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Anastassov S, Filo M, Khammash M. Inteins: A Swiss army knife for synthetic biology. Biotechnol Adv 2024; 73:108349. [PMID: 38552727 DOI: 10.1016/j.biotechadv.2024.108349] [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: 12/18/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024]
Abstract
Inteins are proteins found in nature that execute protein splicing. Among them, split inteins stand out for their versatility and adaptability, presenting creative solutions for addressing intricate challenges in various biological applications. Their exquisite attributes, including compactness, reliability, orthogonality, low toxicity, and irreversibility, make them of interest to various fields including synthetic biology, biotechnology and biomedicine. In this review, we delve into the inherent challenges of using inteins, present approaches for overcoming these challenges, and detail their reliable use for specific cellular tasks. We will discuss the use of conditional inteins in areas like cancer therapy, drug screening, patterning, infection treatment, diagnostics and biocontainment. Additionally, we will underscore the potential of inteins in executing basic logical operations with practical implications. We conclude by showcasing their potential in crafting complex genetic circuits for performing computations and feedback control that achieves robust perfect adaptation.
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Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4056, Switzerland.
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2
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Gharios R, Li A, Kopyeva I, Francis RM, DeForest CA. One-Step Purification and N-Terminal Functionalization of Bioactive Proteins via Atypically Split Inteins. Bioconjug Chem 2024; 35:750-757. [PMID: 38815180 PMCID: PMC11262789 DOI: 10.1021/acs.bioconjchem.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Site-specific installation of non-natural functionality onto proteins has enabled countless applications in biotechnology, chemical biology, and biomaterials science. Though the N-terminus is an attractive derivatization location, prior methodologies targeting this site have suffered from low selectivity, a limited selection of potential chemical modifications, and/or challenges associated with divergent protein purification/modification steps. In this work, we harness the atypically split VidaL intein to simultaneously N-functionalize and purify homogeneous protein populations in a single step. Our method─referred to as VidaL-tagged expression and protein ligation (VEPL)─enables modular and scalable production of N-terminally modified proteins with native bioactivity. Demonstrating its flexibility and ease of use, we employ VEPL to combinatorially install 4 distinct (multi)functional handles (e.g., biotin, alkyne, fluorophores) to the N-terminus of 4 proteins that span three different classes: fluorescent (Enhanced Green Fluorescent Protein, mCherry), enzymatic (β-lactamase), and growth factor (epidermal growth factor). Moving forward, we anticipate that VEPL's ability to rapidly generate and isolate N-modified proteins will prove useful across the growing fields of applied chemical biology.
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Affiliation(s)
- Ryan Gharios
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Annabella Li
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Irina Kopyeva
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Ryan M Francis
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington 98105, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, Washington 98105, United States
- Institute for Protein Design, University of Washington, Seattle ,Washington 98105, United States
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3
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Diao F, Vasudevan D, Heckscher ES, White BH. Hox gene-specific cellular targeting using split intein Trojan exons. Proc Natl Acad Sci U S A 2024; 121:e2317083121. [PMID: 38602904 PMCID: PMC11047080 DOI: 10.1073/pnas.2317083121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
The Trojan exon method, which makes use of intronically inserted T2A-Gal4 cassettes, has been widely used in Drosophila to create thousands of gene-specific Gal4 driver lines. These dual-purpose lines provide genetic access to specific cell types based on their expression of a native gene while simultaneously mutating one allele of the gene to enable loss-of-function analysis in homozygous animals. While this dual use is often an advantage, the truncation mutations produced by Trojan exons are sometimes deleterious in heterozygotes, perhaps by creating translation products with dominant negative effects. Such mutagenic effects can cause developmental lethality as has been observed with genes encoding essential transcription factors. Given the importance of transcription factors in specifying cell type, alternative techniques for generating specific Gal4 lines that target them are required. Here, we introduce a modified Trojan exon method that retains the targeting fidelity and plug-and-play modularity of the original method but mitigates its mutagenic effects by exploiting the self-splicing capabilities of split inteins. "Split Intein Trojan exons" (siTrojans) ensure that the two truncation products generated from the interrupted allele of the native gene are trans-spliced to create a full-length native protein. We demonstrate the efficacy of siTrojans by generating a comprehensive toolkit of Gal4 and Split Gal4 lines for the segmentally expressed Hox transcription factors and illustrate their use in neural circuit mapping by targeting neurons according to their position along the anterior-posterior axis. Both the method and the Hox gene-specific toolkit introduced here should be broadly useful.
