1
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Wang XB, Zhang CH, Zhang T, Li HZ, Liu YL, Xu ZG, Lei G, Cai CJ, Guo ZY. An efficient peptide ligase engineered from a bamboo asparaginyl endopeptidase. FEBS J 2024; 291:2918-2936. [PMID: 38525648 DOI: 10.1111/febs.17111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024]
Abstract
In recent years, a few asparaginyl endopeptidases (AEPs) from certain higher plants have been identified as efficient peptide ligases with wide applications in protein labeling and cyclic peptide synthesis. Recently, we developed a NanoLuc Binary Technology (NanoBiT)-based peptide ligase activity assay to identify more AEP-type peptide ligases. Herein, we screened 61 bamboo species from 16 genera using this assay and detected AEP-type peptide ligase activity in the crude extract of all tested bamboo leaves. From a popular bamboo species, Bambusa multiplex, we identified a full-length AEP-type peptide ligase candidate (BmAEP1) via transcriptomic sequencing. After its zymogen was overexpressed in Escherichia coli and self-activated in vitro, BmAEP1 displayed high peptide ligase activity, but with considerable hydrolytic activity. After site-directed mutagenesis of its ligase activity determinants, the mutant zymogen of [G238V]BmAEP1 was normally overexpressed in E. coli, but failed to activate itself. To resolve this problem, we developed a novel protease-assisted activation approach in which trypsin was used to cleave the mutant zymogen and was then conveniently removed via ion-exchange chromatography. After the noncovalently bound cap domain was dissociated from the catalytic core domain under acidic conditions, the recombinant [G238V]BmAEP1 displayed high peptide ligase activity with much lower hydrolytic activity and could efficiently catalyze inter-molecular protein ligation and intramolecular peptide cyclization. Thus, the engineered bamboo-derived peptide ligase represents a novel tool for protein labeling and cyclic peptide synthesis.
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Affiliation(s)
- Xin-Bo Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cong-Hui Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Teng Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hao-Zheng Li
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ya-Li Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeng-Guang Xu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Gang Lei
- Sanya Research Base of International Centre for Bamboo and Rattan, China
| | - Chun-Ju Cai
- Sanya Research Base of International Centre for Bamboo and Rattan, China
- International Center for Bamboo and Rattan, State Forestry and Grassland Administration Key Laboratory of Bamboo and Rattan, Beijing, China
| | - Zhan-Yun Guo
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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2
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Tang TMS, Luk LYP. Towards controlling activity of a peptide asparaginyl ligase (PAL) by lumazine synthetase compartmentalization. Faraday Discuss 2024. [PMID: 38832470 DOI: 10.1039/d4fd00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Peptide asparaginyl ligases (PALs) hold significant potential in protein bioconjugation due to their excellent kinetic properties and broad substrate compatibility. However, realizing their full potential in biocatalytic applications requires precise control of their activity. Inspired by nature, we aimed to compartmentalize a representative PAL, OaAEP1-C247A, within protein containers to create artificial organelles with substrate sorting capability. Two encapsulation approaches were explored using engineered lumazine synthases (AaLS). The initial strategy involved tagging the PAL with a super-positively charged GFP(+36) for encapsulation into the super-negatively charged AaLS-13 variant, but it resulted in undesired truncation of the enzyme. The second approach involved genetic fusion of the OaAEP1-C247A with a circularly permutated AaLS variant (cpAaLS) and its co-production with AaLS-13, which successfully enabled compartmentalization of the PAL within a patch-work protein cage. Although the caged PAL retained its activity, it was significantly reduced compared to the free enzyme (∼30-40-fold), likely caused by issues related to OaAEP1-C247A stability and folding. Nevertheless, these findings demonstrated the feasibility of the AaLS encapsulation approach and encourage further optimization in the design of peptide-ligating artificial organelles in E. coli, aiming for a more effective and stable system for protein modifications.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Main Building, Room 1.54, Park Place, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Main Building, Room 1.54, Park Place, Cardiff, CF10 3AT, UK.
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3
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Rehm FBH, Tyler TJ, Zhou Y, Huang YH, Wang CK, Lawrence N, Craik DJ, Durek T. Repurposing a plant peptide cyclase for targeted lysine acylation. Nat Chem 2024:10.1038/s41557-024-01520-1. [PMID: 38789555 DOI: 10.1038/s41557-024-01520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/25/2024] [Indexed: 05/26/2024]
Abstract
Transpeptidases are powerful tools for protein engineering but are largely restricted to acting at protein backbone termini. Alternative enzymatic approaches for internal protein labelling require bulky recognition motifs or non-proteinogenic reaction partners, potentially restricting which proteins can be modified or the types of modification that can be installed. Here we report a strategy for labelling lysine side chain ε-amines by repurposing an engineered asparaginyl ligase, which naturally catalyses peptide head-to-tail cyclization, for versatile isopeptide ligations that are compatible with peptidic substrates. We find that internal lysines with an adjacent leucine residue mimic the conventional N-terminal glycine-leucine substrate. This dipeptide motif enables efficient intra- or intermolecular ligation through internal lysine side chains, minimally leaving an asparagine C-terminally linked to the lysine side chain via an isopeptide bond. The versatility of this approach is demonstrated by the chemoenzymatic synthesis of peptides with non-native C terminus-to-side chain topology and the conjugation of chemically modified peptides to recombinant proteins.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Yan Zhou
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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4
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Frazier CL, Deb D, Weeks AM. Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein C termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593989. [PMID: 38798401 PMCID: PMC11118369 DOI: 10.1101/2024.05.13.593989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In biological systems, ATP provides an energetic driving force for peptide bond formation, but protein chemists lack tools that emulate this strategy. Inspired by the eukaryotic ubiquitination cascade, we developed an ATP-driven platform for C-terminal activation and peptide ligation based on E. coli MccB, a bacterial ancestor of ubiquitin-activating (E1) enzymes that natively catalyzes C-terminal phosphoramidate bond formation. We show that MccB can act on non-native substrates to generate an O-AMPylated electrophile that can react with exogenous nucleophiles to form diverse C-terminal functional groups including thioesters, a versatile class of biological intermediates that have been exploited for protein semisynthesis. To direct this activity towards specific proteins of interest, we developed the Thioesterification C-terminal Handle (TeCH)-tag, a sequence that enables high-yield, ATP-driven protein bioconjugation via a thioester intermediate. By mining the natural diversity of the MccB family, we developed two additional MccB/TeCH-tag pairs that are mutually orthogonal to each other and to the E. coli system, facilitating the synthesis of more complex bioconjugates. Our method mimics the chemical logic of peptide bond synthesis that is widespread in biology for high-yield in vitro manipulation of protein structure with molecular precision.
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Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
| | - Debashrito Deb
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin – Madison, Madison, WI, USA 53706
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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5
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Tang J, Hao M, Liu J, Chen Y, Wufuer G, Zhu J, Zhang X, Zheng T, Fang M, Zhang S, Li T, Ge S, Zhang J, Xia N. Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs. Commun Chem 2024; 7:87. [PMID: 38637620 PMCID: PMC11026461 DOI: 10.1038/s42004-024-01173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the "Asn-Ala-Leu" motif and an N-terminus "Arg-Leu" as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, "Asn-Ala-Leu" and "Arg-Leu" under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.
