51
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Rubin GM, Ding Y. Recent advances in the biosynthesis of RiPPs from multicore-containing precursor peptides. J Ind Microbiol Biotechnol 2020; 47:659-674. [PMID: 32617877 PMCID: PMC7666021 DOI: 10.1007/s10295-020-02289-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) compose a large structurally and functionally diverse family of natural products. The biosynthesis system of RiPPs typically involves a precursor peptide comprising of a leader and core motif and nearby processing enzymes that recognize the leader and act on the core for producing modified peptides. Interest in RiPPs has increased substantially in recent years as improvements in genome mining techniques have dramatically improved access to these peptides and biochemical and engineering studies have supported their applications. A less understood, intriguing feature in the RiPPs biosynthesis is the precursor peptides of multiple RiPPs families produced by bacteria, fungi and plants carrying multiple core motifs, which we term "multicore". Herein, we present the prevalence of the multicore systems, their biosynthesis and engineering for applications.
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Affiliation(s)
- Garret M Rubin
- Department of Medicinal Chemistry, and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA.
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52
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Xiao Q, Ashton DS, Jones ZB, Thompson KP, Price JL. Long-range PEG Stapling: Macrocyclization for Increased Protein Conformational Stability and Resistance to Proteolysis. RSC Chem Biol 2020; 1:273-280. [PMID: 33796855 PMCID: PMC8009319 DOI: 10.1039/d0cb00075b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We previously showed that long-range stapling of two Asn-linked O-allyl PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW domain through an entropic effect. The impact of stapling was more favorable when the staple connected positions that were far apart in primary sequence but close in the folded tertiary structure. Here we validate these criteria by identifying new stabilizing PEG-stapling sites within the WW domain and the SH3 domain, both β-sheet proteins. We find that stapling via olefin metathesis vs. the copper(i)-catalyzed azide/alkyne cycloaddition (CuAAC) results in similar energetic benefits, suggesting that olefin and triazole staples can be used interchangeably. Proteolysis assays of selected WW variants reveal that the observed staple-based increases in conformational stability lead to enhanced proteolytic resistance. Finally, we find that an intermolecular staple dramatically increases the quaternary structural stability of an α-helical GCN4 coiled-coil heterodimer. Long-range stapling of two Asn-linked PEG oligomers via olefin metathesis substantially increases the conformational stability of the WW and SH3 domain tertiary structures and the GCN4 coiled-coil quaternary structure.![]()
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Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dallin S Ashton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Zachary B Jones
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Katherine P Thompson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua L Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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53
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Kalmankar NV, Venkatesan R, Balaram P, Sowdhamini R. Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis. Sci Rep 2020; 10:12658. [PMID: 32728092 PMCID: PMC7391643 DOI: 10.1038/s41598-020-69452-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/10/2020] [Indexed: 01/20/2023] Open
Abstract
Clitoria ternatea a perennial climber of the Fabaceae family, is well known for its agricultural and medical applications. It is also currently the only known member of the Fabaceae family that produces abundant amounts of the ultra-stable macrocyclic peptides, cyclotides, across all tissues. Cyclotides are a class of gene-encoded, disulphide-rich, macrocyclic peptides (26–37 residues) acting as defensive metabolites in several plant species. Previous transcriptomic studies have demonstrated the genetic origin of cyclotides from the Fabaceae plant family to be embedded in the albumin-1 genes, unlike its counterparts in other plant families. However, the complete mechanism of its biosynthesis and the repertoire of enzymes involved in cyclotide folding and processing remains to be understood. In this study, using RNA-Seq data and de novo transcriptome assembly of Clitoria ternatea, we have identified 71 precursor genes of cyclotides. Out of 71 unique cyclotide precursor genes obtained, 51 sequences display unique cyclotide domains, of which 26 are novel cyclotide sequences, arising from four individual tissues. MALDI-TOF mass spectrometry analysis of fractions from different tissue extracts, coupled with precursor protein sequences obtained from transcriptomic data, established the cyclotide diversity in this plant species. Special focus in this study has also been on identifying possible enzymes responsible for proper folding and processing of cyclotides in the cell. Transcriptomic mining for oxidative folding enzymes such as protein-disulphide isomerases (PDI), ER oxidoreductin-1 (ERO1) and peptidylprolyl cis-trans isomerases (PPIases)/cyclophilins, and their levels of expression are also reported. In particular, it was observed that the CtPDI genes formed plant-specific clusters among PDI genes as compared to those from other plant species. Collectively, this work provides insights into the biogenesis of the medicinally important cyclotides and establishes the expression of certain key enzymes participating in peptide biosynthesis. Also, several novel cyclotide sequences are reported and precursor sequences are analysed in detail. In the absence of a published reference genome, a comprehensive transcriptomics approach was adopted to provide an overview of diverse properties and constituents of C. ternatea.
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Affiliation(s)
- Neha V Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), #74/2, Jarakabande Kaval, Post Attur, Via Yelahanka, Bangalore, Karnataka, 560064, India
| | - Radhika Venkatesan
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,Department of Biological Sciences, Indian Institute of Science, Education and Research, Kolkata, Mohanpur, West Bengal, 741246, India
| | - Padmanabhan Balaram
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.