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Affiliation(s)
- Fengqiu Diao
- Laboratory of Molecular Biology, Section on Neural Function, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Deeptha Vasudevan
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Ellie S. Heckscher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Benjamin H. White
- Laboratory of Molecular Biology, Section on Neural Function, National Institute of Mental Health, NIH, Bethesda, MD20892
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4
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Snoj J, Lapenta F, Jerala R. Preorganized cyclic modules facilitate the self-assembly of protein nanostructures. Chem Sci 2024; 15:3673-3686. [PMID: 38455016 PMCID: PMC10915844 DOI: 10.1039/d3sc06658d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
The rational design of supramolecular assemblies aims to generate complex systems based on the simple information encoded in the chemical structure. Programmable molecules such as nucleic acids and polypeptides are particularly suitable for designing diverse assemblies and shapes not found in nature. Here, we describe a strategy for assembling modular architectures based on structurally and covalently preorganized subunits. Cyclization through spontaneous self-splicing of split intein and coiled-coil dimer-based interactions of polypeptide chains provide structural constraints, facilitating the desired assembly. We demonstrate the implementation of a strategy based on the preorganization of the subunits by designing a two-chain coiled-coil protein origami (CCPO) assembly that adopts a tetrahedral topology only when one or both subunit chains are covalently cyclized. Employing this strategy, we further design a 109 kDa trimeric CCPO assembly comprising 24 CC-forming segments. In this case, intein cyclization was crucial for the assembly of a concave octahedral scaffold, a newly designed protein fold. The study highlights the importance of preorganization of building modules to facilitate the self-assembly of higher-order supramolecular structures.
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Affiliation(s)
- Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- Interdisciplinary Doctoral Program in Biomedicine, University of Ljubljana Kongresni trg 12 SI-1000 Ljubljana Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- EN-FIST Centre of Excellence Trg OF 13 SI-1000 Ljubljana Slovenia
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5
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Ray DM, Flood JR, David Y. Harnessing Split-Inteins as a Tool for the Selective Modification of Surface Receptors in Live Cells. Chembiochem 2023; 24:e202200487. [PMID: 36178424 PMCID: PMC9977608 DOI: 10.1002/cbic.202200487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/29/2022] [Indexed: 02/04/2023]
Abstract
Biochemical studies of integral membrane proteins are often hampered by low purification yields and technical limitations such as aggregation causing in vitro manipulations to be challenging. The ability of controlling proteins in live cells bypasses these limitations while broadening the scope of accessible questions owing to the proteins being in their native environment. Here we take advantage of the intein biorthogonality to mammalian systems, site specificity, fast kinetics, and auto-processing nature as an attractive option for modifying surface proteins. Using EGFR as a model, we demonstrate that the split-intein pair AvaN /NpuC can be used to efficiently and specifically modify target membrane proteins with a synthetic adduct for downstream live cell application.
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Affiliation(s)
- Devin M Ray
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Julia R Flood
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA
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6
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Khoo ATT, Kim PJ, Kim HM, Je HS. Neural circuit analysis using a novel intersectional split intein-mediated split-Cre recombinase system. Mol Brain 2020; 13:101. [PMID: 32616061 PMCID: PMC7331137 DOI: 10.1186/s13041-020-00640-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/23/2020] [Indexed: 11/10/2022] Open
Abstract
The defining features of a neuron are its functional and anatomical connections with thousands of other neurons in the brain. Together, these neurons form functional networks that direct animal behavior. Current approaches that allow the interrogation of specific populations of neurons and neural circuits rely heavily on targeting their gene expression profiles or connectivity. However, these approaches are often unable to delineate specific neuronal populations. Here, we developed a novel intersectional split intein-mediated split-Cre recombinase system that can selectively label specific types of neurons based on their gene expression profiles and structural connectivity. We developed this system by splitting Cre recombinase into two fragments with evolved split inteins and subsequently expressed one fragment under the influence of a cell type-specific promoter in a transgenic animal, and delivered the other fragment via retrograde viral gene transfer. This approach results in the reconstitution of Cre recombinase in only specific population of neurons projecting from a specific brain region or in those of a specific neuronal type. Taken together, our split intein-based split-Cre system will be useful for sophisticated characterization of mammalian brain circuits.