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Affiliation(s)
- Jiabao Tang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mengling Hao
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Junxian Liu
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Yaling Chen
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Gulimire Wufuer
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Jie Zhu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, 213164, Changzhou, China
| | - Xuejie Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingquan Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mujin Fang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Shiyin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
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6
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de Veer SJ, Zhou Y, Durek T, Craik DJ, Rehm FBH. Tertiary amide bond formation by an engineered asparaginyl ligase. Chem Sci 2024; 15:5248-5255. [PMID: 38577369 PMCID: PMC10988630 DOI: 10.1039/d3sc06352f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
Transpeptidases are powerful tools for site-specific protein modification, enabling the production of tailored biologics to investigate protein function and aiding the development of next-generation therapeutics and diagnostics. Although protein labelling at the N- or C-terminus is readily accomplished using a range of established transpeptidases, these reactions are generally limited to forming products that are linked by a standard (secondary) amide bond. Here we show that, unlike other widely used transpeptidases, an engineered asparaginyl ligase is able to efficiently synthesise tertiary amide bonds by accepting diverse secondary amine nucleophiles. These reactions proceed efficiently under mild conditions (near-neutral pH) and allow the optimal recognition elements for asparaginyl ligases (P1 Asn and P2'' Leu) to be preserved. Certain products, particularly proline-containing products, were found to be protected from recognition by the enzyme, allowing for straightforward sequential labelling of proteins. Additionally, incorporation of 4-azidoproline enables one-pot dual labelling directly at the ligation junction. These capabilities further expand the chemical diversity of asparaginyl ligase-catalysed reactions and provide an alternative approach for straightforward, successive modification of protein substrates.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia
| | - Yan Zhou
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia
| | - Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia
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7
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Arnott ZLP, Morgan HE, Hollingsworth K, Stevenson CME, Collins LJ, Tamasanu A, Machin DC, Dolan JP, Kamiński TP, Wildsmith GC, Williamson DJ, Pickles IB, Warriner SL, Turnbull WB, Webb ME. Quantitative N- or C-Terminal Labelling of Proteins with Unactivated Peptides by Use of Sortases and a d-Aminopeptidase. Angew Chem Int Ed Engl 2024; 63:e202310862. [PMID: 38072831 DOI: 10.1002/anie.202310862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 01/13/2024]
Abstract
Quantitative and selective labelling of proteins is widely used in both academic and industrial laboratories, and catalytic labelling of proteins using transpeptidases, such as sortases, has proved to be a popular strategy for such selective modification. A major challenge for this class of enzymes is that the majority of procedures require an excess of the labelling reagent or, alternatively, activated substrates rather than simple commercially sourced peptides. We report the use of a coupled enzyme strategy which enables quantitative N- and C-terminal labelling of proteins using unactivated labelling peptides. The use of an aminopeptidase in conjunction with a transpeptidase allows sequence-specific degradation of the peptide by-product, shifting the equilibrium to favor product formation, which greatly enhances the reaction efficiency. Subsequent optimisation of the reaction allows N-terminal labelling of proteins using essentially equimolar ratios of peptide label to protein and C-terminal labelling with only a small excess. Minimizing the amount of substrate required for quantitative labelling has the potential to improve industrial processes and facilitate the use of transpeptidation as a method for protein labelling.
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Affiliation(s)
- Zoe L P Arnott
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present address: Centre for Process Innovation, Central Park, The Nigel Perry Building, 1 Union St, Darlington, DL1 1GL, United Kingdom
| | - Holly E Morgan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: Ashfield MedComms, City Tower, Piccadilly Plaza, Manchester, M1 4BT, United Kingdom
| | - Kristian Hollingsworth
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Charlotte M E Stevenson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Lawrence J Collins
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Alexandra Tamasanu
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Darren C Machin
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Jonathan P Dolan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: School of Chemical and Physical Sciences & Centre for Glycoscience Research and Training, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Tomasz P Kamiński
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Gemma C Wildsmith
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Daniel J Williamson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: Iksuda Therapeutics, The Biosphere, Draymans Way, Newcastle upon Tyne, NE4 5BX, United Kingdom
| | - Isabelle B Pickles
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Present Address: York Structural Biology Laboratory, Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Stuart L Warriner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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8
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Lu Z, Ge R, Zheng B, Zheng P. Enzymatic Protein Immobilization for Nanobody Array. Molecules 2024; 29:366. [PMID: 38257279 PMCID: PMC10820937 DOI: 10.3390/molecules29020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Antibody arrays play a pivotal role in the detection and quantification of biomolecules, with their effectiveness largely dependent on efficient protein immobilization. Traditional methods often use heterobifunctional cross-linking reagents for attaching functional residues in proteins to corresponding chemical groups on the substrate surface. However, this method does not control the antibody's anchoring point and orientation, potentially leading to reduced binding efficiency and overall performance. Another method using anti-antibodies as intermediate molecules to control the orientation can be used but it demonstrates lower efficiency. Here, we demonstrate a site-specific protein immobilization strategy utilizing OaAEP1 (asparaginyl endopeptidase) for building a nanobody array. Moreover, we used a nanobody-targeting enhanced green fluorescent protein (eGFP) as the model system to validate the protein immobilization method for building a nanobody array. Finally, by rapidly enriching eGFP, this method further highlights its potential for rapid diagnostic applications. This approach, characterized by its simplicity, high efficiency, and specificity, offers an advancement in the development of surface-modified protein arrays. It promises to enhance the sensitivity and accuracy of biomolecule detection, paving the way for broader applications in various research and diagnostic fields.
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Affiliation(s)
| | | | | | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; (Z.L.); (R.G.); (B.Z.)
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9
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Tang TM, Mason JM. Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins. JACS AU 2023; 3:3290-3296. [PMID: 38155637 PMCID: PMC10751764 DOI: 10.1021/jacsau.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/30/2023]
Abstract
Peptide backbone cyclization is commonly observed in nature and is increasingly applied to proteins and peptides to improve thermal and chemical stability and resistance to proteolytic enzymes and enhance biological activity. However, chemical synthesis of head-to-tail cyclic peptides and proteins is challenging, is often low yielding, and employs toxic and unsustainable reagents. Plant derived asparaginyl endopeptidases such as OaAEP1 have been employed to catalyze the head-to-tail cyclization of peptides in vitro, offering a safer and more sustainable alternative to chemical methods. However, while asparaginyl endopeptidases have been used in vitro and in native and transgenic plant species, they have never been used to generate recombinant cyclic proteins in live recombinant organisms outside of plants. Using dihydrofolate reductase as a proof of concept, we show that a truncated OaAEP1 variant C247A is functional in the Escherichia coli physiological environment and can therefore be coexpressed with a substrate protein to enable concomitant in situ cyclization. The bacterial system is ideal for cyclic protein production owing to the fast growth rate, durability, ease of use, and low cost. This streamlines cyclic protein production via a biocatalytic process with fast kinetics and minimal ligation scarring, while negating the need to purify the enzyme, substrate, and reaction mixtures individually. The resulting cyclic protein was characterized in vitro, demonstrating enhanced thermal stability compared to the corresponding linear protein without impacting enzyme activity. We anticipate this convenient method for generating cyclic peptides will have broad utility in a range of biochemical and chemical applications.
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Affiliation(s)
- T. M.
Simon Tang
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
| | - Jody M. Mason
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
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10
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Zeng Y, Shi W, Liu Z, Xu H, Liu L, Hang J, Wang Y, Lu M, Zhou W, Huang W, Tang F. C-terminal modification and functionalization of proteins via a self-cleavage tag triggered by a small molecule. Nat Commun 2023; 14:7169. [PMID: 37935692 PMCID: PMC10630284 DOI: 10.1038/s41467-023-42977-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
The precise modification or functionalization of the protein C-terminus is essential but full of challenges. Herein, a chemical approach to modify the C-terminus is developed by fusing a cysteine protease domain on the C-terminus of the protein of interest, which could achieve the non-enzymatic C-terminal functionalization by InsP6-triggered cysteine protease domain self-cleavage. This method demonstrates a highly efficient way to achieve protein C-terminal functionalization and is compatible with a wide range of amine-containing molecules and proteins. Additionally, a reversible C-terminal de-functionalization is found by incubating the C-terminal modified proteins with cysteine protease domain and InsP6, providing a tool for protein functionalization and de-functionalization. Last, various applications of protein C-terminal functionalization are provided in this work, as demonstrated by the site-specific assembly of nanobody drug conjugates, the construction of a bifunctional antibody, the C-terminal fluorescent labeling, and the C-terminal transpeptidation and glycosylation.
