1
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Schirer A, Rouch A, Marcheteau E, Stojko J, Sophie Landron, Jeantet E, Fould B, Ferry G, Boutin JA. Further assessments of ligase LplA-mediated modifications of proteins in vitro and in cellulo. Mol Biol Rep 2021; 49:149-161. [PMID: 34718939 DOI: 10.1007/s11033-021-06853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/23/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Posttranslational modifications of proteins are catalyzed by a large family of enzymes catalyzing many chemical modifications. One can hijack the natural use of those enzymes to modify targeted proteins with synthetic chemical moieties. The lipoic acid ligase LplA mutants can be used to introduce onto the lysine sidechain lipoic acid moiety synthetic analogues. Substrate protein candidates of the ligase must obey a few a priori rules. METHODS AND RESULTS In the present report, we technically detailed the use of a cell line stably expressing both the ligase and a model protein (thioredoxin). Although the goal can be reach, and the protein visualized in situ, many experimental difficulties must be fixed. The sequence of events comprises (i) in cellulo labeling of the target protein with a N3-lipoic acid derivative catalyzed by the mutant ligase, (ii) the further introduction by click chemistry onto this lysine sidechain of a fluorophore and (iii) the following of the labeled protein in living cells. One of the main difficulties was to assess the click chemistry step onto the living cells, because images from both control and experimental cells were similar. Alternatively, we describe at that stage, the preferred use of another technique: the Halo-Tag one that led to the obtention of clear images of the targeted protein in its cellular context. Although the ligase-mediated labeling of protein in situ is a rich domain for which many cellular tools must be developed, many difficulties must be considered before entering a systematic use of this approach. CONCLUSIONS In the present contribution, we added several steps of analytical characterization, both in vitro and in cellulo that were previously lacking. Furthermore, we show that the use of the click chemistry should be manipulated with care, as the claimed specificity might be not complete whenever living cells are used. Finally, we added another approach-the Halo Tag-to complete the previously suggested approaches for labelling proteins in cells, as we found difficult to strictly apply the previously reported methodology.
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Affiliation(s)
- Alicia Schirer
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France.,, Techno Parc de Thudinie 2, 6536, Thuin, Belgium
| | - Anne Rouch
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Estelle Marcheteau
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Johann Stojko
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Sophie Landron
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Elodie Jeantet
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Benjamin Fould
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Gilles Ferry
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Jean A Boutin
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France. .,Institut de Recherches Internationales Servier, 50 rue Carnot, 92284, Suresnes, France. .,Faculté de Pharmacie, PHARMADEV (Pharmacochimie et Biologie Pour le Développement), Université Toulouse 3 Paul Sabatier, 35 chemin des maraîchers, 31062, Toulouse Cedex 9, France.
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2
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Aronoff MR, Hiebert P, Hentzen NB, Werner S, Wennemers H. Imaging and targeting LOX-mediated tissue remodeling with a reactive collagen peptide. Nat Chem Biol 2021; 17:865-871. [PMID: 34253910 DOI: 10.1038/s41589-021-00830-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Collagens are fibrous proteins that are integral to the strength and stability of connective tissues. During collagen maturation, lysyl oxidases (LOX) initiate the cross-linking of fibers, but abnormal LOX activity is associated with impaired tissue function as seen in fibrotic and malignant diseases. Visualizing and targeting this dynamic process in healthy and diseased tissue is important, but so far not feasible. Here we present a probe for the simultaneous monitoring and targeting of LOX-mediated collagen cross-linking that combines a LOX-activity sensor with a collagen peptide to chemoselectively target endogenous aldehydes generated by LOX. This synergistic probe becomes covalently anchored and lights up in vivo and in situ in response to LOX at the sites where cross-linking occurs, as demonstrated by staining of normal skin and cancer sections. We anticipate that our reactive collagen-based sensor will improve understanding of collagen remodeling and provide opportunities for the diagnosis of fibrotic and malignant diseases.
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Affiliation(s)
| | - Paul Hiebert
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Nina B Hentzen
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabine Werner
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland.