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Affiliation(s)
- Audrey Tze Ting Khoo
- Neuroscience and Behavioural Disorders Programme, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Paul Jong Kim
- Neuroscience and Behavioural Disorders Programme, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - H Shawn Je
- Neuroscience and Behavioural Disorders Programme, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore.
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Fink T, Stevović B, Verwaal R, Roubos JA, Gaber R, Benčina M, Jerala R, Gradišar H. Metabolic enzyme clustering by coiled coils improves the biosynthesis of resveratrol and mevalonate. AMB Express 2020; 10:97. [PMID: 32448937 PMCID: PMC7246283 DOI: 10.1186/s13568-020-01031-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
The clustering of biosynthetic enzymes is used in nature to channel reaction products and increase the yield of compounds produced by multiple reaction steps. The coupling of multiple enzymes has been shown to increase the biosynthetic product yield. Different clustering strategies have particular advantages as the spatial organization of multiple enzymes creates biocatalytic cascades with a higher efficiency of biochemical reaction. However, there are also some drawbacks, such as misfolding and the variable stability of interaction domains, which may differ between particular biosynthetic reactions and the host organism. Here, we compared different protein-based clustering strategies, including direct fusion, fusion mediated by intein, and noncovalent interactions mediated through small coiled-coil dimer-forming domains. The clustering of enzymes through orthogonally designed coiled-coil interaction domains increased the production of resveratrol in Escherichia coli more than the intein-mediated fusion of biosynthetic enzymes. The improvement of resveratrol production correlated with the stability of the coiled-coil dimers. The coiled-coil fusion-based approach also increased mevalonate production in Saccharomyces cerevisiae, thus demonstrating the wider applicability of this strategy.
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8
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Luan H, Kuzin A, Odenwald WF, White BH. Cre-assisted fine-mapping of neural circuits using orthogonal split inteins. eLife 2020; 9:e53041. [PMID: 32286225 PMCID: PMC7217698 DOI: 10.7554/elife.53041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/11/2020] [Indexed: 01/18/2023] Open
Abstract
Existing genetic methods of neuronal targeting do not routinely achieve the resolution required for mapping brain circuits. New approaches are thus necessary. Here, we introduce a method for refined neuronal targeting that can be applied iteratively. Restriction achieved at the first step can be further refined in a second step, if necessary. The method relies on first isolating neurons within a targeted group (i.e. Gal4 pattern) according to their developmental lineages, and then intersectionally limiting the number of lineages by selecting only those in which two distinct neuroblast enhancers are active. The neuroblast enhancers drive expression of split Cre recombinase fragments. These are fused to non-interacting pairs of split inteins, which ensure reconstitution of active Cre when all fragments are expressed in the same neuroblast. Active Cre renders all neuroblast-derived cells in a lineage permissive for Gal4 activity. We demonstrate how this system can facilitate neural circuit-mapping in Drosophila.
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Affiliation(s)
- Haojiang Luan
- Laboratory of Molecular Biology, National Institute of Mental Health, NIHBethesdaUnited States
| | - Alexander Kuzin
- Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, NIHBethesdaUnited States
| | - Ward F Odenwald
- Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, NIHBethesdaUnited States
| | - Benjamin H White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIHBethesdaUnited States
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9
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Abstract
Protein semisynthesis is a powerful tool for studying proteins and has contributed to a better understanding of protein structure and function and also driven innovations in protein science. Expressed protein ligation (EPL) is a widely used method to generate chemically modified proteins. However, EPL has some limitations, particularly relevant to modify challenging proteins such as antibodies. The method termed streamlined expressed protein ligation (SEPL) overcomes some of the problems of EPL, and other methods of protein semisynthesis, to generate challenging modified proteins such as antibody-drug conjugates (ADCs). ADCs targeting highly cytotoxic molecules to cancer cells, offer an attractive strategy to selectively eliminate tumor cells with improved therapeutic index than the antibodies or cytotoxic molecules themselves. Despite the potential of ADCs, the development of such complex molecules is challenging. We provide here protocols to prepare site-specifically modified ADCs by streamlined expressed protein ligation (SEPL), which does not require the incorporation of unnatural modifications into the antibody. Therefore, fully native antibodies, with only the desired cytotoxic molecules attached, can be generated.
