Article
Chemistry, Analytical
Ian R. Smith, Jimmy K. Eng, Anthony S. Barente, Alexander Hogrebe, Ariadna Llovet, Ricard A. Rodriguez-Mias, Judit Villen
Summary: Stable-isotope labeling with amino acids in cell culture (SILAC)-based metabolic labeling is a widely used proteomics approach for quantitative comparisons. In this study, a new strategy was developed to coisolate and fragment SILAC peptide pairs for relative quantification. The modified database search engine and developed tool facilitated the analysis and quantification of SILAC peptide pairs. The coisolation approach improved the expectation scores and achieved more quantifications compared to traditional methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Patrick Opdensteinen, Laura E. Sperl, Mariam Mohamadi, Nicole Kuendgen-Redding, Franz Hagn, Johannes Felix Buyel
Summary: Nuclear magnetic resonance (NMR) spectroscopy is used to study protein structure and interactions, but requires stable isotope labelling. Traditional labelling methods in E. coli are not suitable for complex proteins. Research shows that cultivating tobacco cell lines in media supplemented with isotope-labelled substrates can efficiently produce labelled proteins for NMR analysis.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Thomas M. Haas, Stephan Mundinger, Danye Qiu, Nikolaus Jork, Kevin Ritter, Tobias Duerr-Mayer, Alexander Ripp, Adolfo Saiardi, Gabriel Schaaf, Henning J. Jessen
Summary: A novel synthetic method for O-18-labelled phosphates is introduced to facilitate access to required standards for stable isotope labelling in quantitative mass spectrometry. The study demonstrates consistent >95% O-18 enrichment ratios and good yields in gram-scale reactions, enabling late-stage labelling and analysis of metabolites in biological samples. The utility of O-18-labelled inositol phosphates and pyrophosphates is shown through assignment of these metabolites from different biological matrices.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Analytical
Yang Zhang, Benjamin Dreyer, Natalia Govorukhina, Alexander M. Heberle, Sasa Koncarevic, Christoph Krisp, Christiane A. . Opitz, Pauline Pfander, Rainer Bischoff, Hartmut Schlueter, Marcel Kwiatkowski, Kathrin Thedieck, Peter L. Horvatovich
Summary: The study compares three different quantitation techniques for tumor tissue phosphoproteomics and highlights the strengths and limitations of each method. The choice of quantitative methodology is critical for study design and comparison of published cancer phosphoproteomes. The results provide a resource for the design and analysis of quantitative phosphoproteomic studies in cancer research and diagnostics.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Applied
Sarah Mazzotta, Giovanna Baron, Laura Fumagalli
Summary: This study reports a procedure to obtain isotopologues of sitosteryl ferulate, one of the major components of gamma-oryzanol, which can be used as an analytical tool to assess the potential nutraceutical exploitation of rice.
Article
Geriatrics & Gerontology
Jordan D. Fuqua, Marcus M. Lawrence, Zachary R. Hettinger, Agnieszka K. Borowik, Parker L. Brecheen, Marcelina M. Szczygiel, Claire B. Abbott, Frederick F. Peelor, Amy L. Confides, Michael Kinter, Sue C. Bodine, Esther E. Dupont-Versteegden, Benjamin F. Miller
Summary: The failure of old muscle to fully recover after disuse is due to impaired protein folding and degradation mechanisms, rather than limitations in protein synthesis.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Biochemistry & Molecular Biology
Meaghan C. S. Courvan, Rachel O. Niederer, Isaac W. Vock, Lea Kiefer, Wendy Gilbert, Matthew D. Simon
Summary: Quantitative comparisons of RNA levels using TILAC can distinguish biological variation from variable sample preparation, making it a valuable tool for improving biological insights. TILAC uses metabolic labels to differentially label RNAs and allows for pooling of experimental and control samples before downstream manipulations. The method has been successfully applied to uncover differences in mRNA association with actively translating ribosomes and identify translationally upregulated transcripts.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Michael Hu, Zihan Ling, Xi Ren
Summary: The extracellular matrix (ECM) plays a crucial role in providing mechanical support and mediating biochemical interactions for cells. Understanding the dynamic changes in ECM composition and structure is essential for studying tissue homeostasis and disease progression. This review discusses the mechanisms of ECM-cell interactions, the modulation of tissue development and disease progression by ECM changes, and the implications of ECM dynamics in tissue engineering.
