1
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [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: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Zou L, Geng X, Li Z, Li T. Design of highly active substrates using molecular docking for microbial transglutaminase detection. RSC Adv 2023; 13:5259-5265. [PMID: 36793302 PMCID: PMC9923216 DOI: 10.1039/d2ra06467g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
The transglutaminase (TGase) family catalyzes a transamidation reaction between glutamine (Gln) and lysine (Lys) residues on protein substrates. Highly active substrates are important for cross-linking and modifying proteins of TGase. In the present work, high-activity substrates have been designed based on the principles of enzyme-substrate interaction, using microbial transglutaminase (mTGase) as a research model of the TGase family. Substrates with high activity were screened using a combination of molecular docking and traditional experiments. Twenty-four sets of peptide substrates all produced good catalytic activity with mTGase. FFKKAYAV as the acyl acceptor and VLQRAY as the acyl donor group had the best reaction efficiency with highly sensitive detection of 26 nM mTGase. In addition, the substrate grouping, KAYAV and AFQSAY, detected 130 nM mTGase under physiological conditions (37 °C, pH 7.4), producing 20-fold higher activity than the natural substrate, collagen. The experimental results confirmed the potential for design of high-activity substrates by a combination of molecular docking and traditional experiments under physiological conditions.
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Affiliation(s)
- Longhao Zou
- Key Laboratory for Molecular Enzymology & Engineering, The Ministry of Education, School of Life Sciences, Jilin University Changchun China
| | - Xu Geng
- Key Laboratory for Molecular Enzymology & Engineering, The Ministry of Education, School of Life Sciences, Jilin University Changchun China
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology & Engineering, The Ministry of Education, School of Life Sciences, Jilin University Changchun China
| | - Tao Li
- Key Laboratory for Molecular Enzymology & Engineering, The Ministry of Education, School of Life Sciences, Jilin University Changchun China
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3
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Bowler MM, Glavatskikh M, Pecot CV, Kireev D, Bower s AA. Enzymatic Macrolactamization of mRNA Display Libraries for Inhibitor Selection. ACS Chem Biol 2023; 18:166-175. [PMID: 36490372 PMCID: PMC9868075 DOI: 10.1021/acschembio.2c00828] [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] [Indexed: 12/13/2022]
Abstract
mRNA display is a powerful, high-throughput technology for discovering novel, peptide ligands for protein targets. A number of methods have been used to expand the chemical diversity of mRNA display libraries beyond the 20 canonical amino acids, including genetic code reprogramming and biorthogonal chemistries. To date, however, there have been few reports using enzymes as biocompatible reagents for diversifying mRNA display libraries. Here, we report the evaluation and implementation of the common industrial enzyme, microbial transglutaminase (mTG), as a versatile biocatalyst for cyclization of mRNA display peptide libraries via lysine-to-glutamine isopeptide bonds. We establish two separate display-based assays to validate the compatibility of mTG with mRNA-linked peptide substrates. These assays indicate that mTG has a high degree of substrate tolerance and low single round bias. To demonstrate the potential benefits of mTG-mediated cyclization in ligand discovery, high diversity mTG-modified libraries were employed in two separate affinity selections: (1) one against the calcium and integrin binding protein, CIB1, and (2) the second against the immune checkpoint protein and emerging therapeutic target, B7-H3. Both selections resulted in the identification of potent, cyclic, low nanomolar binders, and subsequent structure-activity studies demonstrate the importance of the cyclization to the observed activity. Notably, cyclization in the CIB1 binder stabilizes an α-helical conformation, while the B7-H3 inhibitor employs two bridges, one mTG-derived lactam and a second disulfide to achieve its potency. Together, these results demonstrate potential benefits of enzyme-based biocatalysts in mRNA display ligand selections and establish a framework for employing mTG in mRNA display.