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10
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Abstract
In recent years, split inteins have seen widespread use as molecular platforms for the design of a variety of peptide and protein chemistry technologies, most notably protein ligation. The development of these approaches is dependent on the identification and/or design of split inteins with robust activity, stability, and solubility. Here, we describe two approaches to characterize and compare the activities of newly identified or engineered split inteins. The first assay employs an E. coli-based selection system to rapidly screen the activities of many inteins and can be repurposed for directed evolution. The second assay utilizes reverse-phase high-performance liquid chromatography (RP-HPLC) to provide insights into individual chemical steps in the protein splicing reaction, information that can guide further engineering efforts. These techniques provide useful alternatives to common assays that utilize SDS-PAGE to analyze splicing reaction progress.
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11
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Abstract
The development of expressed protein ligation (EPL) widened the scope of questions that could be addressed by mechanistic biochemistry. Protein trans-splicing (PTS) relies on the same basic chemical principles, but utilizes split inteins to tracelessly ligate distinct peptide or polypeptide fragments together with native peptide bonds. Here we present a method to adapt PTS methodologies for their use in live cells, in order to deliver synthetic or native histone modifications. As an example, we provide a protocol to incorporate a small molecule fluorophore into chromatinized histones. The protocol should be easily adaptable to incorporate other modifications to chromatin in vivo.
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Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins. Methods Enzymol 2019; 626:203-222. [PMID: 31606075 DOI: 10.1016/bs.mie.2019.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many cellular processes as well as their associated pathologies are regulated by protein post-translational modifications (PTMs). Understanding the precise roles of these adducts hinges on the development of methods to robustly and site-specifically manipulate proteins in their physiological environments. Recently, ultrafast intein protein trans-splicing (PTS) was harnessed to incorporate site-specific modifications on cellular chromatin in live cells. In this chapter, we present the protocols for the generation of synthetic modifications on native chromatin as well as highlight the capabilities of this methodology.
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Matern JCJ, Friedel K, Binschik J, Becher KS, Yilmaz Z, Mootz HD. Altered Coordination of Individual Catalytic Steps in Different and Evolved Inteins Reveals Kinetic Plasticity of the Protein Splicing Pathway. J Am Chem Soc 2018; 140:11267-11275. [PMID: 30111090 DOI: 10.1021/jacs.8b04794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein splicing performed by inteins provides powerful opportunities to manipulate protein structure and function, however, detailed mechanistic knowledge of the multistep pathway to help engineering optimized inteins remains scarce. A typical intein has to coordinate three steps to maximize the product yield of ligated exteins. We have revealed a new type of coordination in the Ssp DnaB intein, in which the initial N- S acyl shift appears rate-limiting and acts as an up-regulation switch to dramatically accelerate the last step of succinimide formation, which is thus coupled to the first step. The structure-activity relationship at the N-terminal scissile bond was studied with atomic precision using a semisynthetic split intein. We show that the removal of the extein acyl group from the α-amino moiety of the intein's first residue is strictly required and sufficient for the up-regulation switch. Even an acetyl group as the smallest possible extein moiety completely blocked the switch. Furthermore, we investigated the M86 intein, a mutant with faster splicing kinetics previously obtained by laboratory evolution of the Ssp DnaB intein, and the individual impact of its eight mutations. The succinimide formation was decoupled from the first step in the M86 intein, but the acquired H143R mutation acts as a brake to prevent premature C-terminal cleavage and thereby maximizes splicing yields. Together, these results revealed a high degree of plasticity in the kinetic coordination of the splicing pathway. Furthermore, our study led to the rational design of improved M86 mutants with the highest yielding trans-splicing and fastest trans-cleavage activities.
