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Emenike B, Czabala P, Farhi J, Swaminathan J, Anslyn EV, Spangle J, Raj M. Tertiary Amine Coupling by Oxidation for Selective Labeling of Dimethyl Lysine Post-Translational Modifications. J Am Chem Soc 2024; 146:10621-10631. [PMID: 38584362 PMCID: PMC11027136 DOI: 10.1021/jacs.4c00253] [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: 01/07/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Lysine dimethylation (Kme2) is a crucial post-translational modification (PTM) that regulates biological processes and is implicated in diseases. There is significant interest in globally identifying these methylation marks. Unfortunately, this remains challenging due to the lack of robust technologies for selectively labeling Kme2. To address this, we present a chemical method named tertiary amine coupling by oxidation (TACO). This method selectively modifies Kme2 to aldehydes using Selectfluor and a base. The resulting aldehydes from Kme2 were then functionalized using reductive amination, thiolamine, and oxime chemistry. We successfully demonstrated the versatility of TACO in selectively labeling Kme2 peptides and proteins in complex cell lysate mixtures with varying payloads, including affinity tags and fluorophores. We further showed the application of TACO chemistry for the identification of Kme2 sites at a single-molecule level by fluorosequencing. We discovered novel 30 Kme2 sites, in addition to previously known 5 Kme2 sites, by proteomics analysis of TACO-modified nuclear extracts. Our work establishes a unique strategy for covalently modifying Kme2, facilitating the global identification of low-abundance Kme2-PTMs and their sites within complex cell lysate mixtures.
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Affiliation(s)
- Benjamin Emenike
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Patrick Czabala
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan Farhi
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Jagannath Swaminathan
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer Spangle
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Monika Raj
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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2
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Nong K, Zhao YL, Yi S, Zhang X, Wei S, Yao ZJ. 3-Acyl-4-Pyranone as a Lysine Residue-Selective Bioconjugation Reagent for Peptide and Protein Modification. Bioconjug Chem 2024; 35:286-299. [PMID: 38451202 DOI: 10.1021/acs.bioconjchem.3c00447] [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: 03/08/2024]
Abstract
Chemoselective protein modification plays extremely important roles in various biological, medical, and pharmaceutical investigations. Mimicking the mechanism of the chemoselective reaction between natural azaphilones and primary amines, this work successfully simplified the azaphilone scaffold into much simpler 3-acyl-4-pyranones. Examinations confirmed that these slim-size mimics perfectly kept the unique reactivity for selective conjugation with the primary amines including lysine residues of peptides and proteins. The newly developed pyranone tool presents remarkably increased aqueous solubility and compatible second-order rate constant by comparison with the original azaphilone. Additional advantages also include the ease of biorthogonal combinative use with a copper-catalyzed azide-alkyne Click reaction, which was conveniently applied to decorate lysozyme with neutral-, positive- and negative-charged functionalities in parallel. Moderate-degree modification of lysozyme with positively charged quaternary ammoniums was revealed to increase the enzymatic activities.
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Affiliation(s)
- Keyi Nong
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Yi-Lu Zhao
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Shandong Yi
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Xuchun Zhang
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Siyuan Wei
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Zhu-Jun Yao
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
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Gao F, Chang M, Meng X, Xu H, Gnawali G, Dong Y, Lopez B, Wang W. Site-Selective Modification of Secondary Amine Moieties on Native Peptides, Proteins, and Natural Products with Ynones. Bioconjug Chem 2023; 34:1553-1562. [PMID: 37646420 DOI: 10.1021/acs.bioconjchem.3c00246] [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: 09/01/2023]
Abstract
Site-selective modification of biologically relevant secondary amines in peptides, proteins, and natural products has been challenging due to the similar reactivity between primary and secondary amines. Even for the secondary amines, their reactivities are significantly influenced by their structures and environment. Herein, we report a ynone Michael bioconjugation method for selective modification of secondary amines in unprotected peptides and proteins and complex natural products. We show that fine tuning the electronic effect of the ynones enables controlling the Michael acceptor reactivity for the selective reaction with the structurally different secondary amines in densely functionalized complex structures and complicated biological environment.