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Affiliation(s)
- Matthew M. Bowler
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Chad V. Pecot
- UNC Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Albert A. Bower s
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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4
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Damnjanović J, Odake N, Fan J, Camagna M, Jia B, Kojima T, Nemoto N, Hitomi K, Nakano H. Comprehensive analysis of transglutaminase substrate preference by cDNA display coupled with next-generation sequencing and bioinformatics. Sci Rep 2022; 12:13578. [PMID: 35945258 PMCID: PMC9363462 DOI: 10.1038/s41598-022-17494-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
cDNA display is an in vitro display technology based on a covalent linkage between a protein and its corresponding mRNA/cDNA, widely used for the selection of proteins and peptides from large libraries (1012) in a high throughput manner, based on their binding affinity. Here, we developed a platform using cDNA display and next-generation sequencing (NGS) for rapid and comprehensive substrate profiling of transglutaminase 2 (TG2), an enzyme crosslinking glutamine and lysine residues in proteins. After screening and selection of the control peptide library randomized at the reactive glutamine, a combinatorial library of displayed peptides randomized at positions - 1, + 1, + 2, and + 3 from the reactive glutamine was screened followed by NGS and bioinformatic analysis, which indicated a strong preference of TG2 towards peptides with glutamine at position - 1 (Gln-Gln motif), and isoleucine or valine at position + 3. The highly enriched peptides indeed contained the indicated sequence and showed a higher reactivity as TG2 substrates than the peptide previously selected by phage display, thus representing the novel candidate peptide probes for TG2 research. Furthermore, the obtained information on substrate profiling can be used to identify potential TG2 protein targets. This platform will be further used for the substrate profiling of other TG isozymes, as well as for the selection and evolution of larger biomolecules.
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Affiliation(s)
- Jasmina Damnjanović
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Nana Odake
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Jicheng Fan
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Tigermed, Hangzhou, China
| | - Maurizio Camagna
- Laboratory of Plant Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Beixi Jia
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, 468-8502, Japan
| | - Naoto Nemoto
- Laboratory of Evolutionary Molecular Engineering, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kiyotaka Hitomi
- Laboratory of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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5
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Semkova ME, Hsuan JJ. Mass Spectrometric Identification of a Novel Factor XIIIa Cross-Linking Site in Fibrinogen. Proteomes 2021; 9:proteomes9040043. [PMID: 34842803 PMCID: PMC8628943 DOI: 10.3390/proteomes9040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Transglutaminases are a class of enzymes that catalyze the formation of a protein:protein cross-link between a lysine and a glutamine residue. These cross-links play important roles in diverse biological processes. Analysis of cross-linking sites in target proteins is required to elucidate their molecular action on target protein function and the molecular specificity of different transglutaminase isozymes. Mass-spectrometry using settings designed for linear peptide analysis and software designed for the analysis of disulfide bridges and chemical cross-links have previously been employed to identify transglutaminase cross-linking sites in proteins. As no control peptide with which to assess and improve the mass spectrometric analysis of TG cross-linked proteins was available, we developed a method for the enzymatic synthesis of a well-defined transglutaminase cross-linked peptide pair that mimics a predicted tryptic digestion product of collagen I. We then used this model peptide to determine optimal score thresholds for correct peptide identification from y- and b-ion series of fragments produced by collision-induced dissociation. We employed these settings in an analysis of fibrinogen cross-linked by the transglutaminase Factor XIIIa. This approach resulted in identification of a novel cross-linked peptide in the gamma subunit. We discuss the difference in behavior of ions derived from different cross-linked peptide sequences and the consequent demand for a more tailored mass spectrometry approach for cross-linked peptide identification compared to that routinely used for linear peptide analysis.
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6
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Wang H, Wang Y, Yuan Z, Wang Y, Li X, Song P, Lu F, Liu Y. Insight into the cross-linking preferences and characteristics of the transglutaminase from Bacillus subtilis by in vitro RNA display. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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8
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Fuchsbauer HL. Approaching transglutaminase from Streptomyces bacteria over three decades. FEBS J 2021; 289:4680-4703. [PMID: 34102019 DOI: 10.1111/febs.16060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
Transglutaminases are protein cross-linking and protein-modifying enzymes that have attracted considerable interest due to their causal involvement in various diseases and versatility in industrial applications. In particular, microbial transglutaminases (MTG) from Streptomyces bacteria have managed in recent years to evolve from simple food additives to specialized enzymes for the site-directed modification of therapeutic proteins. The review summarizes relevant studies from the beginning dealing with the occurrence, production, structure, catalysis, and substrate molecules of MTG enzymes. It also addresses biotechnological procedures with MTG from S. mobaraensis (SmMTG) as the most prominent representative in focus. Reassessment of the available data revealed unexpected insights into catalysis of SmMTG and other transglutaminases, suggesting selection of glutamine donor proteins by subsites at the front vestibule and the existence of distinct lysine pockets. Flexibility of the SmMTG-accessible glutamine donor substrate regions seems to be more important than the glutamine environment. Nevertheless, residues in close vicinity to glutamines also determine interaction with the SmMTG subsites. The apparent lack of subsites for lysine donor proteins suggests self-assembly of the substrate proteins prior to enzymatic cross-linking. The study of natural substrate proteins, especially their mutual interaction, is proposed to further illuminate catalysis of SmMTG. To this end, structure and function of the characterized substrate proteins from S. mobaraensis are discussed in conclusion.
