Article
Chemistry, Analytical
Guopan Liu, Ming Ho Choi, Haiying Ma, Xuejiao Guo, Pui-Chi Lo, Jinyong Kim, Liang Zhang
Summary: Surface biotinylation is widely used to analyze the cellular proteome associated with the plasma membrane. However, it is prone to interference from cytoplasmic biotin-associated proteins. This study established a new workflow (BCAP) that utilizes a bioorthogonal conjugation reaction to minimize interference and efficiently isolate surface proteins.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
He Wang, Zhiting Wang, Hang Gao, Jianhui Liu, Zichun Qiao, Baofeng Zhao, Zhen Liang, Bo Jiang, Lihua Zhang, Yukui Zhang
Summary: This paper presents a photo-oxidation driven proximity labeling strategy for profiling the mitochondrial proteome with high spatiotemporal resolution in living cells. By selectively labeling mitochondrial proteins and quantifying their dynamics, this strategy provides solid technical support for the study of subcellular biology.
Article
Chemistry, Multidisciplinary
Jiaying Li, Jiahua Zhou, Kailu Tian, He Zhu, Yao Chen, Yangyu Huang, Guosheng Wang, Zhou Gong, Hongqiang Qin, Mingliang Ye, Hao Xu
Summary: The quantitative profiling of residue reactivity in proteins can help identify covalent druggable targets for precise therapy. In this study, a chemical proteomics platform was developed to analyze the reactivity of histidine (His) residues. Through this platform, the reactivity of His residues in the human proteome was characterized, and a large number of His residues with high reactivity were identified. The findings suggest that these highly reactive residues are less likely to be phosphorylation sites, which requires further research to understand the underlying mechanism. This comprehensive map of His residue reactivity provides potential bindable sites for disrupting protein activities and offers new opportunities for developing covalent inhibitors using acrolein derivatives as reactive warheads.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Zheng Zhang, Tong Liu, Hangyan Dong, Jian Li, Haofan Sun, Xiaohong Qian, Weijie Qin
Summary: RNA-protein interactions are crucial in biological regulation, and the development of the PP method for RNA tagging and RNP enrichment has enabled successful screening and analysis of RBPs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Yi-Rong Jiang, Le Zhu, Lan-Rui Cao, Qiong Wu, Jian-Bo Chen, Yu Wang, Jie Wu, Tian-Yu Zhang, Zhao-Lun Wang, Zhi-Ying Guan, Qin-Qin Xu, Qian-Xi Fan, Shao-Wen Shi, Hui-Feng Wang, Jian-Zhan Pan, Xu-Dong Fu, Yongcheng Wang, Qun Fang
Summary: A new single-cell analysis platform, capable of simultaneously analyzing the transcriptome and proteome, provides an important resource for understanding the relationship between transcription and translation in cells. By applying this platform to mouse oocytes, we investigated the correlation between RNA and protein, as well as the meiosis regulatory network, and identified specific oocyte maturational signatures.
Article
Chemistry, Analytical
Li Yang, Shuang Weng, Xiaohong Qian, Mingchao Wang, Wantao Ying
Summary: Peripheral blood mononuclear cells (PBMCs) play vital roles in disease monitoring and physiological processes. Researchers have developed a microscale apparatus (PBMC-mCap) to enrich and analyze the proteome of PBMCs from small volumes of peripheral blood. This approach provides a convenient clinical toolkit for disease diagnosis and monitoring of the healthy state.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Runsheng Zheng, Natalia Govorukhina, Tabiwang N. Arrey, Christopher Pynn, Ate van der Zee, Gyorgy Marko-Varga, Rainer Bischoff, Alexander Boychenko
Summary: This study compares 1D-nanoLC-MS with an automated online-2D high-pH RP x low pH RP separation method for deep proteome profiling, demonstrating that the new method can increase peptide and protein identifications without the need for extra sample handling. Serum sample preparation related changes were revealed, which should be taken into account when planning multicentric biomarker discovery and validation studies.
