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Bulangalire N, Claeyssen C, Douffi S, Agbulut O, Cieniewski-Bernard C. A novel 2D-electrophoresis method for the simultaneous visualization of phosphorylated and O-GlcNAcylated proteoforms of a protein. Electrophoresis 2024; 45:1618-1629. [PMID: 38700120 DOI: 10.1002/elps.202400043] [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: 08/08/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Post-translational modifications (PTMs), such as phosphorylation and O-N-acetyl-β-d-glucosaminylation (O-GlcNAcylation), are involved in the fine spatiotemporal regulation of protein functions, and their dynamic interplay is at the heart of protein language. The coexistence of phosphorylation and O-GlcNAcylation on a protein leads to the diversification of proteoforms. It is therefore essential to decipher the phosphorylation/O-GlcNAcylation interplay on protein species that orchestrates cellular processes in a specific physiological or pathophysiological context. However, simultaneous visualization of phosphorylation and O-GlcNAcylation patterns on a protein of interest remains a challenge. To map the proteoforms of a protein, we have developed an easy-to-use two-dimensional electrophoresis method with a single sample processing permitting simultaneous visualization of the phosphorylated and the O-GlcNAcylated forms of the protein of interest. This method, we termed 2D-WGA-Phos-tag-PAGE relies on proteoforms retardation by affinity gel electrophoresis. With this novel approach, we established the cartography of phospho- and glycoforms of αB-crystallin and desmin in the whole extract and the cytoskeleton protein subfraction in skeletal muscle cells. Interestingly, we have shown that the pattern of phosphorylation and O-GlcNAcylation depends of the subcellular subfraction. Moreover, we have also shown that proteotoxic stress condition increased the complexity of the pattern of PTMs on αB-crystallin.
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Affiliation(s)
- Nathan Bulangalire
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
- CHU Lille, Université de Lille, F-59000, Lille, France
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Charlotte Claeyssen
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Sana Douffi
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Caroline Cieniewski-Bernard
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
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2
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Nalawansha DA, Mangano K, den Besten W, Potts PR. TAC-tics for Leveraging Proximity Biology in Drug Discovery. Chembiochem 2024; 25:e202300712. [PMID: 38015747 DOI: 10.1002/cbic.202300712] [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: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.
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Affiliation(s)
| | - Kyle Mangano
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Willem den Besten
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
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3
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Zakopcanik M, Kavan D, Novak P, Loginov DS. Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis. J Proteome Res 2024; 23:609-617. [PMID: 38158558 PMCID: PMC10845142 DOI: 10.1021/acs.jproteome.3c00390] [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: 06/30/2023] [Revised: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging.
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Affiliation(s)
- Marek Zakopcanik
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12820 Prague, Czech Republic
| | - Daniel Kavan
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
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4
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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5
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Schwein PA, Ge Y, Yang B, D’Souza A, Mody A, Shen D, Woo CM. Writing and Erasing O-GlcNAc on Casein Kinase 2 Alpha Alters the Phosphoproteome. ACS Chem Biol 2022; 17:1111-1121. [PMID: 35467332 DOI: 10.1021/acschembio.1c00987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
O-GlcNAc is an essential carbohydrate modification that intersects with phosphorylation signaling pathways via crosstalk on protein substrates or by direct modification of the kinases that write the phosphate modification. Casein kinase 2 alpha (CK2α), the catalytic subunit of the ubiquitously expressed and constitutively active kinase CK2, is modified by O-GlcNAc, but the effect of this modification on the phosphoproteome in cells is unknown. Here, we apply complementary targeted O-GlcNAc editors, nanobody-OGT and -splitOGA, to selectively write and erase O-GlcNAc from a tagged CK2α to measure the effects on the phosphoproteome in cells. These tools effectively and selectively edit the Ser347 glycosite on CK2α. Using quantitative phosphoproteomics, we report 51 phosphoproteins whose enrichment changes as a function of editing O-GlcNAc on CK2α, including HDAC1, HDAC2, ENSA, SMARCAD1, and PABPN1. Specific phosphosites on HDAC1 Ser393 and HDAC2 Ser394, both reported CK2 substrates, are significantly enhanced by O-GlcNAcylation of CK2α. These data will propel future studies on the crosstalk between O-GlcNAc and phosphorylation.