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Affiliation(s)
- Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
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9
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Zhuang R, Khosla C. Substrates, inhibitors, and probes of mammalian transglutaminase 2. Anal Biochem 2020; 591:113560. [PMID: 31874171 PMCID: PMC6948143 DOI: 10.1016/j.ab.2019.113560] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023]
Abstract
Transglutaminase 2 (TG2) is a ubiquitous but enigmatic mammalian protein to which a number of biological functions have been ascribed but not definitively proven. As a member of the transglutaminase family, TG2 can catalyze deamidation or alternatively transamidation of selected Gln residues in proteins and peptides. It is also known to harbor other enzymatic properties, including protein disulfide isomerase, GTP-dependent signal transduction, and ATP dependent protein kinase activity. Given its multifunctional chemistry, it is unsurprising that a long list of proteins from the mammalian proteome have been identified as substrates and/or binding partners; however, the biological relevance of none of these protein-protein interactions has been clarified as yet. Remarkably, the most definitive insights into the biology of TG2 stem from its pathophysiological role in gluten peptide deamidation in celiac disease. Meanwhile our understanding of TG2 chemistry has been leveraged to engineer a spectrum of inhibitors and other molecular probes of TG2 biology in vivo. This review summarizes our current knowledge of the enzymology and regulation of human TG2 with a focus on its physiological substrates as well as tool molecules whose engineering was inspired by their identities.
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Affiliation(s)
- Ruize Zhuang
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Department of Chemistry, Stanford University, Stanford, CA, USA; Stanford ChEM-H, Stanford University, Stanford, CA, USA.
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10
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Deweid L, Avrutina O, Kolmar H. Microbial transglutaminase for biotechnological and biomedical engineering. Biol Chem 2019; 400:257-274. [PMID: 30291779 DOI: 10.1515/hsz-2018-0335] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/04/2018] [Indexed: 12/17/2022]
Abstract
Research on bacterial transglutaminase dates back to 1989, when the enzyme has been isolated from Streptomyces mobaraensis. Initially discovered during an extensive screening campaign to reduce costs in food manufacturing, it quickly appeared as a robust and versatile tool for biotechnological and pharmaceutical applications due to its excellent activity and simple handling. While pioneering attempts to make use of its extraordinary cross-linking ability resulted in heterogeneous polymers, currently it is applied to site-specifically ligate diverse biomolecules yielding precisely modified hybrid constructs comprising two or more components. This review covers the extensive and rapidly growing field of microbial transglutaminase-mediated bioconjugation with the focus on pharmaceutical research. In addition, engineering of the enzyme by directed evolution and rational design is highlighted. Moreover, cumbersome drawbacks of this technique mainly caused by the enzyme's substrate indiscrimination are discussed as well as the ways to bypass these limitations.
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Affiliation(s)
- Lukas Deweid
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287 Darmstadt, Germany
| | - Olga Avrutina
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287 Darmstadt, Germany
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11
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Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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12
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Juettner NE, Schmelz S, Kraemer A, Knapp S, Becker B, Kolmar H, Scrima A, Fuchsbauer HL. Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase. FEBS J 2018; 285:4684-4694. [PMID: 30318745 DOI: 10.1111/febs.14678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/28/2018] [Accepted: 10/11/2018] [Indexed: 01/10/2023]
Abstract
The protein cross-linking enzyme transglutaminase from Streptomyces mobaraensis (MTG) is frequently used to modify therapeutic proteins. In order to reveal the binding mode of glutamine donor substrates, we have now crystallized MTG covalently linked to large inhibitory peptides. A series of peptide structures were examined but DIPIGSKMTG, which was chloroacetylated at serine, was the only inhibitory molecule that resulted in an interpretable density map. We found that, besides the warhead (modified Ser6), Ile4 and Gly5 of the inhibitory peptide occupy the tight but extended hydrophobic bottom of the MTG-binding cleft. Both termini of the peptide protrude along the cleft walls almost perpendicular to the bottom of the extended cleft. This peptide model suggests a zipper-like cross-linking mechanism of self-assembled substrate proteins by MTG.
