1
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Feng F, Gao Y, Zhao Q, Luo T, Yang Q, Zhao N, Xiao Y, Han Y, Pan J, Feng S, Zhang L, Wu M. Single-electron transfer between sulfonium and tryptophan enables site-selective photo crosslinking of methyllysine reader proteins. Nat Chem 2024; 16:1267-1277. [PMID: 39079947 DOI: 10.1038/s41557-024-01577-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 06/12/2024] [Indexed: 08/15/2024]
Abstract
The identification of readers, an important class of proteins that recognize modified residues at specific sites, is essential to uncover the biological roles of post-translational modifications. Photoreactive crosslinkers are powerful tools for investigating readers. However, existing methods usually employ synthetically challenging photoreactive warheads, and their high-energy intermediates generated upon irradiation, such as nitrene and carbene, may cause substantial non-specific crosslinking. Here we report dimethylsulfonium as a methyllysine mimic that binds to specific readers and subsequently crosslinks to a conserved tryptophan inside the binding pocket through single-electron transfer under ultraviolet irradiation. The crosslinking relies on a protein-templated σ-π electron donor-acceptor interaction between sulfonium and indole, ensuring excellent site selectivity for tryptophan in the active site and orthogonality to other methyllysine readers. This method could escalate the discovery of methyllysine readers from complex cell samples. Furthermore, this photo crosslinking strategy could be extended to develop other types of microenvironment-dependent conjugations to site-specific tryptophan.
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Affiliation(s)
- Feng Feng
- Department of Chemistry, Zhejiang University, Hangzhou, China
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Yingxiao Gao
- Department of Chemistry, Fudan University, Shanghai, China
| | - Qun Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ting Luo
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Qingyun Yang
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Nan Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yihang Xiao
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yusong Han
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Jinheng Pan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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2
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Lee J, Bao X. Comparative Review on Cancer Pathology from Aberrant Histone Chaperone Activity. Int J Mol Sci 2024; 25:6403. [PMID: 38928110 PMCID: PMC11203986 DOI: 10.3390/ijms25126403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Histone chaperones are integral to chromatin dynamics, facilitating the assembly and disassembly of nucleosomes, thereby playing a crucial role in regulating gene expression and maintaining genomic stability. Moreover, they prevent aberrant histone interactions prior to chromatin assembly. Disruption in histone chaperone function may result in genomic instability, which is implicated in pathogenesis. This review aims to elucidate the role of histone chaperones in cancer pathologies and explore their potential as therapeutic targets. Histone chaperones have been found to be dysregulated in various cancers, with alterations in expression levels, mutations, or aberrant interactions leading to tumorigenesis and cancer progression. In addition, this review intends to highlight the molecular mechanisms of interactions between histone chaperones and oncogenic factors, underscoring their roles in cancer cell survival and proliferation. The dysregulation of histone chaperones is significantly correlated with cancer development, establishing them as active contributors to cancer pathology and viable targets for therapeutic intervention. This review advocates for continued research into histone chaperone-targeted therapies, which hold potential for precision medicine in oncology. Future advancements in understanding chaperone functions and interactions are anticipated to lead to novel cancer treatments, enhancing patient care and outcomes.
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Affiliation(s)
| | - Xiucong Bao
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China;
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3
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Walrant A, Sachon E. Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse? MASS SPECTROMETRY REVIEWS 2024. [PMID: 38576378 DOI: 10.1002/mas.21880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.
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Affiliation(s)
- Astrid Walrant
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
- Sorbonne Université, Mass Spectrometry Sciences Sorbonne Université, MS3U platform, Fédération de Chimie moléculaire de Paris centre, Paris, France
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4
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Zong Y, Weiss N, Wang K, Pagano AE, Heissel S, Perveen S, Huang J. Development of Complementary Photo-arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307526. [PMID: 38298064 PMCID: PMC11005723 DOI: 10.1002/advs.202307526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/03/2023] [Indexed: 02/02/2024]
Abstract
Arginine and lysine, frequently appearing as a pair on histones, have been proven to carry diverse modifications and execute various epigenetic regulatory functions. However, the most context-specific and transient effectors of these marks, while significant, have evaded study as detection methods have thus far not reached a standard to capture these ephemeral events. Herein, a pair of complementary photo-arginine/δ-photo-lysine (R-dz/K-dz) probes is developed and involve these into histone peptide, nucleosome, and chromatin substrates to capture and explore the interactomes of Arg and Lys hPTMs. By means of these developed tools, this study identifies that H3R2me2a can recruit MutS protein homolog 6 (MSH6), otherwise repelDouble PHD fingers 2 (DPF2), Retinoblastoma binding protein 4/7 (RBBP4/7). And it is disclosed that H3R2me2a inhibits the chromatin remodeling activity of the cBAF complex by blocking the interaction between DPF2 (one component of cBAF) and the nucleosome. In addition, the novel pairs of H4K5 PTMs and respective readers are highlighted, namely H4K5me-Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2), H4K5me2-L3MBTL2, and H4K5acK8ac-YEATS domain-containing protein 4 (YEATS4). These powerful tools pave the way for future investigation of related epigenetic mechanisms including but not limited to hPTMs.