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3
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Kudriaeva AA, Livneh I, Baranov MS, Ziganshin RH, Tupikin AE, Zaitseva SO, Kabilov MR, Ciechanover A, Belogurov AA. In-depth characterization of ubiquitin turnover in mammalian cells by fluorescence tracking. Cell Chem Biol 2021; 28:1192-1205.e9. [PMID: 33675681 DOI: 10.1016/j.chembiol.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/29/2020] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Despite almost 40 years having passed from the initial discovery of ubiquitin (Ub), fundamental questions related to its intracellular metabolism are still enigmatic. Here we utilized fluorescent tracking for monitoring ubiquitin turnover in mammalian cells, resulting in obtaining qualitatively new data. In the present study we report (1) short Ub half-life estimated as 4 h; (2) for a median of six Ub molecules per substrate as a dynamic equilibrium between Ub ligases and deubiquitinated enzymes (DUBs); (3) loss on average of one Ub molecule per four acts of engagement of polyubiquitinated substrate by the proteasome; (4) direct correlation between incorporation of Ub into the distinct type of chains and Ub half-life; and (5) critical influence of the single lysine residue K27 on the stability of the whole Ub molecule. Concluding, our data provide a comprehensive understanding of ubiquitin-proteasome system dynamics on the previously unreachable state of the art.
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Affiliation(s)
- Anna A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Ido Livneh
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russian Federation
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Snizhana O Zaitseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Aaron Ciechanover
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russian Federation.
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4
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Sadiki A, Vaidya SR, Abdollahi M, Bhardwaj G, Dolan ME, Turna H, Arora V, Sanjeev A, Robinson TD, Koid A, Amin A, Zhou ZS. Site-specific conjugation of native antibody. Antib Ther 2020; 3:271-284. [PMID: 33644685 PMCID: PMC7906296 DOI: 10.1093/abt/tbaa027] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Traditionally, non-specific chemical conjugations, such as acylation of amines on lysine or alkylation of thiols on cysteines, are widely used; however, they have several shortcomings. First, the lack of site-specificity results in heterogeneous products and irreproducible processes. Second, potential modifications near the complementarity-determining region may reduce binding affinity and specificity. Conversely, site-specific methods produce well-defined and more homogenous antibody conjugates, ensuring developability and clinical applications. Moreover, several recent side-by-side comparisons of site-specific and stochastic methods have demonstrated that site-specific approaches are more likely to achieve their desired properties and functions, such as increased plasma stability, less variability in dose-dependent studies (particularly at low concentrations), enhanced binding efficiency, as well as increased tumor uptake. Herein, we review several standard and practical site-specific bioconjugation methods for native antibodies, i.e., those without recombinant engineering. First, chemo-enzymatic techniques, namely transglutaminase (TGase)-mediated transamidation of a conserved glutamine residue and glycan remodeling of a conserved asparagine N-glycan (GlyCLICK), both in the Fc region. Second, chemical approaches such as selective reduction of disulfides (ThioBridge) and N-terminal amine modifications. Furthermore, we list site-specific antibody–drug conjugates in clinical trials along with the future perspectives of these site-specific methods.
