1
|
Pan CR, Knutson SD, Huth SW, MacMillan DWC. µMap proximity labeling in living cells reveals stress granule disassembly mechanisms. Nat Chem Biol 2024:10.1038/s41589-024-01721-2. [PMID: 39215100 DOI: 10.1038/s41589-024-01721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Phase-separated condensates are membrane-less intracellular structures comprising dynamic protein interactions that organize essential biological processes. Understanding the composition and dynamics of these organelles advances our knowledge of cellular behaviors and disease pathologies related to granule dysregulation. In this study, we apply microenvironment mapping with a HaloTag-based platform (HaloMap) to characterize intracellular stress granule dynamics in living cells. After validating the robustness and sensitivity of this approach, we then profile the stress granule proteome throughout the formation and disassembly and under pharmacological perturbation. These experiments reveal several ubiquitin-related modulators, including the HECT (homologous to E6AP C terminus) E3 ligases ITCH and NEDD4L, as well as the ubiquitin receptor toll-interacting protein TOLLIP, as key mediators of granule disassembly. In addition, we identify an autophagy-related pathway that promotes granule clearance. Collectively, this work establishes a general photoproximity labeling approach for unraveling intracellular protein interactomes and uncovers previously unexplored regulatory mechanisms of stress granule dynamics.
Collapse
Affiliation(s)
- Chenmengxiao Roderick Pan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Sean W Huth
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
2
|
Takato M, Sakamoto S, Nonaka H, Tanimura Valor FY, Tamura T, Hamachi I. Photoproximity labeling of endogenous receptors in the live mouse brain in minutes. Nat Chem Biol 2024:10.1038/s41589-024-01692-4. [PMID: 39090312 DOI: 10.1038/s41589-024-01692-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Understanding how protein-protein interaction networks in the brain give rise to cognitive functions necessitates their characterization in live animals. However, tools available for this purpose require potentially disruptive genetic modifications and lack the temporal resolution necessary to track rapid changes in vivo. Here we leverage affinity-based targeting and photocatalyzed singlet oxygen generation to identify neurotransmitter receptor-proximal proteins in the live mouse brain using only small-molecule reagents and minutes of photoirradiation. Our photooxidation-driven proximity labeling for proteome identification (named PhoxID) method not only recapitulated the known interactomes of three endogenous neurotransmitter receptors (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR), inhibitory γ-aminobutyric acid type A receptor and ionotropic glutamate receptor delta-2) but also uncovered age-dependent shifts, identifying NECTIN3 and IGSF3 as developmentally regulated AMPAR-proximal proteins in the cerebellum. Overall, this work establishes a flexible and generalizable platform to study receptor microenvironments in genetically intact specimens with an unprecedented temporal resolution.
Collapse
Affiliation(s)
- Mikiko Takato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Fátima Yuri Tanimura Valor
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan.
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan.
| |
Collapse
|
3
|
Yao Y, Jia R, Liu C, Wang H, Li T, Zheng X, Zhong T, Feng N, Sun J, Li K, Xie R, Ding L, Yan C, Ding L, Ju H. An In-Situ-Tag-Generation Proximity Labeling Technology for Recording Cellular Interactions. Angew Chem Int Ed Engl 2024; 63:e202407109. [PMID: 38702296 DOI: 10.1002/anie.202407109] [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: 04/15/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
Obtaining information about cellular interactions is fundamental to the elucidation of physiological and pathological processes. Proximity labeling technologies have been widely used to report cellular interactions in situ; however, the reliance on addition of tag molecules typically restricts their application to regions where tags can readily diffuse, while the application in, for example, solid tissues, is susceptible. Here, we propose an "in-situ-tag-generation mechanism" and develop the GalTag technology based on galactose oxidase (GAO) for recording cellular interactions within three-dimensional biological solid regions. GAO mounted on bait cells can in situ generate bio-orthogonal aldehyde tags as interaction reporters on prey cells. Using GalTag, we monitored the dynamics of cellular interactions and assessed the targeting ability of engineered cells. In particular, we recorded, for the first time, the footprints of Bacillus Calmette-Guérin (BCG) invasion into the bladder tissue of living mice, providing a valuable perspective to elucidate the anti-tumor mechanism of BCG.
Collapse
Affiliation(s)
- Yunyan Yao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ru Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, P. R. China
| | - Chuanming Liu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, 210008, Nanjing, P. R. China
- Center for Molecular Reproductive Medicine, Nanjing University, 210008, Nanjing, P. R. China
| | - Haiqi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ting Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Xiaocui Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Tong Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Nan Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Jiahui Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ke Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, P. R. China
| | - Lijun Ding
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, 210008, Nanjing, P. R. China
- Center for Molecular Reproductive Medicine, Nanjing University, 210008, Nanjing, P. R. China
| | - Chao Yan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, P. R. China
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, 210023, Nanjing, P. R. China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| |
Collapse
|
4
|
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science 2024; 385:eadl5763. [PMID: 39024454 DOI: 10.1126/science.adl5763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.
