Article
Chemistry, Multidisciplinary
Mikail E. Abbasov, Madeline E. Kavanagh, Taka-Aki Ichu, Michael R. Lazear, Yongfeng Tao, Vincent M. Crowley, Christopher W. am Ende, Stephan M. Hacker, Jordan Ho, Melissa M. Dix, Radu Suciu, Matthew M. Hayward, Laura L. Kiessling, Benjamin F. Cravatt
Summary: Recent advances in chemical proteomics have identified and characterized a wide range of uncharted aminophilic chemotypes that greatly expand the ligandable lysines in human proteins. Aminophilic electrophiles showed varying proteomic reactivities, from selective interactions with specific lysines to broad engagement with covalent small-molecule-lysine interactions. The study demonstrates the potential of covalent chemistry in targeting functional lysines in the human proteome, perturbing diverse biochemical functions.
Review
Chemistry, Multidisciplinary
Wai Cheung Chan, Shabnam Sharifzadeh, Sara J. Buhrlage, Jarrod A. Marto
Summary: Covalent drugs are essential in modern medicine, and there has been a recent surge in interest in the development of covalent inhibitors, particularly utilizing mass spectrometry-based chemoproteomic methods. This review highlights the practical applications of these techniques in target identification, hit discovery, and lead characterization/optimization in covalent drug discovery, with case studies to demonstrate their real-world significance and future opportunities.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Cell Biology
Bishoy Wadie, Vitalii Kleshchevnikov, Elissavet Sandaltzopoulou, Caroline Benz, Evangelia Petsalaki
Summary: Linear motifs play a crucial role in cell functions, but their identification has been challenging. This study uses systematic motif prediction and functional filters to identify viral protein motifs that have evolved convergently with human motifs. The findings improve motif prediction sensitivity and provide a comprehensive catalog of potential human motifs that contribute to understanding the human domain-linear motif code and viral interference mechanisms.
Review
Biochemistry & Molecular Biology
Rita Capela, Rita Felix, Marta Clariano, Diogo Nunes, Maria de Jesus Perry, Francisca Lopes
Summary: Mycobacterium tuberculosis is the cause of tuberculosis, and drug discovery for TB is challenging due to resistance and incomplete knowledge. The limited permeability of the cell wall and presence of efflux pumps hinder drug accumulation. Lack of suitable models is a limiting factor. Only a small percentage of bacterial proteins are targeted in current therapeutic regimens.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Bianbian Huo, Yuanyuan Liu, Lingjun Li, Weijie Qin
Summary: The study developed a novel chemical enrichment method (AFT-OCAP) for simultaneous analysis of O-GlcNAc chromatin-associated proteins (OCAPs) and mapping their binding DNA, providing valuable tools for understanding the functions of OCAPs and the regulatory machinery of O-GlcNAcylation on gene transcription.
Article
Chemistry, Analytical
Carolina Rojas Ramirez, Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii
Summary: Monitoring protein structure before and after environmental alterations can provide insights into protein function. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry allows for monitoring of structural rearrangements by exposing proteins to radicals. However, the challenges of processing FPOP data have limited its proteome-scale uses. In this study, a computational workflow was developed to analyze FPOP data sets more efficiently, enabling the identification of modified peptide spectra at a faster rate than previous methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Louis P. Conway, Appaso M. Jadhav, Rick A. Homan, Weichao Li, Juanita Sanchez Rubiano, Richard Hawkins, R. Michael Lawrence, Christopher G. Parker
Summary: The study systematically evaluated several diazirine-containing FF tags and found that these tags have profound effects on the proteomic profiles of chemical probes.
Article
Biochemical Research Methods
Weili Miao, Jiekai Yin, Douglas F. Porter, Xiaogang Jiang, Paul A. Khavari, Yinsheng Wang
Summary: In this study, a probe and proteomic methods were used to identify a large number of AMP-binding kinases and revealed the potential involvement of AMP in the MAPK pathway.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Matthew Domnauer, Fan Zheng, Liying Li, Yanxiao Zhang, Catherine E. Chang, Jay R. Unruh, Juliana Conkright-Fincham, Scott McCroskey, Laurence Florens, Ying Zhang, Christopher Seidel, Benjamin Fong, Birgit Schilling, Rishi Sharma, Arvind Ramanathan, Kausik Si, Chuankai Zhou
Summary: The study shows that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to reduction of temperature-sensitive proteins and re-localizing a portion of its proteome. Additionally, many proteins adopt an alternative conformation. These findings reveal mechanisms of adaptation to prolonged temperature change in organisms.
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
Chemistry, Multidisciplinary
Antonie J. van der Zouwen, Aike Jeucken, Roy Steneker, Katharina F. Hohmann, Jonas Lohse, Dirk J. Slotboom, Martin D. Witte
Summary: Chemical probes that covalently modify proteins are powerful tools for biological research. Choosing the right reactive group for the design of a probe is crucial, and a modular approach has been developed in this study for easy coupling of reactive groups to ligands. The iminoboronate probes synthesized in this study selectively label target proteins and can be further modified using transimination reactions with aminohydrazides, for example, to introduce fluorophores.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Oncology
Varshni Rajagopal, Astrid-Solveig Loubal, Niklas Engel, Elsa Wassmer, Jeanette Seiler, Oliver Schilling, Maiwen Caudron-Herger, Sven Diederichs
Summary: In this study, we identified RNA-dependent proteins in A549 lung cancer cells, providing insights into their role in cancer. The dataset is available in the R-DeeP 2.0 database, which offers detailed information on RNA-dependent proteins in A549 and HeLa cells.
