1
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Zhan Q, Shi C, Jiang Y, Gao X, Lin Y. Efficient splicing of the CPE intein derived from directed evolution of the Cryptococcus neoformans PRP8 intein. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1310-1318. [PMID: 37489009 PMCID: PMC10448054 DOI: 10.3724/abbs.2023135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/19/2023] [Indexed: 07/26/2023] Open
Abstract
Intein-mediated protein splicing has been widely used in protein engineering; however, the splicing efficiency and extein specificity usually limit its further application. Thus, there is a demand for more general inteins that can overcome these limitations. Here, we study the trans-splicing of CPE intein obtained from the directed evolution of Cne PRP8, which shows that its splicing rate is ~29- fold higher than that of the wild-type. When the +1 residue of C-extein is changed to cysteine, CPE also shows high splicing activity. Faster association and higher affinity may contribute to the high splicing rate compared with wild-type intein. These findings have important implications for the future engineering of inteins and provide clues for fundamental studies of protein structure and folding.
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Affiliation(s)
- Qin Zhan
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Changhua Shi
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Yu Jiang
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Xianling Gao
- Shandong Guoli Biotechnology Co.Ltd.Jinan250101China
| | - Ying Lin
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
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2
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Pasch T, Schröder A, Kattelmann S, Eisenstein M, Pietrokovski S, Kümmel D, Mootz HD. Structural and biochemical analysis of a novel atypically split intein reveals a conserved histidine specific to cysteine-less inteins. Chem Sci 2023; 14:5204-5213. [PMID: 37206380 PMCID: PMC10189870 DOI: 10.1039/d3sc01200j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/23/2023] [Indexed: 05/21/2023] Open
Abstract
Protein trans-splicing mediated by a split intein reconstitutes a protein backbone from two parts. This virtually traceless autoprocessive reaction provides the basis for numerous protein engineering applications. Protein splicing typically proceeds through two thioester or oxyester intermediates involving the side chains of cysteine or serine/threonine residues. A cysteine-less split intein has recently attracted particular interest as it can splice under oxidizing conditions and is orthogonal to disulfide or thiol bioconjugation chemistries. Here, we report the split PolB16 OarG intein, a second such cysteine-independent intein. As a unique trait, it is atypically split with a short intein-N precursor fragment of only 15 amino acids, the shortest characterized to date, which was chemically synthesized to enable protein semi-synthesis. By rational engineering we obtained a high-yielding, improved split intein mutant. Structural and mutational analysis revealed the dispensability of the usually crucial conserved motif N3 (block B) histidine as an obvious peculiar property. Unexpectedly, we identified a previously unnoticed histidine in hydrogen-bond forming distance to the catalytic serine 1 as critical for splicing. This histidine has been overlooked so far in multiple sequence alignments and is highly conserved only in cysteine-independent inteins as a part of a newly discovered motif NX. The motif NX histidine is thus likely of general importance to the specialized environment in the active site required in this intein subgroup. Together, our study advances the toolbox as well as the structural and mechanistic understanding of cysteine-less inteins.
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Affiliation(s)
- Tim Pasch
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Alexander Schröder
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Sabrina Kattelmann
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Miriam Eisenstein
- Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100 Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100 Israel
| | - Daniel Kümmel
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Münster Corrensstr. 36 48149 Münster Germany
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3
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Sekar G, Stevens AJ, Mostafavi AZ, Sashi P, Muir TW, Cowburn D. A Conserved Histidine Residue Drives Extein Dependence in an Enhanced Atypically Split Intein. J Am Chem Soc 2022; 144:19196-19203. [PMID: 36194550 PMCID: PMC10241006 DOI: 10.1021/jacs.2c08985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Split intein-mediated protein trans-splicing (PTS) is widely applied in chemical biology and biotechnology to carry out traceless and specific protein ligation. However, the external residues immediately flanking the intein (exteins) can reduce the splicing rate, thereby limiting certain applications of PTS. Splicing by a recently developed intein with atypical split architecture ("Cat") exhibits a stark dependence on the sequence of its N-terminal extein residues. Here, we further developed Cat using error-prone polymerase chain reaction (PCR) and a cell-based selection assay to produce Cat*, which exhibits greatly enhanced PTS activity in the presence of unfavorable N-extein residues. We then applied solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations to explore how the dynamics of a conserved B-block histidine residue (His78) contribute to this extein dependence. The enhanced extein tolerance of Cat* reported here should expand the applicability of atypically split inteins, and the mechanism highlights common principles that contribute to extein dependence.