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Affiliation(s)
- Yue Zeng
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Wei Shi
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Zhi Liu
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Hao Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Liya Liu
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Jiaying Hang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Yongqin Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Mengru Lu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Zhou
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Huang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Feng Tang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China.
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11
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Liu Q, Li D, Pan X, Liang Y. Targeted therapy using engineered extracellular vesicles: principles and strategies for membrane modification. J Nanobiotechnology 2023; 21:334. [PMID: 37717008 PMCID: PMC10505332 DOI: 10.1186/s12951-023-02081-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/26/2023] [Indexed: 09/18/2023] Open
Abstract
Extracellular vesicles (EVs) are 30-150 nm membrane-bound vesicles naturally secreted by cells and play important roles in intercellular communication by delivering regulatory molecules such as proteins, lipids, nucleic acids and metabolites to recipient cells. As natural nano-carriers, EVs possess desirable properties such as high biocompatibility, biological barrier permeability, low toxicity, and low immunogenicity, making them potential therapeutic delivery vehicles. EVs derived from specific cells have inherent targeting capacity towards specific cell types, which is yet not satisfactory enough for targeted therapy development and needs to be improved. Surface modifications endow EVs with targeting abilities, significantly improving their therapeutic efficiency. Herein, we first briefly introduce the biogenesis, composition, uptake and function of EVs, and review the cargo loading approaches for EVs. Then, we summarize the recent advances in surface engineering strategies of EVs, focusing on the applications of engineered EVs for targeted therapy. Altogether, EVs hold great promise for targeted delivery of various cargos, and targeted modifications show promising effects on multiple diseases.
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Affiliation(s)
- Qisong Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
- Department of Orthopaedics, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), China, Shenzhen, 518000, China
| | - Defeng Li
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Xiaohua Pan
- Department of Orthopaedics, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), China, Shenzhen, 518000, China.
| | - Yujie Liang
- Department of Orthopaedics, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), China, Shenzhen, 518000, China.
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Institute of Mental Health, Shenzhen Mental Health Center, Shenzhen Clinical Research Center for Mental Disorders, Shenzhen, 518020, Guangdong, China.
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12
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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13
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Abstract
A variant originated from Oldenlandia affinis asparaginyl ligase, OaAEP1-C247A, has emerged as an ideal tool for protein labeling. However, its preparation was laborious and time-consuming. It is recombinantly produced as a zymogen, requiring acid activation and four chromatographic steps; despite these extensive steps, the catalytically active enzyme exhibited only moderate purity. Here, we report a novel preparation protocol, in which the cap and catalytically active core domains are produced as separate entities. The active enzyme can be obtained in two chromatographic steps, immobilized metal affinity chromatography (IMAC) and size exclusion chromatography (SEC), with no acid activation required, thereby shortening the purification procedure from at least 2 days to less than 6 h. In addition to the original C247A mutation which enhanced reaction with various amino nucleophiles, an extra D29E mutation was introduced to prevent self-cleavage, which led to noticeable improvements in homogeneity and activity of the enzyme. Indeed, the resulting "split AEP" (i.e., core domain of OaAEP1-D29E/C247A) exhibited improved catalytic efficiency constant (kcat/KM) that was found to be ∼3-fold higher than that of the original acid-activated counterpart (OaAEP1-C247A). Furthermore, we described a protein labeling protocol that couples the enzymatic reaction with an irreversible chemical transformation, thereby enabling high conversion of labeled protein with a lowered amount of reagent. Precisely, an alternative Asn-Cys-Leu (NCL) recognition sequence was used for substrate recognition. As the byproduct contains an N-terminal cysteine, it can be transformed into an inert 1,2 aminothiol motif by reacting with formylphenyl boronic acid (FPBA). Finally, the opportunities and challenges associated with the use of asparaginyl ligase are discussed.
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Affiliation(s)
- Muge Ma
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Simon T M Tang
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Matthew T Dickerson
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom.
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14
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Singh AK, Krężel A. Calcium-assisted sortase A cleavage of SUMOylated metallothionein constructs leads to high-yield production of human MT3. Microb Cell Fact 2023; 22:125. [PMID: 37434134 DOI: 10.1186/s12934-023-02134-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/24/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Mammalian metallothioneins (MTs) are small (6-7 kDa), intracellular, cysteine-rich, metal-binding proteins involved, inter alia, in the homeostasis of zinc and copper, detoxification of heavy metals, antioxidation against reactive oxygen species, and protection against DNA damage. The high cysteine content (~ 30%) in MTs makes them toxic to bacterial cells during protein production, resulting in low yield. To address this issue, we present for the first time a combinatorial approach using the small ubiquitin-like modifier (SUMO) and/or sortase as fusion tags for high-level expression of human MT3 in E. coli and its purification by three different strategies. RESULTS Three different plasmids were generated using SUMO, sortase A pentamutant (eSrtA), and sortase recognition motif (LPETG) as removable fusion tags for high-level expression and purification of human MT3 from the bacterial system. In the first strategy, SUMOylated MT3 was expressed and purified using Ulp1-mediated cleavage. In the second strategy, SUMOylated MT3 with a sortase recognition motif at the N-terminus of MT3 was expressed and purified using sortase-mediated cleavage. In the final strategy, the fusion protein His6-SUMO-eSrtA-LPETG-MT3 was expressed and purified by one-step sortase-mediated inducible on-bead autocleavage. Using these three strategies the apo-MT3 was purified in a yield of 11.5, 11, and 10.8 mg/L, respectively, which is the highest yield achieved for MT expression and purification to date. No effect of MT3 on Ni2+-containing resin was observed. CONCLUSION The SUMO/sortase-based strategy used as the production system for MT3 resulted in a very high expression level and protein production yield. The apo-MT3 purified by this strategy contained an additional glycine residue and had similar metal binding properties as WT-MT3. This SUMO-sortase fusion system is a simple, robust, and inexpensive one-step purification approach for various MTs as well as other toxic proteins with very high yield via immobilized metal affinity chromatography (IMAC).
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Affiliation(s)
- Avinash Kumar Singh
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383, Wrocław, Poland.