Collapse
Affiliation(s)
- Zhi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zi Yao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrea Fossati
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ajikarunia Palar
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
5
|
Knutson SD, Buksh BF, Huth SW, Morgan DC, MacMillan DWC. Current advances in photocatalytic proximity labeling. Cell Chem Biol 2024; 31:1145-1161. [PMID: 38663396 PMCID: PMC11193652 DOI: 10.1016/j.chembiol.2024.03.012] [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: 12/20/2023] [Revised: 01/31/2024] [Accepted: 03/29/2024] [Indexed: 06/23/2024]
Abstract
Understanding the intricate network of biomolecular interactions that govern cellular processes is a fundamental pursuit in biology. Over the past decade, photocatalytic proximity labeling has emerged as one of the most powerful and versatile techniques for studying these interactions as well as uncovering subcellular trafficking patterns, drug mechanisms of action, and basic cellular physiology. In this article, we review the basic principles, methodologies, and applications of photocatalytic proximity labeling as well as examine its modern development into currently available platforms. We also discuss recent key studies that have successfully leveraged these technologies and importantly highlight current challenges faced by the field. Together, this review seeks to underscore the potential of photocatalysis in proximity labeling for enhancing our understanding of cell biology while also providing perspective on technological advances needed for future discovery.
Collapse
Affiliation(s)
- Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Benito F Buksh
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Sean W Huth
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Danielle C Morgan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
6
|
Pani S, Qiu T, Kentala K, Azizi SA, Dickinson BC. Bioorthogonal masked acylating agents for proximity-dependent RNA labelling. Nat Chem 2024; 16:717-726. [PMID: 38594368 DOI: 10.1038/s41557-024-01493-1] [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: 04/20/2023] [Accepted: 02/28/2024] [Indexed: 04/11/2024]
Abstract
RNA localization is highly regulated, with subcellular organization driving context-dependent cell physiology. Although proximity-based labelling technologies that use highly reactive radicals or carbenes provide a powerful method for unbiased mapping of protein organization within a cell, methods for unbiased RNA mapping are scarce and comparably less robust. Here we develop α-alkoxy thioenol and chloroenol esters that function as potent acylating agents upon controlled ester unmasking. We pair these probes with subcellular-localized expression of a bioorthogonal esterase to establish a platform for spatial analysis of RNA: bioorthogonal acylating agents for proximity labelling and sequencing (BAP-seq). We demonstrate that, by selectively unmasking the enol probe in a locale of interest, we can map RNA distribution in membrane-bound and membrane-less organelles. The controlled-release acylating agent chemistry and corresponding BAP-seq method expand the scope of proximity labelling technologies and provide a powerful approach to interrogate the cellular organization of RNAs.
Collapse
Affiliation(s)
- Shubhashree Pani
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Tian Qiu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Kaitlin Kentala
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
7
|
Long MJC, Aye Y. Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms. Chembiochem 2024; 25:e202400005. [PMID: 38511872 DOI: 10.1002/cbic.202400005] [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: 01/02/2024] [Revised: 02/07/2024] [Indexed: 03/22/2024]
Abstract
Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin species for this purpose. We then consider ways to add new dimensions to these experimental regimens, principally by releasing less reactive (i. e., more selective) (preter)natural electrophiles. Although electrophile release methods may have lower resolution and label fewer proteins than biotinylation methods, their ability to probe simultaneously protein function and locale raises new and interesting possibilities for the field.
Collapse
Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, 1015, Switzerland
| |
Collapse
|
8
|
Xie Z, Cao B, Zhao J, Liu M, Lao Y, Luo H, Zhong Z, Xiong X, Wei W, Zou T. Ion Pairing Enables Targeted Prodrug Activation via Red Light Photocatalysis: A Proof-of-Concept Study with Anticancer Gold Complexes. J Am Chem Soc 2024; 146:8547-8556. [PMID: 38498689 DOI: 10.1021/jacs.4c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Photocatalysis has found increasing applications in biological systems, for example, in localized prodrug activation; however, high-energy light is usually required without giving sufficient efficiency and target selectivity. In this work, we report that ion pairing between photocatalysts and prodrugs can significantly improve the photoactivation efficiency and enable tumor-targeted activation by red light. This is exemplified by a gold-based prodrug (1d) functionalized with a morpholine moiety. Such a modification causes 1d to hydrolyze in aqueous solution, forming a cationic species that tightly interacts with anionic photosensitizers including Eosin Y (EY) and Rose Bengal (RB), along with a significant bathochromic shift of absorption tailing to the far-red region. As a result, a high photoactivation efficiency of 1d by EY or RB under low-energy light was found, leading to an effective release of active gold species in living cells, as monitored by a gold-specific biosensor (GolS-mCherry). Importantly, the morpholine moiety, with pKa ∼6.9, in 1d brings in a highly pH-sensitive and preferential ionic interaction under a slightly acidic condition over the normal physiological pH, enabling tumor-targeted prodrug activation by red light irradiation in vitro and in vivo. Since a similar absorption change was found in other morpholine/amine-containing clinic drugs, photocages, and precursors of reactive labeling intermediates, it is believed that the ion-pairing strategy could be extended for targeted activation of different prodrugs and for mapping of an acidic microenvironment by low-energy light.