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Affiliation(s)
- Julian C J Matern
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Kristina Friedel
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Jens Binschik
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Kira-Sophie Becher
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Zahide Yilmaz
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Henning D Mootz
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
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Bachmann AL, Mootz HD. N-terminal chemical protein labeling using the naturally split GOS-TerL intein. J Pept Sci 2017; 23:624-630. [PMID: 28332258 DOI: 10.1002/psc.2996] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/07/2022]
Abstract
Chemoselective and regioselective chemical protein labeling is of great importance, yet no current technique is sufficiently general and simple to perform. Protein trans-splicing by split inteins can be used to ligate short tags with chemical labels to either the N or the C terminus of a protein. The CysTag approach exploits split intein fragments without a cysteine fused with such a short tag containing a single cysteine that is easily amenable to selective modification using classical cysteine bioconjugation. Labeling of the protein of interest is achieved through transfer of the pre-labeled tag by protein trans-splicing. This protocol keeps other cysteines unmodified. While split inteins for C-terminal CysTag labeling were previously reported, no high-yielding and naturally split intein for N-terminal labeling has been available. In this work, the recently discovered GOS-TerL intein was explored as the only known naturally split intein that both lacks a cysteine in its N-terminal fragment and is active under ambient conditions. Thioredoxin as a model protein and a camelid nanobody were labeled with a synthetic fluorophore by transferring the pre-labeling CysTag in the protein trans-splicing reaction with yields of about 50 to 90%. The short N-terminal intein fragment was also chemically synthesized with a tag to enable protein labeling by semi-synthetic protein trans-splicing. Our results expand the scope of the CysTag labeling strategy, which achieves selective chemical modification without the requirement for sophisticated biorthogonal functional groups and rather builds on the plethora of commercially available reagents directed at the thiol side chain of cysteine. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Anne-Lena Bachmann
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
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15
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Fischle W, Mootz HD, Schwarzer D. Synthetic histone code. Curr Opin Chem Biol 2015; 28:131-40. [PMID: 26256563 DOI: 10.1016/j.cbpa.2015.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/04/2015] [Accepted: 07/12/2015] [Indexed: 01/17/2023]
Abstract
Chromatin is the universal template of genetic information in all eukaryotic cells. This complex of DNA and histone proteins not only packages and organizes genomes but also regulates gene expression. A multitude of posttranslational histone modifications and their combinations are thought to constitute a code for directing distinct structural and functional states of chromatin. Methods of protein chemistry, including protein semisynthesis, amber suppression technology, and cysteine bioconjugation, have enabled the generation of so-called designer chromatin containing histones in defined and homogeneous modification states. Several of these approaches have matured from proof-of-concept studies into efficient tools and technologies for studying the biochemistry of chromatin regulation and for interrogating the histone code. We summarize pioneering experiments and recent developments in this exciting field of chemical biology.
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Affiliation(s)
- Wolfgang Fischle
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, 48149 Muenster, Germany.
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.
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16
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Abstract
The first crystal trans-structure of a naturally occurring split intein has been determined for the Npu (Nostoc punctiforme PCC73102) DnaE split intein. Guided by this structure, the residues NArg50 and CSer35, well conserved in DnaE split inteins, are identified to be critical in the trans-splicing of Npu DnaE split intein. An in vitro splicing assay demonstrates that NArg50 and CSer35 play synergistic roles in modulating its intein activity. The C-terminal CAsn36 exhibits two orientations of its side chain and interacts with both NArg50 and CSer35 through hydrogen bonding. These interactions likely facilitate the cyclization of asparagine in the course of protein splicing. The mutation of either residue reduces intein activity, and correlates with the low activity of the Ssp (Cyanobacterium synechocystis sp. strain PCC6803) DnaE split intein. On the other hand, NArg50 also forms a hydrogen bond with the highly conserved F-block CAsp17, thus influencing the N-S acyl shift during N-terminal cleavage. Sequence alignments show that residues NArg50 and CSer35 are rather conserved in those split inteins that lack a penultimate histidine residue. The conserved non-catalytic residues of split inteins modulate the efficiency of protein trans-splicing by hydrogen-bond interactions with the catalytic residues at the splice junction.
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17
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SpyLigase peptide-peptide ligation polymerizes affibodies to enhance magnetic cancer cell capture. Proc Natl Acad Sci U S A 2014; 111:E1176-81. [PMID: 24639550 DOI: 10.1073/pnas.1315776111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Individual proteins can now often be modified with atomic precision, but there are still major obstacles to connecting proteins into larger assemblies. To direct protein assembly, ideally, peptide tags would be used, providing the minimal perturbation to protein function. However, binding to peptides is generally weak, so assemblies are unstable over time and disassemble with force or harsh conditions. We have recently developed an irreversible protein-peptide interaction (SpyTag/SpyCatcher), based on a protein domain from Streptococcus pyogenes, that locks itself together via spontaneous isopeptide bond formation. Here we develop irreversible peptide-peptide interaction, through redesign of this domain and genetic dissection into three parts: a protein domain termed SpyLigase, which now ligates two peptide tags to each other. All components expressed efficiently in Escherichia coli and peptide tags were reactive at the N terminus, at the C terminus, or at internal sites. Peptide-peptide ligation enabled covalent and site-specific polymerization of affibodies or antibodies against the tumor markers epidermal growth factor receptor (EGFR) and HER2. Magnetic capture of circulating tumor cells (CTCs) is one of the most promising approaches to improve cancer prognosis and management, but CTC capture is limited by inefficient recovery of cells expressing low levels of tumor antigen. SpyLigase-assembled protein polymers made possible the isolation of cancerous cells expressing lower levels of tumor antigen and should have general application in enhancing molecular capture.
