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Vogl DP, Conibear AC, Becker CFW. Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins. RSC Chem Biol 2021; 2:1441-1461. [PMID: 34704048 PMCID: PMC8496066 DOI: 10.1039/d1cb00045d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
| | - Anne C Conibear
- The University of Queensland, School of Biomedical Sciences St Lucia Brisbane 4072 QLD Australia
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
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2
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Niu J, Shi Y, Huang K, Zhong Y, Chen J, Sun Z, Luan M, Chen J. Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:149. [PMID: 32843898 PMCID: PMC7441727 DOI: 10.1186/s13068-020-01789-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 08/16/2020] [Indexed: 06/07/2023]
Abstract
BACKGROUND Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. RESULTS In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. CONCLUSIONS Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.
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Affiliation(s)
- Juan Niu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Yaliang Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Kunyong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Yicheng Zhong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Jing Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Zhimin Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
| | - Jianhua Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Xianjiahu West Road, Changsha, 410205 Hunan Province People’s Republic of China
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Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. J Mol Biol 2020; 432:4092-4107. [PMID: 32439331 PMCID: PMC7327521 DOI: 10.1016/j.jmb.2020.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022]
Abstract
Transcription elongation factor Spt6 associates with RNA polymerase II (RNAP II) via a tandem SH2 (tSH2) domain. The mechanism and significance of the RNAP II–Spt6 interaction is still unclear. Recently, it was proposed that Spt6-tSH2 is recruited via a newly described phosphorylated linker between the Rpb1 core and its C-terminal domain (CTD). Here, we report binding studies with isolated tSH2 of Spt6 (Spt6-tSH2) and Spt6 lacking the first unstructured 297 residues (Spt6ΔN) with a minimal CTD substrate of two repetitive heptads phosphorylated at different sites. The data demonstrate that Spt6 also binds the phosphorylated CTD, a site that was originally proposed as a recognition epitope. We also show that an extended CTD substrate harboring 13 repetitive heptads of the tyrosine-phosphorylated CTD binds Spt6-tSH2 and Spt6ΔN with tighter affinity than the minimal CTD substrate. The enhanced binding is achieved by avidity originating from multiple phosphorylation marks present in the CTD. Interestingly, we found that the steric effects of additional domains in the Spt6ΔN construct partially obscure the binding of the tSH2 domain to the multivalent ligand. We show that Spt6-tSH2 binds various phosphorylation patterns in the CTD and found that the studied combinations of phospho-CTD marks (1,2; 1,5; 2,4; and 2,7) all facilitate the interaction of CTD with Spt6. Our structural studies reveal a plasticity of the tSH2 binding pockets that enables the accommodation of CTDs with phosphorylation marks in different registers. High-affinity Pol II CTD-binding by Spt6 is achieved by avidity originating from multiple phosphorylation marks presented in the CTD, suggesting how phosphorylation levels fine-tune the CTD interactome. Structure of RNAP II CTD bound with tandem SH2 domain of Spt6 reveals how phosphorylated CTD is recognized. Isolated tSH2 of Spt6 binds the extended CTD substrate with tighter affinity than nearly full-length Spt6, suggesting that the steric effects of additional domains in Spt6 influence the binding of the tSH2 domain to the multivalent CTD ligand.
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Yang Y, He M, Wei T, Sun J, Wu S, Gao T, Guo Z. Photo-affinity pulling down of low-affinity binding proteins mediated by post-translational modifications. Anal Chim Acta 2020; 1107:164-171. [PMID: 32200891 DOI: 10.1016/j.aca.2020.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/14/2020] [Accepted: 02/06/2020] [Indexed: 11/19/2022]
Abstract
Weak and transient protein-protein interactions (PPIs) mediated by the post-translational modifications (PTMs) play key roles in biological systems. However, technical challenges to investigate the PTM-mediated PPIs have impeded many research advances. In this work, we develop a photo-affinity pull-down assay method to pull-down low-affinity binding proteins, thus for the screen of PTM-mediated PPIs. In this method, the PTM-mediated non-covalent interactions can be converted to the covalent interactions by the photo-activated linkage, so as to freeze frame the low-affinity binding interactions. The fabricated photo-affinity magnetic beads (PAMBs) ensure high specificity and resolution to capture the interacted proteins. Besides, the introduction of PEG passivation layer on PAMB has significantly reduced the non-specific interaction as compared to the traditional pull-down assay. For proof-of-concept, by using this newly developed assay method, we have identified a set of proteins that can interact with a specific methylation site on Flap Endonuclease 1 (FEN1) protein. Less interfering proteins (decreased over 80%) and more proteins sub-classes are profiled as compared to the traditional biotin-avidin pull-down system. Therefore, this new pull-down method may provide a useful tool for the study of low-affinity PPIs, and contribute to the discovery of potential targets for renewed PTM-mediated interactions that is fundamentally needed in biomedical research.