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Affiliation(s)
- Yu Zong
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | - Nicole Weiss
- Program of PharmacologyWeill Cornell Medical College of Cornell UniversityNew York10065USA
| | - Ke Wang
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | | | - Søren Heissel
- Proteomics Resource CenterRockefeller UniversityNew York10065USA
| | - Sumera Perveen
- Structural Genomics ConsortiumUniversity of TorontoTorontoM5S3H2Canada
| | - Jian Huang
- Department of Molecular BiologyPrinceton UniversityPrinceton08544USA
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5
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Hananya N, Koren S, Muir TW. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 2024; 25:255-271. [PMID: 37985791 PMCID: PMC11176933 DOI: 10.1038/s41576-023-00664-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Genetic and genomic techniques have proven incredibly powerful for identifying and studying molecular players implicated in the epigenetic regulation of DNA-templated processes such as transcription. However, achieving a mechanistic understanding of how these molecules interact with chromatin to elicit a functional output is non-trivial, owing to the tremendous complexity of the biochemical networks involved. Advances in protein engineering have enabled the reconstitution of 'designer' chromatin containing customized post-translational modification patterns, which, when used in conjunction with sophisticated biochemical and biophysical methods, allow many mechanistic questions to be addressed. In this Review, we discuss how such tools complement established 'omics' techniques to answer fundamental questions on chromatin regulation, focusing on chromatin mark establishment and protein-chromatin interactions.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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6
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Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
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Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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7
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Chen S, Zhang W, Li X, Cao Z, Liu C. DNA polymerase beta connects tumorigenicity with the circadian clock in liver cancer through the epigenetic demethylation of Per1. Cell Death Dis 2024; 15:78. [PMID: 38245510 PMCID: PMC10799862 DOI: 10.1038/s41419-024-06462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
The circadian-controlled DNA repair exhibits a strong diurnal rhythm. Disruption in circadian clock and DNA repair is closely linked with hepatocellular carcinoma (HCC) progression, but the mechanism remains unknown. Here, we show that polymerase beta (POLB), a critical enzyme in the DNA base excision repair pathway, is rhythmically expressed at the translational level in mouse livers. Hepatic POLB dysfunction dampens clock homeostasis, whereas retards HCC progression, by mediating the methylation of the 4th CpG island on the 5'UTR of clock gene Per1. Clinically, POLB is overexpressed in human HCC samples and positively associated with poor prognosis. Furthermore, the hepatic rhythmicity of POLB protein expression is orchestrated by Calreticulin (CALR). Our findings provide important insights into the molecular mechanism underlying the synergy between clock and food signals on the POLB-driven BER system and reveal new clock-dependent carcinogenetic effects of POLB. Therefore, chronobiological modulation of POLB may help to promote precise interventions for HCC.
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Affiliation(s)
- Siyu Chen
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Wenxiang Zhang
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiao Li
- Department of Pathology, First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zhengyu Cao
- Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China.
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8
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Guo X, Wang Y, An Y, Liu Z, Liu J, Chen J, Zhan MM, Liang M, Hou Z, Wan C, Yin F, Wang R, Li Z. Development of Lysine Crotonyl-Mimic Probe to Covalently Identify H3K27Cr Interacting Proteins. Chemistry 2023; 29:e202301624. [PMID: 37587551 DOI: 10.1002/chem.202301624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Histone lysine crotonylation (Kcr) is one newly discovered acylation modification and regulates numerous pathophysiological processes. The binding affinity between Kcr and its interacting proteins is generally weak, which makes it difficult to effectively identify Kcr-interacting partners. Changing the amide of crotonyl to an ester increased reactivity with proximal cysteines and retained specificity for Kcr antibody. The probe "H3g27Cr" was designed by incorporating the ester functionality into a H3K27 peptide. Using this probe, multiple Kcr-interacting partners including STAT3 were successfully identified, and this has not been reported previously. Further experiments suggested that STAT3 possibly could form complexes with Histone deacetylase HDACs to downregulate the acetylation and crotonylation of Histone H3K27. Our unique design provided intriguing tools to further explore Kcr-interacting proteins and elucidate their working mechanisms.
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Affiliation(s)
- Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yuhao An
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zhihong Liu
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Jianbo Liu
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Jiaxin Chen
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Mei-Miao Zhan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Mingcha Liang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Feng Yin
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Rui Wang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
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9
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Tang JH, Shu QY, Guo YY, Zhu H, Li YM. Cell-Permeable Ubiquitin and Histone Tools for Studying Post-translational Modifications. Chembiochem 2023; 24:e202300169. [PMID: 37060212 DOI: 10.1002/cbic.202300169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/16/2023]
Abstract
Protein post-translational modifications (PTMs) regulate nearly all biological processes in eukaryotic cells, and synthetic PTM protein tools are widely used to detect the activity of the related enzymes and identify the interacting proteins in cell lysates. Recently, the study of these enzymes and the interacting proteome has been accomplished in live cells using cell-permeable PTM protein tools. In this concept, we will introduce cell penetrating techniques, the syntheses of cell-permeable PTM protein tools, and offer some future perspective.
