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Abstract
As an important epigenetic mark, lysine methylations play critical roles in the regulation of both chromatin and non-chromatin proteins. There are three levels of lysine methylation, mono-, di-, and trimethylation. Each one has turned out to be biologically distinctive. For the biochemical characterization of proteins with lysine methylation, multiple chemical biology methods have been developed. This concept article will highlight these developments and their applications in epigenetic investigation of protein functions.
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Affiliation(s)
- Zhipeng A. Wang
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R. Liu
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
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Chen M, Zhang M, Zhai L, Hu H, Liu P, Tan M. Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study. J Proteome Res 2017; 16:3460-3469. [PMID: 28730820 DOI: 10.1021/acs.jproteome.7b00373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin, and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence-dependent manner. Kinetic studies revealed that the optimal digestion time and enzyme-to-substrate ratio for the cleavage of dimethylated lysine by trypsin was around 16 h and 1:50, respectively. We further showed the tryptic C-terminal lysine-dimethylated (C-Kme2) peptides could contribute to a significant portion of substrate identification in the proteomic study, which utilizes the chemical dimethylation labeling approach. More than 120 tryptic C-Kme2 peptides (7% of total peptides identified) were identified in chemically lysine-dimethyl-labeled HeLa whole cell lysate by a single-shot nanoflow high performance liquid chromatography with tandem mass spectrometry (nano-HPLC-MS/MS) analysis. Moreover, in an assay for substrate identification of protease Glu-C using stable isotope dimethyl labeling approach, our data showed the tryptic C-Kme2 peptides accounted for more than 13% of total tryptic peptides. Additionally, our in vivo methylome profiling data revealed some C-Kme2 peptides, which is of importance to identification and quantification of biologically relevant protein and lysine-methylated site. Therefore, we reason that the tryptic peptides bearing C-terminal dimethylated lysine need to be considered in the mass spectrometric analysis of lysine dimethylation.
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Affiliation(s)
- Ming Chen
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China.,University of Chinese Academy of Sciences , Beijing 100049, PR China
| | - Min Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China.,University of Chinese Academy of Sciences , Beijing 100049, PR China
| | - Linhui Zhai
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China
| | - Hao Hu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China
| | - Ping Liu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China.,University of Chinese Academy of Sciences , Beijing 100049, PR China
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Wang ZA, Zeng Y, Kurra Y, Wang X, Tharp JM, Vatansever EC, Hsu WW, Dai S, Fang X, Liu WR. A Genetically Encoded Allysine for the Synthesis of Proteins with Site-Specific Lysine Dimethylation. Angew Chem Int Ed Engl 2016; 56:212-216. [PMID: 27910233 DOI: 10.1002/anie.201609452] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 01/01/2023]
Abstract
Using the amber suppression approach, Nϵ -(4-azidobenzoxycarbonyl)-δ,ϵ-dehydrolysine, an allysine precursor is genetically encoded in E. coli. Its genetic incorporation followed by two sequential biocompatible reactions allows convenient synthesis of proteins with site-specific lysine dimethylation. Using this approach, dimethyl-histone H3 and p53 proteins have been synthesized and used to probe functions of epigenetic enzymes including histone demethylase LSD1 and histone acetyltransferase Tip60. We confirmed that LSD1 is catalytically active toward H3K4me2 and H3K9me2 but inert toward H3K36me2, and methylation at p53 K372 directly activates Tip60 for its catalyzed acetylation at p53 K120.
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Affiliation(s)
- Zhipeng A Wang
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Yu Zeng
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Xin Wang
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics, Office of the Taxes State Chemist, Department of Veterinary Pathobiology, College Station, TX, 77843, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Erol C Vatansever
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Willie W Hsu
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Susie Dai
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics, Office of the Taxes State Chemist, Department of Veterinary Pathobiology, College Station, TX, 77843, USA
| | - Xinqiang Fang
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou, Fujian, 350002, P.R. China
| | - Wenshe R Liu
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
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