1
|
Karasev MM, Verkhusha VV, Shcherbakova DM. Near-Infrared Optogenetic Module for Conditional Protein Splicing. J Mol Biol 2023; 435:168360. [PMID: 37949312 PMCID: PMC10842711 DOI: 10.1016/j.jmb.2023.168360] [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: 04/17/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Optogenetics has emerged as a powerful tool for spatiotemporal control of biological processes. Near-infrared (NIR) light, with its low phototoxicity and deep tissue penetration, holds particular promise. However, the optogenetic control of polypeptide bond formation has not yet been developed. In this study, we introduce a NIR optogenetic module for conditional protein splicing (CPS) based on the gp41-1 intein. We optimized the module to minimize background signals in the darkness and to maximize the contrast between light and dark conditions. Next, we engineered a NIR CPS gene expression system based on the protein ligation of a transcription factor. We applied the NIR CPS for light-triggered protein cleavage to activate gasdermin D, a pore-forming protein that induces pyroptotic cell death. Our NIR CPS optogenetic module represents a promising tool for controlling molecular processes through covalent protein linkage and cleavage.
Collapse
Affiliation(s)
- Maksim M Karasev
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Daria M Shcherbakova
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| |
Collapse
|
2
|
Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
Collapse
Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Yao Z, Aboualizadeh F, Kroll J, Akula I, Snider J, Lyakisheva A, Tang P, Kotlyar M, Jurisica I, Boxem M, Stagljar I. Split Intein-Mediated Protein Ligation for detecting protein-protein interactions and their inhibition. Nat Commun 2020; 11:2440. [PMID: 32415080 PMCID: PMC7229206 DOI: 10.1038/s41467-020-16299-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Here, to overcome many limitations accompanying current available methods to detect protein-protein interactions (PPIs), we develop a live cell method called Split Intein-Mediated Protein Ligation (SIMPL). In this approach, bait and prey proteins are respectively fused to an intein N-terminal fragment (IN) and C-terminal fragment (IC) derived from a re-engineered split intein GP41-1. The bait/prey binding reconstitutes the intein, which splices the bait and prey peptides into a single intact protein that can be detected by regular protein detection methods such as Western blot analysis and ELISA, serving as readouts of PPIs. The method is robust and can be applied not only in mammalian cell lines but in animal models such as C. elegans. SIMPL demonstrates high sensitivity and specificity, and enables exploration of PPIs in different cellular compartments and tracking of kinetic interactions. Additionally, we establish a SIMPL ELISA platform that enables high-throughput screening of PPIs and their inhibitors. Protein-protein interactions are fundamental to the regulation of protein activity and cellular phyisology. Here the authors present Split Intein-Mediated Protein Ligation, which uses bait and prey proteins fused to intein fragments to generate single intact proteins upon interaction.
Collapse
Affiliation(s)
- Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Jason Kroll
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Indira Akula
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Priscilla Tang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Mike Boxem
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000, Split, Croatia.
| |
Collapse
|
5
|
Yang Y, Dong Z, Hu H, Peng J, Sheng Y, Tong Y, Yuan S, Li Z, Yang J, Wells T, Qu Y, Farrell NP, Liu Y. The facile and visualizable identification of broad-spectrum inhibitors of MDM2/p53 using co-expressed protein complexes. Analyst 2019; 144:3773-3781. [PMID: 31089613 DOI: 10.1039/c9an00350a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
MDM2 is a well-known oncoprotein overexpressed in a variety of cancers, and the identification of inhibitors that disrupt the MDM2/p53 interaction is of great interest in anticancer drug development. Here we designed a platform for the facile and visualizable identification of inhibitors of MDM2 using co-expressed protein complexes of MDM2/p53. A hexahistidine-tag on MDM2 allows the binding of the protein complex to the Ni-NTA affinity resin, while the fluorescent protein fused to p53 enables the direct visualization of the interaction of p53 with MDM2. Hence, the inhibition of the MDM2/p53 interaction can be observed with the naked eye. The assay can be set up by directly loading cell lysate to the Ni-NTA affinity resin, and no chemical modification of proteins is needed. In addition to the qualitative analyses, the binding affinity of inhibitors to the MDM2 protein can be quantified by fluorescence titration. The applications of this system have been verified using small molecules and peptide inhibitors. As a proof of concept, we screened a small library using this platform. Interestingly, two types of novel inhibitors of MDM2, including cyclohexyl-triphenylamine derivatives and platinum complexes, were identified and their binding affinities were obtained. Quantitative measurements show that these new types of inhibitors demonstrate a high binding affinity (up to Kd = 51.9 nM) to MDM2.