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Affiliation(s)
- Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Anahita Z. Mostafavi
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Pulikallu Sashi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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4
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Kang W, Ding C, Zheng D, Ma X, Yi L, Tong X, Wu C, Xue C, Yu Y, Zhou Q. Nanobody Conjugates for Targeted Cancer Therapy and Imaging. Technol Cancer Res Treat 2021; 20:15330338211010117. [PMID: 33929911 PMCID: PMC8111546 DOI: 10.1177/15330338211010117] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Conventional antibody-based targeted cancer therapy is one of the most promising avenues of successful cancer treatment, with the potential to reduce toxic side effects to healthy cells surrounding tumor cells. However, the full potential of antibodies is severely limited due to their large size, low stability, slow clearance, and high immunogenicity. Alternatively, recently discovered nanobodies, which are the smallest naturally occurring antigen-binding format, have shown great potential for addressing these limitations. Bioconjugation of nanobodies to functional groups such as toxins, enzymes, radionucleotides, and fluorophores can improve the efficacy and potency of nanobodies, enhance their in vivo pharmacokinetics, and expand the range of potential applications. Herein, we review the superior characteristics of nanobodies in comparison to conventional antibodies and provide insight into recent developments in nanobody conjugates for targeted cancer therapy and imaging.
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Affiliation(s)
- Wei Kang
- School of Bioengineering, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Chuanfeng Ding
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Danni Zheng
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiao Ma
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lun Yi
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xinyi Tong
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Chuang Wu
- Xiamen Medical College, Xiamen, China
| | - Chuang Xue
- School of Bioengineering, Dalian University of Technology, Dalian, China.,Ningbo Institute of Dalian University of Technology, Ningbo, China
| | - Yongsheng Yu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qian Zhou
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
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5
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Ho TYH, Shao A, Lu Z, Savilahti H, Menolascina F, Wang L, Dalchau N, Wang B. A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction. Nat Commun 2021; 12:2200. [PMID: 33850130 PMCID: PMC8044194 DOI: 10.1038/s41467-021-22404-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.
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Affiliation(s)
- Trevor Y H Ho
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Hangzhou Innovation Centre, Zhejiang University, Hangzhou, China.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Alexander Shao
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Microsoft Research, Cambridge, UK
| | - Zeyu Lu
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Filippo Menolascina
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, UK
| | - Lei Wang
- School of Engineering, Westlake University, Hangzhou, China
| | | | - Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. .,Hangzhou Innovation Centre, Zhejiang University, Hangzhou, China. .,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China. .,ZJU-UoE Joint Research Centre for Engineering Biology, Zhejiang University, Haining, China.