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Affiliation(s)
- Jia-Hui Tang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Qing-Yao Shu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Yan Guo
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Huixia Zhu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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10
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Yan B, Guo J, Wang Z, Ning J, Wang H, Shu L, Hu K, Chen L, Shi Y, Zhang L, Liu S, Tao Y, Xiao D. The ubiquitin-specific protease 5 mediated deubiquitination of LSH links metabolic regulation of ferroptosis to hepatocellular carcinoma progression. MedComm (Beijing) 2023; 4:e337. [PMID: 37492786 PMCID: PMC10363799 DOI: 10.1002/mco2.337] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/27/2023] Open
Abstract
Epigenetic regulators and posttranslational modifications of proteins play important roles in various kinds of cancer cell death, including ferroptosis, a non-apoptotic form of cell death. However, the interplay of chromatin modifiers and deubiquitinase (DUB) in ferroptosis remains unclear. Here, we found that ubiquitin-specific protease 5 (USP5) is regarded as a bona fide DUB of lymphoid-specific helicase (LSH), a DNA methylation repressor, in hepatocellular carcinoma (HCC). Functional studies reveal that USP5 interacts with LSH and stabilizes LSH by a deubiquitylation activity-dependent process. Furthermore, the USP5-mediated deubiquitination of LSH facilitates the tumorigenesis of HCC by upregulating solute carrier family 7 member 11 (SLC7A11) to suppress ferroptosis of liver cancer cells. Moreover, the USP5 inhibitor degrasyn inhibits DUB activities of USP5 to LSH to suppress the progression of HCC. Additionally, USP5 and LSH are positively correlated and both are overexpressed and linked to poor prognosis in HCC patients. Together, our findings show that USP5 interacts with LSH directly and enhances LSH protein stability through deubiquitination, which, in turn, promotes the development of HCC by suppressing ferroptosis of liver cancer cells, suggesting that USP5 may be a potential therapeutic target for HCC.
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Affiliation(s)
- Bokang Yan
- Department of PathologyZhuzhou Hospital Affiliated to Xiangya School of MedicineCentral South UniversityZhuzhouHunanChina
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Jiaxing Guo
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Zuli Wang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Jieling Ning
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Haiyan Wang
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Long Shu
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Kuan Hu
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
- Department of Hepatobiliary SurgeryXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Ling Chen
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Ying Shi
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Lingqiang Zhang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of Radiation MedicineCollaborative Innovation Center for Cancer MedicineBeijingChina
| | - Shuang Liu
- Department of OncologyInstitute of Medical SciencesNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education)Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaHunanChina
- Department of Thoracic SurgeryHunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung CancerSecond Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Desheng Xiao
- Department of PathologyXiangya HospitalCentral South UniversityChangshaHunanChina
- Department of PathologySchool of Basic MedicineCentral South UniversityChangshaHunanChina
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11
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Wang S, Fairall L, Pham TK, Ragan TJ, Vashi D, Collins M, Dominguez C, Schwabe JR. A potential histone-chaperone activity for the MIER1 histone deacetylase complex. Nucleic Acids Res 2023; 51:6006-6019. [PMID: 37099381 PMCID: PMC10325919 DOI: 10.1093/nar/gkad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 04/27/2023] Open
Abstract
Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.
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Affiliation(s)
- Siyu Wang
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Trong Khoa Pham
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Timothy J Ragan
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Dipti Vashi
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Cyril Dominguez
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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12
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Yan B, Guo J, Deng S, Chen D, Huang M. A pan-cancer analysis of the role of USP5 in human cancers. Sci Rep 2023; 13:8972. [PMID: 37268697 DOI: 10.1038/s41598-023-35793-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023] Open
Abstract
Posttranslational modifications (PTM) such as acetylation, deubiquitination, and phosphorylation of proteins, play important roles in various kinds of cancer progression. Ubiquitin-specific proteinase 5 (USP5), a unique member of deubiquitinating enzymes (DUBs) which recognizes unanchored polyubiquitin specifically, could regulate the stability of many tumorigenesis-associated proteins to influence cancer initiation and progression. However, the diverse biological significance of USP5 in pan-cancer has not been systematically and comprehensively studied. Here, we explored the role of USP5 in pan-cancer using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database, and we also acquired and analyzed data via various software and web platforms such as R, GEPIA2.0, HPA, TISIDB, cBioPortal, UALCAN, TIMER 2.0, CancerSEA and BioGRID. USP5 expression was high in most cancers and differed significantly in different molecular and immune subtypes of cancers. In addition, USP5 had certain diagnostic value in multiple cancers, and high expression of USP5 generally predicted poor prognosis for cancer patients. We also found that the most frequent genetic alterations type of USP5 was mutation, and the DNA methylation level of USP5 decreased in various cancers. Furthermore, USP5 expression correlated with cancer-associated fibroblasts (CAFs), endothelial cells (EC) and genetic markers of immunodulators in cancers. Moreover, the result from single cell sequencing showed that USP5 could regulate several tumor biological behaviors such as apoptosis, DNA damage and metastasis. Gene enrichment analysis indicated "spliceosome" and "RNA splicing" may be the critical mechanism for USP5 to involve in cancer. Taken together, our study elucidates the biological significance of USP5 in the diagnosis, prognosis and immune in human pan-cancer.