ANALYTICAL CHEMISTRY
(2021)
Article
Ecology
Shimon Bershtein, Daniel Kleiner, Dan Mishmar
Summary: Recent advances in AI-based 3D protein structure prediction have the potential to address health-related questions and impact evolution. Integration of structural predictions with functional genomic studies is emphasized for a comprehensive understanding of protein properties and their effects on fitness.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Pharmacology & Pharmacy
Congcong Ma, Yanwei Li, Jie Li, Lei Song, Liangyu Chen, Na Zhao, Xueping Li, Ning Chen, Lixia Long, Jin Zhao, Xin Hou, Li Ren, Xubo Yuan
Summary: This study synthesized zeolite NaY and developed a method to comprehensively profile plasma proteome using the plasma protein corona formed on zeolite NaY, which is important for the development of novel pharmacodynamic biomarkers.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Chemistry, Multidisciplinary
Maxwell Zimmerman, Justin R. Porter, Michael D. Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M. Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D. Chodera, Gregory R. Bowman
Summary: Researchers utilized the Folding@home project to simulate the viral proteome of SARS-CoV-2 and discovered 'cryptic' epitopes, with spike variants affecting the balance between receptor binding and immune evasion. The data and models generated provide valuable insight for the design of antiviral drugs.
Article
Biochemical Research Methods
Niels M. Leijten, Petra Bakker, Herman P. Spaink, Jeroen den Hertog, Simone Lemeer
Summary: Thermal proteome profiling (TPP) enables unbiased detection of drug-target protein engagements in vivo. By using whole zebrafish embryo lysate, this study identified potential protein targets of napabucasin, including oxidoreductase PORA, which may affect Stat3 signaling.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Chemistry, Multidisciplinary
Qianqian Jiang, He Wang, Zichun Qiao, Yutong Hou, Zhigang Sui, Baofeng Zhao, Zhen Liang, Bo Jiang, Yukui Zhang, Lihua Zhang
Summary: Systematic analysis of the membrane proteome of living cells is crucial for understanding cellular processes and relationships between membrane-bound organelles. However, enriching and analyzing membrane proteins in their native state remains challenging. To address this, researchers developed a cell surface engineering method that uses biomembrane fusion to map the membrane proteome. This approach bypasses traditional fractionation methods and enables specific and comprehensive analysis of membrane proteins.
Article
Multidisciplinary Sciences
Haizhu Zhang, Zhaoyu Qin, Xuetong Yue, Yang Liu, Xiaogang Sun, Jinwen Feng, Ziyan Xu, Jiangyan Zhao, Kai Li, Jiange Qiu, Wenjun Yang, Fuchu He, Chen Ding
Summary: ATAC-MS is a method to identify transcriptional protein complexes assembled on accessible chromatin, providing insight into the protein machinery in open chromatin. Combined with ATAC-seq, it allows for high-resolution profiling of chromatin-transcriptional machinery. Additionally, the fusion protein ctATAC-MS enables systematic pinpointing of the transcriptional machinery at specific open chromatin regions.
Article
Cell Biology
Jing Yan, Bei Xie, Ye Tian, Li Huang, Shuli Zou, Zhiheng Peng, Zhuan Liu, Linjing Li
Summary: Insulin resistance (IR) is associated with poor prognosis in hepatocellular carcinoma (HCC). This study identified differentially expressed proteins (DEPs) in insulin resistant HepG2 cells, and found that these DEPs are involved in tumorigenesis and tumor progression. High expression of SOX9 and PRKD3 is strongly associated with reduced patient survival rate.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Coline Mahe, Regis Lavigne, Emmanuelle Com, Charles Pineau, Yann Locatelli, Aleksandra Maria Zlotkowska, Carmen Alminana, Guillaume Tsikis, Pascal Mermillod, Jennifer Schoen, Marie Saint-Dizier
Summary: Understanding the composition of oviduct fluid is crucial for understanding the microenvironment of sperm capacitation, fertilization, and early embryo development. This study analyzed the proteome of oviduct fluid samples from different regions, stages, and sides of the oviduct, and found that protein abundance was mainly influenced by the oviduct region, followed by the proximity of the ovulating ovary and the peri-ovulatory stage.
SCIENTIFIC REPORTS
(2022)