Collapse
Affiliation(s)
- Zhiying Xie
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bei Cao
- Warshel Institute for Computational Biology, and General Education Division, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Education Sciences, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511453, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Moyi Liu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuhan Lao
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Hejiang Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhi Zhong
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiaolin Xiong
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Taotao Zou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China
| |
Collapse
|
9
|
Li M, Zhang X, Zhang Y, Xu X, Liu Y, Zhang Y, He Z, Wang J, Liang Y. Effect of interaction between dissolved organic matter and iron/manganese (hydrogen) oxides on the degradation of organic pollutants by in-situ advanced oxidation techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170351. [PMID: 38307288 DOI: 10.1016/j.scitotenv.2024.170351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/26/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024]
Abstract
Iron and manganese (hydrogen) oxides (IMHOs) exhibit excellent redox capabilities for environmental pollutants and are commonly used in situ chemical oxidation (ISCO) technologies for the degradation of organic pollutants. However, the coexisting dissolved organic matter (DOMs) in surface environments would influence the degradation behavior and fate of organic pollutants in IMHOs-based ISCO. This review has summarized the interactions and mechanisms between DOMs and IMHOs, as well as the properties of DOM-IMHOs complexes. Importantly, the promotion or inhibition impact of DOM was discussed from three perspectives. First, the presence of DOMs may hinder the accessibility of active sites on IMHOs, thus reducing their efficiency in degrading organic pollutants. The formation of compounds between DOMs and IMHOs alters their stability and activity in the degradation process. Second, the presence of DOMs may also affect the generation and transport of active species, thereby influencing the oxidative degradation process of organic pollutants. Third, specific components within DOMs also participate and affect the degradation pathways and rates. A comprehensive understanding of the interaction between DOMs and IMHOs helps to better understand and predict the degradation process of organic pollutants mediated by IMHOs in real environmental conditions and contributes to the further development and application of IMHO-mediated ISCO technology.
Collapse
Affiliation(s)
- Mengke Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Xin Zhang
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Yan Zhang
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Xin Xu
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Yun Liu
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China.
| | - Yaoyao Zhang
- Chinese Academy of Geological Sciences, Beijing 100037, China.
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Jieyi Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Yuting Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| |
Collapse
|
10
|
Huang Y, Zhai G, Fu Y, Li Y, Zang Y, Lin Y, Zhang K. A proximity labeling-based orthogonal trap strategy identifies HDAC8 promotes cell motility by modulating cortactin acetylation. Cell Chem Biol 2024; 31:514-522.e4. [PMID: 38460516 DOI: 10.1016/j.chembiol.2024.02.003] [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: 04/19/2023] [Revised: 12/14/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
It is a challenge for the traditional affinity methods to capture transient interactions of enzyme-post-translational modification (PTM) substrates in vivo. Herein we presented a strategy termed proximity labeling-based orthogonal trap approach (ProLORT), relying upon APEX2-catalysed proximity labeling and an orthogonal trap pipeline as well as quantitative proteomics to directly investigate the transient interactome of enzyme-PTM substrates in living cells. As a proof of concept, ProLORT allows for robust evaluation of a known HDAC8 substrate, histone H3K9ac. By leveraging this approach, we identified numerous of putative acetylated proteins targeted by HDAC8, and further confirmed CTTN as a bona fide substrate in vivo. Next, we demonstrated that HDAC8 facilitates cell motility via deacetylation of CTTN at lysine 144 that attenuates its interaction with F-actin, expanding the underlying regulatory mechanisms of HDAC8. We developed a general strategy to profile the transient enzyme-substrate interactions mediated by PTMs, providing a powerful tool for identifying the spatiotemporal PTM-network regulated by enzymes in living cells.
Collapse
Affiliation(s)
- Yepei Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China; Laboratory of Biochemistry and Molecular Biology Research, Department of Clinical Laboratory, Fujian Medical University Cancer Hospital, No. 420 Fuma Road, Jin'an District, Fuzhou 350014, Fujian Province, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.
| | - Yun Fu
- Fujian Provincial Sperm bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Yanan Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yong Zang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, United States.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.
| |
Collapse
|
11
|
Milione RR, Schell BB, Douglas CJ, Seath CP. Creative approaches using proximity labeling to gain new biological insights. Trends Biochem Sci 2024; 49:224-235. [PMID: 38160064 PMCID: PMC10939868 DOI: 10.1016/j.tibs.2023.12.005] [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: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
At its most fundamental level, life is a collection of synchronized cellular processes driven by interactions among biomolecules. Proximity labeling has emerged as a powerful technique to capture these interactions in native settings, revealing previously unexplored elements of biology. This review highlights recent developments in proximity labeling, focusing on methods that push the fundamental technologies beyond the classic bait-prey paradigm, such as RNA-protein interactions, ligand/small-molecule-protein interactions, cell surface protein interactions, and subcellular protein trafficking. The advancement of proximity labeling methods to address different biological problems will accelerate our understanding of the complex biological systems that make up life.