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54
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Hemu X, El Sahili A, Hu S, Zhang X, Serra A, Goh BC, Darwis DA, Chen MW, Sze SK, Liu CF, Lescar J, Tam JP. Turning an Asparaginyl Endopeptidase into a Peptide Ligase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02078] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xinya Hemu
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Abbas El Sahili
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
| | - Side Hu
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
| | - Xiaohong Zhang
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Aida Serra
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- IMDEA Food Research Institute, Carr. de Canto Blanco, 8, Madrid 28049, Spain
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
- Antimicrobial Resistance Interdisciplinary Research Group, SMART, 1 CREATE Way, Singapore 138602
| | - Dina A. Darwis
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Ming Wei Chen
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Chuan-fa Liu
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Julien Lescar
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
| | - James P. Tam
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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55
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Hebbrecht T, Liu J, Zwaenepoel O, Boddin G, Van Leene C, Decoene K, Madder A, Braeckmans K, Gettemans J. Nanobody click chemistry for convenient site-specific fluorescent labelling, single step immunocytochemistry and delivery into living cells by photoporation and live cell imaging. N Biotechnol 2020; 59:33-43. [PMID: 32659511 DOI: 10.1016/j.nbt.2020.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/20/2020] [Accepted: 05/23/2020] [Indexed: 12/18/2022]
Abstract
While conventional antibodies have been an instrument of choice in immunocytochemistry for some time, their small counterparts known as nanobodies have been much less frequently used for this purpose. In this study we took advantage of the availability of nanobody cDNAs to site-specifically introduce a non-standard amino acid carrying an azide/alkyne moiety, allowing subsequent Cu(I)-catalyzed Azide-Alkyne Click Chemistry (CuAAC). This generated a fluorescently labelled nanobody that can be used in single step immunocytochemistry as compared to conventional two step immunocytochemistry. Two strategies were explored to label nanobodies with Alexa Fluor 488. The first involved enzymatic addition of an alkyne-containing peptide to nanobodies using sortase A, while the second consisted of incorporating para-azido phenylalanine at the nanobody C-terminus. Through these approaches, the fluorophore was covalently and site-specifically attached. It was demonstrated that cortactin and β-catenin, cytoskeletal and adherens junction proteins respectively, can be imaged in cells in this manner through single step immunocytochemistry. However, fixation and permeabilization of cells can alter native protein structure and form a dense cross-linked protein network, encumbering antibody binding. It was shown that photoporation prior to fixation not only allowed delivery of nanobodies into living cells, but also facilitated β-catenin nanobody Nb86 imaging of its target, which was not possible in fixed cells. Pharmacological inhibitors are lacking for many non-enzymatic proteins, and it is therefore expected that new biological information will be obtained through photoporation of fluorescent nanobodies, which allows the study of short term effects, independent of gene-dependent (intrabody) expression.
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Affiliation(s)
- Tim Hebbrecht
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Jing Liu
- Laboratory of General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent B-9000, Belgium
| | - Olivier Zwaenepoel
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Gaëlle Boddin
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Chloé Van Leene
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Klaas Decoene
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Ghent B-9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Ghent B-9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent B-9000, Belgium; Center for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
| | - Jan Gettemans
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium.
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56
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PolyTag: A peptide tag that affords scaffold-less covalent protein assembly catalyzed by microbial transglutaminase. Anal Biochem 2020; 600:113700. [DOI: 10.1016/j.ab.2020.113700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
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57
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Frazier CL, Weeks AM. Engineered peptide ligases for cell signaling and bioconjugation. Biochem Soc Trans 2020; 48:1153-1165. [PMID: 32539119 PMCID: PMC8350744 DOI: 10.1042/bst20200001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Abstract
Enzymes that catalyze peptide ligation are powerful tools for site-specific protein bioconjugation and the study of cellular signaling. Peptide ligases can be divided into two classes: proteases that have been engineered to favor peptide ligation, and protease-related enzymes with naturally evolved peptide ligation activity. Here, we provide a review of key natural peptide ligases and proteases engineered to favor peptide ligation activity. We cover the protein engineering approaches used to generate and improve these tools, along with recent biological applications, advantages, and limitations associated with each enzyme. Finally, we address future challenges and opportunities for further development of peptide ligases as tools for biological research.
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Affiliation(s)
- Clara L. Frazier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy M. Weeks
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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58
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Shinbara K, Liu W, van Neer RHP, Katoh T, Suga H. Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies. Front Chem 2020; 8:447. [PMID: 32626683 PMCID: PMC7314982 DOI: 10.3389/fchem.2020.00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.
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Affiliation(s)
| | | | | | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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59
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Du J, Yap K, Chan LY, Rehm FBH, Looi FY, Poth AG, Gilding EK, Kaas Q, Durek T, Craik DJ. A bifunctional asparaginyl endopeptidase efficiently catalyzes both cleavage and cyclization of cyclic trypsin inhibitors. Nat Commun 2020; 11:1575. [PMID: 32221295 PMCID: PMC7101308 DOI: 10.1038/s41467-020-15418-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
Asparaginyl endopeptidases (AEPs) catalyze the key backbone cyclization step during the biosynthesis of plant-derived cyclic peptides. Here, we report the identification of two AEPs from Momordica cochinchinensis and biochemically characterize MCoAEP2 that catalyzes the maturation of trypsin inhibitor cyclotides. Recombinantly produced MCoAEP2 catalyzes the backbone cyclization of a linear cyclotide precursor (MCoTI-II-NAL) with a kcat/Km of 620 mM−1 s−1, making it one of the fastest cyclases reported to date. We show that MCoAEP2 can mediate both the N-terminal excision and C-terminal cyclization of cyclotide precursors in vitro. The rate of cyclization/hydrolysis is primarily influenced by varying pH, which could potentially control the succession of AEP-mediated processing events in vivo. Furthermore, MCoAEP2 efficiently catalyzes the backbone cyclization of an engineered MCoTI-II analog with anti-angiogenic activity. MCoAEP2 provides enhanced synthetic access to structures previously inaccessible by direct chemistry approaches and enables the wider application of trypsin inhibitor cyclotides in biotechnology applications. Asparaginyl endopeptidases (AEPs) catalyze the cyclization step during the biosynthesis of cyclic peptides in plants. Here, the authors report a recombinantly produced AEP that catalyzes the backbone cyclization of a linear cyclotide precursor and an engineered analog with high efficiency and in a pH-dependent manner.
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Affiliation(s)
- Junqiao Du
- 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
| | - Lai Yue Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fabian B H Rehm
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fong Yang Looi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Thomas Durek
- 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.
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60
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Marmelstein AM, Lobba MJ, Mogilevsky CS, Maza JC, Brauer DD, Francis MB. Tyrosinase-Mediated Oxidative Coupling of Tyrosine Tags on Peptides and Proteins. J Am Chem Soc 2020; 142:5078-5086. [PMID: 32093466 DOI: 10.1021/jacs.9b12002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidative coupling (OC) through o-quinone intermediates has been established as an efficient and site-selective way to modify protein N-termini and the unnatural amino acid p-aminophenylalanine (paF). Recently, we reported that the tyrosinase-mediated oxidation of phenol-tagged cargo molecules is a particularly convenient method of generating o-quinones in situ. The coupling partners can be easily prepared and stored, the reaction takes place under mild conditions (phosphate buffer, pH 6.5, 4 to 23 °C), and dissolved oxygen is the only oxidant required. Here, we show an important extension of this chemistry for the activation of tyrosine residues that project into solution from the N or C-termini of peptide and protein substrates. Generating the o-quinone electrophiles from tyrosine allows greater flexibility in choosing the nucleophilic coupling partner and expands the scope of the reaction to include C-terminal positions. We also introduce a new bacterial tyrosinase enzyme that shows improved activation for some tyrosine substrates. The efficacy of several secondary amines and aniline derivatives was evaluated in the coupling reactions, providing important information for coupling partner design. This strategy was used to modify the C-termini of an antibody scFv construct and of Protein L, a human IgG kappa light chain binding protein. The use of the modified proteins as immunolabeling agents was also demonstrated.