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6
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Bhagawati M, Hoffmann S, Höffgen KS, Piehler J, Busch KB, Mootz HD. In Cellulo Protein Semi‐Synthesis from Endogenous and Exogenous Fragments Using the Ultra‐Fast Split Gp41‐1 Intein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maniraj Bhagawati
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Simon Hoffmann
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Katharina S. Höffgen
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics University of Osnabrück Barbarastrasse 11 49076 Osnabrück Germany
| | - Karin B. Busch
- Institute of Molecular Cell Biology University of Münster Schlossplatz 5 48149 Münster Germany
| | - Henning D. Mootz
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
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7
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Bhagawati M, Hoffmann S, Höffgen KS, Piehler J, Busch KB, Mootz HD. In Cellulo Protein Semi-Synthesis from Endogenous and Exogenous Fragments Using the Ultra-Fast Split Gp41-1 Intein. Angew Chem Int Ed Engl 2020; 59:21007-21015. [PMID: 32777124 PMCID: PMC7693240 DOI: 10.1002/anie.202006822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/15/2020] [Indexed: 12/19/2022]
Abstract
Protein semi-synthesis inside live cells from exogenous and endogenous parts offers unique possibilities for studying proteins in their native context. Split-intein-mediated protein trans-splicing is predestined for such endeavors and has seen some successes, but a much larger variety of established split inteins and associated protocols is urgently needed. We characterized the association and splicing parameters of the Gp41-1 split intein, which favorably revealed a nanomolar affinity between the intein fragments combined with the exceptionally fast splicing rate. Following bead-loading of a chemically modified intein fragment precursor into live mammalian cells, we fluorescently labeled target proteins on their N- and C-termini with short peptide tags, thus ensuring minimal perturbation of their structure and function. In combination with a nuclear-entrapment strategy to minimize cytosolic fluorescence background, we applied our technique for super-resolution imaging and single-particle tracking of the outer mitochondrial protein Tom20 in HeLa cells.
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Affiliation(s)
- Maniraj Bhagawati
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Simon Hoffmann
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Katharina S. Höffgen
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Jacob Piehler
- Department of Biology and Center for Cellular NanoanalyticsUniversity of OsnabrückBarbarastrasse 1149076OsnabrückGermany
| | - Karin B. Busch
- Institute of Molecular Cell BiologyUniversity of MünsterSchlossplatz 548149MünsterGermany
| | - Henning D. Mootz
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
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8
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Jedlitzke B, Mootz HD. Photocaged Nanobodies Delivered into Cells for Light Activation of Biological Processes. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Benedikt Jedlitzke
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Correns-Str. 36 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Correns-Str. 36 48149 Münster Germany
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9
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Hoffmann S, Terhorst TME, Singh RK, Kümmel D, Pietrokovski S, Mootz HD. Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein. Chembiochem 2020; 22:364-373. [PMID: 32813312 PMCID: PMC7891396 DOI: 10.1002/cbic.202000509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Indexed: 12/31/2022]
Abstract
Split inteins are indispensable tools for protein engineering because their ligation and cleavage reactions enable unique modifications of the polypeptide backbone. Three different classes of inteins have been identified according to the nature of the covalent intermediates resulting from the acyl rearrangements in the multistep protein‐splicing pathway. Class 3 inteins employ a characteristic internal cysteine for a branched thioester intermediate. A bioinformatic database search of non‐redundant protein sequences revealed the absence of split variants in 1701 class 3 inteins. We have discovered the first reported split class 3 intein in a metagenomics data set and report its biochemical, mechanistic and structural analysis. The AceL NrdHF intein exhibits low sequence conservation with other inteins and marked deviations in residues at conserved key positions, including a variation of the typical class‐3 WCT triplet motif. Nevertheless, functional analysis confirmed the class 3 mechanism of the intein and revealed excellent splicing yields within a few minutes over a wide range of conditions and with barely detectable cleavage side reactions. A high‐resolution crystal structure of the AceL NrdHF precursor and a mutagenesis study explained the importance and roles of several residues at the key positions. Tolerated substitutions in the flanking extein residues and a high affinity between the split intein fragments further underline the intein's future potential as a ligation tool.