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Affiliation(s)
- Bokang Yan
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Jiaxing Guo
- Department of Hematology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Shuang Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Dongliang Chen
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
| | - Meiyuan Huang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
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13
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Wu Y, Bertran MT, Joshi D, Maslen SL, Hurd C, Walport LJ. Identification of photocrosslinking peptide ligands by mRNA display. Commun Chem 2023; 6:103. [PMID: 37258712 PMCID: PMC10232439 DOI: 10.1038/s42004-023-00898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - M Teresa Bertran
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics, The Francis Crick Institute, London, NW1 1AT, UK
| | - Catherine Hurd
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK.
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14
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Liu Z, Wu Y, Mao X, Kwan KCJ, Cheng X, Li X, Jing Y, Li XD. Development of multifunctional synthetic nucleosomes to interrogate chromatin-mediated protein interactions. SCIENCE ADVANCES 2023; 9:eade5186. [PMID: 37134166 PMCID: PMC10156118 DOI: 10.1126/sciadv.ade5186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Various proteins bind to chromatin to regulate DNA and its associated processes such as replication, transcription, and damage repair. The identification and characterization of these chromatin-associating proteins remain a challenge, as their interactions with chromatin often occur within the context of the local nucleosome or chromatin structure, which makes conventional peptide-based strategies unsuitable. Here, we developed a simple and robust protein labeling chemistry to prepare synthetic multifunctional nucleosomes that carry a photoreactive group, a biorthogonal handle, and a disulfide moiety to examine chromatin-protein interactions in a nucleosomal context. Using the prepared protein- and nucleosome-based photoaffinity probes, we examined a number of protein-protein and protein-nucleosome interactions. In particular, we (i) mapped the binding sites for the HMGN2-nucleosome interaction, (ii) provided the evidence for transition between the active and poised states of DOT1L in recognizing H3K79 within the nucleosome, and (iii) identified OARD1 and LAP2α as nucleosome acidic patch-associating proteins. This study provides powerful and versatile chemical tools for interrogating chromatin-associating proteins.
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Affiliation(s)
- Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yiping Wu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xin Mao
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Xinxin Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen 518055, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
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15
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Liu Z, Chen X, Yang S, Tian R, Wang F. Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization. Curr Opin Chem Biol 2023; 74:102305. [PMID: 37071953 DOI: 10.1016/j.cbpa.2023.102305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023]
Abstract
The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shirui Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Carraro M, Hendriks IA, Hammond CM, Solis-Mezarino V, Völker-Albert M, Elsborg JD, Weisser MB, Spanos C, Montoya G, Rappsilber J, Imhof A, Nielsen ML, Groth A. DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Mol Cell 2023; 83:1075-1092.e9. [PMID: 36868228 PMCID: PMC10114496 DOI: 10.1016/j.molcel.2023.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.
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Affiliation(s)
- Massimo Carraro
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin M Hammond
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | | | | | - Jonas D Elsborg
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Melanie B Weisser
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Axel Imhof
- EpiQMAx GmbH, Planegg, Germany; Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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17
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Fedoryshchak RO, Gorelik A, Shen M, Shchepinova MM, Pérez-Dorado I, Tate EW. Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes. Chem Sci 2023; 14:2419-2430. [PMID: 36873846 PMCID: PMC9977449 DOI: 10.1039/d2sc06116c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in biology. Despite the development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report the design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N-myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions in the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein 1 (FSP1) and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome without the requirement for genetic modification, which may prove broadly applicable to other PTMs.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Andrii Gorelik
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Mengjie Shen
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Maria M Shchepinova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
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18
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Lin J, Wu Y, Tian G, Yu D, Yang E, Lam WH, Liu Z, Jing Y, Dang S, Bao X, Wong JWH, Zhai Y, Li XD. Menin "reads" H3K79me2 mark in a nucleosomal context. Science 2023; 379:717-723. [PMID: 36795828 DOI: 10.1126/science.adc9318] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Methylation of histone H3 lysine-79 (H3K79) is an epigenetic mark for gene regulation in development, cellular differentiation, and disease progression. However, how this histone mark is translated into downstream effects remains poorly understood owing to a lack of knowledge about its readers. We developed a nucleosome-based photoaffinity probe to capture proteins that recognize H3K79 dimethylation (H3K79me2) in a nucleosomal context. In combination with a quantitative proteomics approach, this probe identified menin as a H3K79me2 reader. A cryo-electron microscopy structure of menin bound to an H3K79me2 nucleosome revealed that menin engages with the nucleosome using its fingers and palm domains and recognizes the methylation mark through a π-cation interaction. In cells, menin is selectively associated with H3K79me2 on chromatin, particularly in gene bodies.
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Affiliation(s)
- Jianwei Lin
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Yiping Wu
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Gaofei Tian
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Daqi Yu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Eunjeong Yang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China.,Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Wai Hei Lam
- School of Biological Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Zheng Liu
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, China
| | - Shangyu Dang
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Xiucong Bao
- School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China.,Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Yuanliang Zhai
- School of Biological Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Xiang David Li
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China.,Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, China
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19
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Long MJC, Liu J, Aye Y. Finding a vocation for validation: taking proteomics beyond association and location. RSC Chem Biol 2023; 4:110-120. [PMID: 36794020 PMCID: PMC9906375 DOI: 10.1039/d2cb00214k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022] Open
Abstract
First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision-making processes. With an ever-growing inventory of these advanced proteomics tools, the onus is upon the researchers to understand their individual advantages and limitations, such that we can ensure rigorous implementation and conclusions derived from critical data interpretations backed up by orthogonal series of functional validations. This perspective-based on the authors' experience in applying varied proteomics workflows in complex living models-underlines key book-keeping considerations, comparing and contrasting most-commonly-deployed modern proteomics profiling technologies. We hope this article stimulates thoughts among expert users and equips new-comers with practical knowhow of what has become an indispensable tool in chemical biology, drug discovery, and broader life-science investigations.