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Affiliation(s)
- Alan M Marmelstein
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Marco J Lobba
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Casey S Mogilevsky
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Daniel D Brauer
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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61
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Hemu X, To J, Zhang X, Tam JP. Immobilized Peptide Asparaginyl Ligases Enhance Stability and Facilitate Macrocyclization and Site-Specific Ligation. J Org Chem 2019; 85:1504-1512. [DOI: 10.1021/acs.joc.9b02524] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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62
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Nuijens T, Toplak A, Schmidt M, Ricci A, Cabri W. Natural Occurring and Engineered Enzymes for Peptide Ligation and Cyclization. Front Chem 2019; 7:829. [PMID: 31850317 PMCID: PMC6895249 DOI: 10.3389/fchem.2019.00829] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
The renaissance of peptides as prospective therapeutics has fostered the development of novel strategies for their synthesis and modification. In this context, besides the development of new chemical peptide ligation approaches, especially the use of enzymes as a versatile tool has gained increased attention. Nowadays, due to their inherent properties such as excellent regio- and chemoselectivity, enzymes represent invaluable instruments in both academic and industrial laboratories. This mini-review focuses on natural- and engineered peptide ligases that can form a new peptide (amide) bond between the C-terminal carboxy and N-terminal amino group of a peptide and/or protein. The pro's and cons of several enzyme classes such as Sortases, Asparaginyl Endoproteases, Trypsin related enzymes and as a central focus subtilisin-derived variants are summarized. Most recent developments with regards to ligation and cyclization are highlighted.
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Affiliation(s)
- Timo Nuijens
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Ana Toplak
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Marcel Schmidt
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | | | - Walter Cabri
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands.,Fresenius Kabi iPSUM Srl, Villadose, Italy
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63
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Matsuda K, Kuranaga T, Wakimoto T. A New Cyclase Family Catalyzing Head-to-Tail Macrolactamization of Non-ribosomal Peptides. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.1106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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64
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65
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A suite of kinetically superior AEP ligases can cyclise an intrinsically disordered protein. Sci Rep 2019; 9:10820. [PMID: 31346249 PMCID: PMC6658665 DOI: 10.1038/s41598-019-47273-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are a class of enzymes commonly associated with proteolysis in the maturation of seed storage proteins. However, a subset of AEPs work preferentially as peptide ligases, coupling release of a leaving group to formation of a new peptide bond. These “ligase-type” AEPs require only short recognition motifs to ligate a range of targets, making them useful tools in peptide and protein engineering for cyclisation of peptides or ligation of separate peptides into larger products. Here we report the recombinant expression, ligase activity and cyclisation kinetics of three new AEPs from the cyclotide producing plant Oldenlandia affinis with superior kinetics to the prototypical recombinant AEP ligase OaAEP1b. These AEPs work preferentially as ligases at both acidic and neutral pH and we term them “canonical AEP ligases” to distinguish them from other AEPs where activity preferences shift according to pH. We show that these ligases intrinsically favour ligation over hydrolysis, are highly efficient at cyclising two unrelated peptides and are compatible with organic co-solvents. Finally, we demonstrate the broad scope of recombinant AEPs in biotechnology by the backbone cyclisation of an intrinsically disordered protein, the 25 kDa malarial vaccine candidate Plasmodium falciparum merozoite surface protein 2 (MSP2).
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66
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Chow HY, Zhang Y, Matheson E, Li X. Ligation Technologies for the Synthesis of Cyclic Peptides. Chem Rev 2019; 119:9971-10001. [PMID: 31318534 DOI: 10.1021/acs.chemrev.8b00657] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cyclic peptides have been attracting a lot of attention in recent decades, especially in the area of drug discovery, as more and more naturally occurring cyclic peptides with diverse biological activities have been discovered. Chemical synthesis of cyclic peptides is essential when studying their structure-activity relationships. Conventional peptide cyclization methods via direct coupling have inherent limitations, like the susceptibility to epimerization at the C-terminus, poor solubility of fully protected peptide precursors, and low yield caused by oligomerization. In this regard, chemoselective ligation-mediated cyclization methods have emerged as effective strategies for cyclic peptide synthesis. The toolbox for cyclic peptide synthesis has been expanded substantially in the past two decades, allowing more efficient synthesis of cyclic peptides with various scaffolds and modifications. This Review will explore different chemoselective ligation technologies used for cyclic peptide synthesis that generate both native and unnatural peptide linkages. The practical issues and limitations of different methods will be discussed. The advance in cyclic peptide synthesis will benefit the biological and medicinal study of cyclic peptides, an important class of macrocycles with potentials in numerous fields, notably in therapeutics.
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Affiliation(s)
- Hoi Yee Chow
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong SAR , P. R. China
| | - Yue Zhang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong SAR , P. R. China
| | - Eilidh Matheson
- School of Chemistry , University of Edinburgh , Edinburgh EH8 9LE , United Kingdom
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong SAR , P. R. China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , P. R. China
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67
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Protein engineering through tandem transamidation. Nat Chem 2019; 11:737-743. [PMID: 31263208 DOI: 10.1038/s41557-019-0281-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/10/2019] [Indexed: 01/01/2023]
Abstract
Semisynthetic proteins engineered to contain non-coded elements such as post-translational modifications (PTMs) represent a powerful class of tools for interrogating biological processes. Here, we introduce a one-pot, chemoenzymatic method that allows broad access to chemically modified proteins. The approach involves a tandem transamidation reaction cascade that integrates intein-mediated protein splicing with enzyme-mediated peptide ligation. We show that this approach can be used to introduce PTMs and biochemical probes into a range of proteins including Cas9 nuclease and the transcriptional regulator MeCP2, which causes Rett syndrome when mutated. The versatility of the approach is further illustrated through the chemical tailoring of histone proteins within a native chromatin setting. We expect our approach will extend the scope of semisynthesis in protein engineering.