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Affiliation(s)
- Simon Hoffmann
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Tobias M E Terhorst
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Rohit K Singh
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
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10
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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11
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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12
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Pinto F, Thornton EL, Wang B. An expanded library of orthogonal split inteins enables modular multi-peptide assemblies. Nat Commun 2020; 11:1529. [PMID: 32251274 PMCID: PMC7090010 DOI: 10.1038/s41467-020-15272-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
Inteins are protein segments capable of joining adjacent residues via a peptide bond. In this process known as protein splicing, the intein itself is not present in the final sequence, thus achieving scarless peptide ligation. Here, we assess the splicing activity of 34 inteins (both uncharacterized and known) using a rapid split fluorescent reporter characterization platform, and establish a library of 15 mutually orthogonal split inteins for in vivo applications, 10 of which can be simultaneously used in vitro. We show that orthogonal split inteins can be coupled to multiple split transcription factors to implement complex logic circuits in living organisms, and that they can also be used for the in vitro seamless assembly of large repetitive proteins with biotechnological relevance. Our work demonstrates the versatility and vast potential of an expanded library of orthogonal split inteins for their use in the fields of synthetic biology and protein engineering.
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Affiliation(s)
- Filipe Pinto
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Ella Lucille Thornton
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
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13
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A mesophilic cysteine-less split intein for protein trans-splicing applications under oxidizing conditions. Proc Natl Acad Sci U S A 2019; 116:22164-22172. [PMID: 31611397 DOI: 10.1073/pnas.1909825116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Split intein-mediated protein trans-splicing has found extensive applications in chemical biology, protein chemistry, and biotechnology. However, an enduring limitation of all well-established split inteins has been the requirement to carry out the reaction in a reducing environment due to the presence of 1 or 2 catalytic cysteines that need to be in a reduced state for splicing to occur. The concomitant exposure of the fused proteins to reducing agents severely limits the scope of protein trans-splicing by excluding proteins sensitive to reducing conditions, such as those containing critical disulfide bonds. Here we report the discovery, characterization, and engineering of a completely cysteine-less split intein (CL intein) that is capable of efficient trans-splicing at ambient temperatures, without a denaturation step, and in the absence of reducing agents. We demonstrate its utility for the site-specific chemical modification of nanobodies and an antibody Fc fragment by N- and C-terminal trans-splicing with short peptide tags (CysTag) that consist of only a few amino acids and have been prelabeled on a single cysteine using classical cysteine bioconjugation. We also synthesized the short N-terminal fragment of the atypically split CL intein by solid-phase peptide synthesis. Furthermore, using the CL intein in combination with a nanobody-epitope pair as a high-affinity mediator, we showed chemical labeling of the extracellular domain of a cell surface receptor on living mammalian cells with a short CysTag containing a synthetic fluorophore. The CL intein thus greatly expands the scope of applications for protein trans-splicing.
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14
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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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15
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Schumacher D, Helma J, Schneider AFL, Leonhardt H, Hackenberger CPR. Nanobodies: Chemical Functionalization Strategies and Intracellular Applications. Angew Chem Int Ed Engl 2018; 57:2314-2333. [PMID: 28913971 PMCID: PMC5838514 DOI: 10.1002/anie.201708459] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Indexed: 01/12/2023]
Abstract
Nanobodies can be seen as next-generation tools for the recognition and modulation of antigens that are inaccessible to conventional antibodies. Due to their compact structure and high stability, nanobodies see frequent usage in basic research, and their chemical functionalization opens the way towards promising diagnostic and therapeutic applications. In this Review, central aspects of nanobody functionalization are presented, together with selected applications. While early conjugation strategies relied on the random modification of natural amino acids, more recent studies have focused on the site-specific attachment of functional moieties. Such techniques include chemoenzymatic approaches, expressed protein ligation, and amber suppression in combination with bioorthogonal modification strategies. Recent applications range from sophisticated imaging and mass spectrometry to the delivery of nanobodies into living cells for the visualization and manipulation of intracellular antigens.