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Affiliation(s)
- Norbert E Juettner
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Stefan Schmelz
- Structural Biology of Autophagy Group, Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Andreas Kraemer
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt, Germany
| | - Bastian Becker
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Andrea Scrima
- Structural Biology of Autophagy Group, Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
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13
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Juettner NE, Classen M, Colin F, Hoffmann SB, Meyners C, Pfeifer F, Fuchsbauer HL. Features of the transglutaminase-activating metalloprotease from Streptomyces mobaraensis DSM 40847 produced in Escherichia coli. J Biotechnol 2018; 281:115-122. [PMID: 29981445 DOI: 10.1016/j.jbiotec.2018.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 01/21/2023]
Abstract
Transglutaminase from Streptomyces mobaraensis (MTG) is an important enzyme for numerous industrial applications. Recombinant production requires proteolytic activation of the zymogen. The study provides a convenient procedure for the preparation of the transglutaminase-activating metalloprotease (TAMP) in Escherichia coli. In contrast to wtTAMP, rTAMP exhibited the P domain of convertases as molecular mass of 55.7 kDa suggested. Protein integrity was beneficially influenced by 2-5 mM CaCl2. Study of pH and temperature optima assigned rTAMP to the neutral metalloproteases, more heat-resistant than Dispase but not thermolysin. Zinc had no inhibiting effect but 3.1 μM EDTA completely reduced activity of 5 nM TAMP. MTG, exceeding concentration of rTAMP by three orders of magnitude, was largely activated within few minutes. The kinetic parameters KM (1.31 ± 0.05 mM) and kcat (135 ± 4.3 s-1), monitored by isothermal titration calorimetry (ITC), further highlighted catalytic efficiency (103,053 M-1 s-1) of rTAMP and rapid processing of MTG. ITC even revealed that inhibition of rTAMP by its intrinsic inhibitory protein SSTI was an enthalpy-driven process resulting in Kd of 199 ± 37.9 nM. The production procedure of rTAMP in E. coli closes the gap between production and application of recombinant MTG and may enhance relevance of MTG-mediated reactions in pharmaceutical processes.
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Affiliation(s)
- Norbert E Juettner
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295, Darmstadt, Germany; Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Moritz Classen
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295, Darmstadt, Germany
| | - Felix Colin
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295, Darmstadt, Germany
| | - Sascha B Hoffmann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295, Darmstadt, Germany
| | - Christian Meyners
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295, Darmstadt, Germany
| | - Felicitas Pfeifer
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295, Darmstadt, Germany.
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14
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Oteng-Pabi SK, Clouthier CM, Keillor JW. Design of a glutamine substrate tag enabling protein labelling mediated by Bacillus subtilis transglutaminase. PLoS One 2018; 13:e0197956. [PMID: 29847605 PMCID: PMC5976192 DOI: 10.1371/journal.pone.0197956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/13/2018] [Indexed: 02/07/2023] Open
Abstract
Transglutaminases (TGases) are enzymes that catalyse protein cross-linking through a transamidation reaction between the side chain of a glutamine residue on one protein and the side chain of a lysine residue on another. Generally, TGases show low substrate specificity with respect to their amine substrate, such that a wide variety of primary amines can participate in the modification of specific glutamine residue. Although a number of different TGases have been used to mediate these bioconjugation reactions, the TGase from Bacillus subtilis (bTG) may be particularly suited to this application. It is smaller than most TGases, can be expressed in a soluble active form, and lacks the calcium dependence of its mammalian counterparts. However, little is known regarding this enzyme and its glutamine substrate specificity, limiting the scope of its application. In this work, we designed a FRET-based ligation assay to monitor the bTG-mediated conjugation of the fluorescent proteins Clover and mRuby2. This assay allowed us to screen a library of random heptapeptide glutamine sequences for their reactivity with recombinant bTG in bacterial cells, using fluorescence assisted cell sorting. From this library, several reactive sequences were identified and kinetically characterized, with the most reactive sequence (YAHQAHY) having a kcat/KM value of 19 ± 3 μM-1 min-1. This sequence was then genetically appended onto a test protein as a reactive 'Q-tag' and fluorescently labelled with dansyl-cadaverine, in the first demonstration of protein labelling mediated by bTG.