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Affiliation(s)
- Marcus J. C. Long
- University of Lausanne (UNIL)Switzerland,NCCR Chemical Biology, University of Geneva (UNIGE)Switzerland
| | - Jinmin Liu
- Swiss Federal Institute of Technology Lausanne (EPFL) Switzerland .,NCCR Chemical Biology, University of Geneva (UNIGE) Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL) Switzerland .,NCCR Chemical Biology, University of Geneva (UNIGE) Switzerland
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20
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Hong X, Li N, Lv J, Zhang Y, Li J, Zhang J, Chen HF. PTMint database of experimentally verified PTM regulation on protein-protein interaction. Bioinformatics 2022; 39:6957085. [PMID: 36548389 PMCID: PMC9848059 DOI: 10.1093/bioinformatics/btac823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Post-translational modification (PTM) is an important biochemical process. which includes six most well-studied types: phosphorylation, acetylation, methylation, sumoylation, ubiquitylation and glycosylation. PTM is involved in various cell signaling pathways and biological processes. Abnormal PTM status is closely associated with severe diseases (such as cancer and neurologic diseases) by regulating protein functions, such as protein-protein interactions (PPIs). A set of databases was constructed separately for PTM sites and PPI; however, the resource of regulation for PTM on PPI is still unsolved. RESULTS Here, we firstly constructed a public accessible database of PTMint (PTMs that are associated with PPIs) (https://ptmint.sjtu.edu.cn/) that contains manually curated complete experimental evidence of the PTM regulation on PPIs in multiple organisms, including Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Currently, the first version of PTMint encompassed 2477 non-redundant PTM sites in 1169 proteins affecting 2371 protein-protein pairs involving 357 diseases. Various annotations were systematically integrated, such as protein sequence, structure properties and protein complex analysis. PTMint database can help to insight into disease mechanism, disease diagnosis and drug discovery associated with PTM and PPI. AVAILABILITY AND IMPLEMENTATION PTMint is freely available at: https://ptmint.sjtu.edu.cn/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ningshan Li
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics and Data Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiyang Lv
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Li
- To whom correspondence should be addressed. or or
| | - Jian Zhang
- To whom correspondence should be addressed. or or
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21
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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22
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Pardal AJ, Bowman AJ. A specific role for importin-5 and NASP in the import and nuclear hand-off of monomeric H3. eLife 2022; 11:e81755. [PMID: 36066346 PMCID: PMC9560165 DOI: 10.7554/elife.81755] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/04/2022] [Indexed: 12/04/2022] Open
Abstract
Core histones package chromosomal DNA and regulate genomic transactions, with their nuclear import and deposition involving importin-β proteins and a dedicated repertoire of histone chaperones. Previously, a histone H3-H4 dimer has been isolated bound to importin-4 (Imp4) and the chaperone ASF1, suggesting that H3 and H4 fold together in the cytoplasm before nuclear import. However, other studies have shown the existence of monomeric H3 in the nucleus, indicating a post-import folding pathway. Here, we report that the predominant importin associated with cytoplasmic H3 is importin-5 (Imp5), which hands off its monomeric cargo to nuclear sNASP. Imp5, in contrast to Imp4, binds to both H3 and H4 containing constitutively monomeric mutations and binds to newly synthesised, monomeric H3 tethered in the cytoplasm. Constitutively monomeric H3 retains its interaction with NASP, whereas monomeric H4 retains interactions specifically with HAT1 and RBBP7. High-resolution separation of NASP interactors shows the 's' isoform but not the 't' isoform associates with monomeric H3, whilst both isoforms associate with H3-H4 dimers in at least three discrete multi-chaperoning complexes. In vitro binding experiments show mutual exclusivity between sNASP and Imp5 in binding H3, suggesting direct competition for interaction sites, with the GTP-bound form of Ran required for histone transfer. Finally, using pulse-chase analysis, we show that cytoplasm-tethered histones do not interact with endogenous NASP until they reach the nucleus, whereupon they bind rapidly. We propose an Imp5-specific import pathway for monomeric H3 that hands off to sNASP in the nucleus, with a parallel H4 pathway involving Imp5 and the HAT1-RBBP7 complex, followed by nuclear folding and hand-off to deposition factors.