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Affiliation(s)
- Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Mengyuan He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tianxiang Wei
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Junhua Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Shaohua Wu
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), College of Chemistry, Fuzhou University, Fuzhou, 350108, PR China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China.
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Zhao L, Ehrt C, Koch O, Wu YW. One-Pot N2C/C2C/N2N Ligation To Trap Weak Protein-Protein Interactions. Angew Chem Int Ed Engl 2016; 55:8129-33. [PMID: 27213482 DOI: 10.1002/anie.201601299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/13/2016] [Indexed: 01/19/2023]
Abstract
Weak transient protein-protein interactions (PPIs) play an essential role in cellular dynamics. However, it is challenging to obtain weak protein complexes owing to their short lifetime. Herein we present a general and facile method for trapping weak PPIs in an unbiased manner using proximity-induced ligations. To expand the chemical ligation spectrum, we developed novel N2N (N-terminus to N-terminus) and C2C (C-terminus to C-terminus) ligation approaches. By using N2C (N-terminus to C-terminus), N2N, and C2C ligations in one pot, the interacting proteins were linked. The weak Ypt1:GDI interaction drove C2C ligation with t1/2 of 4.8 min and near quantitative conversion. The Ypt1-GDI conjugate revealed that binding of Ypt1 G-domain causes opening of the lipid-binding site of GDI, which can accommodate one prenyl group, giving insights into Rab membrane recycling. Moreover, we used this strategy to trap the KRas homodimer, which plays an important role in Ras signaling.
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Affiliation(s)
- Lei Zhao
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - Christiane Ehrt
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Oliver Koch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.
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Zhao L, Ehrt C, Koch O, Wu YW. Eintopf-N2C/C2C/N2N-Proteinligationsstrategien zur Analyse schwacher Protein-Protein-Wechselwirkungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lei Zhao
- Chemical Genomics Center der Max-Planck-Gesellschaft; Otto-Hahn-Straße 15 44227 Dortmund Deutschland
| | - Christiane Ehrt
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Oliver Koch
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Center der Max-Planck-Gesellschaft; Otto-Hahn-Straße 15 44227 Dortmund Deutschland
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Gianazza E, Parravicini C, Primi R, Miller I, Eberini I. In silico prediction and characterization of protein post-translational modifications. J Proteomics 2015; 134:65-75. [PMID: 26436211 DOI: 10.1016/j.jprot.2015.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/17/2015] [Accepted: 09/23/2015] [Indexed: 01/06/2023]
Abstract
This review outlines the computational approaches and procedures for predicting post translational modification (PTM)-induced changes in protein conformation and their influence on protein function(s), the latter being assessed as differential affinity in interaction with either low (ligands for receptors or transporters, substrates for enzymes) or high molecular mass molecules (proteins or nucleic acids in supramolecular assemblies). The scope for an in silico approach is discussed against a summary of the in vitro evidence on the structural and functional outcome of protein PTM.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Sezione di Scienze Farmacologiche, Via Balzaretti 9, I-20133 Milan, Italy.
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
| | - Roberto Primi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
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Reimann O, Smet‐Nocca C, Hackenberger CPR. Spurlose Aufreinigung und Desulfurierung von Ligationsprodukten des Tau‐Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Oliver Reimann
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin (Deutschland)
| | - Caroline Smet‐Nocca
- UMR CNRS 8576, Lille 1 Science and Technology University, 59655 Villeneuve d'Ascq Cedex (Frankreich)
| | - Christian P. R. Hackenberger
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin (Deutschland)
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Reimann O, Smet‐Nocca C, Hackenberger CPR. Traceless Purification and Desulfurization of Tau Protein Ligation Products. Angew Chem Int Ed Engl 2014; 54:306-10. [DOI: 10.1002/anie.201408674] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Oliver Reimann
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Strasse 2, 12489 Berlin (Germany)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
| | - Caroline Smet‐Nocca
- UMR CNRS 8576—Lille 1 Science and Technology University, 59655 Villeneuve d'Ascq Cedex (France)
| | - Christian P. R. Hackenberger
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Strasse 2, 12489 Berlin (Germany)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
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