Article
Genetics & Heredity
Jingning Zhang, Diptavo Dutta, Anna Koettgen, Adrienne Tin, Pascal Schlosser, Morgan E. Grams, Benjamin Harvey, Bing Yu, Eric Boerwinkle, Josef Coresh, Nilanjan Chatterjee
Summary: Improved understanding of genetic regulation of the proteome can help identify causal mechanisms for complex traits. This study analyzed data from two large population studies and identified proteins associated with genetic variants in European American and African American individuals. The study also demonstrated the potential of proteome-wide association studies in predicting and treating diseases like gout.
Article
Multidisciplinary Sciences
Junki Uchiyama, Rohini Roy, Dan Ohtan Wang, Kazuya Morikawa, Yuka Kawahara, Mio Iwasaki, Chiaki Yoshino, Yuichiro Mishima, Yasushi Ishihama, Koshi Imami
Summary: pSNAP is a novel method for proteome-wide profiling of NPCs without the need for ribosome purification and/or chemical labeling, capturing bona fide NPCs and their characteristics. It can be used to evaluate the effect of potential molecular therapies on translation and study modifications on NPCs and their interactions with ribosome-associated factors.
Article
Biochemistry & Molecular Biology
Zhiqian Zhang, Brandon Sie, Aiquan Chang, Yumei Leng, Christopher Nardone, Richard T. Timms, Stephen J. Elledge
Summary: This study establishes a strategy for identifying and mapping critical residues of internal degrons on a proteome-scale using global protein stability profiling and machine learning. By combining this with scanning mutagenesis, the researchers determined the critical residues for over 5,000 predicted degrons. They focused on Cullin-RING ligase degrons and generated mutational fingerprints for 219 degrons, developing the DegronID algorithm for clustering degron peptides with similar motifs. The study also uncovered 16 E3-degron pairs with extensive degron variability and structural determinants.
Article
Biochemical Research Methods
Sunkyu Choi, Jonathan Kelber, Xinning Jiang, Jan Strnadel, Ken Fujimura, Martina Pasillas, Judith Coppinger, Richard Klemke
ANALYTICAL BIOCHEMISTRY
(2014)
Article
Chemistry, Analytical
Xinning Jiang, Mingliang Ye, Guanghui Han, Xiaoli Dong, Hanfa Zou
ANALYTICAL CHEMISTRY
(2010)
Article
Chemistry, Analytical
Fangjun Wang, Chunxia Song, Kai Cheng, Xinning Jiang, Mingliang Ye, Hanfa Zou
ANALYTICAL CHEMISTRY
(2011)
Article
Chemistry, Multidisciplinary
Liu Xiaoyan, Song Chunxia, Chen Rui, Jiang Xinning, Jin Yan, Zou Hanfa
CHINESE JOURNAL OF CHEMISTRY
(2010)
Article
Biochemical Research Methods
Guanghui Han, Mingliang Ye, Hongwei Liu, Chunxia Song, Deguang Sun, Yifeng Wu, Xinning Jiang, Rui Chen, Chunli Wang, Liming Wang, Hanfa Zou
Article
Biotechnology & Applied Microbiology
Hongwei Liu, Xin Zhao, Fangjun Wang, Xinning Jiang, Sufang Zhang, Mingliang Ye, Zongbao K. Zhao, Hanfa Zou
FEMS YEAST RESEARCH
(2011)
Article
Biochemistry & Molecular Biology
Yingchun Wang, Feng Yang, Yi Fu, Xiahe Huang, Wei Wang, Xinning Jiang, Marina A. Gritsenko, Rui Zhao, Matthew E. Monore, Olivier C. Pertz, Samuel O. Purvine, Daniel J. Orton, Jon M. Jacobs, David G. Camp, Richard D. Smith, Richard L. Klemke
JOURNAL OF BIOLOGICAL CHEMISTRY
(2011)
Article
Biochemical Research Methods
Xiaoli Dong, Lei Xiong, Xinning Jiang, Yinsheng Wang
JOURNAL OF PROTEOME RESEARCH
(2010)
Article
Biochemical Research Methods
Xinning Jiang, Mingliang Ye, Kai Cheng, Hanfa Zou
JOURNAL OF PROTEOME RESEARCH
(2010)
Article
Biochemical Research Methods
Lei Xiong, Jing Zhang, Bifeng Yuan, Xiaoli Dong, Xinning Jiang, Yinsheng Wang
JOURNAL OF PROTEOME RESEARCH
(2010)
Article
Biochemical Research Methods
Xiaoli Dong, Yongsheng Xiao, Xinning Jiang, Yinsheng Wang
JOURNAL OF PROTEOME RESEARCH
(2011)
Article
Chemistry, Analytical
Fangjun Wang, Guanghui Han, Zhiyuan Yu, Xinning Jiang, Shutao Sun, Rui Chen, Mingliang Ye, Hanfa Zou
JOURNAL OF SEPARATION SCIENCE
(2010)
Article
Biochemical Research Methods
Chunxia Song, Mingliang Ye, Zexian Liu, Han Cheng, Xinning Jiang, Guanghui Han, Zhou Songyang, Yexiong Tan, Hongyang Wang, Jian Ren, Yu Xue, Hanfa Zou
MOLECULAR & CELLULAR PROTEOMICS
(2012)
Article
Biochemical Research Methods
Chunli Wang, Mingliang Ye, Guanghui Han, Rui Chen, Manyu Zhang, Xinning Jiang, Kai Cheng, Fangjun Wang, Hanfa Zou