Collapse
Affiliation(s)
- Ryan R Milione
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Bin-Bin Schell
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Cameron J Douglas
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Ciaran P Seath
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
12
|
D’Avino C, Gutiérrez S, Feldhaus MJ, Tomás-Gamasa M, Mascareñas JL. Intracellular Synthesis of Indoles Enabled by Visible-Light Photocatalysis. J Am Chem Soc 2024; 146:2895-2900. [PMID: 38277674 PMCID: PMC10859955 DOI: 10.1021/jacs.3c13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/14/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Performing abiotic synthetic transformations in live cell environments represents a new, promising approach to interrogate and manipulate biology and to uncover new types of biomedical tools. We now found that photocatalytic bond-forming reactions can be added to the toolbox of bioorthogonal synthetic chemistry. Specifically, we demonstrate that exogenous styryl aryl azides can be converted into indoles inside living mammalian cells under photocatalytic conditions.
Collapse
Affiliation(s)
- Cinzia D’Avino
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Sara Gutiérrez
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Max J. Feldhaus
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - María Tomás-Gamasa
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS),
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| |
Collapse
|
13
|
Cabanero DC, Kariofillis SK, Johns AC, Kim J, Ni J, Park S, Parker DL, Ramil CP, Roy X, Shah NH, Rovis T. Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light. J Am Chem Soc 2024; 146:1337-1345. [PMID: 38165744 DOI: 10.1021/jacs.3c09545] [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] [Indexed: 01/04/2024]
Abstract
State-of-the-art methods in photoproximity labeling center on the targeted generation and capture of short-lived reactive intermediates to provide a snapshot of local protein environments. Diazirines are the current gold standard for high-resolution proximity labeling, generating short-lived aryl(trifluoromethyl) carbenes. Here, we present a method to access aryl(trifluoromethyl) carbenes from a stable diazo source via tissue-penetrable, deep red to near-infrared light (600-800 nm). The operative mechanism of this activation involves Dexter energy transfer from photoexcited osmium(II) photocatalysts to the diazo, thus revealing an aryl(trifluoromethyl) carbene. The labeling preferences of the diazo probe with amino acids are studied, showing high reactivity toward heteroatom-H bonds. Upon the synthesis of a biotinylated diazo probe, labeling studies are conducted on native proteins as well as proteins conjugated to the Os photocatalyst. Finally, we demonstrate that the conjugation of a protein inhibitor to the photocatalyst also enables selective protein labeling in the presence of spectator proteins and achieves specific labeling of a membrane protein on the surface of mammalian cells via a two-antibody photocatalytic system.
Collapse
Affiliation(s)
- David C Cabanero
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Stavros K Kariofillis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Andrew C Johns
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jinwoo Kim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jizhi Ni
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sangho Park
- Discovery Biology, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Dann L Parker
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carlo P Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Xavier Roy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| |
Collapse
|
14
|
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564055. [PMID: 37961561 PMCID: PMC10634877 DOI: 10.1101/2023.10.28.564055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The cell membrane proteome is the primary biohub for cell communication, yet we are only beginning to understand the dynamic protein neighborhoods that form on the cell surface and between cells. Proximity labeling proteomics (PLP) strategies using chemically reactive probes are powerful approaches to yield snapshots of protein neighborhoods but are currently limited to one single resolution based on the probe labeling radius. Here, we describe a multi-scale PLP method with tunable resolution using a commercially available histological dye, Eosin Y, which upon visible light illumination, activates three different photo-probes with labeling radii ranging from ∼100 to 3000 Å. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor (EGFR) and orthogonally validated >20 neighbors using immuno-assays and AlphaFold-Multimer prediction that generated plausible binary interaction models. We further profiled the protein neighborhoods of cell-cell synapses induced by bi-specific T-cell engagers (BiTEs) and chimeric antigen receptor (CAR)T cells at longer length scales. This integrated multi-scale PLP platform maps local and distal protein networks on cell surfaces and between cells. We believe this information will aid in the systematic construction of the cell surface interactome and reveal new opportunities for immunotherapeutics.