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Affiliation(s)
- Paul A. Schwein
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Yun Ge
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Alexandria D’Souza
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Alison Mody
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
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6
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Abstract
Post-translational modification with O-linked β-N-acetylglucosamine (O-GlcNAc), a process referred to as O-GlcNAcylation, occurs on a vast variety of proteins. Mounting evidence in the past several decades has clearly demonstrated that O-GlcNAcylation is a unique and ubiquitous modification. Reminiscent of a code, protein O-GlcNAcylation functions as a crucial regulator of nearly all cellular processes studied. The primary aim of this review is to summarize the developments in our understanding of myriad protein substrates modified by O-GlcNAcylation from a systems perspective. Specifically, we provide a comprehensive survey of O-GlcNAcylation in multiple species studied, including eukaryotes (e.g., protists, fungi, plants, Caenorhabditis elegans, Drosophila melanogaster, murine, and human), prokaryotes, and some viruses. We evaluate features (e.g., structural properties and sequence motifs) of O-GlcNAc modification on proteins across species. Given that O-GlcNAcylation functions in a species-, tissue-/cell-, protein-, and site-specific manner, we discuss the functional roles of O-GlcNAcylation on human proteins. We focus particularly on several classes of relatively well-characterized human proteins (including transcription factors, protein kinases, protein phosphatases, and E3 ubiquitin-ligases), with representative O-GlcNAc site-specific functions presented. We hope the systems view of the great endeavor in the past 35 years will help demystify the O-GlcNAc code and lead to more fascinating studies in the years to come.
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Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
| | - Chunyan Hou
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, United States
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7
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Xu Y, Zhang H. Putting the pieces together: mapping the O-glycoproteome. Curr Opin Biotechnol 2021; 71:130-136. [PMID: 34358979 PMCID: PMC8629430 DOI: 10.1016/j.copbio.2021.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/26/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Protein glycosylation is the most diverse and omnipresent protein modification. Glycosylation provides glycoproteins with important structural and functional properties to facilitate critical biological processes. Despite the significance of protein glycosylation, the investigation of glycoproteome, especially O-linked glycoproteome, remains elusive due to the lack of a comprehensive methodology to conform with the diversity of O-linked glycoforms of O-linked glycoproteins. In recent years, mass spectrometry has become an indispensable tool for the characterization of O-linked glycosylated proteins across biological systems. We herein highlight the recent developments in MS-based O-linked glycoproteomic technologies, quantitative data acquisition strategy and bioinformatic tools, with a special focus on mucin-type O-linked glycosylation.
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Affiliation(s)
- Yuanwei Xu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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8
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Roberts DS, Mann M, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Top-Down Mass Spectrometry. J Am Chem Soc 2021; 143:12014-12024. [PMID: 34328324 PMCID: PMC8353889 DOI: 10.1021/jacs.1c02713] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry, and the S protein glycosylation plays key roles in altering the viral binding/function and infectivity. However, the molecular structures and glycan heterogeneity of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis by conventional bottom-up glycoproteomic approaches. Here, we report the complete structural elucidation of intact O-glycan proteoforms through a hybrid native and denaturing top-down mass spectrometry (MS) approach employing both trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight and ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR)-MS. Native top-down TIMS-MS/MS separates the protein conformers of the S-RBD to reveal their gas-phase structural heterogeneity, and top-down FTICR-MS/MS provides in-depth glycoform analysis for unambiguous identification of the glycan structures and their glycosites. A total of eight O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that this hybrid top-down MS approach can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants as well as other O-glycoproteins in general.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Morgan Mann
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Allan R Brasier
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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9
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Chen S, Wu D, Robinson CV, Struwe WB. Native Mass Spectrometry Meets Glycomics: Resolving Structural Detail and Occupancy of Glycans on Intact Glycoproteins. Anal Chem 2021; 93:10435-10443. [PMID: 34279906 DOI: 10.1021/acs.analchem.1c01460] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycoproteins are inherently heterogeneous and therefore resolving structures in their entirety remains a major challenge in structural biology. Native mass spectrometry has transformed our ability to study glycoproteins, and despite advances in high-resolution instrumentation, there are comparatively a few studies demonstrating its potential with data largely limited to an overall measure of monosaccharide composition for all glycans across glycosylation sites for a given protein. Clearly, these readouts lack glycan topology information, namely, monosaccharide linkage and glycan branching. To address this deficiency, we developed a new approach that joins native mass spectrometry with glycan exoglycosidase sequencing, the combination of which provides remarkable glycoprotein structural details. We show how N-glycan branching, terminal fucosylation, LacNAc extensions, and N- and O-glycan occupancy (i.e., total number of glycans) can be directly characterized on intact glycoproteins with minimal sample preparation. Taken together, native exoglycosidase sequencing mass spectrometry (NES-MS) notably improves our ability to characterize protein glycosylation, addressing a significant need in structural biology that will enable new routes to understand glycoprotein function.