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15
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Obeng EM, Fulcher AJ, Wagstaff KM. Harnessing sortase A transpeptidation for advanced targeted therapeutics and vaccine engineering. Biotechnol Adv 2023; 64:108108. [PMID: 36740026 DOI: 10.1016/j.biotechadv.2023.108108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The engineering of potent prophylactic and therapeutic complexes has always required careful protein modification techniques with seamless capabilities. In this light, methods that favor unobstructed multivalent targeting and correct antigen presentations remain essential and very demanding. Sortase A (SrtA) transpeptidation has exhibited these attributes in various settings over the years. However, its applications for engineering avidity-inspired therapeutics and potent vaccines have yet to be significantly noticed, especially in this era where active targeting and multivalent nanomedications are in great demand. This review briefly presents the SrtA enzyme and its associated transpeptidation activity and describes interesting sortase-mediated protein engineering and chemistry approaches for achieving multivalent therapeutic and antigenic responses. The review further highlights advanced applications in targeted delivery systems, multivalent therapeutics, adoptive cellular therapy, and vaccine engineering. These innovations show the potential of sortase-mediated techniques in facilitating the development of simple plug-and-play nanomedicine technologies against recalcitrant diseases and pandemics such as cancer and viral infections.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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16
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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17
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Xia Y, Li F, Zhang X, Balamkundu S, Tang F, Hu S, Lescar J, Tam JP, Liu CF. A Cascade Enzymatic Reaction Scheme for Irreversible Transpeptidative Protein Ligation. J Am Chem Soc 2023; 145:6838-6844. [PMID: 36924109 DOI: 10.1021/jacs.2c13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Enzymatic peptide ligation holds great promise in the study of protein functions and development of protein therapeutics. Owing to their high catalytic efficiency and a minimal tripeptide recognition motif, peptidyl asparaginyl ligases (PALs) are particularly useful tools for bioconjugation. However, as an inherent limitation of transpeptidases, PAL-mediated ligation is reversible, requiring a large excess of one of the ligation partners to shift the reaction equilibrium in the forward direction. Herein, we report a method to make PAL-mediated intermolecular ligation irreversible by coupling it to glutaminyl cyclase (QC)-catalyzed pyroglutamyl formation. In this method, the acyl donor substrate of PALs is designed to have glutamine at the P1' position of the Asn-P1'-P2' tripeptide PAL recognition motif. Upon ligation with an acyl acceptor substrate, the acyl donor substrate releases a leaving group in which the exposed N-terminal glutamine is cyclized by QC, quenching the Gln Nα-amine in a lactam. Using this method, PAL-mediated ligation can achieve near-quantitative yields even at an equal molar ratio between the two ligation partners. We have demonstrated this method for a wide range of applications, including protein-to-protein ligations. We anticipate that this cascade enzymatic reaction scheme will make PAL enzymes well suited for numerous new uses in biotechnology.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Fupeng Li
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Fan Tang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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18
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Antonenko A, Singh AK, Mosna K, Krężel A. OaAEP1 Ligase-Assisted Chemoenzymatic Synthesis of Full Cysteine-Rich Metal-Binding Cyanobacterial Metallothionein SmtA. Bioconjug Chem 2023. [PMID: 36921066 PMCID: PMC10119931 DOI: 10.1021/acs.bioconjchem.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Among all approaches used for the semisynthesis of natural or chemically modified products, enzyme-assisted ligation is among the most promising and dynamically developing approaches. Applying an efficient C247A mutant of Oldenlandia affinis plant ligase OaAEP1 and solid-phase peptide synthesis chemistry, we present the chemoenzymatic synthesis of a complete sequence of the cysteine-rich and metal-binding cyanobacterial metallothionein Synechococcus metallothionein A (SmtA). Zn(II) and Cd(II) binding to the newly synthesized SmtA showed identical properties to the protein expressed in Escherichia coli. The presented approach is the first example of the use of OaAEP1 mutant for total protein synthesis of metallothionein, which occurs in mild conditions preventing cysteine thiol oxidation. The recognition motif of the applied enzyme could naturally occur in the protein structure or be synthetically or genetically incorporated in some loops or secondary structure elements. Therefore, we envision that this strategy can be used for efficiently obtaining SmtA and for a wide range of proteins and their derivatives.
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Affiliation(s)
- Anastasiia Antonenko
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Avinash Kumar Singh
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Karolina Mosna
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
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19
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Dunleavy R, Chandrasekaran S, Crane BR. Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy. Bioconjug Chem 2023:10.1021/acs.bioconjchem.3c00029. [PMID: 36921260 PMCID: PMC10502183 DOI: 10.1021/acs.bioconjchem.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.
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Affiliation(s)
- Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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20
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Hemu X, Zhang X, Chang HY, Poh JE, Tam JP. Consensus design and engineering of an efficient and high-yield peptide asparaginyl ligase for protein cyclization and ligation. J Biol Chem 2023; 299:102997. [PMID: 36764523 PMCID: PMC10017362 DOI: 10.1016/j.jbc.2023.102997] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Plant legumains are Asn/Asp-specific endopeptidases that have diverse functions in plants. Peptide asparaginyl ligases (PALs) are a special legumain subtype that primarily catalyze peptide bond formation rather than hydrolysis. PALs are versatile protein engineering tools but are rarely found in nature. To overcome this limitation, here we describe a two-step method to design and engineer a high-yield and efficient recombinant PAL based on commonly found asparaginyl endopeptidases. We first constructed a consensus sequence derived from 1500 plant legumains to design the evolutionarily stable legumain conLEG that could be produced in E. coli with 20-fold higher yield relative to that for natural legumains. We then applied the ligase-activity determinant hypothesis to exploit conserved residues in PAL substrate-binding pockets and convert conLEG into conPAL1-3. Functional studies showed that conLEG is primarily a hydrolase, whereas conPALs are ligases. Importantly, conPAL3 is a superefficient and broadly active PAL for protein cyclization and ligation.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hong Yi Chang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Jin En Poh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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21
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Okuda A, Shimizu M, Inoue R, Urade R, Sugiyama M. Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance. Angew Chem Int Ed Engl 2023; 62:e202214412. [PMID: 36347766 DOI: 10.1002/anie.202214412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/10/2022]
Abstract
Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.
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Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
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22
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Ma Q, He B, Tang G, Xie R, Zheng P. Enzymatic Protein Immobilization on Amino-Functionalized Nanoparticles. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010379. [PMID: 36615576 PMCID: PMC9822503 DOI: 10.3390/molecules28010379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
The immobilization of proteins on nanoparticles has received much attention in recent years. Among different approaches, enzymatic protein immobilization shows unique advantages because of its site-specific connection. OaAEP1 is a recently engineered peptide ligase which can specifically recognize an N-terminal GL residue (NH2-Gly-Leu) and a C-terminal NGL amino acid residue (Asn-Gly-Leu-COOH) and ligates them efficiently. Herein, we report OaAEP1-mediated protein immobilization on synthetic magnetic nanoparticles. Our work showed that OaAEP1 could mediate C-terminal site-specific protein immobilization on the amino-functionalized Fe3O4 nanoparticles. Our work demonstrates a new method for site-specific protein immobilization on nanoparticles.
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23
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Morgan H, Arnott ZLP, Kamiński TP, Turnbull WB, Webb ME. Combined Application of Orthogonal Sortases and Depsipeptide Substrates for Dual Protein Labeling. Bioconjug Chem 2022; 33:2341-2347. [PMID: 36356167 PMCID: PMC9782347 DOI: 10.1021/acs.bioconjchem.2c00411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Staphylococcus aureus sortase A is a transpeptidase that has been extensively exploited for site-specific modification of proteins and was originally used to attach a labeling reagent containing an LPXTG recognition sequence to a protein or peptide with an N-terminal glycine. Sortase mutants with other recognition sequences have also been reported, but in all cases, the reversibility of the transpeptidation reaction limits the efficiency of sortase-mediated labeling reactions. For the wildtype sortase, depsipeptide substrates, in which the scissile peptide bond is replaced with an ester, allow effectively irreversible sortase-mediated labeling as the alcohol byproduct is a poor competing nucleophile. In this paper, the use of depsipeptide substrates for evolved sortase variants is reported. Substrate specificities of three sortases have been investigated allowing identification of an orthogonal pair of enzymes accepting LPEToG and LPESoG depsipeptides, which have been applied to dual N-terminal labeling of a model protein mutant containing a second, latent N-terminal glycine residue. The method provides an efficient orthogonal site-specific labeling technique that further expands the biochemical protein labeling toolkit.