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Affiliation(s)
- Alonso Javier Pardal
- Division of Biomedical Sciences, Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of WarwickCoventryUnited Kingdom
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23
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Huang Y, Zhai G, Li Y, Han Y, Chen C, Lu C, Zhang K. Deciphering the Interactome of Histone Marks in Living Cells via Genetic Code Expansion Combined with Proximity Labeling. Anal Chem 2022; 94:10705-10714. [PMID: 35862615 DOI: 10.1021/acs.analchem.2c01042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deciphering the endogenous interactors of histone post-translational modifications (hPTMs, also called histone marks) is essential to understand the mechanisms of epigenetic regulation. However, most of the analytical methods to determine hPTM interactomes are in vitro settings, lacking interrogating native chromatin. Although lysine crotonylation (Kcr) has recently been considered an important hPTM for the regulation of gene transcription, the interactors of Kcr still remain to be explored. Herein, we present a general approach relying upon a genetic code expansion system, APEX2 (engineered peroxidase)-mediated proximity labeling, and quantitative proteomics to profile interactomes of the selected hPTMs in living cells. We genetically fused APEX2 to the recombinant histone H3 with a crotonyl lysine inserted site specifically to generate APEX2-H3K9cr that incorporated into native chromatin. Upon activation, APEX2 triggered in vivo biotin labeling of H3K9cr interactors that can then be enriched with streptavidin beads and identified by mass spectrometry. Proteomic analysis further revealed the endogenous interactomes of H3K9cr and confirmed the reliability of the method. Moreover, DPF2 was identified as a candidate interactor, and the binding interaction of DPF2 to H3K9c was further characterized and verified. This study provides a novel strategy for the identification of hPTM interactomes in living cells, and we envision that this is key to elucidating epigenetic regulatory pathways.
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Affiliation(s)
- Yepei Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Micro-environment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yanan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yue Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chen Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Congcong Lu
- College of Life Sciences, Nankai University, Tianjin 300070, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Micro-environment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
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24
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Wang S, Osgood AO, Chatterjee A. Uncovering post-translational modification-associated protein-protein interactions. Curr Opin Struct Biol 2022; 74:102352. [PMID: 35334254 PMCID: PMC9464464 DOI: 10.1016/j.sbi.2022.102352] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 02/05/2023]
Abstract
In living systems, the chemical space and functional repertoire of proteins are dramatically expanded through the post-translational modification (PTM) of various amino acid residues. These modifications frequently trigger unique protein-protein interactions (PPIs) - for example with reader proteins that directly bind the modified amino acid residue - which leads to downstream functional outcomes. The modification of a protein can also perturb its PPI network indirectly, for example, through altering its conformation or subcellular localization. Uncovering the network of unique PTM-triggered PPIs is essential to fully understand the roles of an ever-expanding list of PTMs in our biology. In this review, we discuss established strategies and current challenges associated with this endeavor.
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Affiliation(s)
- Shu Wang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Arianna O Osgood
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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25
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Xie Y, Du S, Liu Z, Liu M, Xu Z, Wang X, Kee JX, Yi F, Sun H, Yao SQ. Chemical Biology Tools for Protein Lysine Acylation. Angew Chem Int Ed Engl 2022; 61:e202200303. [PMID: 35302274 DOI: 10.1002/anie.202200303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 01/10/2023]
Abstract
Lysine acylation plays pivotal roles in cell physiology, including DNA transcription and repair, signal transduction, immune defense, metabolism, and many other key cellular processes. Molecular mechanisms of dysregulated lysine acylation are closely involved in the pathophysiological progress of many human diseases, most notably cancers. In recent years, chemical biology tools have become instrumental in studying the function of post-translational modifications (PTMs), identifying new "writers", "erasers" and "readers", and in targeted therapies. Here, we describe key developments in chemical biology approaches that have advanced the study of lysine acylation and its regulatory proteins (2016-2021). We further discuss the discovery of ligands (inhibitors and PROTACs) that are capable of targeting regulators of lysine acylation. Next, we discuss some current challenges of these chemical biology probes and suggest how chemists and biologists can utilize chemical probes with more discriminating capacity. Finally, we suggest some critical considerations in future studies of PTMs from our perspective.
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Affiliation(s)
- Yusheng Xie
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Shubo Du
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Zhiyang Liu
- Department of Chemistry, COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Min Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Zhiqiang Xu
- Department of Chemistry, COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Xiaojie Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Jia Xuan Kee
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Fan Yi
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Hongyan Sun
- Department of Chemistry, COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
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26
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Qin Y, Zheng Z, Chu B, Kong Q, Ke M, Voss C, Li SSC, Tian R. Generic Plug-and-Play Strategy for High-Throughput Analysis of PTM-Mediated Protein Complexes. Anal Chem 2022; 94:6799-6808. [PMID: 35471023 DOI: 10.1021/acs.analchem.2c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein complexes mediated by various post-translational modifications (PTMs) play important roles in almost every aspect of biological processes. PTM-mediated protein complexes often have weak and transient binding properties, which limit their unbiased profiling especially in complex biological samples. Here, we developed a plug-and-play chemical proteomic approach for high-throughput analyis of PTM-mediated protein complexes. Taking advantage of the glutathione-S-transferase (GST) tag, which is the gold standard for protein purification and has wide access to a variety of proteins of interest (POIs), a glutathione (GSH) group- and photo-cross-linking group-containing trifunctional chemical probe was developed to tag POIs and assembled onto a streptavidin-coated 96-well plate for affinity purification, photo-cross-linking, and proteomics sample preparation in a fully integrated manner. Compared with the previously developed photo-pTyr-scaffold strategy, by assembling the tyrosine phosphorylation (pTyr) binding domain through covalent NHS chemistry, the new plug-and-play strategy using a noncovalent GST-GSH interaction has comparable enrichment efficiency for EGF stimulation-dependent pTyr protein complexes. To further prove its feasibility, we additionally assembled four pTyr-binding domains in the 96-well plate and selectively identified their pTyr-dependent interacting proteins. Importantly, we systematically optimized and applied the plug-and-play approach for exploring protein methylation-mediated protein complexes, which are difficult to be characterized due to their weak binding affinity and the lack of efficient enrichment strategies. We explored a comprehensive protein methylation-mediated interaction network assembled by five protein methylation binding domains including the chromo domain of MPP8, tandem tudor domain of KDM4A, full-length CBX1, PHD domain of RAG2, and tandem tudor domain of TP53BP1 and validated the chromo domain- and tudor domain-mediated interaction with histone H3. Collectively, this plug-and-play approach provides a convenient and generic strategy for exploring PTM-dependent protein complexes for any POIs with the GST tag.
