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Zane HK, Doh JK, Enns CA, Beatty KE. Versatile Interacting Peptide (VIP) Tags for Labeling Proteins with Bright Chemical Reporters. Chembiochem 2017; 18:470-474. [PMID: 28052473 PMCID: PMC5785092 DOI: 10.1002/cbic.201600627] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence microscopy is an essential tool for the biosciences, enabling the direct observation of proteins in their cellular environment. New methods that facilitate attachment of photostable synthetic fluorophores with genetic specificity are needed to advance the frontiers of biological imaging. Here, we describe a new set of small, selective, genetically encoded tags for proteins based on a heterodimeric coiled-coil interaction between two peptides: CoilY and CoilZ. Proteins expressed as a fusion to CoilZ were selectively labeled with the complementary CoilY fluorescent probe peptide. Fluorophore-labeled target proteins were readily detected in cell lysates with high specificity and sensitivity. We found that these versatile interacting peptide (VIP) tags allowed rapid and specific delivery of bright organic dyes or quantum dots to proteins displayed on living cells. Additionally, we validated that either CoilY or CoilZ could serve as the VIP tag, which enabled us to observe two distinct cell-surface protein targets with this one heterodimeric pair.
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Affiliation(s)
- Hannah K Zane
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Julia K Doh
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Caroline A Enns
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Kimberly E Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
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2
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DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells. ACTA ACUST UNITED AC 2016; 22:1671-9. [PMID: 26687484 DOI: 10.1016/j.chembiol.2015.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/10/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Polypeptide-tag/small-molecule pairs for specific cellular protein labeling are useful for visualizing cellular proteins and controlling their activity. Here, we report the development of an in vitro evolution-based (poly)peptide tag identification system named the DIVERSE (Directed In Vitro Evolution of Reactive peptide tags via Sequential Enrichment) system. In this system, an extremely diverse (10(14)) library of peptide tags, displayed by covalent attachment to their encoding cDNAs, is continuously prepared from the DNA library in a one-pot approach. Using this system, we demonstrated de novo creation of non-enzymatically covalent-labeling peptide tags for a synthetic small-molecule target from a random peptide library. Protein labeling with these tags was applicable to N- and C-terminal fusions, multiple different proteins and fluorophores, and intracellular labeling. The DIVERSE system can be used not only for the de novo creation of polypeptide tags but also sequence optimization of existing polypeptide tags from extremely diverse libraries.
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Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1. Cell 2013; 154:737-47. [PMID: 23953109 PMCID: PMC3950538 DOI: 10.1016/j.cell.2013.07.030] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/30/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
Mitochondria have long been implicated in the pathogenesis of Parkinson's disease (PD). Mutations in the mitochondrial kinase PINK1 that reduce kinase activity are associated with mitochondrial defects and result in an autosomal-recessive form of early-onset PD. Therapeutic approaches for enhancing the activity of PINK1 have not been considered because no allosteric regulatory sites for PINK1 are known. Here, we show that an alternative strategy, a neo-substrate approach involving the ATP analog kinetin triphosphate (KTP), can be used to increase the activity of both PD-related mutant PINK1(G309D) and PINK1(WT). Moreover, we show that application of the KTP precursor kinetin to cells results in biologically significant increases in PINK1 activity, manifest as higher levels of Parkin recruitment to depolarized mitochondria, reduced mitochondrial motility in axons, and lower levels of apoptosis. Discovery of neo-substrates for kinases could provide a heretofore-unappreciated modality for regulating kinase activity.