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24
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Scinto SL, Reagle TR, Fox JM. Affinity Bioorthogonal Chemistry (ABC) Tags for Site-Selective Conjugation, On-Resin Protein-Protein Coupling, and Purification of Protein Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207661. [PMID: 36058881 PMCID: PMC10029600 DOI: 10.1002/anie.202207661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 11/12/2022]
Abstract
The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the nickel-iminodiacetate (Ni-IDA) resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity-based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC-tagging works with a range of site-selective bioconjugation methods with proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions to provide protein-protein conjugates.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Tyler R Reagle
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
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25
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Fottner M, Heimgärtner J, Gantz M, Mühlhofer R, Nast-Kolb T, Lang K. Site-Specific Protein Labeling and Generation of Defined Ubiquitin-Protein Conjugates Using an Asparaginyl Endopeptidase. J Am Chem Soc 2022; 144:13118-13126. [PMID: 35850488 PMCID: PMC9335880 DOI: 10.1021/jacs.2c02191] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Asparaginyl endopeptidases
(AEPs) have recently been widely utilized
for peptide and protein modification. Labeling is however restricted
to protein termini, severely limiting flexibility and scope in creating
diverse conjugates as needed for therapeutic and diagnostic applications.
Here, we use genetic code expansion to site-specifically modify target
proteins with an isopeptide-linked glycylglycine moiety that serves
as an acceptor nucleophile in AEP-mediated transpeptidation with various
probes containing a tripeptidic recognition motif. Our approach allows
simple and flexible labeling of recombinant proteins at any internal
site and leaves a minimal, entirely peptidic footprint (NGG) in the
conjugation product. We show site-specific labeling of diverse target
proteins with various biophysical probes, including dual labeling
at an internal site and the N-terminus. Furthermore, we harness AEP-mediated
transpeptidation for generation of ubiquitin- and ubiquitin-like-modifier
conjugates bearing a native isopeptide bond and only one point mutation
in the linker region.
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Affiliation(s)
- Maximilian Fottner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Johannes Heimgärtner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maximilian Gantz
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Rahel Mühlhofer
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Timon Nast-Kolb
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27), Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Kathrin Lang
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.,Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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26
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Wang Z, Zhao Z, Li G, Zheng P. Single-Molecule Force Spectroscopy Reveals the Dynamic HgS Coordination Site in the De Novo-Designed Metalloprotein α 3DIV. J Phys Chem Lett 2022; 13:5372-5378. [PMID: 35678420 DOI: 10.1021/acs.jpclett.2c01316] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The de novo-designed metalloprotein α3DIV binds to mercury via three cysteine residues under dynamic conditions. An unusual trigonal three-coordinate HgS3 site is formed in the protein in basic solution, whereas a linear two-coordinate HgS2 site is formed in acidic solution. Furthermore, it is unknown whether the two coordinated cysteines in the HgS2 site are fixed or not, which may lead to more dynamics. However, the signal for HgS2 sites with different cysteines may be similar or may be averaged and indistinguishable. To circumvent this problem, we adopt a single-molecule approach to study one mercury site at a time. Using atomic force microscopy-based single-molecule force spectroscopy, the protein is unfolded, and the HgS site is ruptured. The results confirm the formation of HgS3 and HgS2 sites at different pH values. Moreover, it is found that any two of the three cysteines in the protein bind to mercury in the HgS2 site.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Zhongxing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
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27
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Nie JY, Song GB, Deng YB, Zheng P. Single-Molecule Force Spectroscopy Reveals Stability of mitoNEET and its [2Fe2Se] Cluster in Weakly Acidic and Basic Solutions. Chemistry 2022; 11:e202200056. [PMID: 35608094 PMCID: PMC9127745 DOI: 10.1002/open.202200056] [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: 03/16/2022] [Revised: 04/21/2022] [Indexed: 11/05/2022]
Abstract
The outer mitochondrial membrane protein mitoNEET (mNT) is a recently identified iron-sulfur protein containing a unique Fe2 S2 (His)1 (Cys)3 metal cluster with a single Fe-N(His87) coordinating bond. This labile Fe-N bond led to multiple unfolding/rupture pathways of mNT and its cluster by atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), one of most common tools for characterizing the molecular mechanics. Although previous ensemble studies showed that this labile Fe-N(His) bond is essential for protein function, they also indicated that the protein and its [2Fe2S] cluster are stable under acidic conditions. Thus, we applied AFM-SMFS to measure the stability of mNT and its cluster at pH values of 6, 7, and 8. Indeed, all previous multiple unfolding pathways of mNT were still observed. Moreover, single-molecule measurements revealed that the stabilities of the protein and the [2Fe2S] cluster are consistent at these pH values with only ≈20 pN force differences. Thus, we found that the behavior of the protein is consistent in both weakly acidic and basic solutions despite a labile Fe-N bond.
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Affiliation(s)
- Jing-Yuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Guo-Bin Song
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yi-Bing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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28
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Morgan HE, Turnbull WB, Webb ME. Challenges in the use of sortase and other peptide ligases for site-specific protein modification. Chem Soc Rev 2022; 51:4121-4145. [PMID: 35510539 PMCID: PMC9126251 DOI: 10.1039/d0cs01148g] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Site-specific protein modification is a widely-used biochemical tool. However, there are many challenges associated with the development of protein modification techniques, in particular, achieving site-specificity, reaction efficiency and versatility. The engineering of peptide ligases and their substrates has been used to address these challenges. This review will focus on sortase, peptidyl asparaginyl ligases (PALs) and variants of subtilisin; detailing how their inherent specificity has been utilised for site-specific protein modification. The review will explore how the engineering of these enzymes and substrates has led to increased reaction efficiency mainly due to enhanced catalytic activity and reduction of reversibility. It will also describe how engineering peptide ligases to broaden their substrate scope is opening up new opportunities to expand the biochemical toolkit, particularly through the development of techniques to conjugate multiple substrates site-specifically onto a protein using orthogonal peptide ligases. We highlight chemical and biochemical strategies taken to optimise peptide and protein modification using peptide ligases.![]()
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Affiliation(s)
- Holly E Morgan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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29
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Yang E, Liu Q, Huang G, Liu J, Wei W. Engineering nanobodies for next-generation molecular imaging. Drug Discov Today 2022; 27:1622-1638. [PMID: 35331925 DOI: 10.1016/j.drudis.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/04/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
In recent years, nanobodies have emerged as ideal imaging agents for molecular imaging. Molecular nanobody imaging combines the specificity of nanobodies with the sensitivity of state-of-the-art molecular imaging modalities, such as positron emission tomography (PET). Given that modifications of nanobodies alter their pharmacokinetics (PK), the engineering strategies that combine nanobodies with radionuclides determine the effectiveness, reliability, and safety of the molecular imaging probes. In this review, we introduce conjugation strategies that have been applied to nanobodies, including random conjugation, 99mTc tricarbonyl chemistry, sortase A-mediated site-specific conjugation, maleimide-cysteine chemistry, and click chemistries. We also summarize the latest advances in nanobody tracers, emphasizing their preclinical and clinical use. In addition, we elaborate on nanobody-based near-infrared fluorescence (NIRF) imaging and image-guided surgery.
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Affiliation(s)
- Erpeng Yang
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China
| | - Qiufang Liu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Gang Huang
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China.
| | - Weijun Wei
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China.