JOURNAL OF BIOLOGICAL ENGINEERING
(2022)
Review
Biochemistry & Molecular Biology
Nicole C. Beller, Amanda B. Hummon
Summary: The SILAC technique in proteomics uses stable isotope labeling in cell culture to differentiate and quantify unlabeled and labeled cells. The pulsed SILAC technique provides a new quantitative dimension for temporal analysis in proteomics. These innovative techniques have contributed to the development of various SILAC-based temporal and spatial labeling applications.
Article
Biochemical Research Methods
Jimena Tejerina, Jason Ryan, Mikhail Vyssotski, Kirill Lagutin, Yinrong Lu, Gabriel Visnovsky
Summary: EPA is an essential omega-3 polyunsaturated fatty acid that plays a critical role in marine life, primarily produced by phytoplankton and specific marine bacteria. Labelling a marine bacterium with stable isotope 13C proved to be an effective method to reveal the contribution of bacterial EPA, showing potential for further research.
JOURNAL OF MICROBIOLOGICAL METHODS
(2023)
Article
Cell Biology
Chongde Wu, Qian Ba, Dayun Lu, Wenxue Li, Barbora Salovska, Pingfu Hou, Torsten Mueller, George Rosenberger, Erli Gao, Yi Di, Hu Zhou, Eugenio F. Fornasiero, Yansheng Liu
Summary: The DeltaSILAC method quantitatively assesses the impact of site-specific phosphorylation on protein turnover, revealing a delay of protein turnover at many phosphorylation sites and an acceleration at functionally selected sites. This approach provides a valuable resource for understanding the effects of phosphorylation sites on protein lifetime in the context of cell signaling and disease biology.
DEVELOPMENTAL CELL
(2021)
Article
Chemistry, Analytical
Peilin Jiang, Wenjing Peng, Jingfu Zhao, Mona Goli, Yifan Huang, Yunxiang Li, Yehia Mechref
Summary: The complexity and heterogeneity of protein glycosylation present challenges in characterization and quantitation. This study introduces a metabolic isotope labeling strategy called GlyProSILC, which can label both the glycan motif and peptide backbone in the same batch of cells. It provides an accurate and effective quantitation approach for glycomics, proteomics, and glycoproteomics in a cell culture system.
ANALYTICAL CHEMISTRY
(2023)
Article
Food Science & Technology
Zi-Han Wang, Jing-Xian Zhang, Ming Gao, Wei-Qi Cui, Lu Xu, Xiao-lin Zhu, Jin-Jin Li, Zhi-E Huang, Dilshad Hussain, Jing-Yu Zhang, Di Chen, Xia Xu
Summary: This work presented a SIL-FIA-MS method for high throughput analysis of HMF in drinks, using 3-NPH and C-13(6)-3-NPH as labelling reagents. The method achieved rapid sample pretreatment and MS detection, with a total procedure time of 3 min per sample. By utilizing specific labelling and internal standard strategies, accurate and precise detection of HMF was ensured, demonstrating high reproducibility in real sample analysis.