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Affiliation(s)
- Samuel K. Oteng-Pabi
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis and Research Innovation, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario, Canada
| | - Christopher M. Clouthier
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis and Research Innovation, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario, Canada
| | - Jeffrey W. Keillor
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis and Research Innovation, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario, Canada
- * E-mail:
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15
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Juettner NE, Schmelz S, Bogen JP, Happel D, Fessner WD, Pfeifer F, Fuchsbauer HL, Scrima A. Illuminating structure and acyl donor sites of a physiological transglutaminase substrate from Streptomyces mobaraensis. Protein Sci 2018; 27:910-922. [PMID: 29430769 DOI: 10.1002/pro.3388] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 11/11/2022]
Abstract
Transglutaminase from Streptomyces mobaraensis (MTG) has become a powerful tool to covalently and highly specifically link functional amines to glutamine donor sites of therapeutic proteins. However, details regarding the mechanism of substrate recognition and interaction of the enzyme with proteinaceous substrates still remain mostly elusive. We have determined the crystal structure of the Streptomyces papain inhibitory protein (SPIp ), a substrate of MTG, to study the influence of various substrate amino acids on positioning glutamine to the active site of MTG. SPIp exhibits a rigid, thermo-resistant double-psi-beta-barrel fold that is stabilized by two cysteine bridges. Incorporation of biotin cadaverine identified Gln-6 as the only amine acceptor site on SPIp accessible for MTG. Substitution of Lys-7 demonstrated that small and hydrophobic residues in close proximity to Gln-6 favor MTG-mediated modification and are likely to facilitate introduction of the substrate into the front vestibule of MTG. Moreover, exchange of various surface residues of SPIp for arginine and glutamate/aspartate outside the glutamine donor region influences the efficiency of modification by MTG. These results suggest the occurrence of charged contact areas between MTG and the acyl donor substrates beyond the front vestibule, and pave the way for protein engineering approaches to improve the properties of artificial MTG-substrates used in biomedical applications.
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Affiliation(s)
- Norbert E Juettner
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Darmstadt, Germany.,The Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Schmelz
- The Young Investigator Group Structural Biology of Autophagy, Department of Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Jan P Bogen
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Darmstadt, Germany
| | - Dominic Happel
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Darmstadt, Germany
| | - Wolf-Dieter Fessner
- The Department of Chemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Felicitas Pfeifer
- The Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Darmstadt, Germany
| | - Andrea Scrima
- The Young Investigator Group Structural Biology of Autophagy, Department of Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany
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16
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Fiebig D, Schmelz S, Zindel S, Ehret V, Beck J, Ebenig A, Ehret M, Fröls S, Pfeifer F, Kolmar H, Fuchsbauer HL, Scrima A. Structure of the Dispase Autolysis-inducing Protein from Streptomyces mobaraensis and Glutamine Cross-linking Sites for Transglutaminase. J Biol Chem 2016; 291:20417-26. [PMID: 27493205 DOI: 10.1074/jbc.m116.731109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 11/06/2022] Open
Abstract
Transglutaminase from Streptomyces mobaraensis (MTG) is an important enzyme for cross-linking and modifying proteins. An intrinsic substrate of MTG is the dispase autolysis-inducing protein (DAIP). The amino acid sequence of DAIP contains 5 potential glutamines and 10 lysines for MTG-mediated cross-linking. The aim of the study was to determine the structure and glutamine cross-linking sites of the first physiological MTG substrate. A production procedure was established in Escherichia coli BL21 (DE3) to obtain high yields of recombinant DAIP. DAIP variants were prepared by replacing four of five glutamines for asparagines in various combinations via site-directed mutagenesis. Incorporation of biotin cadaverine revealed a preference of MTG for the DAIP glutamines in the order of Gln-39 ≫ Gln-298 > Gln-345 ∼ Gln-65 ≫ Gln-144. In the structure of DAIP the preferred glutamines do cluster at the top of the seven-bladed β-propeller. This suggests a targeted cross-linking of DAIP by MTG that may occur after self-assembly in the bacterial cell wall. Based on our biochemical and structural data of the first physiological MTG substrate, we further provide novel insight into determinants of MTG-mediated modification, specificity, and efficiency.