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30
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Rehm FBH, Tyler TJ, de Veer SJ, Craik DJ, Durek T. Enzymatic C-to-C Protein Ligation. Angew Chem Int Ed Engl 2022; 61:e202116672. [PMID: 35018698 PMCID: PMC9303898 DOI: 10.1002/anie.202116672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 01/11/2023]
Abstract
Transpeptidase‐catalyzed protein and peptide modifications have been widely utilized for generating conjugates of interest for biological investigation or therapeutic applications. However, all known transpeptidases are constrained to ligating in the N‐to‐C orientation, limiting the scope of attainable products. Here, we report that an engineered asparaginyl ligase accepts diverse incoming nucleophile substrate mimetics, particularly when a means of selectively quenching the reactivity of byproducts released from the recognition sequence is employed. In addition to directly catalyzing formation of l‐/d‐ or α‐/β‐amino acid junctions, we find C‐terminal Leu‐ethylenediamine (Leu‐Eda) motifs to be bona fide mimetics of native N‐terminal Gly‐Leu sequences. Appending a C‐terminal Leu‐Eda to synthetic peptides or, via an intein‐splicing approach, to recombinant proteins enables direct transpeptidase‐catalyzed C‐to‐C ligations. This work significantly expands the synthetic scope of enzyme‐catalyzed protein transpeptidation reactions.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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31
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Ji F, Ren J, Vincke C, Jia L, Muyldermans S. Nanobodies: From Serendipitous Discovery of Heavy Chain-Only Antibodies in Camelids to a Wide Range of Useful Applications. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:3-17. [PMID: 35157266 DOI: 10.1007/978-1-0716-2075-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The presence of unique heavy chain-only antibodies (HCAbs) in camelids was discovered at Vrije Universiteit Brussel (VUB, Brussels, Belgium) at a time when many researchers were exploring the cloning and expression of smaller antigen-binding fragments (Fv and Fab) from hybridoma-derived antibodies. The potential importance of this discovery was anticipated, and efforts were immediately undertaken to understand the emergence and ontogeny of these HCAbs as well as to investigate the applications of the single-domain antigen-binding variable domains of HCAbs (nanobodies). Nanobodies were demonstrated to possess multiple biochemical and biophysical advantages over other antigen-binding antibody fragments and alternative scaffolds. Today, nanobodies have a significant and growing impact on research, biotechnology, and medicine.
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Affiliation(s)
- Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Cécile Vincke
- Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.,Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China. .,Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.
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32
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Rodríguez V. Insights into post-translational modification enzymes from RiPPs: A toolkit for applications in peptide synthesis. Biotechnol Adv 2022; 56:107908. [PMID: 35032597 DOI: 10.1016/j.biotechadv.2022.107908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 12/30/2021] [Accepted: 01/09/2022] [Indexed: 11/02/2022]
Abstract
The increasing length and complexity of peptide drug candidates foster the development of novel strategies for their manufacture, which should include sustainable and efficient technologies. In this context, including enzymatic catalysis in the production of peptide molecules has gained interest. Here, several enzymes from ribosomally synthesized and post-translationally modified peptides biosynthesis pathways are reviewed, with attention to their capacity to introduce stability-promoting structural features on peptides, providing an initial framework towards their use in therapeutic peptide production processes.
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Affiliation(s)
- Vida Rodríguez
- Faculty of Engineering, Science and Technology, Bernardo O'Higgins University, Viel 1497, Santiago, Chile.
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33
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Rehm FBH, Tyler TJ, de Veer SJ, Craik DJ, Durek T. Enzymatic C‐to‐C Protein Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fabian B. H. Rehm
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - Tristan J. Tyler
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - Simon J. de Veer
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - David J. Craik
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - Thomas Durek
- The University of Queensland Institute for Molecular Bioscience 306 Carmody RdLvl 7 North 4072 Brisbane AUSTRALIA
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34
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Li D, Peng Q, Huang C, Zang B, Ren J, Ji F, Muyldermans S, Jia L. Cytoplasmic Expression of Nanobodies with Formylglycine Generating Enzyme Tag and Conversion to a Bio-Orthogonal Aldehyde Group. Methods Mol Biol 2022; 2446:357-371. [PMID: 35157283 DOI: 10.1007/978-1-0716-2075-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanobodies (Nbs) can be successfully retrieved following phage, bacterial, yeast, or ribosome display of immune, synthetic, or naïve libraries. However, after panning, multiple individual Nb clones need to be screened and assessed for solubility, antigen specificity, affinity, and potential biological function. Therefore, it is highly desirable to have a convenient expression strategy to obtain sufficient protein for in-depth characterization of the Nbs. The presence of a purification and detection tag, as well as a chemically reactive group to enable simple generation of Nb derivatives, would be of great help in this regard. Here, we provide a general protocol for high yield cytoplasmic expression and purification of formylglycine generating enzyme (FGE)-tagged Nbs. The cysteine within the FGE tag is easily converted to formylglycine by passing the FGE-tag containing Nb over a continuous-flow bio-catalysis system. The aldehyde group within the formylglycine side chain at the C-terminal end of the Nb is suitably located for subsequent bio-orthogonal reactions to fluorescent dyes, biotin, polyethylene glycol, or chromatography resins. We also include methods for production of high yield recombinant FGE, as well as conditions for its immobilization on Sepharose to produce the continuous-flow bio-catalysis system.
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Affiliation(s)
- Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Qiang Peng
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Chungdong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Berlin Zang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China.
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
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35
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Rehm FBH, Tyler TJ, Yap K, de Veer SJ, Craik DJ, Durek T. Enzymatic C-Terminal Protein Engineering with Amines. J Am Chem Soc 2021; 143:19498-19504. [PMID: 34761936 DOI: 10.1021/jacs.1c08976] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemoenzymatic protein and peptide modification is a powerful means of generating defined, homogeneous conjugates for a range of applications. However, the use of transpeptidases is limited by the need to prepare synthetic peptide conjugates to be ligated, bulky recognition tags remaining in the product, and inefficient substrate turnover. Here, we report a peptide/protein labeling strategy that utilizes a promiscuous, engineered transpeptidase to irreversibly incorporate diverse, commercially available amines at a C-terminal asparagine. To demonstrate the utility of this approach, we prepare a protein-drug conjugate, generate a genetically inaccessible C-to-C protein fusion, and site specifically label both termini of a single protein in sequential steps.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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36
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Tran HNT, Tran P, Deuis JR, McMahon KL, Yap K, Craik DJ, Vetter I, Schroeder CI. Evaluation of Efficient Non-reducing Enzymatic and Chemical Ligation Strategies for Complex Disulfide-Rich Peptides. Bioconjug Chem 2021; 32:2407-2419. [PMID: 34751572 PMCID: PMC10167913 DOI: 10.1021/acs.bioconjchem.1c00452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Double-knotted peptides identified in venoms and synthetic bivalent peptide constructs targeting ion channels are emerging tools for the study of ion channel pharmacology and physiology. These highly complex and disulfide-rich peptides contain two individual cystine knots, each comprising six cysteines and three disulfide bonds. Until now, native double-knotted peptides, such as Hi1a and DkTx, have only been isolated from venom or produced recombinantly, whereas engineered double-knotted peptides have successfully been produced through enzymatic ligation using sortase A to form a seamless amide bond at the ligation site between two knotted toxins, and by alkyne/azide click chemistry, joining two peptide knots via a triazole linkage. To further pursue these double-knotted peptides as pharmacological tools or probes for therapeutically relevant ion channels, we sought to identify a robust methodology resulting in a high yield product that lends itself to rapid production and facile mutational studies. In this study, we evaluated the ligation efficiency of enzymatic (sortase A5°, butelase 1, wild-type OaAEP 1, C247A-OaAEP 1, and peptiligase) and mild chemical approaches (α-ketoacid-hydroxylamine, KAHA) for forming a native amide bond linking the toxins while maintaining the native disulfide connectivity of each pre-folded peptide. We used two NaV1.7 inhibitors: PaurTx3, a spider-derived gating modifier peptide, and KIIIA, a small cone snail-derived pore blocker peptide, which have previously been shown to increase affinity and inhibitory potency on hNaV1.7 when ligated together. Correctly folded peptides were successfully ligated in varying yields, without disulfide bond shuffling or reduction, with sortase A5° being the most efficient, resulting in 60% ligation conversion within 15 min. In addition, electrophysiology studies demonstrated that for these two peptides, the amino acid composition of the linker did not affect the activity of the double-knotted peptides. This study demonstrates the powerful application of enzymes in efficiently ligating complex disulfide-rich peptides, paving the way for facile production of double-knotted peptides.