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Affiliation(s)
- Feng Gao
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, 1703 E Mabel Street, Tucson, Arizona 85721, United States
| | - Mengyang Chang
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd., Tucson, Arizona 85721, United States
| | - Xiang Meng
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, 1703 E Mabel Street, Tucson, Arizona 85721, United States
| | - Hang Xu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, 1703 E Mabel Street, Tucson, Arizona 85721, United States
| | - Giri Gnawali
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, 1703 E Mabel Street, Tucson, Arizona 85721, United States
| | - Yue Dong
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, 1703 E Mabel Street, Tucson, Arizona 85721, United States
| | - Byrdie Lopez
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd., Tucson, Arizona 85721, United States
| | - Wei Wang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, 1703 E Mabel Street, Tucson, Arizona 85721, United States
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd., Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, 3838 N. Campbell Avenue, Tucson, Arizona 85719, United States
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Yates NDJ, Hatton NE, Fascione MA, Parkin A. Site-Selective Aryl Diazonium Installation onto Protein Surfaces at Neutral pH using a Maleimide-Functionalized Triazabutadiene. Chembiochem 2023; 24:e202300313. [PMID: 37311168 DOI: 10.1002/cbic.202300313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
Aryl diazonium cations are versatile bioconjugation reagents due to their reactivity towards electron-rich aryl residues and secondary amines, but historically their usage has been hampered by both their short lifespan in aqueous solution and the harsh conditions required to generate them in situ. Triazabutadienes address many of these issues as they are stable enough to endure multiple-step chemical syntheses and can persist for several hours in aqueous solution, yet upon UV-exposure rapidly release aryl diazonium cations under biologically-relevant conditions. This paper describes the synthesis of a novel maleimide-functionalized triazabutadiene suitable for site-selectively installing aryl diazonium cations into proteins at neutral pH; we show reaction with this molecule and a surface-cysteine of a thiol disulfide oxidoreductase. Through photoactivation of the site-selectively installed triazabutadiene motifs, we generate aryl diazonium functionality, which we further derivatize via azo-bond formation to electron-rich aryl species, showcasing the potential utility of this strategy for the generation of photoswitches or protein-drug conjugates.
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Affiliation(s)
- Nicholas D J Yates
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
| | - Natasha E Hatton
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
| | - Martin A Fascione
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
| | - Alison Parkin
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
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Li Z, Wang Q, Wang K, Zhang W, Ye M. An antibody-free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis. Proteomics 2023; 23:e2100378. [PMID: 35532377 DOI: 10.1002/pmic.202100378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Accepted: 05/03/2022] [Indexed: 11/06/2022]
Abstract
Protein lysine monomethylation is an important post-translational modification participated in regulating many biological processes. There is growing interest in identifying these methylation events. However, the introduction of one methyl group on lysine residues has negligible effect on changing the physical and chemical properties of proteins or peptides, making enriching and identifying monomethylated lysine (Kme1) proteins or peptides extraordinarily challenging. In this study, we proposed an antibody-free chemical proteomics approach to capture Kme1 peptides from complex protein digest. By exploiting reductive glutaraldehydation, 5-aldehyde-pentanyl modified Kme1 residues and piperidine modified primary amines were generated at the same time. The peptides with aldehyde modified Kme1 residues were then enriched by solid-phase hydrazide chemistry. This chemical proteomics approach was validated by using several synthetic peptides. It was demonstrated that it can enrich and detect Kme1 peptide from peptide mixture containing 5000-fold more bovine serum albumin tryptic digest. Besides, we extended our approach to profile Kme1 using heavy methyl stable isotope labeling by amino acids in cell culture (hmSILAC) labeled Jurkat T cells and Hela cells. Totally, 29 Kme1 sites on 25 proteins were identified with high confidence and 11 Kme1 sites were identified in both two types cells. This is the first antibody-free chemical proteomics approach to enrich Kme1 peptides from complex protein digest, and it provides a potential avenue for the analysis of methylome.
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Affiliation(s)
- Zhouxian Li
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Qi Wang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Keyun Wang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
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Wu CS, Cheng L. Recent Advances towards the Reversible Chemical Modification of Proteins. Chembiochem 2023; 24:e202200468. [PMID: 36201252 DOI: 10.1002/cbic.202200468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/05/2022] [Indexed: 01/20/2023]
Abstract
Proteins are intriguing biomacromolecules for all living systems, not only as essential building blocks of organisms, but also as participants in almost every aspect of cellular activity such as metabolism and gene transcription/expression. Developing chemical biology tools that are capable of labeling/modifying proteins is a powerful method for decoding their detailed structures and functions. However, most current approaches heavily rely on the installation of permanent tags or genetic engineering of unnatural amino acids. There has been slow development in reversible chemical labeling using small organic probes and bioorthogonal transformations to construct site-selectively modified proteins and conditionally restore their activities or structures. This review summarizes recent advances in the field of chemical regulation of proteins with reversible transformations towards distinct motifs, including amino acid residues, amide backbones and native post-translational lysine. Finally, current challenges and future perspectives are discussed.
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Affiliation(s)
- Chuan-Shuo Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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Emenike B, Nwajiobi O, Raj M. Covalent Chemical Tools for Profiling Post-Translational Modifications. Front Chem 2022; 10:868773. [PMID: 35860626 PMCID: PMC9289218 DOI: 10.3389/fchem.2022.868773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs); a process that involves the proteolytic processing or catalytic attachment of diverse functional groups onto proteins. These modifications modulate a host of biological activities and responses. Consequently, anomalous PTMs often correlate to a host of diseases, hence there is a need to detect these transformations, both qualitatively and quantitatively. One technique that has gained traction is the use of robust chemical strategies to label different PTMs. By utilizing the intrinsic chemical reactivity of the different chemical groups on the target amino acid residues, this strategy can facilitate the delineation of the overarching and inclusionary roles of these different modifications. Herein, we will discuss the current state of the art in post-translational modification analysis, with a direct focus on covalent chemical methods used for detecting them.
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