Article
Biochemical Research Methods
Zhou Xin, Li Ruo-Qi, Wang Cong, Ma Xiao-Xia, Sun Ying, Song Wen-Xuan, Wei Xue-Bing, Li Dong-Hua, Ma Xiao, Wang Ren-Qi
Summary: CKs are important plant hormones, and a new chemical isotope labelling LC-MS analytical method has been developed to enhance sensitivity and monitor the impact of fertilizers on endogenous CKs metabolism.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Review
Cell Biology
Muhammad U. Anwar, F. Gisou van der Goot
Summary: S-acylation is an important posttranslational modification that regulates cellular processes. This reversible lipid modification affects cellular pathways and physiological processes, and the enzymes and proteins involved in S-acylation are still being discovered and studied.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Ainoa Rueda-Zubiaurre, Sabrina Yahiya, Oliver J. Fischer, Xiaojun Hu, Charlie N. Saunders, Sachi Sharma, Ursula Straschil, Junting Shen, Edward W. Tate, Michael J. Delves, Jake Baum, Anna Barnard, Matthew J. Fuchter
JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Chemistry, Medicinal
Andrew S. Bell, Zhiyong Yu, Jennie A. Hutton, Megan H. Wright, James A. Brannigan, Daniel Paape, Shirley M. Roberts, Charlotte L. Sutherell, Markus Ritzefeld, Anthony J. Wilkinson, Deborah F. Smith, Robin J. Leatherbarrow, Edward W. Tate
JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Cassandra R. Kennedy, Andrea Goya Grocin, Tristan Kovacic, Ravi Singh, Jennifer A. Ward, Avinash R. Shenoy, Edward W. Tate
Summary: Inhibition of the inflammasome and pyroptotic pathways is a promising strategy for treating autoimmune and inflammatory disorders. The study introduces a novel probe, IMP2070, which directly engages with NLRP3 and inhibits inflammasome activation in macrophages. Chemical proteomics identified potential off-targets, such as carbonic anhydrase 2, suggesting biological mechanisms for off-target effects of MCC950 and its derivatives in preclinical or clinical studies.
ACS CHEMICAL BIOLOGY
(2021)
Review
Oncology
Milon Mondal, Daniel Conole, Jaya Nautiyal, Edward W. Tate
Summary: Breast cancer, particularly metastatic ER- breast cancer and TNBC subtypes, has limited treatment options and low survival rates. UCHL1, highly expressed in these cancers, has emerged as a potential drug target in breast cancer with the recent discovery of small-molecule inhibitors.
BRITISH JOURNAL OF CANCER
(2022)
Article
Biochemistry & Molecular Biology
Maria Sladowska, Michal Turek, Min-Ji Kim, Krzysztof Drabikowski, Ben Hur Marins Mussulini, Karthik Mohanraj, Remigiusz A. Serwa, Ulrike Topf, Agnieszka Chacinska
Summary: Defects in mitochondrial function trigger compensatory responses in the cell, activating the mitochondrial unfolded protein response and proteasomal activity in the cytosol. This compensatory response plays a crucial role in promoting longevity.
Article
Biochemical Research Methods
Wouter W. Kallemeijn, Thomas Lanyon-Hogg, Nattawadee Panyain, Andrea Goya Grocin, Paulina Ciepla, Julia Morales-Sanfrutos, Edward W. Tate
Summary: Protein lipidation is a widespread post-translational modification in nature that regulates protein function, structure, and subcellular localization. Lipid transferases and their substrate proteins are of interest as drug targets due to their dysregulation in disease. The hydrophobic and dynamic nature of lipid modifications poses challenges for detection, but chemical proteomics offers a powerful approach to identify and quantify them.
Review
Pharmacology & Pharmacy
Andrea Goya Grocin, Wouter W. Kallemeijn, Edward W. Tate
Summary: MetAP2 has been a potential drug target for over three decades for the treatment of cancer, obesity, and autoimmune diseases, but no MetAP2 inhibitors have successfully reached clinical trials yet despite significant investment by major pharmaceutical companies. This review summarizes the key series of MetAP2 inhibitors developed so far, discusses their clinical progress and issues, and highlights the need to address gaps in knowledge for successful development of MetAP2 inhibitors in clinical settings.
TRENDS IN PHARMACOLOGICAL SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Federico Dona, Cagakan Ozbalci, Andrea Paquola, Federica Ferrentino, Stephen J. Terry, Elisabeth M. Storck, Gaoge Wang, Ulrike S. Eggert
Summary: The membrane protein stomatin is found to be involved in the cytokinesis step of cell division, even though it is not a lipid biosynthetic enzyme. Depletion of stomatin leads to changes in cellular lipidomes, and exogenous phosphatidylcholines can rescue these defects.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Microbiology
Lalita Priyamvada, Wouter W. Kallemeijn, Monica Faronato, Kimberly Wilkins, Cynthia S. Goldsmith, Catherine A. Cotter, Suany Ojeda, Roberto Solari, Bernard Moss, Edward W. Tate, Panayampalli Subbian Satheshkumar
Summary: N-myristoylation plays a critical role in VACV infection, and the NMT inhibitor IMP-1088 can effectively inhibit viral replication and infectivity.