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Affiliation(s)
- David Fiebig
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and the Department of Chemistry and
| | - Stefan Schmelz
- From the Helmholtz-Centre for Infection Research, Braunschweig, 38124 Germany
| | - Stephan Zindel
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and the Department of Chemistry and
| | - Vera Ehret
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and
| | - Jan Beck
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and the Department of Chemistry and
| | - Aileen Ebenig
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and the Department of Chemistry and
| | - Marina Ehret
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and
| | - Sabrina Fröls
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Felicitas Pfeifer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | | | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, 64287 Darmstadt, Germany, and
| | - Andrea Scrima
- From the Helmholtz-Centre for Infection Research, Braunschweig, 38124 Germany,
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17
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Siegmund V, Schmelz S, Dickgiesser S, Beck J, Ebenig A, Fittler H, Frauendorf H, Piater B, Betz UAK, Avrutina O, Scrima A, Fuchsbauer H, Kolmar H. Locked by Design: A Conformationally Constrained Transglutaminase Tag Enables Efficient Site‐Specific Conjugation. Angew Chem Int Ed Engl 2015; 54:13420-4. [DOI: 10.1002/anie.201504851] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Vanessa Siegmund
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
| | - Stefan Schmelz
- Arbeitsgruppe Strukturbiologie der Autophagie, Abteilung Struktur und Funktion der Proteine, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstr. 7, 38124 Braunschweig (Germany)
| | - Stephan Dickgiesser
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
| | - Jan Beck
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
| | - Aileen Ebenig
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
| | - Heiko Fittler
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
| | - Holm Frauendorf
- Institut für Organische und Biomolekulare Chemie, Zentrale Analytik/Massenspektrometrie, Georg‐August‐Universität Göttingen, Tammannstr. 2, 37077 Göttingen (Germany)
| | - Birgit Piater
- Merck KGaA, Frankfurterstr. 250, 64293 Darmstadt (Germany)
| | | | - Olga Avrutina
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
| | - Andrea Scrima
- Arbeitsgruppe Strukturbiologie der Autophagie, Abteilung Struktur und Funktion der Proteine, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstr. 7, 38124 Braunschweig (Germany)
| | - Hans‐Lothar Fuchsbauer
- Fachbereich Chemie‐ und Biotechnologie, Hochschule Darmstadt, Schnittspahnstraße 12, 64287 Darmstadt (Germany)
| | - Harald Kolmar
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Germany)
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18
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Siegmund V, Schmelz S, Dickgiesser S, Beck J, Ebenig A, Fittler H, Frauendorf H, Piater B, Betz UAK, Avrutina O, Scrima A, Fuchsbauer H, Kolmar H. Durch Design verbrückt: ein konformativ eingeschränkter Transglutaminase‐Marker ermöglicht effiziente ortsspezifische Konjugation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504851] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vanessa Siegmund
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
| | - Stefan Schmelz
- Arbeitsgruppe Strukturbiologie der Autophagie, Abteilung Struktur und Funktion der Proteine, Helmholtz‐Zentrum für Infektionsforschung, Braunschweig (Deutschland)
| | - Stephan Dickgiesser
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
| | - Jan Beck
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
| | - Aileen Ebenig
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
| | - Heiko Fittler
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
| | - Holm Frauendorf
- Institut für Organische und Biomolekulare Chemie, Zentrale Analytik/Massenspektrometrie, Universität Göttingen (Deutschland)
| | | | | | - Olga Avrutina
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
| | - Andrea Scrima
- Arbeitsgruppe Strukturbiologie der Autophagie, Abteilung Struktur und Funktion der Proteine, Helmholtz‐Zentrum für Infektionsforschung, Braunschweig (Deutschland)
| | | | - Harald Kolmar
- Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich‐Weiss‐Straße 4, 64287 Darmstadt (Deutschland)
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19
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Malešević M, Migge A, Hertel TC, Pietzsch M. A fluorescence-based array screen for transglutaminase substrates. Chembiochem 2015; 16:1169-74. [PMID: 25940638 DOI: 10.1002/cbic.201402709] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 01/05/2023]
Abstract
Transglutaminases (EC 2.3.2.13) form an enzyme family that catalyzes the formation of isopeptide bonds between the γ-carboxamide group of glutamine and the ε-amine group of lysine residues of peptides and proteins. Other primary amines can be accepted in place of lysine. Because of their important physiological and pathophysiological functions, transglutaminases have been studied for 60 years. However, the substrate preferences of this enzyme class remain largely elusive. In this study, we used focused combinatorial libraries of 400 peptides to investigate the influence of the amino acids adjacent to the glutamine and lysine residues on the catalysis of isopeptide bond formation by microbial transglutaminase. Using the peptide microarray technology we found a strong positive influence of hydrophobic and basic amino acids, especially arginine, tyrosine, and leucine. Several tripeptide substrates were synthesized, and enzymatic kinetic parameters were determined both by microarray analysis and in solution.
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Affiliation(s)
- Miroslav Malešević
- Institute of Biochemistry and Biotechnology, Department of Enzymology, Project Group gFP5, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany)
| | - Andreas Migge
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Faculty of Sciences I, Biosciences, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany)
| | - Thomas C Hertel
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Faculty of Sciences I, Biosciences, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany)
| | - Markus Pietzsch
- Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Faculty of Sciences I, Biosciences, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle/Saale (Germany).
