Chemical Synthesis of Diubiquitin‐Based Photoaffinity Probes for Selectively Profiling Ubiquitin‐Binding Proteins

Liang, Jun; Zhang, Lin; Tan, Xiang-Long; Qi, Yun‐Kun; Feng, Shan; Deng, Haiteng; Yan, YiJing; Zheng, Ji‐Min; Liu, Lei; Tian, Changlin

doi:10.1002/ange.201611659

Cited by 15 publications

(5 citation statements)

References 55 publications

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“…Finally, chemical biology, combined with structural information, has yielded a wealth of activity-based probes that can be used to manipulate and study key enzymes in ubiquitin research (see for an overview for example [39][40][41]). Chemical and semi-chemical probes have been developed that target E1, E2 and E3 enzymes and E3substrate interactions [42][43][44], DUBs [45][46][47][48], UBDs [49] or can be applied for the induction of protein degradation, such as proteolysis-targeting chimeras (PROTACs) [50][51][52][53][54].…”

Section: Biochemical Approaches To Study Ubiquitinationmentioning

confidence: 99%

Visualizing ubiquitination in mammalian cells

et al. 2019

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Covalent modification of proteins with ubiquitin is essential for the majority of biological processes in mammalian cells. Numerous proteins are conjugated with single or multiple ubiquitin molecules or chains in a dynamic fashion, often determining protein half‐lives, localization or function. Experimental approaches to study ubiquitination have been dominated by genetic and biochemical analysis of enzyme structure–function relationships, reaction mechanisms and physiological relevance. Here, we provide an overview of recent developments in microscopy‐based imaging of ubiquitination, available reagents and technologies. We discuss the progress in direct and indirect imaging of differentially linked ubiquitin chains in fixed and living cells using confocal fluorescence microscopy and super‐resolution microscopy, illustrated by the role of ubiquitin in antibacterial autophagy and pro‐inflammatory signalling. Finally, we speculate on future developments and forecast a transition from qualitative to quantitative super‐resolution approaches to understand fundamental aspects of ubiquitination and the formation and distribution of functional E3 ligase protein complexes in their native environment.

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Section: Biochemical Approaches To Study Ubiquitinationmentioning

confidence: 99%

Visualizing ubiquitination in mammalian cells

et al. 2019

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“…Chang-Lin Tian et al [ 104 ] described the chemical synthesis of diubiquitin-based photo-affinity probes for the identification ubiquitin-binding proteins (Fig. 37 ).…”

Section: Comparative Probesmentioning

confidence: 99%

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

et al. 2016

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Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.

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“…Although the incorporation of amino acid analogs with photoreactive functional groups into proteins can be achieved via chemical [23] or genetic [24] methods, they are laborious. When a crosslinker is introduced randomly into a protein, site‐specificity is impaired; therefore, various alternative methods are required.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Selenoprotein F Binding to UDP‐Glucose:Glycoprotein Glucosyltransferase (UGGT) by a Photoreactive Crosslinker

et al. 2022

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In the endoplasmic reticulum glycoprotein quality control system, UDP-glucose : glycoprotein glucosyltransferase (UGGT) functions as a folding sensor. Although it is known to form a heterodimer with selenoprotein F (SelenoF), the details of the complex formation remain obscure. A pulldown assay using cotransfected SelenoF and truncated mutants of human UGGT1 (HUGT1) revealed that SelenoF binds to the TRXL2 domain of HUGT1. Additionally, a newly developed photoaffinity crosslinker was selectively introduced into cysteine residues of recombinant SelenoF to determine the spatial orientation of SelenoF to HUGT1. The crosslinking experiments showed that SelenoF formed a covalent bond with amino acids in the TRXL3 region and the interdomain between βS2 and GT24 of HUGT1 via the synthetic crosslinker. SelenoF might play a role in assessing and refining the disulfide bonds of misfolded glycoproteins in the hydrophobic cavity of HUGT1 as it binds to the highly flexible region of HUGT1 to reach its long hydrophobic cavity. Clarification of the SelenoF-binding domain of UGGT and its relative position will help predict and reveal the function of SelenoF from a structural perspective.

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Chemical Synthesis of Diubiquitin‐Based Photoaffinity Probes for Selectively Profiling Ubiquitin‐Binding Proteins

Cited by 15 publications

References 55 publications

Visualizing ubiquitination in mammalian cells

Visualizing ubiquitination in mammalian cells

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

Analysis of Selenoprotein F Binding to UDP‐Glucose:Glycoprotein Glucosyltransferase (UGGT) by a Photoreactive Crosslinker

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