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Affiliation(s)
- Yunqiu Qin
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China.,Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhendong Zheng
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China.,Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bizhu Chu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Mi Ke
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Courtney Voss
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Shawn S C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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27
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Du J, Babik S, Li Y, Deol KK, Eyles SJ, Fejzo J, Tonelli M, Strieter E. A cryptic K48 ubiquitin chain binding site on UCH37 is required for its role in proteasomal degradation. eLife 2022; 11:e76100. [PMID: 35451368 PMCID: PMC9033301 DOI: 10.7554/elife.76100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Degradation by the 26 S proteasome is an intricately regulated process fine tuned by the precise nature of ubiquitin modifications attached to a protein substrate. By debranching ubiquitin chains composed of K48 linkages, the proteasome-associated ubiquitin C-terminal hydrolase UCHL5/UCH37 serves as a positive regulator of protein degradation. How UCH37 achieves specificity for K48 chains is unclear. Here, we use a combination of hydrogen-deuterium mass spectrometry, chemical crosslinking, small-angle X-ray scattering, nuclear magnetic resonance (NMR), molecular docking, and targeted mutagenesis to uncover a cryptic K48 ubiquitin (Ub) chain-specific binding site on the opposite face of UCH37 relative to the canonical S1 (cS1) ubiquitin-binding site. Biochemical assays demonstrate the K48 chain-specific binding site is required for chain debranching and proteasome-mediated degradation of proteins modified with branched chains. Using quantitative proteomics, translation shutoff experiments, and linkage-specific affinity tools, we then identify specific proteins whose degradation depends on the debranching activity of UCH37. Our findings suggest that UCH37 and potentially other DUBs could use more than one S1 site to perform different biochemical functions.
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Affiliation(s)
- Jiale Du
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Sandor Babik
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Yanfeng Li
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Kirandeep K Deol
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Jasna Fejzo
- Biomolecular NMR Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-MadisonMadisonUnited States
| | - Eric Strieter
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
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28
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Xie Y, Du S, Liu Z, Liu M, Xu Z, Wang X, Kee JX, Yi F, Sun H, Yao SQ. Chemical Biology Tools for Protein Lysine Acylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yusheng Xie
- Shandong University School of Basic Medical Science 250012 Jinan CHINA
| | - Shubo Du
- National University of Singapore Department of Chemistry SINGAPORE
| | - Zhiyang Liu
- City University of Hong Kong chemistry HONG KONG
| | - Min Liu
- Shandong University School of Basic Medical Sciences CHINA
| | - Zhiqiang Xu
- City University of Hong Kong Department of Chemistry HONG KONG
| | - Xiaojie Wang
- Shandong University School of Basic Medical Sciences CHINA
| | - Jia Xuan Kee
- National University of Singapore Chemistry SINGAPORE
| | - Fan Yi
- Shandong University School of basic medical sciences CHINA
| | - Hongyan Sun
- City University of Hong Kong department of chemistry HONG KONG
| | - Shao Q. Yao
- National University of Singapore Department of Chemistry 3 Science Dr. 117543 Singapore SINGAPORE
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29
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Chen Y, Wang Y. Mapping histone modification-dependent protein interactions with chemical proteomics. Trends Biochem Sci 2021; 47:189-193. [PMID: 34872818 DOI: 10.1016/j.tibs.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 11/04/2021] [Indexed: 11/29/2022]
Abstract
Post-translational modifications (PTMs) of histones play essential roles in chromatin function and epigenetic regulation. Determining the interaction partners of these modifications is crucial to understanding transcriptional processes related to diverse developmental and pathological cues. We discuss how chemical proteomics can be applied to the simultaneous and global exploration of these interaction networks.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, 450002, Zhengzhou, Henan, China
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30
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Zhang F, Yang J, Liu H. Solubility of N-(9-fluorenylmethoxycarbonyloxy)-succinimide in several aqueous co-solvent solutions revisited: Solvent effect, preferential solvation and dissolution and transfer properties. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Burton AJ, Hamza GM, Zhang AX, Muir TW. Chemical biology approaches to study histone interactors. Biochem Soc Trans 2021; 49:2431-2441. [PMID: 34709376 PMCID: PMC9785950 DOI: 10.1042/bst20210772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/25/2022]
Abstract
Protein-protein interactions (PPIs) in the nucleus play key roles in transcriptional regulation and ensure genomic stability. Critical to this are histone-mediated PPI networks, which are further fine-tuned through dynamic post-translational modification. Perturbation to these networks leads to genomic instability and disease, presenting epigenetic proteins as key therapeutic targets. This mini-review will describe progress in mapping the combinatorial histone PTM landscape, and recent chemical biology approaches to map histone interactors. Recent advances in mapping direct interactors of histone PTMs as well as local chromatin interactomes will be highlighted, with a focus on mass-spectrometry based workflows that continue to illuminate histone-mediated PPIs in unprecedented detail.
