Advances in chemical probing of protein <i>O</i>-GlcNAc glycosylation: structural role and molecular mechanisms

Saha, Abhijit; Bello, Davide; Fernández‐Tejada, Alberto

doi:10.1039/d0cs01275k

Cited by 73 publications

(51 citation statements)

References 266 publications

(438 reference statements)

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“…Therefore, the characteristics of PTMs provide invaluable insights into the cellular functions under the etiological process. The study of PTMs may help clarify and understand the structure and function of proteins, which is also an important research content in proteomics and bioinformatics ( 16–19 ).…”

Section: Introductionmentioning

confidence: 99%

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications

Luo

et al. 2021

Nucleic Acids Research

103

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Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

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Section: Introductionmentioning

confidence: 99%

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications

Luo

et al. 2021

Nucleic Acids Research

103

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“…Some examples of the manifold approaches for the incorporation of S-GlcNAc and O-GlcNAc derivatives are given. An extensive review of O-GlcNAc installation and detection can be found in ( Saha et al, 2021 ). Site-specific O-GlcNAc mimics can be incorporated directly on the cysteine thiol function after Ser/Thr into Cys site-directed mutagenesis or using the gene-editing tool CRISPR-Cas9.…”

Section: Deciphering the Posttranslational Modification Codes Of Amyl...mentioning

confidence: 99%

“…The investigations of the functional impact of amyloid PTMs and PTM dysregulation in cell and in vivo systems require the isolation, detection and analytical characterization of posttranslationally modified proteins which proved to be particularly difficult in the general case of O-GlcNAcylated proteins. Indeed, both detection and/or enrichment of O-GlcNAc proteins usually apply succinylated wheat germ agglutinin (sWGA) lectin or pan-O-GlcNAc monoclonal antibodies, RL2 and CTD110.6, that detect O-GlcNAc proteins in cytosolic and nuclear extracts ( Saha et al, 2021 ). However, sWGA although relatively selective has a low affinity for the single O-GlcNAc sugar while pan-O-GlcNAc antibodies have a low affinity and a limited specificity, sometimes exhibiting cross-reactivity with terminal GlcNAc of branched N-glycans ( Isono, 2011 ; Tashima and Stanley, 2014 ).…”

Section: Deciphering the Posttranslational Modification Codes Of Amyl...mentioning

confidence: 99%

“…However, sWGA although relatively selective has a low affinity for the single O-GlcNAc sugar while pan-O-GlcNAc antibodies have a low affinity and a limited specificity, sometimes exhibiting cross-reactivity with terminal GlcNAc of branched N-glycans ( Isono, 2011 ; Tashima and Stanley, 2014 ). Significant advances using chemical biology tools during the last decade has strongly expanded the detection of O-GlcNAcylated proteins as a long-standing demand, and helped deciphering the functional role of O-GlcNAcylation as extensively reviewed in ( Saha et al, 2021 ). Bioorthogonal chemical reactions have been implemented to afford a wide range of tools and probes for the detection or enrichment of O-GlcNAcylated proteins from in vivo systems ( Figure 7 ).…”

Section: Deciphering the Posttranslational Modification Codes Of Amyl...mentioning

confidence: 99%

“…The former approach uses the manipulation of the UDP-GlcNAc metabolic pathway and the OGT plasticity to a variety of UDP-GlcNAc derivatives (e.g. peracetylated N-azidoacetylglucosamine) to directly incorporate chemical reactive group in the GlcNAc moiety of glycosylated proteins ( Moon et al, 2022 ; Saha et al, 2021 ). The latter approach achieved better efficiency by using a mutant of GalT (GalT-Y289L) tolerant to UDP-GalNAc derivatives, such UDP-GalNAz containing an azide group, as a substrate donor for glycosidic linkage to GlcNAc ( Figure 7 ) ( Khidekel et al, 2003 ).…”

Section: Deciphering the Posttranslational Modification Codes Of Amyl...mentioning

confidence: 99%

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Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools

et al. 2022

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Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer’s and Parkinson’s diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.

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The Essential Role of Water Molecules in the Reaction Mechanism of Protein O‐Fucosyltransferase 2

et al. 2022

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Protein O‐fucosyltransferase 2 (PoFUT2) is an inverting glycosyltransferase (GT) that fucosylates thrombospondin repeats (TSRs) from group 1 and 2. PoFUT2 recognizes a large and diverse number of TSRs through a dynamic network of water‐mediated interactions. By X‐ray structural studies of C. elegans PoFUT2 complexed to a TSR of group 2, we demonstrate that this GT recognizes similarly the 3D structure of TSRs from both groups 1 and 2. Its active site is highly exposed to the solvent, suggesting that water molecules might also play an essential role in the fucosylation mechanism. We applied QM/MM methods using human PoFUT2 as a model, and found that HsPoFUT2 follows a classical SN2 reaction mechanism in which water molecules contribute to a great extent in facilitating the release of the leaving pyrophosphate unit, causing the H transfer from the acceptor nucleophile (Thr/Ser) to the catalytic base, which is the last event in the reaction. This demonstrates the importance of water molecules not only in recognition of the ligands but also in catalysis.

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Advances in chemical probing of protein O-GlcNAc glycosylation: structural role and molecular mechanisms

Abstract: This review describes the recent developments in chemical probing of O-GlcNAcylation with a special focus on its molecular, structural and mechanistic implications.

Cited by 73 publications

References 266 publications

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications

Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools

The Essential Role of Water Molecules in the Reaction Mechanism of Protein O‐Fucosyltransferase 2

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