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68
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Pi N, Gao M, Cheng X, Liu H, Kuang Z, Yang Z, Yang J, Zhang B, Chen Y, Liu S, Huang Y, Su Z. Recombinant Butelase-Mediated Cyclization of the p53-Binding Domain of the Oncoprotein MdmX-Stabilized Protein Conformation as a Promising Model for Structural Investigation. Biochemistry 2019; 58:3005-3015. [DOI: 10.1021/acs.biochem.9b00263] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ni Pi
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
- Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan 430075, China
| | - Huili Liu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei 430071 China
| | - Zhengkun Kuang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Zixin Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Jing Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Bailing Zhang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Yao Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
- Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan 430075, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology and National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, China
- Wuhan Amersino Biodevelop Inc., B1-Building, Biolake Park, Wuhan 430075, China
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69
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James AM, Haywood J, Leroux J, Ignasiak K, Elliott AG, Schmidberger JW, Fisher MF, Nonis SG, Fenske R, Bond CS, Mylne JS. The macrocyclizing protease butelase 1 remains autocatalytic and reveals the structural basis for ligase activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:988-999. [PMID: 30790358 DOI: 10.1111/tpj.14293] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/03/2019] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
Plant asparaginyl endopeptidases (AEPs) are expressed as inactive zymogens that perform maturation of seed storage protein upon cleavage-dependent autoactivation in the low-pH environment of storage vacuoles. The AEPs have attracted attention for their macrocyclization reactions, and have been classified as cleavage or ligation specialists. However, we have recently shown that the ability of AEPs to produce either cyclic or acyclic products can be altered by mutations to the active site region, and that several AEPs are capable of macrocyclization given favorable pH conditions. One AEP extracted from Clitoria ternatea seeds (butelase 1) is classified as a ligase rather than a protease, presenting an opportunity to test for loss of cleavage activity. Here, making recombinant butelase 1 and rescuing an Arabidopsis thaliana mutant lacking AEP, we show that butelase 1 retains cleavage functions in vitro and in vivo. The in vivo rescue was incomplete, consistent with some trade-off for butelase 1 specialization toward macrocyclization. Its crystal structure showed an active site with only subtle differences from cleaving AEPs, suggesting the many differences in its peptide-binding region are the source of its efficient macrocyclization. All considered, it seems that either butelase 1 has not fully specialized or a requirement for autocatalytic cleavage is an evolutionary constraint upon macrocyclizing AEPs.
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Affiliation(s)
- Amy M James
- 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
| | - Julie Leroux
- 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
| | - Katarzyna Ignasiak
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Alysha G Elliott
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld, 4072, Australia
| | - Jason W Schmidberger
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Mark F Fisher
- 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
| | - 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
| | - Ricarda Fenske
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, 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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70
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Oguis GK, Gilding EK, Jackson MA, Craik DJ. Butterfly Pea ( Clitoria ternatea), a Cyclotide-Bearing Plant With Applications in Agriculture and Medicine. FRONTIERS IN PLANT SCIENCE 2019; 10:645. [PMID: 31191573 PMCID: PMC6546959 DOI: 10.3389/fpls.2019.00645] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/29/2019] [Indexed: 05/16/2023]
Abstract
The perennial leguminous herb Clitoria ternatea (butterfly pea) has attracted significant interest based on its agricultural and medical applications, which range from use as a fodder and nitrogen fixing crop, to applications in food coloring and cosmetics, traditional medicine and as a source of an eco-friendly insecticide. In this article we provide a broad multidisciplinary review that includes descriptions of the physical appearance, distribution, taxonomy, habitat, growth and propagation, phytochemical composition and applications of this plant. Notable amongst its repertoire of chemical components are anthocyanins which give C. ternatea flowers their characteristic blue color, and cyclotides, ultra-stable macrocyclic peptides that are present in all tissues of this plant. The latter are potent insecticidal molecules and are implicated as the bioactive agents in a plant extract used commercially as an insecticide. We include a description of the genetic origin of these peptides, which interestingly involve the co-option of an ancestral albumin gene to produce the cyclotide precursor protein. The biosynthesis step in which the cyclic peptide backbone is formed involves an asparaginyl endopeptidase, of which in C. ternatea is known as butelase-1. This enzyme is highly efficient in peptide ligation and has been the focus of many recent studies on peptide ligation and cyclization for biotechnological applications. The article concludes with some suggestions for future studies on this plant, including the need to explore possible synergies between the various peptidic and non-peptidic phytochemicals.
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Affiliation(s)
| | | | | | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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71
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Structural determinants for peptide-bond formation by asparaginyl ligases. Proc Natl Acad Sci U S A 2019; 116:11737-11746. [PMID: 31123145 DOI: 10.1073/pnas.1818568116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Asparaginyl endopeptidases (AEPs) are cysteine proteases which break Asx (Asn/Asp)-Xaa bonds in acidic conditions. Despite sharing a conserved overall structure with AEPs, certain plant enzymes such as butelase 1 act as a peptide asparaginyl ligase (PAL) and catalyze Asx-Xaa bond formation in near-neutral conditions. PALs also serve as macrocyclases in the biosynthesis of cyclic peptides. Here, we address the question of how a PAL can function as a ligase rather than a protease. Based on sequence homology of butelase 1, we identified AEPs and PALs from the cyclic peptide-producing plants Viola yedoensis (Vy) and Viola canadensis (Vc) of the Violaceae family. Using a crystal structure of a PAL obtained at 2.4-Å resolution coupled to mutagenesis studies, we discovered ligase-activity determinants flanking the S1 site, namely LAD1 and LAD2 located around the S2 and S1' sites, respectively, which modulate ligase activity by controlling the accessibility of water or amine nucleophile to the S-ester intermediate. Recombinantly expressed VyPAL1-3, predicted to be PALs, were confirmed to be ligases by functional studies. In addition, mutagenesis studies on VyPAL1-3, VyAEP1, and VcAEP supported our prediction that LAD1 and LAD2 are important for ligase activity. In particular, mutagenesis targeting LAD2 selectively enhanced the ligase activity of VyPAL3 and converted the protease VcAEP into a ligase. The definition of structural determinants required for ligation activity of the asparaginyl ligases presented here will facilitate genomic identification of PALs and engineering of AEPs into PALs.