Article
Chemistry, Multidisciplinary
Roman O. O. Fedoryshchak, Andrii Gorelik, Mengjie Shen, Maria M. M. Shchepinova, Inmaculada Perez-Dorado, Edward W. W. Tate
Summary: Protein-protein interactions (PPIs) play important roles in biology. However, there are limited methods to study interactions driven by specific post-translational modifications (PTMs). In this study, a panel of novel myristic acid analog probes were designed and synthesized to capture PTM-specific interactions. These probes successfully labeled NMT substrates in cells and formed covalent crosslinks with their interacting proteins, allowing the identification of known and novel interactors of myristoylated proteins.
Article
Microbiology
Elizabeth V. K. Ledger, Katie Lau, Edward W. Tate, Andrew M. Edwards
Summary: Pathogenic bacteria need to repair DNA damage from antibiotics and the immune system to survive in the host environment. The SOS response is a vital pathway for bacterial DNA repair and could be targeted for new therapeutics to sensitize bacteria to antibiotics and the immune response. Through a mutant screen, 16 genes potentially involved in the SOS response were identified in Staphylococcus aureus, with 3 genes affecting susceptibility to ciprofloxacin. The loss of the tyrosine recombinase XerC also increased susceptibility to antibiotics and host immune defenses, suggesting that inhibiting XerC could sensitize S. aureus to both antibiotics and the immune response.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Emma C. Couves, Scott Gardner, Tomas B. Voisin, Jasmine K. Bickel, Phillip J. Stansfeld, Edward W. Tate, Doryen Bubeck
Summary: This study reveals the role of CD59 in immune regulation, by preventing the formation of MAC toxins through inhibiting the binding of C8 and C9 to the membrane. CD59 also protects membrane integrity by altering the trajectory of C9 beta-hairpins, restricting MAC polymerization. These findings are significant for understanding the dual roles of CD59 in MAC and its involvement in host-pathogen interactions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Matthew E. H. White, Jesus Gil, Edward W. Tate
Summary: Covalent drug discovery has experienced a resurgence and reactive cysteine profiling has emerged as a platform for ligand discovery. However, the scope of this approach at the whole-proteome level has not been fully explored. By combining AlphaFold2-predicted side-chain accessibilities and a meta-analysis of cysteine profiling datasets, accessibility biases in cysteines were revealed. Analysis of cysteine-fragment interactions showed increased bias against buried cysteine residues. Future directions for increasing coverage were proposed.
CELL CHEMICAL BIOLOGY
(2023)
Article
Geriatrics & Gerontology
Pankaj Thapa, Katarzyna Olek, Agata Kowalska, Remigiusz A. Serwa, Wojciech Pokrzywa
Summary: Supplementation with S-adenosylhomocysteine (SAH) can extend the lifespan of model organisms. This study generated a Caenorhabditis elegans model with a mutation in S-adenosylhomocysteine hydrolase (AHCY-1), resulting in delayed aging. The balance between S-adenosylmethionine (SAM) and SAH appears to play a pivotal role in defining the lifespan of C. elegans.
Article
Biochemistry & Molecular Biology
Nattawadee Panyain, Aurelien Godinat, Aditya Raymond Thawani, Sofia Lachiondo-Ortega, Katie Mason, Sarah Elkhalifa, Lisa M. Smith, Jeanine A. Harrigan, Edward W. Tate
Summary: UCHL1 covalent inhibitor MT16-001 and an activity-based probe MT16-205 were characterized in this study, providing a comprehensive quantitative profile for on- and off-targets. These compounds showed good selectivity for UCHL1 over other DUBs in intact cells, while also engaging with a range of other targets, highlighting the potential of the cyanopyrrolidine warhead as a versatile platform for liganding diverse classes of proteins.
RSC MEDICINAL CHEMISTRY
(2021)