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Affiliation(s)
- Nicholas T. Hertz
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Amandine Berthet
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin L. Sos
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kurt S. Thorn
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Al L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Graduate Programs in Neuroscience and Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
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Ochoa-Leyva A, Barona-Gómez F, Saab-Rincón G, Verdel-Aranda K, Sánchez F, Soberón X. Exploring the Structure-Function Loop Adaptability of a (β/α)(8)-Barrel Enzyme through Loop Swapping and Hinge Variability. J Mol Biol 2011; 411:143-57. [PMID: 21635898 DOI: 10.1016/j.jmb.2011.05.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/31/2011] [Accepted: 05/18/2011] [Indexed: 11/26/2022]
Abstract
Evolution of proteins involves sequence changes that are frequently localized at loop regions, revealing their important role in natural evolution. However, the development of strategies to understand and imitate such events constitutes a challenge to design novel enzymes in the laboratory. In this study, we show how to adapt loop swapping as semiautonomous units of functional groups in an enzyme with the (β/α)(8)-barrel and how this functional adaptation can be measured in vivo. To mimic the natural mechanism providing loop variability in antibodies, we developed an overlap PCR strategy. This includes introduction of sequence diversity at two hinge residues, which connect the new loops with the rest of the protein scaffold, and we demonstrate that this is necessary for a successful exploration of functional sequence space. This design allowed us to explore the sequence requirements to functional adaptation of each loop replacement that may not be sampled otherwise. Libraries generated following this strategy were evaluated in terms of their folding competence and their functional proficiency, an observation that was formalized as a Structure-Function Loop Adaptability value. Molecular details about the function and structure of some variants were obtained by enzyme kinetics and circular dichroism. This strategy yields functional variants that retain the original activity at higher frequencies, suggesting a new strategy for protein engineering that incorporates a more divergent sequence exploration beyond that limited to point mutations. We discuss how this approach may provide insights into the mechanism of enzyme evolution and function.
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Affiliation(s)
- Adrián Ochoa-Leyva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, C.P. 62210, México
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Plass T, Schultz C. Covalent Labeling of Biomolecules in Living Cells. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Abstract
The insertion of peptide loops into the polypeptide chain of proteins at surface-exposed regions is an attractive avenue to modify the protein's properties or to evolve new functionalities. The strategy of peptide loop insertion has, for example, been used to create new binding sites in protein scaffolds and has led to the isolation of proteins with excellent binding affinities for various biological structures. Peptide loops have also been inserted into enzymes to modulate their catalytic properties. We recently used loop insertion mutagenesis to evolve a mutant of O(6)-alkylguanine-DNA-alkyltransferase (AGT) that reacts with the nonnatural substrate O(6)-propargylguanine for applications in molecular imaging. In this chapter, we describe in detail the protocols that we have applied (1) to identify sites in AGT that are permissive to loop insertion, (2) to manipulate DNA to create large loop insertion libraries, and (3) to identify mutants with desired properties. The experimental procedures are general and can easily be adapted for the insertion of peptide loops into other classes of enzymes or into any protein of interest.
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Affiliation(s)
- Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de, Lausanne (EPFL), Lausanne, Switzerland
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Gallagher SS, Sable JE, Sheetz MP, Cornish VW. An in vivo covalent TMP-tag based on proximity-induced reactivity. ACS Chem Biol 2009; 4:547-56. [PMID: 19492849 DOI: 10.1021/cb900062k] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical tags for live cell imaging are emerging as viable alternatives to the fluorescent proteins for labeling proteins with small molecule probes. Among reported chemical tags, trimethoprim (TMP)-tag stands out for having sufficient cell permeability and selectivity to allow imaging of intracellular proteins. TMP-tag provides a noncovalent label in which the protein of interest is fused to E. coli dihydrofolate reductase (DHFR) and then labeled with a cell-permeable TMP-probe heterodimer. To complement the utility of the noncovalent TMP-tag, we sought to render the TMP-tag covalent for applications such as single-molecule tracking and pulse-chase labeling that would benefit from a more permanent modification. On the basis of the long-standing use of proximity-induced reactivity for irreversible inhibitor design and its more recent application to in vitro chemical biology tools, we designed an eDHFR variant with a unique cysteine residue positioned to react with an acrylamide electrophile installed on the TMP-probe label. In vitro experiments show that the eDHFR:L28C nucleophile reacts rapidly and quantitatively with the TMP-acrylamide-probe. Most significantly, the balance in reactivity provided by the acrylamide electrophile allows intracellular proteins tagged with eDHFR:L28C to be labeled with a TMP-acrylamide-fluorescein heterotrimer in live cells with minimal background. Thus, the TMP electrophile described here can be used immediately as a covalent chemical tag in live cells. Moreover, proximity-induced reactivity is shown to be sufficiently selective for use in a living cell, suggesting a general approach for the development of orthogonal covalent chemical tags from existing noncovalent ligand-protein pairs.