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Affiliation(s)
- Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Poanna Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirsten L McMahon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Pharmacy, The University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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37
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Cong M, Tavakolpour S, Berland L, Glöckner H, Andreiuk B, Rakhshandehroo T, Uslu S, Mishra S, Clark L, Rashidian M. Direct N- or C-Terminal Protein Labeling Via a Sortase-Mediated Swapping Approach. Bioconjug Chem 2021; 32:2397-2406. [PMID: 34748323 PMCID: PMC9595177 DOI: 10.1021/acs.bioconjchem.1c00442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Site-specific protein labeling is important in biomedical research and biotechnology. While many methods allow site-specific protein modification, a straightforward approach for efficient N-terminal protein labeling is not available. We introduce a novel sortase-mediated swapping approach for a one-step site-specific N-terminal labeling with a near-quantitative yield. We show that this method allows rapid and efficient cleavage and simultaneous labeling of the N or C termini of fusion proteins. The method does not require any prior modification beyond the genetic incorporation of the sortase recognition motif. This new approach provides flexibility for protein engineering and site-specific protein modifications.
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Affiliation(s)
- Min Cong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Soheil Tavakolpour
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Lea Berland
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Université Côte d'Azur, CNRS, INSERM, IRCAN, 06100 Nice, France
| | - Hannah Glöckner
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Bohdan Andreiuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Taha Rakhshandehroo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Safak Uslu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Medical Scientist Training Program, Hacettepe University Faculty of Medicine, Ankara, 06230, Turkey
| | - Shruti Mishra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Louise Clark
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Mohammad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
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38
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Liu Y, Tian F, Shi S, Deng Y, Zheng P. Enzymatic Protein-Protein Conjugation through Internal Site Verified at the Single-Molecule Level. J Phys Chem Lett 2021; 12:10914-10919. [PMID: 34734720 DOI: 10.1021/acs.jpclett.1c02767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzymes are widely used for protein ligation because of their efficient and site-specific connections under mild conditions. However, many enzymatic ligations are restricted to connections between protein termini while protein-protein conjugation at a specific internal site is limited. Previous work has found that Sortase A (SrtA) conjugates small molecules/peptides to a pilin protein at an internal lysine site via an isopeptide bond. Herein, we apply this noncanonical ligation property of SrtA for protein-protein conjugation at a designed YPKH site. Both a small protein domain, I27, and a large protein, GFP, were ligated at the designed internal site. Moreover, besides characterization by classic methods at the ensemble level, the specific ligation site at the interior YPKH motif is unambiguously verified by atomic force microscopy-based single-molecule force spectroscopy, showing the characteristic unfolding signature at the single-molecule level. Finally, steered molecular dynamics simulations also agreed with the results.
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Affiliation(s)
- Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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39
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Abstract
Proper function of receptors on the cell surface is essential for homeostasis. Compounds that target cell surface receptors to address dysregulation have proven exceptionally successful as therapeutic agents; however, the development of compounds with the desired specificity for receptors, cells, and tissues of choice has proven difficult in some cases. The use of compounds that can engage more than one binding site at the cell surface offers a path toward improving biological specificity or pharmacological properties. In this chapter we summarize historical context for the development of such bivalent compounds. We focus on developments in chemical methods and biological engineering to provide bivalent compounds in which the high affinity and specificity of antibodies are leveraged to create multifunctional conjugates with new and useful properties. The development of methods to meld biological macromolecules with synthetic compounds will facilitate modulation of receptor biology in ways not previously possible.
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40
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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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41
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Xia Y, To J, Chan N, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu C. N
γ
‐Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yiyin Xia
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Janet To
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Ning‐Yu Chan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Side Hu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Heng Tai Liew
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
- Singapore-MIT Alliance for Research and Technology Singapore 138602 Singapore
| | - Xiaohong Zhang
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Julien Lescar
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - James P. Tam
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
| | - Chuan‐Fa Liu
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore
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42
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Xia Y, To J, Chan NY, Hu S, Liew HT, Balamkundu S, Zhang X, Lescar J, Bhattacharjya S, Tam JP, Liu CF. N γ -Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases. Angew Chem Int Ed Engl 2021; 60:22207-22211. [PMID: 34396662 DOI: 10.1002/anie.202108125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/10/2022]
Abstract
Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely Nγ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (Ki =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Seetharamsing Balamkundu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.,Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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43
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Islam A, Pishesha N, Harmand TJ, Heston H, Woodham AW, Cheloha RW, Bousbaine D, Rashidian M, Ploegh HL. Converting an Anti-Mouse CD4 Monoclonal Antibody into an scFv Positron Emission Tomography Imaging Agent for Longitudinal Monitoring of CD4 + T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1468-1477. [PMID: 34408009 PMCID: PMC8387391 DOI: 10.4049/jimmunol.2100274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022]
Abstract
Immuno-positron emission tomography (PET), a noninvasive imaging modality, can provide a dynamic approach for longitudinal assessment of cell populations of interest. Transformation of mAbs into single-chain variable fragment (scFv)-based PET imaging agents would allow noninvasive tracking in vivo of a wide range of possible targets. We used sortase-mediated enzymatic labeling in combination with PEGylation to develop an anti-mouse CD4 scFv-based PET imaging agent constructed from an anti-mouse CD4 mAb. This anti-CD4 scFv can monitor the in vivo distribution of CD4+ T cells by immuno-PET. We tracked CD4+ and CD8+ T cells in wild-type mice, in immunodeficient recipients reconstituted with monoclonal populations of OT-II and OT-I T cells, and in a B16 melanoma model. Anti-CD4 and -CD8 immuno-PET showed that the persistence of both CD4+ and CD8+ T cells transferred into immunodeficient mice improved when recipients were immunized with OVA in CFA. In tumor-bearing animals, infiltration of both CD4+ and CD8+ T cells increased as the tumor grew. The approach described in this study should be readily applicable to convert clinically useful Abs into the corresponding scFv PET imaging agents.
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Affiliation(s)
- Ashraful Islam
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Society of Fellows, Harvard University, Cambridge, MA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Hailey Heston
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Andrew W Woodham
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Djenet Bousbaine
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA
| | - Mohammad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA; and
- Department of Radiology, Harvard Medical School, Boston, MA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA;
- Department of Pediatrics, Harvard Medical School, Boston, MA
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44
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Mogilevsky CS, Lobba MJ, Brauer DD, Marmelstein AM, Maza JC, Gleason JM, Doudna JA, Francis MB. Synthesis of Multi-Protein Complexes through Charge-Directed Sequential Activation of Tyrosine Residues. J Am Chem Soc 2021; 143:13538-13547. [PMID: 34382787 DOI: 10.1021/jacs.1c03079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Site-selective protein-protein coupling has long been a goal of chemical biology research. In recent years, that goal has been realized to varying degrees through a number of techniques, including the use of tyrosinase-based coupling strategies. Early publications utilizing tyrosinase from Agaricus bisporus(abTYR) showed the potential to convert tyrosine residues into ortho-quinone functional groups, but this enzyme is challenging to produce recombinantly and suffers from some limitations in substrate scope. Initial screens of several tyrosinase candidates revealed that the tyrosinase from Bacillus megaterium (megaTYR) is an enzyme that possesses a broad substrate tolerance. We use the expanded substrate preference as a starting point for protein design experiments and show that single point mutants of megaTYR are capable of activating tyrosine residues in various sequence contexts. We leverage this new tool to enable the construction of protein trimers via a charge-directed sequential activation of tyrosine residues (CDSAT).