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20
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Caporale A, Selis F, Sandomenico A, Jotti GS, Tonon G, Ruvo M. The LQSP tetrapeptide is a new highly efficient substrate of microbial transglutaminase for the site-specific derivatization of peptides and proteins. Biotechnol J 2014; 10:154-61. [DOI: 10.1002/biot.201400466] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/13/2014] [Accepted: 10/29/2014] [Indexed: 11/08/2022]
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21
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Kosa NM, Pham KM, Burkart MD. Chemoenzymatic exchange of phosphopantetheine on protein and peptide. Chem Sci 2014; 5:1179-1186. [PMID: 26998215 PMCID: PMC4795179 DOI: 10.1039/c3sc53154f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Evaluation of new acyl carrier protein hydrolase (AcpH, EC 3.1.4.14) homologs from proteobacteria and cyanobacteria reveals significant variation in substrate selectivity and kinetic parameters for phosphopantetheine hydrolysis from carrier proteins. Evaluation with carrier proteins from both primary and secondary metabolic pathways reveals an overall preference for acyl carrier protein (ACP) substrates from type II fatty acid synthases, as well as variable activity for polyketide synthase ACPs and peptidyl carrier proteins (PCP) from non-ribosomal peptide synthases. We also demonstrate the kinetic parameters of these homologs for AcpP and the 11-mer peptide substrate YbbR. These findings enable the fully reversible labeling of all three classes of natural product synthase carrier proteins as well as full and minimal fusion protein constructs.
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Affiliation(s)
- Nicolas M. Kosa
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Kevin M. Pham
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego (UCSD), La Jolla, California, USA
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22
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van Vught R, Pieters RJ, Breukink E. Site-specific functionalization of proteins and their applications to therapeutic antibodies. Comput Struct Biotechnol J 2014; 9:e201402001. [PMID: 24757499 PMCID: PMC3995230 DOI: 10.5936/csbj.201402001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/28/2014] [Accepted: 02/04/2014] [Indexed: 12/19/2022] Open
Abstract
Protein modifications are often required to study structure and function relationships. Instead of the random labeling of lysine residues, methods have been developed to (sequence) specific label proteins. Next to chemical modifications, tools to integrate new chemical groups for bioorthogonal reactions have been applied. Alternatively, proteins can also be selectively modified by enzymes. Herein we review the methods available for site-specific modification of proteins and their applications for therapeutic antibodies.
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Affiliation(s)
- Remko van Vught
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Roland J Pieters
- Department of Medicinal Chemistry and Chemical Biology. Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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23
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Oteng-Pabi SK, Pardin C, Stoica M, Keillor JW. Site-specific protein labelling and immobilization mediated by microbial transglutaminase. Chem Commun (Camb) 2014; 50:6604-6. [DOI: 10.1039/c4cc00994k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microbial transglutaminase (mTG) mediates site-specific propargylation of target proteins, allowing their subsequent modification in in vitro bio-conjugation applications.
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Affiliation(s)
| | | | - Maria Stoica
- Department of Chemistry
- University of Ottawa
- Ottawa, Canada K1N 6N5
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24
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Bains W. Transglutaminse 2 and EGGL, the protein cross-link formed by transglutaminse 2, as therapeutic targets for disabilities of old age. Rejuvenation Res 2013; 16:495-517. [PMID: 23968147 PMCID: PMC3869435 DOI: 10.1089/rej.2013.1452] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/22/2013] [Indexed: 12/17/2022] Open
Abstract
Aging of the extracellular matrix (ECM), the protein matrix that surrounds and penetrates the tissues and binds the body together, contributes significantly to functional aging of tissues. ECM proteins become increasingly cross-linked with age, and this cross-linking is probably important in the decline of the ECM's function. This article reviews the role of ε-(γ-glutamyl)-lysine (EGGL), a cross-link formed by transglutaminase enzymes, and particularly the widely expressed isozyme transglutaminase 2 (TG2), in the aging ECM. There is little direct data on EGGL accumulation with age, and no direct evidence of a role of EGGL in the aging of the ECM with pathology. However, several lines of circumstantial evidence suggest that EGGL accumulates with age, and its association with pathology suggests that this might reflect degradation of ECM function. TG activity increases with age in many circumstances. ECM protein turnover is such that some EGGL made by TG is likely to remain in place for years, if not decades, in healthy tissue, and both EGGL and TG levels are enhanced by age-related diseases. If further research shows EGGL does accumulate with age, removing it could be of therapeutic benefit. Also reviewed is the blockade of TG and active removal of EGGL as therapeutic strategies, with the conclusion that both have promise. EGGL removal may have benefit for acute fibrotic diseases, such as tendinopathy, and for treating generalized decline in ECM function with old age. Extracellular TG2 and EGGL are therefore therapeutic targets both for specific and more generalized diseases of aging.