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Schütz V, Mootz HD. Click-tag and amine-tag: chemical tag approaches for efficient protein labeling in vitro and on live cells using the naturally split Npu DnaE intein. Angew Chem Int Ed Engl 2014; 53:4113-7. [PMID: 24615830 DOI: 10.1002/anie.201309396] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/16/2013] [Indexed: 11/07/2022]
Abstract
Protein labeling with synthetic moieties remains in many cases a technically challenging or unresolved task. Two new and simple concepts are presented. In both approaches, a very short tag of only a few amino acids is prepared with the desired chemical modification and, in a second step, it is transferred to the protein of interest by protein trans-splicing. For the amine-tag, a recombinant intein fragment free of lysine residues was generated such that the amine group of the N terminus could be selectively modified with regular amine-reactive reagents. Thus, standard bioconjugation procedures without any chemical synthesis could be applied without modification of lysines in the protein of interest. For the click-tag, protein trans-splicing was combined with unnatural amino acid mutagenesis and subsequent bioorthogonal side chain modification, as demonstrated for click chemistry using p-azidophenylalanine. By the two-step strategy, exposure of the protein of interest to the copper catalyst was avoided.
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Affiliation(s)
- Vivien Schütz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149 Münster (Germany)
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19
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Schütz V, Mootz HD. Click-Tag and Amine-Tag: Chemical Tag Approaches for Efficient Protein Labeling In Vitro and on Live Cells using the Naturally SplitNpuDnaE Intein. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Topilina NI, Mills KV. Recent advances in in vivo applications of intein-mediated protein splicing. Mob DNA 2014; 5:5. [PMID: 24490831 PMCID: PMC3922620 DOI: 10.1186/1759-8753-5-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/07/2014] [Indexed: 01/27/2023] Open
Abstract
Intein-mediated protein splicing has become an essential tool in modern biotechnology. Fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. Recent work has extended these in vitro applications to the cell or to whole organisms. We review recent advances in intein-mediated protein expression and modification, post-translational processing and labeling, protein regulation by conditional protein splicing, biosensors, and expression of trans-genes.
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Affiliation(s)
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, 1 College Street, Worcester, MA 01610, USA.
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21
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Wang Z, Ding X, Li S, Shi J, Li Y. Engineered fluorescence tags for in vivo protein labelling. RSC Adv 2014. [DOI: 10.1039/c3ra46991c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In vivoprotein labelling with a peptide tag–fluorescent probe system is an important chemical biology strategy for studying protein distribution, interaction and function.
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Affiliation(s)
- Zhipeng Wang
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
- School of Life Sciences
| | - Xiaozhe Ding
- Department of Chemistry
- School of Life Sciences
- Tsinghua University
- Beijing 100084, China
| | - Sijian Li
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
| | - Jing Shi
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
| | - Yiming Li
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
- School of Life Sciences
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22
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Shah NH, Eryilmaz E, Cowburn D, Muir TW. Naturally split inteins assemble through a "capture and collapse" mechanism. J Am Chem Soc 2013; 135:18673-81. [PMID: 24236406 PMCID: PMC3865799 DOI: 10.1021/ja4104364] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Split
inteins are a class of naturally occurring proteins that
carry out protein splicing in trans. The chemical
mechanism of protein trans-splicing is well-understood
and has been exploited to develop several powerful protein engineering
technologies. Split intein chemistry is preceded by efficient molecular
recognition between two protomers that become intertwined in their
bound state. It is currently unclear how this unique topology is achieved
upon fragment association. Using biophysical techniques in conjunction
with protein engineering methods, including segmental isotopic labeling,
we show that one split intein fragment is partly folded, while the
other is completely disordered. These polypeptides capture each other
through their disordered regions and form an ordered intermediate
with native-like structure at their interface. This intermediate then
collapses into the canonical intein fold. This mechanism provides
insight into the evolutionary constraints on split intein assembly
and should enhance the development of split intein-based technologies.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
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23
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Sorci M, Dassa B, Liu H, Anand G, Dutta AK, Pietrokovski S, Belfort M, Belfort G. Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins. Anal Chem 2013; 85:6080-8. [PMID: 23679912 PMCID: PMC3760192 DOI: 10.1021/ac400949t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step, allowing direct intermolecular force measurement of the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1 μm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and nonpolar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski's equality and demonstrated, as expected, that nonequilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair.