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72
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Jackson MA, Yap K, Poth AG, Gilding EK, Swedberg JE, Poon S, Qu H, Durek T, Harris K, Anderson MA, Craik DJ. Rapid and Scalable Plant-Based Production of a Potent Plasmin Inhibitor Peptide. FRONTIERS IN PLANT SCIENCE 2019; 10:602. [PMID: 31156672 PMCID: PMC6530601 DOI: 10.3389/fpls.2019.00602] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/24/2019] [Indexed: 05/03/2023]
Abstract
The backbone cyclic and disulfide bridged sunflower trypsin inhibitor-1 (SFTI-1) peptide is a proven effective scaffold for a range of peptide therapeutics. For production at laboratory scale, solid phase peptide synthesis techniques are widely used, but these synthetic approaches are costly and environmentally taxing at large scale. Here, we developed a plant-based approach for the recombinant production of SFTI-1-based peptide drugs. We show that transient expression in Nicotiana benthamiana allows for rapid peptide production, provided that asparaginyl endopeptidase enzymes with peptide-ligase functionality are co-expressed with the substrate peptide gene. Without co-expression, no target cyclic peptides are detected, reflecting rapid in planta degradation of non-cyclized substrate. We test this recombinant production system by expressing a SFTI-1-based therapeutic candidate that displays potent and selective inhibition of human plasmin. By using an innovative multi-unit peptide expression cassette, we show that in planta yields reach ~60 μg/g dry weight at 6 days post leaf infiltration. Using nuclear magnetic resonance structural analysis and functional in vitro assays, we demonstrate the equivalence of plant and synthetically derived plasmin inhibitor peptide. The methods and insights gained in this study provide opportunities for the large scale, cost effective production of SFTI-1-based therapeutics.
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Affiliation(s)
- Mark A. Jackson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aaron G. Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Edward K. Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Haiou Qu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Karen Harris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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73
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Affiliation(s)
- Yingqin Hou
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
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74
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Schmidt M, Huang YH, Texeira de Oliveira EF, Toplak A, Wijma HJ, Janssen DB, van Maarseveen JH, Craik DJ, Nuijens T. Efficient Enzymatic Cyclization of Disulfide-Rich Peptides by Using Peptide Ligases. Chembiochem 2019; 20:1524-1529. [PMID: 30735312 DOI: 10.1002/cbic.201900033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
Disulfide-rich macrocyclic peptides-cyclotides, for example-represent a promising class of molecules with potential therapeutic use. Despite their potential their efficient synthesis at large scale still represents a major challenge. Here we report new chemoenzymatic strategies using peptide ligase variants-inter alia, omniligase-1-for the efficient and scalable one-pot cyclization and folding of the native cyclotides MCoTI-II, kalata B1 and variants thereof, as well as of the θ-defensin RTD-1. The synthesis of the kB1 variant T20K was successfully demonstrated at multi-gram scale. The existence of several ligation sites for each macrocycle makes this approach highly flexible and facilitates both the larger-scale manufacture and the engineering of bioactive, grafted cyclotide variants, therefore clearly offering a valuable and powerful extension of the existing toolbox of enzymes for peptide head-to-tail cyclization.
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Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands.,Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Eduardo F Texeira de Oliveira
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ana Toplak
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
| | - Hein J Wijma
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dick B Janssen
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Timo Nuijens
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
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75
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Tam JP. Butelase: Linkage‐specific Ligase. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.783.4] [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)
- James P Tam
- School of Biological SciencesNanyang Technological UniversitySingapore, Singapore
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76
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Streefkerk DE, Schmidt M, Ippel JH, Hackeng TM, Nuijens T, Timmerman P, van Maarseveen JH. Synthesis of Constrained Tetracyclic Peptides by Consecutive CEPS, CLIPS, and Oxime Ligation. Org Lett 2019; 21:2095-2100. [PMID: 30912446 PMCID: PMC6456872 DOI: 10.1021/acs.orglett.9b00378] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
In Nature, multicyclic
peptides constitute a versatile molecule
class with various biological functions. For their pharmaceutical
exploitation, chemical methodologies that enable selective consecutive
macrocyclizations are required. We disclose a combination of enzymatic
macrocyclization, CLIPS alkylation, and oxime ligation to prepare
tetracyclic peptides. Five new small molecular scaffolds and differently
sized model peptides featuring noncanonical amino acids were synthesized.
Enzymatic macrocyclization, followed by one-pot scaffold-assisted
cyclizations, yielded 21 tetracyclic peptides in a facile and robust
manner.
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Affiliation(s)
- Dieuwertje E Streefkerk
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands
| | - Marcel Schmidt
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands.,EnzyPep B.V. , Urmonderbaan 22 , 6167 RD Geleen , The Netherlands
| | - Johannes H Ippel
- Department of Biochemistry (CARIM) , University of Maastricht , Universiteitssingel 50, 6229 ER Maastricht , The Netherlands
| | - Tilman M Hackeng
- Department of Biochemistry (CARIM) , University of Maastricht , Universiteitssingel 50, 6229 ER Maastricht , The Netherlands
| | - Timo Nuijens
- EnzyPep B.V. , Urmonderbaan 22 , 6167 RD Geleen , The Netherlands
| | - Peter Timmerman
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands.,Pepscan Therapeutics , Zuidersluisweg 2 , 8243 RC Lelystad , The Netherlands
| | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands
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77
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Varnava KG, Sarojini V. Making Solid-Phase Peptide Synthesis Greener: A Review of the Literature. Chem Asian J 2019; 14:1088-1097. [PMID: 30681290 DOI: 10.1002/asia.201801807] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/24/2019] [Indexed: 11/07/2022]
Abstract
To date, the synthesis of peptides is concurrent with the production of enormous amounts of toxic waste. DMF, CH2 Cl2 , and NMP are three of the most toxic organic solvents used in chemical synthesis and are the most common solvents used for peptide synthesis. Additionally, concerns about the hepatotoxicity caused by exposure to DMF and from the toxic and allergenic nature of additives used in peptide synthesis necessitates the need for a green, environmentally friendly, and safer protocol for peptide synthesis. This review summarizes the current literature on green solid-phase peptide synthesis successes and challenges encountered. The review concludes with suggestions for future research towards a simple and efficient green peptide synthesis protocol.