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Affiliation(s)
- Antony J. Burton
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA 02451
| | - Ghaith M. Hamza
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA 02451
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Andrew X. Zhang
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA 02451
| | - Tom W. Muir
- Frick Chemistry Laboratory, Princeton, NJ 08544
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32
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Lin J, Bao X, Li XD. Chemoproteomic approach for mapping binding sites of post-translational-modification-mediated protein-protein interactions. Trends Biochem Sci 2021; 46:1030-1031. [PMID: 34642109 DOI: 10.1016/j.tibs.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xiucong Bao
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China; School of Biomedical Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Xiang D Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China.
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33
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Li X, Li XD. Integrative Chemical Biology Approaches to Deciphering the Histone Code: A Problem-Driven Journey. Acc Chem Res 2021; 54:3734-3747. [PMID: 34553920 DOI: 10.1021/acs.accounts.1c00463] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The hereditary blueprint of a eukaryotic cell is encoded in its genomic DNA that is tightly compacted into chromatin together with histone proteins. The basic repeating units of chromatin fibers are nucleosomes, in which approximately 1.7 turns of DNA wrap around a proteinaceous octamer consisting of two copies of histones H2A, H2B, H3, and H4. Histones are extensively decorated by a variety of posttranslational modifications (PTMs, e.g., methylation, acetylation, ubiquitylation, phosphorylation, etc.), serving as one of the cellular mechanisms that regulates DNA-templated processes, including but not limited to gene transcription, DNA replication, and DNA damage repair. Most of the histone PTMs exist in dynamic fluctuations, and their on and off states are exquisitely regulated by enzymes known as "writers" and "erasers", respectively. When installed at certain sites, histone PTMs can change the local physicochemical environment and thereby directly influence the nucleosome and chromatin structures. Alternatively, histone PTMs can recruit effectors (or "readers") to signal the downstream events. A "histone code" hypothesis has been proposed in which the combinatory actions of different histone PTMs orchestrate the epigenetic landscape of cells, modulating the activity of the underlying DNA and maintaining the genome stability between generations. Accumulating evidence also suggests that malfunctions of histone PTMs are associated with the pathogenesis of human diseases, such as cancer. It is therefore important to fully decipher the histone code, namely, to dissect the regulatory mechanisms and biological functions of histone PTMs.Owing to the advances in state-of-the-art mass spectrometry, dozens of novel histone modifications have been archived during the past decade. However, most of these newly identified histone PTMs remain poorly explored. To unravel the roles played by these PTMs in histone code, key questions that have driven our study are (i) how to detect the novel histone PTMs; (ii) how to identify the enzymes that catalyze the addition (writers) and removal (erasers) of the histone PTMs along with the regulating mechanisms; (iii) what is the biological significance of the histone PTMs and how do they function, by affecting the nucleosome and chromatin dynamics or by recruiting readers; and (iv) how to develop chemical probes to interrogate the histone PTMs or even serve as potential leads for the drug discovery campaigns to treat diseases caused by abnormalities in the regulation of histone PTMs.This Account focuses on our efforts in developing and applying chemical tools and methods to answer the above questions. Specifically, we review the detection of negatively charged histone acylations by developing and applying chemical reporters; preparing homogeneous nucleosomes carrying negatively charged acylations by protein chemistry approaches and the in vitro biophysical analyses of the effects of the acylations on nucleosome structures; investigating the negatively charged acylations' influence on chromatin dynamics in vivo using yeast genetic approaches; identifying and characterizing protein-protein interactions (PPIs) mediated by histone PTMs in different biological contexts (i.e., to identify the readers and erasers) by establishing a chemical proteomics platform that is enabled by photo-cross-linking chemistry and quantitative proteomics strategies; and manipulating PTM-mediated PPIs by the structure-guided design of inhibitors. We also discuss possible future directions in our journey to fully decipher the histone code.
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Affiliation(s)
- Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077 China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077 China
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34
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Burton NR, Kim P, Backus KM. Photoaffinity labelling strategies for mapping the small molecule-protein interactome. Org Biomol Chem 2021; 19:7792-7809. [PMID: 34549230 PMCID: PMC8489259 DOI: 10.1039/d1ob01353j] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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35
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Coan JP, Liu S, Gozani O. Chemical linguistics: Reading the modified proteome. Mol Cell 2021; 81:2501-2503. [PMID: 34143967 DOI: 10.1016/j.molcel.2021.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this issue of Molecular Cell, Lin et al. (2021) develop a tri-functional amino acid probe for the discovery and characterization of protein domains that sense or "read" protein post-translational modifications, a chemical tool that can facilitate our understanding of how signaling networks act at the molecular level.
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Affiliation(s)
- John P Coan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shuo Liu
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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