Collapse
|
15
|
Schneider Y, Jadhav AP, Legault CY. Synthesis of Indoles Using the Electrophilic Potential of Diazirines. J Org Chem 2023; 88:14809-14819. [PMID: 37779242 DOI: 10.1021/acs.joc.3c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The electrophilic potential of diazirines has been utilized to obtain N-substituted diaziridines that are directly hydrolyzed to produce monosubstituted hydrazines. The hydrazines can undergo the Fisher process with enolizable carbonyls to yield multiple indole derivatives in moderate to high yields. The N-metalated diaziridine intermediates can undergo isomerization prior to electrophilic substitution, to form N,N-disubstituted hydrazones. The latter react with enolizable carbonyls to produce N-protected indole derivatives in a single step. This protocol was used to efficiently synthesize indomethacin, an anti-inflammatory drug.
Collapse
Affiliation(s)
- Yoann Schneider
- University of Sherbrooke, Department of Chemistry, 2500 boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Amol P Jadhav
- University of Sherbrooke, Department of Chemistry, 2500 boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Claude Y Legault
- University of Sherbrooke, Department of Chemistry, 2500 boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| |
Collapse
|
16
|
Shafraz O, Davis CMO, Sivasankar S. Light-activated BioID - an optically activated proximity labeling system to study protein-protein interactions. J Cell Sci 2023; 136:jcs261430. [PMID: 37756605 PMCID: PMC10656424 DOI: 10.1242/jcs.261430] [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: 06/21/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Proximity labeling with genetically encoded enzymes is widely used to study protein-protein interactions in cells. However, the accuracy of proximity labeling is limited by a lack of control over the enzymatic labeling process. Here, we present a light-activated proximity labeling technology for mapping protein-protein interactions at the cell membrane with high accuracy and precision. Our technology, called light-activated BioID (LAB), fuses the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1. We demonstrate, in multiple cell lines, that upon illumination with blue light, CRY2 and CIB1 dimerize, reconstitute split-TurboID and initiate biotinylation. Turning off the light leads to the dissociation of CRY2 and CIB1 and halts biotinylation. We benchmark LAB against the widely used TurboID proximity labeling method by measuring the proteome of E-cadherin, an essential cell-cell adhesion protein. We show that LAB can map E-cadherin-binding partners with higher accuracy and significantly fewer false positives than TurboID.
Collapse
Affiliation(s)
- Omer Shafraz
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | | | - Sanjeevi Sivasankar
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| |
Collapse
|
17
|
Li XM, Huang S, Li XD. Photo-ANA enables profiling of host-bacteria protein interactions during infection. Nat Chem Biol 2023; 19:614-623. [PMID: 36702958 DOI: 10.1038/s41589-022-01245-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023]
Abstract
Bacterial pathogens rapidly change and adapt their proteome to cope with the environment in host cells and secrete effector proteins to hijack host targets and ensure their survival and proliferation during infection. Excessive host proteins make it difficult to profile pathogens' proteome dynamics by conventional proteomics. It is even more challenging to map pathogen-host protein-protein interactions in real time, given the low abundance of bacterial effectors and weak and transient interactions in which they may be involved. Here we report a method for selectively labeling bacterial proteomes using a bifunctional amino acid, photo-ANA, equipped with a bio-orthogonal handle and a photoreactive warhead, which enables simultaneous analysis of bacterial proteome reprogramming and pathogen-host protein interactions of Salmonella enterica serovar Typhimurium (S. Typhimurium) during infection. Using photo-ANA, we identified FLOT1/2 as host interactors of S. Typhimurium effector PipB2 in late-stage infection and globally profiled the extensive interactions between host proteins and pathogens during infection.
Collapse
Affiliation(s)
- Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Siyue Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
18
|
Seath CP, Burton AJ, Sun X, Lee G, Kleiner RE, MacMillan DWC, Muir TW. Tracking chromatin state changes using nanoscale photo-proximity labelling. Nature 2023; 616:574-580. [PMID: 37020029 PMCID: PMC10408239 DOI: 10.1038/s41586-023-05914-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/02/2023] [Indexed: 04/07/2023]
Abstract
Interactions between biomolecules underlie all cellular processes and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects1,2. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health1. However, in the complex environment of the nucleus, it is challenging to determine protein-protein interactions owing to low abundance, transient or multivalent binding and a lack of technologies that are able to interrogate these interactions without disrupting the protein-binding surface under study3. Here, we describe a method for the traceless incorporation of iridium-photosensitizers into the nuclear micro-environment using engineered split inteins. These Ir-catalysts can activate diazirine warheads through Dexter energy transfer to form reactive carbenes within an approximately 10 nm radius, cross-linking with proteins in the immediate micro-environment (a process termed µMap) for analysis using quantitative chemoproteomics4. We show that this nanoscale proximity-labelling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. µMap improves our fundamental understanding of nuclear protein-protein interactions and, in doing so, is expected to have a significant effect on the field of epigenetic drug discovery in both academia and industry.