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Affiliation(s)
| | - Julia E. Sable
- Biological Sciences, Columbia University, New York, New York, 10027
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8
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Meares CF. The chemistry of irreversible capture. Adv Drug Deliv Rev 2008; 60:1383-8. [PMID: 18538444 DOI: 10.1016/j.addr.2008.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 04/16/2008] [Indexed: 10/22/2022]
Abstract
The specific recognition and binding of biological molecules by antibodies is fundamentally important. Natural antibodies are multivalent, having at least two identical ligand-binding sites; this permits them to bind tightly at cell surfaces, which present multiple copies of their target ligands. Antibodies that bind to soluble monovalent ligands, such as most small molecules, do not share this multivalent advantage. Nor do engineered fragments of antibodies, such as single-chain Fv proteins or Fab fragments, which generally possess only a single ligand-binding site. Engineered monovalent antibody/ligand pairs that retain the binding specificity of the antibody, but do not dissociate, are promising components of new delivery systems. These are based on a combination of genetic manipulation of the protein and chemical synthesis of appropriate ligands, examples of which are reviewed here.
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Gautier A, Juillerat A, Heinis C, Corrêa IR, Kindermann M, Beaufils F, Johnsson K. An Engineered Protein Tag for Multiprotein Labeling in Living Cells. ACTA ACUST UNITED AC 2008; 15:128-36. [DOI: 10.1016/j.chembiol.2008.01.007] [Citation(s) in RCA: 609] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 01/12/2008] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
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Lemercier G, Gendreizig S, Kindermann M, Johnsson K. Inducing and sensing protein--protein interactions in living cells by selective cross-linking. Angew Chem Int Ed Engl 2007; 46:4281-4. [PMID: 17465435 DOI: 10.1002/anie.200700408] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guillaume Lemercier
- ISIC-Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Lemercier G, Gendreizig S, Kindermann M, Johnsson K. Inducing and Sensing Protein–Protein Interactions in Living Cells by Selective Cross-linking. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Chen I, Choi YA, Ting AY. Phage display evolution of a peptide substrate for yeast biotin ligase and application to two-color quantum dot labeling of cell surface proteins. J Am Chem Soc 2007; 129:6619-25. [PMID: 17472384 PMCID: PMC2629800 DOI: 10.1021/ja071013g] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific protein labeling with Escherichia coli biotin ligase (BirA) has been used to introduce fluorophores, quantum dots (QDs), and photocross-linkers onto recombinant proteins fused to a 15-amino acid acceptor peptide (AP) substrate for BirA and expressed on the surface of living mammalian cells. Here, we used phage display to engineer a new and orthogonal biotin ligase-AP pair for site-specific protein labeling. Yeast biotin ligase (yBL) does not recognize the AP, but we discovered a new 15-amino acid substrate for yBL called the yeast acceptor peptide (yAP), using two generations of phage display selection from 15-mer peptide libraries. The yAP is not recognized by BirA, and thus, we were able to specifically label AP and yAP fusion proteins coexpressed in the same cell with differently colored QDs. We fused the yAP to a variety of recombinant proteins and demonstrated biotinylation by yBL at the N-terminus, C-terminus, and within a flexible internal region. yBL is extremely sequence-specific, as endogenous proteins on the surface of yeast and HeLa cells are not biotinylated. This new methodology expands the scope of biotin ligase labeling to two-color imaging and yeast-based applications.
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Abstract
The visualization of biologically relevant molecules and activities inside living cells continues to transform cell biology into a truly quantitative science. However, despite the spectacular achievements in some areas of cell biology, the majority of cellular processes still operate invisibly, not illuminated by even our brightest laser beams. Further progress therefore will depend not only on improvements in instrumentation but also increasingly on the development of new fluorophores and fluorescent sensors to target these activities. In the following, we review some of the recent approaches to generating such sensors, the methods to attach them to selected biomolecules, and their applications to various biological problems.
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Affiliation(s)
- Nils Johnsson
- Center for Molecular Biology of Inflammation, Cellular Biochemistry, University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany.
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