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Affiliation(s)
- Siyun Chen
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Di Wu
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
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10
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Mueller T, Ouyang X, Johnson MS, Qian WJ, Chatham JC, Darley-Usmar V, Zhang J. New Insights Into the Biology of Protein O-GlcNAcylation: Approaches and Observations. FRONTIERS IN AGING 2021; 1:620382. [PMID: 35822169 PMCID: PMC9261361 DOI: 10.3389/fragi.2020.620382] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
O-GlcNAcylation is a protein posttranslational modification that results in the addition of O-GlcNAc to Ser/Thr residues. Since its discovery in the 1980s, it has been shown to play an important role in a broad range of cellular functions by modifying nuclear, cytosolic, and mitochondrial proteins. The addition of O-GlcNAc is catalyzed by O-GlcNAc transferase (OGT), and its removal is catalyzed by O-GlcNAcase (OGA). Levels of protein O-GlcNAcylation change in response to nutrient availability and metabolic, oxidative, and proteotoxic stress. OGT and OGA levels, activity, and target engagement are also regulated. Together, this results in adaptive and, on occasions, detrimental responses that affect cellular function and survival, which impact a broad range of pathologies and aging. Over the past several decades, approaches and tools to aid the investigation of the regulation and consequences of protein O-GlcNAcylation have been developed and enhanced. This review is divided into two sections: 1) We will first focus on current standard and advanced technical approaches for assessing enzymatic activities of OGT and OGT, assessing the global and specific protein O-GlcNAcylation and 2) we will summarize in vivo findings of functional consequences of changing protein O-GlcNAcylation, using genetic and pharmacological approaches.
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Affiliation(s)
- Toni Mueller
- Department of Pathology and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Xiaosen Ouyang
- Department of Pathology and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michelle S. Johnson
- Department of Pathology and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - John C. Chatham
- Department of Pathology and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Victor Darley-Usmar
- Department of Pathology and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jianhua Zhang
- Department of Pathology and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Jianhua Zhang,
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11
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Roberts DS, Mann MW, Melby JA, Larson EJ, Zhu Y, Brasier AR, Jin S, Ge Y. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33688648 DOI: 10.1101/2021.02.28.433291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation is strongly implicated in altering viral binding/function and infectivity. However, the structures and relative abundance of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis. Here, we report the complete structural characterization of intact O-glycan proteoforms using native top-down mass spectrometry (MS). By combining trapped ion mobility spectrometry (TIMS), which can separate the protein conformers of S-RBD and analyze their gas phase structural variants, with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analysis, the O-glycoforms of the S-RBD are comprehensively characterized, so that seven O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that native top-down MS can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.
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12
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Ma J, Wu C, Hart GW. Analytical and Biochemical Perspectives of Protein O-GlcNAcylation. Chem Rev 2021; 121:1513-1581. [DOI: 10.1021/acs.chemrev.0c00884] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Ci Wu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington D.C. 20057, United States
| | - Gerald W. Hart
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
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13
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Ning J, Yang H. O-GlcNAcylation in Hyperglycemic Pregnancies: Impact on Placental Function. Front Endocrinol (Lausanne) 2021; 12:659733. [PMID: 34140929 PMCID: PMC8204080 DOI: 10.3389/fendo.2021.659733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/17/2021] [Indexed: 01/16/2023] Open
Abstract
The dynamic cycling of N-acetylglucosamine, termed as O-GlcNAcylation, is a post-translational modification of proteins and is involved in the regulation of fundamental cellular processes. It is controlled by two essential enzymes, O-GlcNAc transferase and O-GlcNAcase. O-GlcNAcylation serves as a modulator in placental tissue; furthermore, increased levels of protein O-GlcNAcylation have been observed in women with hyperglycemia during pregnancy, which may affect the short-and long-term development of offspring. In this review, we focus on the impact of O-GlcNAcylation on placental functions in hyperglycemia-associated pregnancies. We discuss the following topics: effect of O-GlcNAcylation on placental development and its association with hyperglycemia; maternal-fetal nutrition transport, particularly glucose transport, via the mammalian target of rapamycin and AMP-activated protein kinase pathways; and the two-sided regulatory effect of O-GlcNAcylation on inflammation. As O-GlcNAcylation in the placental tissues of pregnant women with hyperglycemia influences near- and long-term development of offspring, research in this field has significant therapeutic relevance.