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Affiliation(s)
- William Bains
- SRF Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge , Cambridge, United Kingdom
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25
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Rachel NM, Pelletier JN. Biotechnological applications of transglutaminases. Biomolecules 2013; 3:870-88. [PMID: 24970194 PMCID: PMC4030973 DOI: 10.3390/biom3040870] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/10/2013] [Accepted: 10/11/2013] [Indexed: 12/28/2022] Open
Abstract
In nature, transglutaminases catalyze the formation of amide bonds between proteins to form insoluble protein aggregates. This specific function has long been exploited in the food and textile industries as a protein cross-linking agent to alter the texture of meat, wool, and leather. In recent years, biotechnological applications of transglutaminases have come to light in areas ranging from material sciences to medicine. There has also been a substantial effort to further investigate the fundamentals of transglutaminases, as many of their characteristics that remain poorly understood. Those studies also work towards the goal of developing transglutaminases as more efficient catalysts. Progress in this area includes structural information and novel chemical and biological assays. Here, we review recent achievements in this area in order to illustrate the versatility of transglutaminases.
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Affiliation(s)
- Natalie M Rachel
- Chimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3T 1J4, Canada.
| | - Joelle N Pelletier
- Chimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3T 1J4, Canada.
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26
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Lee JH, Song E, Lee SG, Kim BG. High-throughput screening for transglutaminase activities using recombinant fluorescent proteins. Biotechnol Bioeng 2013; 110:2865-73. [PMID: 23740563 DOI: 10.1002/bit.24970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/28/2013] [Accepted: 05/28/2013] [Indexed: 01/20/2023]
Abstract
Since detailed evaluation of specific transglutaminases (TGs) from various species requires identification of their substrate specificities, rapid substrate screening method by measurement of their relative activities is in great demand. Here, a novel evaluation method of TG activity was developed using two recombinant fluorescent proteins (FPs), that is, eYFP and DsRed, tagged with TG substrate peptides. By cross-linking the two FPs based on the tagged target peptide sequences at their C-terminus, the expression of co-transformed TG allows quenching of the yellow fluorescence intensities. It was shown that the degree of in vivo fluorescent quenching by the TG activity agrees well with its in vitro reaction data, suggesting that this system can be used to identify relative substrate specificity of TGs for target peptide sequences. Using this method, the lysine substrates of TGs from Bacillus species (BTG) were evaluated, and the newly selected pentapeptide, KTKTN showed almost the same reactivity with the well-known hexa-lysine (K₆) substrate for BTG reaction.
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Affiliation(s)
- Jae-Hun Lee
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Kwanak-Gu, Seoul, South Korea; Institute of Bioengineering, Seoul National University, Kwanak-Gu, Seoul, South Korea
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27
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Microbial transglutaminase displays broad acyl-acceptor substrate specificity. Appl Microbiol Biotechnol 2013; 98:219-30. [PMID: 23615739 DOI: 10.1007/s00253-013-4886-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/20/2013] [Accepted: 03/30/2013] [Indexed: 10/26/2022]
Abstract
The great importance of amide bonds in industrial synthesis has encouraged the search for efficient catalysts of amide bond formation. Microbial transglutaminase (MTG) is heavily utilized in crosslinking proteins in the food and textile industries, where the side chain of a glutamine reacts with the side chain of a lysine, forming a secondary amide bond. Long alkylamines carrying diverse chemical entities can substitute for lysine as acyl-acceptor substrates, to link molecules of interest onto peptides or proteins. Here, we explore short and chemically varied acyl-acceptor substrates, to better understand the nature of nonnatural substrates that are tolerated by MTG, with the aim of diversifying biocatalytic applications of MTG. We show, for the first time, that very short-chain alkyl-based amino acids such as glycine can serve as acceptor substrates. The esterified α-amino acids Thr, Ser, Cys, and Trp--but not Ile--also showed reactivity. Extending the search to nonnatural compounds, a ring near the amine group--particularly if aromatic--was beneficial for reactivity, although ring substituents reduced reactivity. Overall, amines attached to a less hindered carbon increased reactivity. Importantly, very small amines carrying either the electron-rich azide or the alkyne groups required for click chemistry were highly reactive as acyl-acceptor substrates, providing a robust route to minimally modified, "clickable" peptides. These results demonstrate that MTG is tolerant to a variety of chemically varied natural and nonnatural acyl-acceptor substrates, which broadens the scope for modification of Gln-containing peptides and proteins.
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