Collapse
Affiliation(s)
- Yang Yang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhiqiang Dong
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Hongze Hu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Junhui Peng
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Yaping Sheng
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Yang Tong
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Siming Yuan
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China
| | - Jiaxiang Yang
- Department of Chemistry, Anhui University, Hefei 230601, China
| | - Thomas Wells
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284-2006, USA
| | - Yun Qu
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284-2006, USA
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284-2006, USA
| | - Yangzhong Liu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| |
Collapse
|
6
|
Magyar C, Mentes A, Fichó E, Cserző M, Simon I. Physical Background of the Disordered Nature of "Mutual Synergetic Folding" Proteins. Int J Mol Sci 2018; 19:ijms19113340. [PMID: 30373142 PMCID: PMC6274838 DOI: 10.3390/ijms19113340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/17/2018] [Accepted: 10/21/2018] [Indexed: 01/16/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined 3D structure. Their disordered nature enables them to interact with several other proteins and to fulfil their vital biological roles, in most cases after coupled folding and binding. In this paper, we analyze IDPs involved in a new mechanism, mutual synergistic folding (MSF). These proteins define a new subset of IDPs. Recently we collected information on these complexes and created the Mutual Folding Induced by Binding (MFIB) database. These protein complexes exhibit considerable structural variation, and almost half of them are homodimers, but there is a significant amount of heterodimers and various kinds of oligomers. In order to understand the basic background of the disordered character of the monomers found in MSF complexes, the simplest part of the MFIB database, the homodimers are analyzed here. We conclude that MFIB homodimeric proteins have a larger solvent-accessible main-chain surface area on the contact surface of the subunits, when compared to globular homodimeric proteins. The main driving force of the dimerization is the mutual shielding of the water-accessible backbones and the formation of extra intermolecular interactions.
Collapse
Affiliation(s)
- Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Anikó Mentes
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Erzsébet Fichó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Miklós Cserző
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
- Department of Physiology, Faculty of Medicine, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary.
| | - István Simon
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Kulkarni P, Solomon TL, He Y, Chen Y, Bryan PN, Orban J. Structural metamorphism and polymorphism in proteins on the brink of thermodynamic stability. Protein Sci 2018; 27:1557-1567. [PMID: 30144197 PMCID: PMC6194243 DOI: 10.1002/pro.3458] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022]
Abstract
The classical view of the structure-function paradigm advanced by Anfinsen in the 1960s is that a protein's function is inextricably linked to its three-dimensional structure and is encrypted in its amino acid sequence. However, it is now known that a significant fraction of the proteome consists of intrinsically disordered proteins (IDPs). These proteins populate a polymorphic ensemble of conformations rather than a unique structure but are still capable of performing biological functions. At the boundary, between well-ordered and inherently disordered states are proteins that are on the brink of stability, either weakly stable ordered systems or disordered but on the verge of being stable. In such marginal states, even relatively minor changes can significantly alter the energy landscape, leading to large-scale conformational remodeling. Some proteins on the edge of stability are metamorphic, with the capacity to switch from one fold topology to another in response to an environmental trigger (e.g., pH, temperature/salt, redox). Many IDPs, on the other hand, are marginally unstable such that small perturbations (e.g., phosphorylation, ligands) tip the balance over to a range of ordered, partially ordered, or even more disordered states. In general, the structural transitions described by metamorphic fold switches and polymorphic IDPs possess a number of common features including low or diminished stability, large-scale conformational changes, critical disordered regions, latent or attenuated binding sites, and expansion of function. We suggest that these transitions are, therefore, conceptually and mechanistically analogous, representing adjacent regions in the continuum of order/disorder transitions.
Collapse
Affiliation(s)
- Prakash Kulkarni
- W. M. Keck Laboratory for Structural BiologyUniversity of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMaryland20850
| | - Tsega L. Solomon
- W. M. Keck Laboratory for Structural BiologyUniversity of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMaryland20850
| | - Yanan He
- W. M. Keck Laboratory for Structural BiologyUniversity of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMaryland20850
| | - Yihong Chen
- W. M. Keck Laboratory for Structural BiologyUniversity of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMaryland20850
| | - Philip N. Bryan
- W. M. Keck Laboratory for Structural BiologyUniversity of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMaryland20850
| | - John Orban
- W. M. Keck Laboratory for Structural BiologyUniversity of Maryland Institute for Bioscience and Biotechnology ResearchRockvilleMaryland20850
- Department of Chemistry and BiochemistryUniversity of MarylandCollege ParkMaryland20742
| |
Collapse
|
9
|
Gramespacher JA, Stevens AJ, Thompson RE, Muir TW. Improved protein splicing using embedded split inteins. Protein Sci 2018; 27:614-619. [PMID: 29226478 PMCID: PMC5818749 DOI: 10.1002/pro.3357] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 01/24/2023]
Abstract
Naturally split inteins mediate a traceless protein ligation process known as protein trans-splicing (PTS). Although frequently used in protein engineering applications, the efficiency of PTS can be reduced by the tendency of some split intein fusion constructs to aggregate; a consequence of the fragmented nature of the split intein itself or the polypeptide to which it is fused (the extein). Here, we report a strategy to help address this liability. This involves embedding the split intein within a protein sequence designed to stabilize either the intein fragment itself or the appended extein. We expect this approach to increase the scope of PTS-based protein engineering efforts.