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Affiliation(s)
- Jie Ning
- Department of Obstetrics and Gynaecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Foetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
| | - Huixia Yang
- Department of Obstetrics and Gynaecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Foetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
- *Correspondence: Huixia Yang,
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14
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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15
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Abstract
O-GlcNAcylation is an abundant and dynamic protein posttranslational modification (PTM), with crucial roles in metazoans. Studies of this modification are hampered by the lack of convenient methods for detecting native O-GlcNAcylation. Here, we describe a novel gel-based approach, Separation of O-GlcNAcylated Proteins by Polyacrylamide Gel Electrophoresis (SOPAGE), which enables detection of O-GlcNAc levels and dynamics.
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Affiliation(s)
- Chuan Fu
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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16
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Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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17
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Araman C, 't Hart BA. Neurodegeneration meets immunology - A chemical biology perspective. Bioorg Med Chem 2019; 27:1911-1924. [PMID: 30910473 DOI: 10.1016/j.bmc.2019.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/16/2022]
Affiliation(s)
- C Araman
- Leiden Institute of Chemistry and the Institute for Chemical Immunology, Leiden University, Leiden, The Netherlands.
| | - B A 't Hart
- University of Groningen, Department of Biomedical Sciences of Cells and Systems, University Medical Centre, Groningen, The Netherlands; Department Anatomy and Neuroscience, Free University Medical Center (VUmc), Amsterdam, The Netherlands.
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18
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Too sweet to resist: Control of immune cell function by O-GlcNAcylation. Cell Immunol 2018; 333:85-92. [PMID: 29887419 DOI: 10.1016/j.cellimm.2018.05.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 12/31/2022]
Abstract
O-linked β-N-acetyl glucosamine modification (O-GlcNAcylation) is a dynamic, reversible posttranslational modification of cytoplasmic and nuclear proteins. O-GlcNAcylation depends on nutrient availability and the hexosamine biosynthetic pathway (HBP), which produces the donor substrate UDP-GlcNAc. O-GlcNAcylation is mediated by a single enzyme, O-GlcNAc transferase (OGT), which adds GlcNAc and another enzyme, O-GlcNAcase (OGA), which removes O-GlcNAc from proteins. O-GlcNAcylation controls vital cellular processes including transcription, translation, the cell cycle, metabolism, and cellular stress. Aberrant O-GlcNAcylation has been implicated in various pathologies including Alzheimer's disease, diabetes, obesity, and cancer. Growing evidences indicate that O-GlcNAcylation plays crucial roles in regulating immunity and inflammatory responses, especially under hyperglycemic conditions. This review will highlight the emerging functions of O-GlcNAcylation in mammalian immunity under physiological and various pathological conditions.
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19
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The Role of Stress-Induced O-GlcNAc Protein Modification in the Regulation of Membrane Transport. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1308692. [PMID: 29456783 PMCID: PMC5804373 DOI: 10.1155/2017/1308692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/03/2017] [Indexed: 02/06/2023]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a posttranslational modification that is increasingly recognized as a signal transduction mechanism. Unlike other glycans, O-GlcNAc is a highly dynamic and reversible process that involves the addition and removal of a single N-acetylglucosamine molecule to Ser/Thr residues of proteins. UDP-GlcNAc—the direct substrate for O-GlcNAc modification—is controlled by the rate of cellular metabolism, and thus O-GlcNAc is dependent on substrate availability. Serving as a feedback mechanism, O-GlcNAc influences the regulation of insulin signaling and glucose transport. Besides nutrient sensing, O-GlcNAc was also implicated in the regulation of various physiological and pathophysiological processes. Due to improvements of mass spectrometry techniques, more than one thousand proteins were detected to carry the O-GlcNAc moiety; many of them are known to participate in the regulation of metabolites, ions, or protein transport across biological membranes. Recent studies also indicated that O-GlcNAc is involved in stress adaptation; overwhelming evidences suggest that O-GlcNAc levels increase upon stress. O-GlcNAc elevation is generally considered to be beneficial during stress, although the exact nature of its protective effect is not understood. In this review, we summarize the current data regarding the oxidative stress-related changes of O-GlcNAc levels and discuss the implications related to membrane trafficking.