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Affiliation(s)
- Dominik Schumacher
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare, Pharmakologie and Department of ChemistryHumboldt-Universität zu BerlinBerlinGermany
- Department of Biology IILudwig Maximilians Universität München und Center for Integrated Protein Science MunichMartinsriedGermany
| | - Jonas Helma
- Department of Biology IILudwig Maximilians Universität München und Center for Integrated Protein Science MunichMartinsriedGermany
| | - Anselm F. L. Schneider
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare, Pharmakologie and Department of ChemistryHumboldt-Universität zu BerlinBerlinGermany
| | - Heinrich Leonhardt
- Department of Biology IILudwig Maximilians Universität München und Center for Integrated Protein Science MunichMartinsriedGermany
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Schumacher D, Helma J, Schneider AFL, Leonhardt H, Hackenberger CPR. Nanobodys: Strategien zur chemischen Funktionalisierung und intrazelluläre Anwendungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201708459] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dominik Schumacher
- Chemische Biologie, Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Institut für Chemie; Humboldt-Universität zu Berlin; Berlin Deutschland
- Department Biologie II; Ludwig Maximilians Universität München und Center for Integrated Protein Science Munich; Martinsried Deutschland
| | - Jonas Helma
- Department Biologie II; Ludwig Maximilians Universität München und Center for Integrated Protein Science Munich; Martinsried Deutschland
| | - Anselm F. L. Schneider
- Chemische Biologie, Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Institut für Chemie; Humboldt-Universität zu Berlin; Berlin Deutschland
| | - Heinrich Leonhardt
- Department Biologie II; Ludwig Maximilians Universität München und Center for Integrated Protein Science Munich; Martinsried Deutschland
| | - Christian P. R. Hackenberger
- Chemische Biologie, Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Institut für Chemie; Humboldt-Universität zu Berlin; Berlin Deutschland
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17
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Kolesinska B, Wasko J, Kaminski Z, Geueke B, Kohler HPE, Seebach D. Labeling and Protecting N
-Terminal Protein Positions by β
-Peptidyl Aminopeptidase-Catalyzed Attachment of β
-Amino-Acid Residues - Insulin as a First Example. Helv Chim Acta 2018. [DOI: 10.1002/hlca.201700259] [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)
- Beata Kolesinska
- Institute of Organic Chemistry; Technical University of Łodz; Zeromskiego 116 PL-90-924 Łodz Poland
| | - Joanna Wasko
- Institute of Organic Chemistry; Technical University of Łodz; Zeromskiego 116 PL-90-924 Łodz Poland
| | - Zbigniew Kaminski
- Institute of Organic Chemistry; Technical University of Łodz; Zeromskiego 116 PL-90-924 Łodz Poland
| | - Birgit Geueke
- Department of Environmental Microbiology; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Überlandstrasse 133 8600 Dübendorf Switzerland
| | - Hans-Peter E. Kohler
- Department of Environmental Microbiology; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Überlandstrasse 133 8600 Dübendorf Switzerland
| | - Dieter Seebach
- Laboratorium für Organische Chemie; Departement Chemie und Angewandte Biowissenschaften; ETH-Zürich; Hönggerberg HCI, Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
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18
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Enzyme-Based Labeling Strategies for Antibody-Drug Conjugates and Antibody Mimetics. Antibodies (Basel) 2018; 7:antib7010004. [PMID: 31544857 PMCID: PMC6698867 DOI: 10.3390/antib7010004] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 01/25/2023] Open
Abstract
Strategies for site-specific modification of proteins have increased in number, complexity, and specificity over the last years. Such modifications hold the promise to broaden the use of existing biopharmaceuticals or to tailor novel proteins for therapeutic or diagnostic applications. The recent quest for next-generation antibody–drug conjugates (ADCs) sparked research into techniques with site selectivity. While purely chemical approaches often impede control of dosage or locus of derivatization, naturally occurring enzymes and proteins bear the ability of co- or post-translational protein modifications at particular residues, thus enabling unique coupling reactions or protein fusions. This review provides a general overview and focuses on chemo-enzymatic methods including enzymes such as formylglycine-generating enzyme, sortase, and transglutaminase. Applications for the conjugation of antibodies and antibody mimetics are reported.
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