Collapse
Affiliation(s)
| | - Adam J. Stevens
- Department of ChemistryPrinceton University, Frick Laboratory, PrincetonNew Jersey
| | - Robert E. Thompson
- Department of ChemistryPrinceton University, Frick Laboratory, PrincetonNew Jersey
| | - Tom W. Muir
- Department of ChemistryPrinceton University, Frick Laboratory, PrincetonNew Jersey
| |
Collapse
|
10
|
Abstract
Protein splicing in trans by split inteins has increasingly become a powerful protein-engineering tool for protein ligation, both in vivo and in vitro. Over 100 naturally occurring and artificially engineered split inteins have been reported for protein ligation using protein trans-splicing. Here, we review the current status of the reported split inteins in order to delineate an empirical or rational strategy for constructing new split inteins suitable for various applications in biotechnology and chemical biology.
Collapse
Affiliation(s)
- A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute-Frederick, MD 21702, USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Eryilmaz E, Shah NH, Muir TW, Cowburn D. Structural and dynamical features of inteins and implications on protein splicing. J Biol Chem 2014; 289:14506-11. [PMID: 24695731 DOI: 10.1074/jbc.r113.540302] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microorganisms from all domains of life. Despite this broad phylogenetic distribution, all inteins share common structural features such as a horseshoe-like pseudo two-fold symmetric fold, several canonical sequence motifs, and similar splicing mechanisms. Intriguingly, the splicing efficiencies and substrate specificity of different inteins vary considerably, reflecting subtle changes in the chemical mechanism of splicing, linked to their local structure and dynamics. As intein chemistry has widespread use in protein chemistry, understanding the structural and dynamical aspects of inteins is crucial for intein engineering and the improvement of intein-based technologies.
Collapse
Affiliation(s)
- Ertan Eryilmaz
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
| | - Neel H Shah
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - Tom W Muir
- the Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
| | - David Cowburn
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
| |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Vivien Schütz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149 Münster (Germany)
| | | |
Collapse
|
14
|
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]
|
15
|
Abstract
Inteins are auto-processing domains found in organisms from all domains of life. These proteins carry out a process known as protein splicing, which is a multi-step biochemical reaction comprised of both the cleavage and formation of peptide bonds. While the endogenous substrates of protein splicing are specific essential proteins found in intein-containing host organisms, inteins are also functional in exogenous contexts and can be used to chemically manipulate virtually any polypeptide backbone. Given this, protein chemists have exploited various facets of intein reactivity to modify proteins in myriad ways for both basic biological research as well as potential therapeutic applications. Here, we review the intein field, first focusing on the biological context and phylogenetic diversity of inteins, followed by a description of intein structure and biochemical function. Finally, we discuss prevalent inteinbased technologies, focusing on their applications in chemical biology, followed by persistent caveats of intein chemistry and approaches to alleviate these shortcomings. The findings summarized herein describe two and a half decades of research, leading from a biochemical curiosity to the development of powerful protein engineering tools.
Collapse
Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, United States
| |
Collapse
|
16
|
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
![]()
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.
Collapse
Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States
| | | | | | | |
Collapse
|
17
|
Minde DP, Halff EF, Tans S. Designing disorder: Tales of the unexpected tails. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26790. [PMID: 28516025 PMCID: PMC5424805 DOI: 10.4161/idp.26790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 12/24/2022]
Abstract
Protein tags of various sizes and shapes catalyze progress in biosciences. Well-folded tags can serve to solubilize proteins. Small, unfolded, peptide-like tags have become invaluable tools for protein purification as well as protein-protein interaction studies. Intrinsically Disordered Proteins (IDPs), which lack unique 3D structures, received exponentially increasing attention during the last decade. Recently, large ID tags have been developed to solubilize proteins and to engineer the pharmacological properties of protein and peptide pharmaceuticals. Here, we contrast the complementary benefits and applications of both folded and ID tags based on predictions of ID. Less structure often means more function in a shorter tag.
Collapse
Affiliation(s)
| | - Els F Halff
- Crystal and Structural Chemistry; Bijvoet Center for Biomolecular Research; Utrecht University; Utrecht, The Netherlands
| | - Sander Tans
- FOM Institute AMOLF; Amsterdam, The Netherlands
| |
Collapse
|