Collapse
Affiliation(s)
- Ciaran P Seath
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Scripps-UF, Jupiter, FL, USA
| | - Antony J Burton
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Discovery Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Xuemeng Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Gihoon Lee
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
19
|
Zhang Z, Ren J, Dai W, Zhang H, Wang X, He B, Zhang Q. Fast and Dynamic Mapping of the Protein Corona on Nanoparticle Surfaces by Photocatalytic Proximity Labeling. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206636. [PMID: 36477943 DOI: 10.1002/adma.202206636] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Protein corona broadly affects the delivery of nanomedicines in vivo. Although it has been widely studied by multiple strategies like centrifugal sedimentation, the rapidly forming mechanism and the dynamic structure of the protein corona at the seconds level remains challenging. Here, a photocatalytic proximity labeling technology in nanoparticles (nano-PPL) is developed. By fabricating a "core-shell" nanoparticle co-loaded with chlorin e6 catalyst and biotin-phenol probe, nano-PPL technology is validated for the rapid and precise labeling of corona proteins in situ. Nano-PPL significantly improves the temporal resolution of nano-protein interactions to 5 s duration compared with the classical centrifugation method (>30 s duration). Furthermore, nano-PPL achieves the fast and dynamic mapping of the protein corona on anionic and cationic nanoparticles, respectively. Finally, nano-PPL is deployed to verify the effect of the rapidly formed protein corona on the initial interaction of nanoparticles with cells. These findings highlight a significant methodological advance toward nano-protein interactions in the delivery of nanomedicines in vivo.
Collapse
Affiliation(s)
- Zibin Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Junji Ren
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Wenbing Dai
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Hua Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Xueqing Wang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Bing He
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Qiang Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Abstract
The emergence of modern photocatalysis, characterized by mildness and selectivity, has significantly spurred innovative late-stage C-H functionalization approaches that make use of low energy photons as a controllable energy source. Compared to traditional late-stage functionalization strategies, photocatalysis paves the way toward complementary and/or previously unattainable regio- and chemoselectivities. Merging the compelling benefits of photocatalysis with the late-stage functionalization workflow offers a potentially unmatched arsenal to tackle drug development campaigns and beyond. This Review highlights the photocatalytic late-stage C-H functionalization strategies of small-molecule drugs, agrochemicals, and natural products, classified according to the targeted C-H bond and the newly formed one. Emphasis is devoted to identifying, describing, and comparing the main mechanistic scenarios. The Review draws a critical comparison between established ionic chemistry and photocatalyzed radical-based manifolds. The Review aims to establish the current state-of-the-art and illustrate the key unsolved challenges to be addressed in the future. The authors aim to introduce the general readership to the main approaches toward photocatalytic late-stage C-H functionalization, and specialist practitioners to the critical evaluation of the current methodologies, potential for improvement, and future uncharted directions.
Collapse
Affiliation(s)
- Peter Bellotti
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149Münster, Germany
| | - Huan-Ming Huang
- School of Physical Science and Technology, ShanghaiTech University, 201210Shanghai, China
| | - Teresa Faber
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149Münster, Germany
| |
Collapse
|
22
|
Meyer CF, Seath CP, Knutson SD, Lu W, Rabinowitz JD, MacMillan DWC. Photoproximity Labeling of Sialylated Glycoproteins (GlycoMap) Reveals Sialylation-Dependent Regulation of Ion Transport. J Am Chem Soc 2022; 144:23633-23641. [PMID: 36525649 PMCID: PMC10782853 DOI: 10.1021/jacs.2c11094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sialylation, the addition of sialic acid to glycans, is a crucial post-translational modification of proteins, contributing to neurodevelopment, oncogenesis, and immune response. In cancer, sialylation is dramatically upregulated. Yet, the functional biochemical consequences of sialylation remain mysterious. Here, we establish a μMap proximity labeling platform that utilizes metabolically inserted azidosialic acid to introduce iridium-based photocatalysts on sialylated cell-surface glycoproteins as a means to profile local microenvironments across the sialylated proteome. In comparative experiments between primary cervical cells and a cancerous cell line (HeLa), we identify key differences in both the global sialome and proximal proteins, including solute carrier proteins that regulate metabolite and ion transport. In particular, we show that cell-surface interactions between receptors trafficking ethanolamine and zinc are sialylation-dependent and impact intracellular metabolite levels. These results establish a μMap method for interrogating proteoglycan function and support a role for sialylated glycoproteins in regulating cell-surface transporters.
Collapse
Affiliation(s)
- Claudio F. Meyer
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Steve D. Knutson
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Ludwig Institute for Cancer Research, Princeton University, Princeton, New Jersey, 08544, United States
| | - David W. C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
23
|
Bechtel TJ, Bertoch JM, Olow AK, Duich M, White CH, Reyes-Robles T, Fadeyi OO, Oslund RC. Proteomic mapping of intercellular synaptic environments via flavin-dependent photoredox catalysis. Org Biomol Chem 2022; 21:98-106. [PMID: 36477737 DOI: 10.1039/d2ob02103j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Receptor-ligand interactions play essential signaling roles within intercellular contact regions. This is particularly important within the context of the immune synapse where protein communication at the surface of physically interacting T cells and antigen-presenting cells regulate downstream immune signaling responses. To identify protein microenvironments within immunological synapses, we combined a flavin-dependent photocatalytic labeling strategy with quantitative mass spectrometry-based proteomics. Using α-PD-L1 or α-PD-1 single-domain antibody (VHH)-based photocatalyst targeting modalities, we profiled protein microenvironments within the intercellular region of an immune synapse-forming co-culture system. In addition to enrichment of both PD-L1 and PD-1 with either targeting modality, we also observed enrichment of both known immune synapse residing receptor-ligand pairs and surface proteins, as well as previously unknown synapse residing proteins.