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Affiliation(s)
- Kyriakos G Varnava
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
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78
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Abstract
A biomimetic one-step ligase-catalyzed cyclo-oligomerization mediated by butelase 1, an Asn/Asp-specific ligase, is introduced that is time-, concentration-, length-, and sequence-dependent. This reaction yields cyclic mono-, di-, tri-, and tetramers from peptide precursors containing 3-15 amino acids ended with Asn and a His-Val tail. The cyclomonomers were favored when the peptide lengths were >9 amino acids. A turn-forming Pro residue at the P2 position favored the formation of higher-order cyclo-oligomers.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Xiaohong Zhang
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - James P Tam
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
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79
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Hemu X, Zhang X, Bi X, Liu CF, Tam JP. Butelase 1-Mediated Ligation of Peptides and Proteins. Methods Mol Biol 2019; 2012:83-109. [PMID: 31161505 DOI: 10.1007/978-1-4939-9546-2_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structurally, butelase 1 is a cysteine protease of the asparaginyl endoprotease (AEP) family, but functionally, it displays intense Asn/Asp-specific (Asx) ligase activity and is virtually devoid of protease activity. Butelase 1 recognizes specifically a C-terminal Asx-containing tripeptide motif, Asx-His-Val, to form an Asx-Xaa peptide bond (Xaa = any amino acid), either intramolecularly or intermolecularly, resulting in cyclic peptides or site-specific modified peptides/proteins, respectively. Our work in the past 4 years has validated that butelase 1 is a potent and versatile tool for peptide and protein modification. Here we describe our protocols using butelase 1 for efficient and site-specific peptide and protein ligation, N-terminal labeling, preparation of thioesters, and bioconjugation of dendrimers. Additionally, we provide an example using butelase 1 for protein cyclization in combination with genetic code expansion in order to incorporate unnatural building blocks.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaobao Bi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- 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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80
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Wang XW, Zhang WB. SpyTag-SpyCatcher Chemistry for Protein Bioconjugation In Vitro and Protein Topology Engineering In Vivo. Methods Mol Biol 2019; 2033:287-300. [PMID: 31332761 DOI: 10.1007/978-1-4939-9654-4_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of "molecular superglue," such as SpyTag-SpyCatcher chemistry, has tremendously expanded our capability in manipulating protein shape and architecture via conjugation. Telechelic proteins bearing the SpyTag and SpyCatcher reactive sequences can be expressed and purified for bioconjugation in vitro, giving protein conjugates, branched proteins, and circular proteins. By encoding both reactive sequences in the same construct for expression in vivo, the nascent protein undergoes programmed posttranslational modification guided by protein folding and reaction, leading to diverse nonlinear topologies in situ. In this chapter, we present the SpyTag-SpyCatcher chemistry as a versatile platform for protein bioconjugation and topology engineering.
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Affiliation(s)
- Xiao-Wei Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China.
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81
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Wu XL, Liu Y, Liu D, Sun F, Zhang WB. An Intrinsically Disordered Peptide-Peptide Stapler for Highly Efficient Protein Ligation Both in Vivo and in Vitro. J Am Chem Soc 2018; 140:17474-17483. [PMID: 30449090 DOI: 10.1021/jacs.8b08250] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein, we report an intrinsically disordered protein SpyStapler that can catalyze the isopeptide bond formation between two peptide tags, that is, SpyTag and BDTag, both in vitro and in vivo. SpyStapler and BDTag are developed by splitting SpyCatcher-the cognate protein partner of SpyTag-at the more solvent exposed second loop region. Regardless of their locations in protein constructs, SpyStapler enables efficient covalent coupling of SpyTag and BDTag under a variety of mild conditions in vitro (yield ∼80%). Co-expression of SpyStapler with telechelic dihydrofolate reductase (DHFR) bearing a SpyTag at N-terminus and a BDTag at C-terminus leads to direct cellular synthesis of a circular DHFR. Mechanistic studies involving circular dichroism and nuclear magnetic resonance spectrometry reveal that SpyStapler alone is disordered in solution and forms a stable folded structure ( Tm ∼ 55 °C) in the presence of both SpyTag and BDTag upon isopeptide bonding. No ordered structure can be formed in the absence of either tag. The catalytically inactive SpyStapler-EQ mutant cannot form a stable physical complex with SpyTag and BDTag, but it can fold into ordered structure in the presence of the ligated product (SpyTag-BDTag). It suggests that the isopeptide bond is important in stabilizing the complex. Given its efficiency, resilience, and robustness, SpyStapler provides new opportunities for bioconjugation and creation of complex protein architectures.
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Affiliation(s)
- Xia-Ling Wu
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Yajie Liu
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Dong Liu
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Fei Sun
- Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , P. R. China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
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82
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Wu WH, Wei J, Zhang WB. Controlling SpyTag/SpyCatcher Reactivity via Redox-Gated Conformational Restriction. ACS Macro Lett 2018; 7:1388-1393. [PMID: 35651248 DOI: 10.1021/acsmacrolett.8b00668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Herein, we report that the reactivity of genetically encoded SpyTag/SpyCatcher chemistry can be manipulated via redox-gated conformational restriction, which facilitates the preparation of all-protein-based hydrogel with latent reactive sites for subsequent covalent functionalization.
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Affiliation(s)
- Wen-Hao Wu
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Jingjing Wei
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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83
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Stevens AJ, Sekar G, Gramespacher JA, Cowburn D, Muir TW. An Atypical Mechanism of Split Intein Molecular Recognition and Folding. J Am Chem Soc 2018; 140:11791-11799. [PMID: 30156841 PMCID: PMC7232844 DOI: 10.1021/jacs.8b07334] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Split inteins associate to trigger protein splicing in trans, a post-translational modification in which protein sequences fused to the intein pair are ligated together in a traceless manner. Recently, a family of naturally split inteins has been identified that is split at a noncanonical location in the primary sequence. These atypically split inteins show considerable promise in protein engineering applications; however, the mechanism by which they associate is unclear and must be different from that of previously characterized canonically split inteins due to unique topological restrictions. Here, we use a consensus design strategy to generate an atypical split intein pair (Cat) that has greatly improved activity and is amenable to detailed biochemical and biophysical analysis. Guided by the solution structure of Cat, we show that the association of the fragments involves a disorder-to-order structural transition driven by hydrophobic interactions. This molecular recognition mechanism satisfies the topological constraints of the intein fold and, importantly, ensures that premature chemistry does not occur prior to fragment complementation. Our data lead a common blueprint for split intein complementation in which localized structural rearrangements are used to drive folding and regulate protein-splicing activity.