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Leney AC, Tschanz A, Heck AJR. Connecting color with assembly in the fluorescent B‐phycoerythrin protein complex. FEBS J 2017; 285:178-187. [DOI: 10.1111/febs.14331] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre Utrecht University Utrecht The Netherlands
| | - Aline Tschanz
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre Utrecht University Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre Utrecht University Utrecht The Netherlands
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21
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Behrens AJ, Struwe WB, Crispin M. Glycosylation profiling to evaluate glycoprotein immunogens against HIV-1. Expert Rev Proteomics 2017; 14:881-890. [PMID: 28870097 DOI: 10.1080/14789450.2017.1376658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Much of the efforts to develop a vaccine against the human immunodeficiency virus (HIV) have focused on the design of recombinant mimics of the viral attachment glycoprotein (Env). The leading immunogens exhibit native-like antigenic properties and are being investigated for their ability to induce broadly neutralizing antibodies (bNAbs). Understanding the relative abundance of glycans at particular glycosylation sites on these immunogens is important as most bNAbs have evolved to recognize or evade the dense coat of glycans that masks much of the protein surface. Understanding the glycan structures on candidate immunogens enables triaging between native-like conformations and immunogens lacking key structural features as steric constraints limit glycan processing. The sensitivity of the processing state of a particular glycan to its structural environment has led to the need for quantitative glycan profiling and site-specific analysis to probe the structural integrity of immunogens. Areas covered: We review analytical methodologies for HIV immunogen evaluation and discuss how these studies have led to a greater understanding of the structural constraints that control the glycosylation state of the HIV attachment and fusion spike. Expert commentary: Total composition and site-specific glycosylation profiling are emerging as standard methods in the evaluation of Env-based immunogen candidates.
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Affiliation(s)
- Anna-Janina Behrens
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Weston B Struwe
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK
| | - Max Crispin
- a Oxford Glycobiology Institute, Department of Biochemistry , University of Oxford , Oxford , UK.,b Department of Immunology and Microbial Science , The Scripps Research Institute , La Jolla , CA , USA.,c Centre for Biological Sciences and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK
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22
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Leney AC, El Atmioui D, Wu W, Ovaa H, Heck AJR. Elucidating crosstalk mechanisms between phosphorylation and O-GlcNAcylation. Proc Natl Acad Sci U S A 2017. [PMID: 28808029 DOI: 10.1073/pnas.1620529114/suppl_file/pnas.1620529114.sapp.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Proteins can be modified by multiple posttranslational modifications (PTMs), creating a PTM code that controls the function of proteins in space and time. Unraveling this complex PTM code is one of the great challenges in molecular biology. Here, using mass spectrometry-based assays, we focus on the most common PTMs-phosphorylation and O-GlcNAcylation-and investigate how they affect each other. We demonstrate two generic crosstalk mechanisms. First, we define a frequently occurring, very specific and stringent phosphorylation/O-GlcNAcylation interplay motif, (pSp/T)P(V/A/T)(gS/gT), whereby phosphorylation strongly inhibits O-GlcNAcylation. Strikingly, this stringent motif is substantially enriched in the human (phospho)proteome, allowing us to predict hundreds of putative O-GlcNAc transferase (OGT) substrates. A set of these we investigate further and show them to be decent substrates of OGT, exhibiting a negative feedback loop when phosphorylated at the P-3 site. Second, we demonstrate that reciprocal crosstalk does not occur at PX(S/T)P sites, i.e., at sites phosphorylated by proline-directed kinases, which represent 40% of all sites in the vertebrate phosphoproteomes.
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Affiliation(s)
- Aneika C Leney
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, 3584 CH Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Dris El Atmioui
- Chemical Immunology, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, 3584 CH Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Huib Ovaa
- Chemical Immunology, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, 3584 CH Utrecht, The Netherlands;
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht University, 3584 CH Utrecht, The Netherlands
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23
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Elucidating crosstalk mechanisms between phosphorylation and O-GlcNAcylation. Proc Natl Acad Sci U S A 2017; 114:E7255-E7261. [PMID: 28808029 DOI: 10.1073/pnas.1620529114] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteins can be modified by multiple posttranslational modifications (PTMs), creating a PTM code that controls the function of proteins in space and time. Unraveling this complex PTM code is one of the great challenges in molecular biology. Here, using mass spectrometry-based assays, we focus on the most common PTMs-phosphorylation and O-GlcNAcylation-and investigate how they affect each other. We demonstrate two generic crosstalk mechanisms. First, we define a frequently occurring, very specific and stringent phosphorylation/O-GlcNAcylation interplay motif, (pSp/T)P(V/A/T)(gS/gT), whereby phosphorylation strongly inhibits O-GlcNAcylation. Strikingly, this stringent motif is substantially enriched in the human (phospho)proteome, allowing us to predict hundreds of putative O-GlcNAc transferase (OGT) substrates. A set of these we investigate further and show them to be decent substrates of OGT, exhibiting a negative feedback loop when phosphorylated at the P-3 site. Second, we demonstrate that reciprocal crosstalk does not occur at PX(S/T)P sites, i.e., at sites phosphorylated by proline-directed kinases, which represent 40% of all sites in the vertebrate phosphoproteomes.
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