Here, ribosome profiling, quantitative mass spectrometry and RNA-sequencing were conducted on recently established HBV replication system, through which we identified multiomic differentially expressed genes (DEGs) that orchestrated remodel host proteostasis networks. Our multiomics interrogation revealed induced significant changes in both transcription...
Human neutrophil peptide-1 (HNP-1) is a promising antibiotic candidate, but its clinical applications have been hampered by challenges during mass production and an inadequate understanding of bactericidal mechanisms. In this study, we demonstrated that Escherichia coli expressing full-length preproHNP-1 secretes soluble form HNP-1, which can be recovered from the total cell lysate after isopropyl thio-β-d-galactoside (IPTG) induction ultrafiltration. Label-free quantitative proteomics...
Abstract Reactive cysteines often serve as functional sites on proteins and play important regulatory roles in various biological processes. A chemoproteomic method named “isoTOP‐ABPP” has enabled global profiling of cysteine reactivity native systems greatly increased our understanding reactive cysteinome. This elegant its derived technologies are now widely applied cysteinome the associated post‐translational modifications, discovery covalent ligands for undruggable targets well...
Activity-based proteome profiling (ABPP) is a powerful chemoproteomic technology for global of protein activity and modifications. The tandem orthogonal proteolysis-ABPP (TOP-ABPP) strategy utilizes clickable enrichment tag with cleavable linkers to enable direct identification probe-labeled residue sites within the target proteins. However, such site-specific workflow requires long operation time complex sample preparation procedures, limiting its wide applications. In current study, we...
Polyubiquitination encompasses complex topologies through various linkage types to deliver diverse cellular signals, which has been recognized as a sophisticated ubiquitin code. Accurate comparison of polyubiquitination signals is critical for revealing the dynamic ubiquitination-regulated events. Western blotting (WB) most widely used biochemical method quantify proteins and posttranslational modifications under physiological conditions. The accuracy sensitivity WB mainly depend on quality...
Rationale LysargiNase is a novel characterized metalloprotease that can cleave the N‐terminii of lysine or arginine residues. The peptides generated by are just mirrors to those trypsin. These characteristics provide powerful tool for mass spectrometry (MS)‐based proteomics research. A highly active and stable produced an easy inexpensive method could greatly benefit Here, we report soluble recombinant expression, purification acetyl modification in Escherichia coli . Methods coding sequence...
Mass spectrometry (MS)-based identification of ubiquitinated sites requires trypsin digestion prior to MS analysis, and a signature peptide was produced with diglycine residue attached the lysine (K-ε-GG peptide). However, missed cleavage modified lysines by results in peptides increased length charge, whose detection analysis is suppressed vast majority internally unmodified peptides. LysargiNase, mirrored trypsin, reported cleave before arginine residues be favorable for methylation...
Protein ubiquitylation is an important posttranslational modification that governs most cellular processes. Signaling functions of are very diverse and involve proteolytic as well nonproteolytic events, such localization, regulation protein interactions, control activity. The intricacy ubiquitin signaling further complicated by several different polyubiquitin chain types likely recognized interpreted readers. For example, K48-linked chains represent the abundant topology canonical...
Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction a sample-specific database variants predicted from next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed identification SAP peptides, thus validating...
Polyubiquitination signal deliver diverse cellular signal, which have been recognized as a sophisticated ubiquitin code. The perception and transduction of ubiquitination depend on the specificity sensitivity ubiquitin-binding domain. Accurate sensitive detection polyubiquitination is crucial for revealing dynamic ubiquitin-regulated events. Western blotting (WB) immunohistochemistry (IHC) are most widely used biochemical strategies to detect substrates under physiological pathological...