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Affiliation(s)
- Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Josef A. Gramespacher
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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84
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Accessing Structure, Dynamics and Function of Biological Macromolecules by NMR Through Advances in Isotope Labeling. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0085-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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85
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86
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87
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Molecular basis for the production of cyclic peptides by plant asparaginyl endopeptidases. Nat Commun 2018; 9:2411. [PMID: 29925835 PMCID: PMC6010433 DOI: 10.1038/s41467-018-04669-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/09/2018] [Indexed: 11/08/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are proteases that have crucial roles in plant defense and seed storage protein maturation. Select plant AEPs, however, do not function as proteases but as transpeptidases (ligases) catalyzing the intra-molecular ligation of peptide termini, which leads to peptide cyclization. These ligase-type AEPs have potential biotechnological applications ranging from in vitro peptide engineering to plant molecular farming, but the structural features enabling these enzymes to catalyze peptide ligation/cyclization rather than proteolysis are currently unknown. Here, we compare the sequences, structures, and functions of diverse plant AEPs by combining molecular modeling, sequence space analysis, and functional testing in planta. We find that changes within the substrate-binding pocket and an adjacent loop, here named the “marker of ligase activity”, together play a key role for AEP ligase efficiency. Identification of these structural determinants may facilitate the discovery of more ligase-type AEPs and the engineering of AEPs with tailored catalytic properties. Asparaginyl endopeptidases (AEPs) are plant proteases that can also function as ligases, catalyzing the production of cyclic plant peptides. Here, the authors identify structural features that govern AEP ligase activity, providing insights to aid the discovery and engineering of ligase-type AEPs.
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88
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Bi X, Yin J, Hemu X, Rao C, Tam JP, Liu CF. Immobilization and Intracellular Delivery of Circular Proteins by Modifying a Genetically Incorporated Unnatural Amino Acid. Bioconjug Chem 2018; 29:2170-2175. [DOI: 10.1021/acs.bioconjchem.8b00244] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiaobao Bi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | | | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Chang Rao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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89
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Banerjee A, Howarth M. Nanoteamwork: covalent protein assembly beyond duets towards protein ensembles and orchestras. Curr Opin Biotechnol 2018; 51:16-23. [DOI: 10.1016/j.copbio.2017.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
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90
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James AM, Haywood J, Mylne JS. Macrocyclization by asparaginyl endopeptidases. THE NEW PHYTOLOGIST 2018; 218:923-928. [PMID: 28322452 DOI: 10.1111/nph.14511] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/24/2017] [Indexed: 05/18/2023]
Abstract
Contents Summary 923 I. Introduction 923 II. Plant AEPs with macrocyclizing ability 924 III. Mechanism of macrocyclization by AEPs 925 IV. Conclusions 927 Acknowledgements 927 References 927 SUMMARY: Plant asparaginyl endopeptidases (AEPs) are important for the post-translational processing of seed storage proteins via cleavage of precursor proteins. Some AEPs also function as peptide bond-makers during the biosynthesis of several unrelated classes of cyclic peptides, namely the kalata-type cyclic peptides, PawS-Derived Peptides and cyclic knottins. These three families of gene-encoded peptides have different evolutionary origins, but all have recruited AEPs for their maturation. In the last few years, the field has advanced rapidly, with the biochemical characterization of three plant AEPs capable of peptide macrocyclization, and insights have been gained from the first AEP crystal structures, albeit mammalian ones. Although the biochemical studies have improved our understanding of the mechanism of action, the focus now is to understand what changes in AEP sequence and structure enable some plant AEPs to perform macrocyclization reactions.
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Affiliation(s)
- Amy M James
- School of Molecular Sciences & 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 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 ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
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91
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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92
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Zauner FB, Elsässer B, Dall E, Cabrele C, Brandstetter H. Structural analyses of Arabidopsis thaliana legumain γ reveal differential recognition and processing of proteolysis and ligation substrates. J Biol Chem 2018; 293:8934-8946. [PMID: 29628443 PMCID: PMC5995516 DOI: 10.1074/jbc.m117.817031] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 02/18/2018] [Indexed: 11/06/2022] Open
Abstract
Legumain is a dual-function protease-peptide ligase whose activities are of great interest to researchers studying plant physiology and to biotechnological applications. However, the molecular mechanisms determining the specificities for proteolysis and ligation are unclear because structural information on the substrate recognition by a fully activated plant legumain is unavailable. Here, we present the X-ray structure of Arabidopsis thaliana legumain isoform γ (AtLEGγ) in complex with the covalent peptidic Ac-YVAD chloromethyl ketone (CMK) inhibitor targeting the catalytic cysteine. Mapping of the specificity pockets preceding the substrate-cleavage site explained the known substrate preference. The comparison of inhibited and free AtLEGγ structures disclosed a substrate-induced disorder-order transition with synergistic rearrangements in the substrate-recognition sites. Docking and in vitro studies with an AtLEGγ ligase substrate, sunflower trypsin inhibitor (SFTI), revealed a canonical, protease substrate-like binding to the active site-binding pockets preceding and following the cleavage site. We found the interaction of the second residue after the scissile bond, P2'-S2', to be critical for deciding on proteolysis versus cyclization. cis-trans-Isomerization of the cyclic peptide product triggered its release from the AtLEGγ active site and prevented inadvertent cleavage. The presented integrative mechanisms of proteolysis and ligation (transpeptidation) explain the interdependence of legumain and its preferred substrates and provide a rational framework for engineering optimized proteases, ligases, and substrates.
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Affiliation(s)
- Florian B Zauner
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Brigitta Elsässer
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Elfriede Dall
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Chiara Cabrele
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Hans Brandstetter
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
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93
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Zhang XJ, Wu XL, Wang XW, Liu D, Yang S, Zhang WB. SpyCatcher-NTEV: A Circularly Permuted, Disordered SpyCatcher Variant for Less Trace Ligation. Bioconjug Chem 2018; 29:1622-1629. [DOI: 10.1021/acs.bioconjchem.8b00131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xue-Jian Zhang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, P. R. China
| | - Xia-Ling Wu
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Wei Wang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dong Liu
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Shuguang Yang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University, Shanghai 201620, P. R. China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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94
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Ongpipattanakul C, Nair SK. Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides. Biochemistry 2018; 57:3201-3209. [PMID: 29553721 DOI: 10.1021/acs.biochem.8b00114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Circular peptides have long been sought after as scaffolds for drug design as they demonstrate protein-like properties in the context of small, constrained peptides. Traditional routes toward the production of cyclic peptides rely on synthesis or semisynthetic methods, which restrict their use as platforms for the production of large, structurally diverse chemical libraries. Here, we discuss the biosynthetic routes toward the N-C macrocyclization of linear peptide precursors, specifically, those transformations that are catalyzed by peptidases. While canonical peptidases catalyze the proteolysis of linear peptides, the biosynthetic macrocyclases couple proteolytic cleavage with cyclization to produce macrocyclic compounds. In this Perspective, we explore the different structural features that impart on each of these biosynthetic proteases the distinct ability to perform macrocyclization and focus on their potential use in biotechnology.