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Affiliation(s)
- Casey S Mogilevsky
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Marco J Lobba
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel D Brauer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alan M Marmelstein
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jamie M Gleason
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States.,Gladstone Institutes, San Francisco, California 94158, United States.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States.,Innovative Genomics Institute, University of California, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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45
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Harmand TJ, Pishesha N, Rehm FBH, Ma W, Pinney WB, Xie YJ, Ploegh HL. Asparaginyl Ligase-Catalyzed One-Step Cell Surface Modification of Red Blood Cells. ACS Chem Biol 2021; 16:1201-1207. [PMID: 34129316 DOI: 10.1021/acschembio.1c00216] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Red blood cells (RBCs) can serve as vascular carriers for drugs, proteins, peptides, and nanoparticles. Human RBCs remain in the circulation for ∼120 days, are biocompatible, and are immunologically largely inert. RBCs are cleared by the reticuloendothelial system and can induce immune tolerance to foreign components attached to the RBC surface. RBC conjugates have been pursued in clinical trials to treat cancers and autoimmune diseases and to correct genetic disorders. Still, most methods used to modify RBCs require multiple steps, are resource-intensive and time-consuming, and increase the risk of inflicting damage to the RBCs. Here, we describe direct conjugation of peptides and proteins onto the surface of RBCs in a single step, catalyzed by a highly efficient, recombinant asparaginyl ligase under mild, physiological conditions. In mice, the modified RBCs remain intact in the circulation, display a normal circulatory half-life, and retain their immune tolerance-inducing properties, as shown for protection against an accelerated model for type 1 diabetes. We conjugated different nanobodies to RBCs with retention of their binding properties, and these modified RBCs can target cancer cells in vitro. This approach provides an appealing alternative to current methods of RBC engineering. It provides ready access to more complex RBC constructs and highlights the general utility of asparaginyl ligases for the modification of native cell surfaces.
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Affiliation(s)
- Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
| | - Fabian B H Rehm
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Weiyi Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
| | - William B Pinney
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
| | - Yushu J Xie
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachussets 02115, United States
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46
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Li X, Zhang L, Wang S, Liu X, Lin Y. Site-specific internal protein labeling through trans-splicing. Int J Biol Macromol 2021; 186:40-46. [PMID: 34246886 DOI: 10.1016/j.ijbiomac.2021.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/26/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Atypical S1 and S11 split inteins have been used for N-terminal or C-terminal protein labeling. Here we reported a novel site-specific internal protein labeling method based on two atypical split inteins, Ter DnaE3 S11 and Rma DnaB S1. Protein-peptide trans-splicing activity was first demonstrated in vitro between a short peptide (Flag tag, FLAG) and two recombinant proteins (Maltose binding protein, MBP, and Thioredoxin, Trx) by trans-splicing between MBP-TE3S11N (MBP-N fragment of Ter DnaE3 S11), TE3S11C-FLAG-RBS1N (C fragment of Ter DnaE3 S11-FLAG-N fragment of Rma DnaB S1), and RBS1C-Trx (C fragment of Rma DnaB S1-Trx). To minimize the middle synthetic peptide (TE3S11C-linker-RBS1N), we reduced the number of native extein amino acids, which may play a role in protein trans-splicing. The results showed at least 3 (CKG) native extein amino acids were required for detectable trans-splicing activity. This method was further demonstrated to be effective in facilitating the incorporation of fluorescent probe (FITC) to the internal site of recombinant protein, generating the FITC-labeled protein. Besides the fluorescent group, these two split inteins can also be useful for adding any desirable chemical groups into a protein of interest, which may include biotin, modified and unnatural amino acids, or drug molecules.
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Affiliation(s)
- Xue Li
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, PR China
| | - Lu Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, PR China
| | - Suyang Wang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, PR China
| | - Xiangqin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Ying Lin
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, PR China.
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47
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Tang TMS, Luk LYP. Asparaginyl endopeptidases: enzymology, applications and limitations. Org Biomol Chem 2021; 19:5048-5062. [PMID: 34037066 PMCID: PMC8209628 DOI: 10.1039/d1ob00608h] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Asparaginyl endopeptidases (AEP) are cysteine proteases found in mammalian and plant cells. Several AEP isoforms from plant species were found to exhibit transpeptidase activity which is integral for the key head-to-tail cyclisation reaction during the biosynthesis of cyclotides. Since many plant AEPs exhibit excellent enzyme kinetics for peptide ligation via a relatively short substrate recognition sequence, they have become appealing tools for peptide and protein modification. In this review, research focused on the enzymology of AEPs and their applications in polypeptide cyclisation and labelling will be presented. Importantly, the limitations of using AEPs and opportunities for future research and innovation will also be discussed.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
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48
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Zhang D, Wang Z, Hu S, Balamkundu S, To J, Zhang X, Lescar J, Tam JP, Liu CF. pH-Controlled Protein Orthogonal Ligation Using Asparaginyl Peptide Ligases. J Am Chem Soc 2021; 143:8704-8712. [PMID: 34096285 DOI: 10.1021/jacs.1c02638] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptide asparaginyl ligases (PALs) catalyze transpeptidation at the Asn residue of a short Asn-Xaa1-Xaa2 tripeptide motif. Due to their high catalytic activity toward the P1-Asn substrates at around neutral pH, PALs have been used extensively for peptide ligation at asparaginyl junctions. PALs also bind to aspartyl substrates, but only when the γCOOH of P1-Asp remains in its neutral, protonated form, which usually requires an acidic pH. However, this limits the availability of the amine nucleophile and, consequently, the ligation efficiency at aspartyl junctions. Because of this perceived inefficiency, the use of PALs for Asp-specific ligation remains largely unexplored. We found that PAL enzymes, such as VyPAL2, display appreciable catalytic activities toward P1-Asp substrates at pH 4-5, which are at least 2 orders of magnitude higher than that of sortase A, making them practically useful for both intra- and intermolecular ligations. This also allows sequential ligations, first at Asp and then at Asn junctions, because the newly formed aspartyl peptide bond is resistant to the ligase at the pH used for asparaginyl ligation in the second step. Using this pH-controlled orthogonal ligation method, we dually labeled truncated sfGFP with a cancer-targeting peptide and a doxorubicin derivative at the respective N- and C-terminal ends in the N-to-C direction. In addition, a fluorescein tag and doxorubicin derivative were tagged to an EGFR-targeting affibody in the C-to-N direction. This study shows that the pH-dependent catalytic activity of PAL enzymes can be exploited to prepare multifunction protein biologics for pharmacological applications.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | | | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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49
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Nonis SG, Haywood J, Mylne JS. Plant asparaginyl endopeptidases and their structural determinants of function. Biochem Soc Trans 2021; 49:965-976. [PMID: 33666219 PMCID: PMC8106488 DOI: 10.1042/bst20200908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.
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Affiliation(s)
- Samuel G. Nonis
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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50
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Rehm FBH, Tyler TJ, Xie J, Yap K, Durek T, Craik DJ. Asparaginyl Ligases: New Enzymes for the Protein Engineer's Toolbox. Chembiochem 2021; 22:2079-2086. [PMID: 33687132 DOI: 10.1002/cbic.202100071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/08/2021] [Indexed: 01/11/2023]
Abstract
Enzyme-catalysed site-specific protein modifications enable the precision manufacture of conjugates for the study of protein function and/or for therapeutic or diagnostic applications. Asparaginyl ligases are a class of highly efficient transpeptidases with the capacity to modify proteins bearing only a tripeptide recognition motif. Herein, we review the types of protein modification that are accessible using these enzymes, including N- and C-terminal protein labelling, head-to-tail cyclisation, and protein-protein conjugation. We describe the progress that has been made to engineer highly efficient ligases as well as efforts to chemically manipulate the enzyme reaction to favour product formation. These enzymes are powerful additions to the protein engineer's toolbox.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jing Xie
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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