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Affiliation(s)
- Mirco Sorci
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Bareket Dassa
- Molecular Genetics Department, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hongwei Liu
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Gaurav Anand
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Amit K. Dutta
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Shmuel Pietrokovski
- Molecular Genetics Department, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marlene Belfort
- Department of Biological Sciences, University at Albany, SUNY, Albany, NY 12222
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, Troy, NY 12180
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24
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Shah NH, Eryilmaz E, Cowburn D, Muir TW. Extein residues play an intimate role in the rate-limiting step of protein trans-splicing. J Am Chem Soc 2013; 135:5839-47. [PMID: 23506399 PMCID: PMC3630739 DOI: 10.1021/ja401015p] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Split
inteins play an important role in modern protein semisynthesis
techniques. These naturally occurring protein splicing domains can
be used for in vitro and in vivo protein modification, peptide and
protein cyclization, segmental isotopic labeling, and the construction
of biosensors. The most well-characterized family of split inteins,
the cyanobacterial DnaE inteins, show particular promise, as many
of these can splice proteins in less than 1 min. Despite this fact,
the activity of these inteins is context-dependent: certain peptide
sequences surrounding their ligation junction (called local N- and
C-exteins) are strongly preferred, while other sequences cause a dramatic
reduction in the splicing kinetics and yield. These sequence constraints
limit the utility of inteins, and thus, a more detailed understanding
of their participation in protein splicing is needed. Here we present
a thorough kinetic analysis of the relationship between C-extein composition
and split intein activity. The results of these experiments were used
to guide structural and molecular dynamics studies, which revealed
that the motions of catalytic residues are constrained by the second
C-extein residue, likely forcing them into an active conformation
that promotes rapid protein splicing. Together, our structural and
functional studies also highlight a key region of the intein structure
that can be re-engineered to increase intein promiscuity.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
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25
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Volkmann G, Mootz HD. Recent progress in intein research: from mechanism to directed evolution and applications. Cell Mol Life Sci 2013; 70:1185-206. [PMID: 22926412 PMCID: PMC11113529 DOI: 10.1007/s00018-012-1120-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 07/23/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
Abstract
Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.
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Affiliation(s)
- Gerrit Volkmann
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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26
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Binschik J, Mootz HD. Chemical bypass of intein-catalyzed N-S acyl shift in protein splicing. Angew Chem Int Ed Engl 2013; 52:4260-4. [PMID: 23468274 DOI: 10.1002/anie.201208863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/13/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Jens Binschik
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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27
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Binschik J, Mootz HD. Chemischer “Bypass” des Intein-katalysierten N-S-Acyltransfers im Proteinspleißen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Vila-Perelló M, Liu Z, Shah NH, Willis JA, Idoyaga J, Muir TW. Streamlined expressed protein ligation using split inteins. J Am Chem Soc 2012; 135:286-92. [PMID: 23265282 PMCID: PMC3544275 DOI: 10.1021/ja309126m] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified proteins are invaluable tools for studying the molecular details of biological processes, and they also hold great potential as new therapeutic agents. Several methods have been developed for the site-specific modification of proteins, one of the most widely used being expressed protein ligation (EPL) in which a recombinant α-thioester is ligated to an N-terminal Cys-containing peptide. Despite the widespread use of EPL, the generation and isolation of the required recombinant protein α-thioesters remain challenging. We describe here a new method for the preparation and purification of recombinant protein α-thioesters using engineered versions of naturally split DnaE inteins. This family of autoprocessing enzymes is closely related to the inteins currently used for protein α-thioester generation, but they feature faster kinetics and are split into two inactive polypeptides that need to associate to become active. Taking advantage of the strong affinity between the two split intein fragments, we devised a streamlined procedure for the purification and generation of protein α-thioesters from cell lysates and applied this strategy for the semisynthesis of a variety of proteins including an acetylated histone and a site-specifically modified monoclonal antibody.
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Affiliation(s)
- Miquel Vila-Perelló
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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