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95
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Ludewig H, Czekster CM, Oueis E, Munday ES, Arshad M, Synowsky SA, Bent AF, Naismith JH. Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates. ACS Chem Biol 2018; 13:801-811. [PMID: 29377663 PMCID: PMC5859912 DOI: 10.1021/acschembio.8b00050] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cyclic ribosomally derived peptides possess diverse bioactivities and are currently of major interest in drug development. However, it can be chemically challenging to synthesize these molecules, hindering the diversification and testing of cyclic peptide leads. Enzymes used in vitro offer a solution to this; however peptide macrocyclization remains the bottleneck. PCY1, involved in the biosynthesis of plant orbitides, belongs to the class of prolyl oligopeptidases and natively displays substrate promiscuity. PCY1 is a promising candidate for in vitro utilization, but its substrates require an 11 to 16 residue C-terminal recognition tail. We have characterized PCY1 both kinetically and structurally with multiple substrate complexes revealing the molecular basis of recognition and catalysis. Using these insights, we have identified a three residue C-terminal extension that replaces the natural recognition tail permitting PCY1 to operate on synthetic substrates. We demonstrate that PCY1 can macrocyclize a variety of substrates with this short tail, including unnatural amino acids and nonamino acids, highlighting PCY1's potential in biocatalysis.
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Affiliation(s)
- Hannes Ludewig
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
| | - Clarissa M. Czekster
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
| | - Emilia Oueis
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
| | - Elizabeth S. Munday
- EaStChem, School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
| | - Mohammed Arshad
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom
| | - Silvia A. Synowsky
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
| | - Andrew F. Bent
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, United Kingdom
- Biotherapy Centre, Sichuan University, Chengdu, China
- Research Complex at Harwell, Didcot, OX11 0FA, United Kingdom
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, United Kingdom
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96
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Buldun CM, Jean JX, Bedford MR, Howarth M. SnoopLigase Catalyzes Peptide–Peptide Locking and Enables Solid-Phase Conjugate Isolation. J Am Chem Soc 2018; 140:3008-3018. [DOI: 10.1021/jacs.7b13237] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Can M. Buldun
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Jisoo X. Jean
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | | | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
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97
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Hou Y, Zhou Y, Wang H, Wang R, Yuan J, Hu Y, Sheng K, Feng J, Yang S, Lu H. Macrocyclization of Interferon-Poly(α-amino acid) Conjugates Significantly Improves the Tumor Retention, Penetration, and Antitumor Efficacy. J Am Chem Soc 2018; 140:1170-1178. [PMID: 29262256 DOI: 10.1021/jacs.7b13017] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cyclization and polymer conjugation are two commonly used approaches for enhancing the pharmacological properties of protein drugs. However, cyclization of parental proteins often only affords a modest improvement in biochemical or cell-based in vitro assays. Moreover, very few studies have included a systematic pharmacological evaluation of cyclized protein-based therapeutics in live animals. On the other hand, polymer-conjugated proteins have longer circulation half-lives but usually show poor tumor penetration and suboptimal pharmacodynamics due to increased steric hindrance. We herein report the generation of a head-to-tail interferon-poly(α-amino acid) macrocycle conjugate circ-P(EG3Glu)20-IFN by combining the aforementioned two approaches. We then compared the antitumor pharmacological activity of this macrocycle conjugate against its linear counterparts, N-P(EG3Glu)20-IFN, C-IFN-P(EG3Glu)20, and C-IFN-PEG. Our results found circ-P(EG3Glu)20-IFN to show considerably greater stability, binding affinity, and in vitro antiproliferative activity toward OVCAR3 cells than the three linear conjugates. More importantly, circ-P(EG3Glu)20-IFN exhibited longer circulation half-life, remarkably higher tumor retention, and deeper tumor penetration in vivo. As a result, administration of the macrocyclic conjugate could effectively inhibit tumor progression and extend survival in mice bearing established xenograft human OVCAR3 or SKOV3 tumors without causing severe paraneoplastic syndromes. Taken together, our study provided until now the most relevant experimental evidence in strong support of the in vivo benefit of macrocyclization of protein-polymer conjugates and for its application in next-generation therapeutics.
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Affiliation(s)
- Yingqin Hou
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China
| | - Yu Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China , Chengdu 610054, People's Republic of China
| | - Hao Wang
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China
| | - Ruijue Wang
- College of Chemistry and Environment Protection Engineering, Southwest University for Nationalities , Chengdu 610041, People's Republic of China
| | - Jingsong Yuan
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China
| | - Yali Hu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China.,Peking-Tsinghua Center for Life Sciences, Peking University , Beijing 100871, People's Republic of China
| | - Kai Sheng
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China
| | - Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China , Chengdu 610054, People's Republic of China
| | - Shengtao Yang
- College of Chemistry and Environment Protection Engineering, Southwest University for Nationalities , Chengdu 610041, People's Republic of China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China
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98
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Otaka A, Shigenaga A. Protein Synthetic Chemistry Inspired by Intein-mediated Protein Splicing. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akira Otaka
- Institutes of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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99
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100
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Schmidt M, Toplak A, Quaedflieg PJLM, van Maarseveen JH, Nuijens T. Enzyme-catalyzed peptide cyclization. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:11-16. [PMID: 29249237 DOI: 10.1016/j.ddtec.2017.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 10/18/2022]
Abstract
The recent advancement of peptide macrocycles as promising therapeutics creates a need for novel methodologies for their efficient synthesis and (large scale) production. Within this context, due to the favorable properties of biocatalysts, enzyme-mediated methodologies have gained great interest. Enzymes such as sortase A, butelase 1, peptiligase and omniligase-1 represent extremely powerful and valuable enzymatic tools for peptide ligation, since they can be applied to generate complex cyclic peptides with exquisite biological activity. Therefore, the use of enzymatic strategies will effectively supplement the scope of existing chemical methodologies and will accelerate the development of future cyclic peptide therapeutics. The advantages and disadvantages of the different enzymatic methodologies will be discussed in this review.
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Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands; Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Ana Toplak
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | | | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Timo Nuijens
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
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