Collapse
Affiliation(s)
- Tyler J Bechtel
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | - Jayde M Bertoch
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | - Aleksandra K Olow
- Genetics and Pharmacogenomics, Merck & Co., Inc., South San Francisco, CA, 94080, USA
| | - Margaret Duich
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | - Cory H White
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| | | | | | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA.
| |
Collapse
|
24
|
Santorelli L, Caterino M, Costanzo M. Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:633-649. [PMID: 36445175 DOI: 10.1089/omi.2022.0137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The majority of processes that occur in daily cell life are modulated by hundreds to thousands of dynamic protein-protein interactions (PPI). The resulting protein complexes constitute a tangled network that, with its continuous remodeling, builds up highly organized functional units. Thus, defining the dynamic interactome of one or more proteins allows determining the full range of biological activities these proteins are capable of. This conceptual approach is poised to gain further traction and significance in the current postgenomic era wherein the treatment of severe diseases needs to be tackled at both genomic and PPI levels. This also holds true for COVID-19, a multisystemic disease affecting biological networks across the biological hierarchy from genome to proteome to metabolome. In this overarching context and the current historical moment of the COVID-19 pandemic where systems biology increasingly comes to the fore, cross-linking mass spectrometry (XL-MS) has become highly relevant, emerging as a powerful tool for PPI discovery and characterization. This expert review highlights the advanced XL-MS approaches that provide in vivo insights into the three-dimensional protein complexes, overcoming the static nature of common interactomics data and embracing the dynamics of the cell proteome landscape. Many XL-MS applications based on the use of diverse cross-linkers, MS detection methods, and predictive bioinformatic tools for single proteins or proteome-wide interactions were shown. We conclude with a future outlook on XL-MS applications in the field of structural proteomics and ways to sustain the remarkable flexibility of XL-MS for dynamic interactomics and structural studies in systems biology and planetary health.
Collapse
Affiliation(s)
- Lucia Santorelli
- Department of Oncology and Hematology-Oncology, University of Milano, Milan, Italy.,IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| |
Collapse
|
25
|
Yu S, Chang W, Hua R, Jie X, Zhang M, Zhao W, Chen J, Zhang D, Qiu H, Liang Y, Hu W. An enantioselective four-component reaction via assembling two reaction intermediates. Nat Commun 2022; 13:7088. [PMID: 36400780 PMCID: PMC9674633 DOI: 10.1038/s41467-022-34913-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
A reaction intermediate is a key molecular entity that has been used in explaining how starting materials converts into the final products in the reaction, and it is usually unstable, highly reactive, and short-lived. Extensive efforts have been devoted in identifying and characterizing such species via advanced physico-chemical analytical techniques. As an appealing alternative, trapping experiments are powerful tools in this field. This trapping strategy opens an opportunity to discover multicomponent reactions. In this work, we report various highly diastereoselective and enantioselective four-component reactions (containing alcohols, diazoesters, enamines/indoles and aldehydes) which involve the coupling of in situ generated intermediates (iminium and enol). The reaction conditions presented herein to produce over 100 examples of four-component reaction products proceed under mild reaction conditions and show high functional group tolerance to a broad range of substrates. Based on experimental and computational analyses, a plausible mechanism of this multicomponent reaction is proposed.
Collapse
Affiliation(s)
- Sifan Yu
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Wenju Chang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 PR China
| | - Ruyu Hua
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Xiaoting Jie
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Mengchu Zhang
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Wenxuan Zhao
- grid.41156.370000 0001 2314 964XState Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 PR China
| | - Jinzhou Chen
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Dan Zhang
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Huang Qiu
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| | - Yong Liang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 PR China
| | - Wenhao Hu
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 PR China
| |
Collapse
|
26
|
Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. J Biol Chem 2022; 298:102343. [PMID: 35933017 PMCID: PMC9437848 DOI: 10.1016/j.jbc.2022.102343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.
Collapse
Affiliation(s)
- Murat Artan
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter (VBC), Vienna, Austria
| | - Weiqiang Chen
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter (VBC), Vienna, Austria
| | - Mario de Bono
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| |
Collapse
|
27
|
Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Nat Commun 2022; 13:4906. [PMID: 35987950 PMCID: PMC9392063 DOI: 10.1038/s41467-022-32689-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/11/2022] [Indexed: 12/18/2022] Open
Abstract
AbstractEnzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein interactors in living cells. However, activated esters are poorly reactive which leads to a wide labeling radius and phenoxy radicals generated by peroxide treatment may disturb redox-sensitive pathways. Herein, we report a photoactivation-dependent proximity labeling (PDPL) method designed by genetically attaching photosensitizer protein miniSOG to a protein of interest. Triggered by blue light and tunned by irradiation time, singlet oxygen is generated, thereafter enabling spatiotemporally-resolved aniline probe labeling of histidine residues. We demonstrate its high-fidelity through mapping of organelle-specific proteomes. Side-by-side comparison of PDPL with TurboID reveals more specific and deeper proteomic coverage by PDPL. We further apply PDPL to the disease-related transcriptional coactivator BRD4 and E3 ligase Parkin, and discover previously unknown interactors. Through over-expression screening, two unreported substrates Ssu72 and SNW1 are identified for Parkin, whose degradation processes are mediated by the ubiquitination-proteosome pathway.
Collapse
|
28
|
Buksh BF, Knutson SD, Oakley JV, Bissonnette NB, Oblinsky DG, Schwoerer MP, Seath CP, Geri JB, Rodriguez-Rivera FP, Parker DL, Scholes GD, Ploss A, MacMillan DW. μMap-Red: Proximity Labeling by Red Light Photocatalysis. J Am Chem Soc 2022; 144:6154-6162. [PMID: 35363468 PMCID: PMC9843638 DOI: 10.1021/jacs.2c01384] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Modern proximity labeling techniques have enabled significant advances in understanding biomolecular interactions. However, current tools primarily utilize activation modes that are incompatible with complex biological environments, limiting our ability to interrogate cell- and tissue-level microenvironments in animal models. Here, we report μMap-Red, a proximity labeling platform that uses a red-light-excited SnIV chlorin e6 catalyst to activate a phenyl azide biotin probe. We validate μMap-Red by demonstrating photonically controlled protein labeling in vitro through several layers of tissue, and we then apply our platform in cellulo to label EGFR microenvironments and validate performance with STED microscopy and quantitative proteomics. Finally, to demonstrate labeling in a complex biological sample, we deploy μMap-Red in whole mouse blood to profile erythrocyte cell-surface proteins. This work represents a significant methodological advance toward light-based proximity labeling in complex tissue environments and animal models.
Collapse
Affiliation(s)
- Benito F. Buksh
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Steve D. Knutson
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - James V. Oakley
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Noah B. Bissonnette
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Michael P. Schwoerer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Jacob B. Geri
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Dann L. Parker
- Discovery Chemistry, Merck & Co., Kenilworth, NJ, 07033, USA
| | | | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - David W.C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, USA,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA,Corresponding Author: David W. C. MacMillan − Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States;
| |
Collapse
|
29
|
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] [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.
Collapse
|
30
|
Neveselý T, Wienhold M, Molloy JJ, Gilmour R. Advances in the E → Z Isomerization of Alkenes Using Small Molecule Photocatalysts. Chem Rev 2021; 122:2650-2694. [PMID: 34449198 DOI: 10.1021/acs.chemrev.1c00324] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Geometrical E → Z alkene isomerization is intimately entwined in the historical fabric of organic photochemistry and is enjoying a renaissance (Roth et al. Angew. Chem., Int. Ed. Engl. 1989 28, 1193-1207). This is a consequence of the fundamental stereochemical importance of Z-alkenes, juxtaposed with frustrations in thermal reactivity that are rooted in microscopic reversibility. Accessing excited state reactivity paradigms allow this latter obstacle to be circumnavigated by exploiting subtle differences in the photophysical behavior of the substrate and product chromophores: this provides a molecular basis for directionality. While direct irradiation is operationally simple, photosensitization via selective energy transfer enables augmentation of the alkene repertoire to include substrates that are not directly excited by photons. Through sustained innovation, an impressive portfolio of tailored small molecule catalysts with a range of triplet energies are now widely available to facilitate contra-thermodynamic and thermo-neutral isomerization reactions to generate Z-alkene fragments. This review is intended to serve as a practical guide covering the geometric isomerization of alkenes enabled by energy transfer catalysis from 2000 to 2020, and as a logical sequel to the excellent treatment by Dugave and Demange (Chem. Rev. 2003 103, 2475-2532). The mechanistic foundations underpinning isomerization selectivity are discussed together with induction models and rationales to explain the counterintuitive directionality of these processes in which very small energy differences distinguish substrate from product. Implications for subsequent stereospecific transformations, application in total synthesis, regioselective polyene isomerization, and spatiotemporal control of pre-existing alkene configuration in a broader sense are discussed.
Collapse
Affiliation(s)
- Tomáš Neveselý
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Max Wienhold
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - John J Molloy
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Ryan Gilmour
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Münster, Germany
| |
Collapse
|