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Affiliation(s)
- Amissi Sadiki
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Shefali R Vaidya
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Mina Abdollahi
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Gunjan Bhardwaj
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Michael E Dolan
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA.,Downstream Development, Biologics Process Development, Millennium Pharmaceuticals, Inc., (a wholly-owned subsidiary of Takeda Pharmaceuticals Company Limited), Cambridge, Massachusetts 02139, USA
| | - Harpreet Turna
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Varnika Arora
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Athul Sanjeev
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Timothy D Robinson
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Andrea Koid
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Aashka Amin
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
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5
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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6
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Shigemitsu H, Matsuda K, Mori T, Nakatsuji H, Matsusaki M, Kida T. Enhancing Photostability of a Coumarin Dye by Self‐inclusion into a Cyclodextrin Cavity in Aqueous Solution and Living Cells. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hajime Shigemitsu
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
- Frontier Research Base for Global Young Researchers Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565–0871 Japan
- Global Center for Medical Engineering and Informatics Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Keigo Matsuda
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Tadashi Mori
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Hirotaka Nakatsuji
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Michiya Matsusaki
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
| | - Toshiyuki Kida
- Department of Applied Chemistry Graduate School of Engineering Osaka University 2-1 Yamadaoka Suita 565-0871 Japan
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7
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Mohammad-Beigi H, Scavenius C, Jensen PB, Kjaer-Sorensen K, Oxvig C, Boesen T, Enghild JJ, Sutherland DS, Hayashi Y. Tracing the In Vivo Fate of Nanoparticles with a "Non-Self" Biological Identity. ACS NANO 2020; 14:10666-10679. [PMID: 32806026 DOI: 10.1021/acsnano.0c05178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanoparticles can acquire a biomolecular corona with a species-specific biological identity. However, "non-self" incompatibility of recipient biological systems is often not considered, for example, when rodents are used as a model organism for preclinical studies of biomolecule-inspired nanomedicines. Using zebrafish embryos as an emerging model for nanobioimaging, here we unravel the in vivo fate of intravenously injected 70 nm SiO2 nanoparticles with a protein corona preformed from fetal bovine serum (FBS), representing a non-self biological identity. Strikingly rapid sequestration and endolysosomal acidification of nanoparticles with the preformed FBS corona were observed in scavenger endothelial cells within minutes after injection. This led to loss of blood vessel integrity and to inflammatory activation of macrophages over the course of several hours. As unmodified nanoparticles or the equivalent dose of FBS proteins alone failed to induce the observed pathophysiology, this signifies how the corona enriched with a differential repertoire of proteins can determine the fate of the nanoparticles in vivo. Our findings thus reveal the adverse outcome triggered by incompatible protein coronas and indicate a potential pitfall in the use of mismatched species combinations during nanomedicine development.
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Affiliation(s)
- Hossein Mohammad-Beigi
- iNANO Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Pia Bomholt Jensen
- iNANO Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kasper Kjaer-Sorensen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Claus Oxvig
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Thomas Boesen
- iNANO Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Duncan S Sutherland
- iNANO Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Yuya Hayashi
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
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8
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Liu J, Cui Z. Fluorescent Labeling of Proteins of Interest in Live Cells: Beyond Fluorescent Proteins. Bioconjug Chem 2020; 31:1587-1595. [PMID: 32379972 DOI: 10.1021/acs.bioconjchem.0c00181] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Live cell imaging brings us into a new era of direct visualization of biological processes and molecular dynamics in real time. To visualize dynamic cellular processes and virus-host interactions, fluorescent labeling of proteins of interest is often necessary. Fluorescent proteins are widely used for protein imaging, but they have some intrinsic deficiencies such as big size, photobleaching, and spectrum restriction. Thus, a variety of labeling strategies have been established and continuously developed. To protect the natural biological function(s) of the protein of interest, especially in viral life cycle, in vivo labeling requires smaller-sized tags, more specificity, and lower cytotoxicity. Here, we briefly summarized the principles, development, and their applications mainly in the virology field of three strategies for fluorescent labeling of proteins of interest including self-labeling enzyme derivatives, stainable peptide tags, and non-canonical amino acid incorporation. These labeling techniques greatly expand the fluorescent labeling toolbox and provide new opportunities for imaging biological processes.
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Affiliation(s)
- Ji Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Doh JK, Enns CA, Beatty KE. Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy. Bio Protoc 2019; 9:e3413. [PMID: 32665966 PMCID: PMC7360171 DOI: 10.21769/bioprotoc.3413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
Genetically-encoded tags are useful tools for multicolor and multi-scale cellular imaging. Versatile Interacting Peptide (VIP) tags, such as VIPER, are new genetically-encoded tags that can be used in various imaging applications. VIP tags consist of a coiled-coil heterodimer, with one peptide serving as the genetic tag and the other ("probe peptide") delivering a reporter compatible with imaging. Heterodimer formation is rapid and specific, allowing proteins to be selectively labeled for live-cell and fixed-cell imaging. In this Bio-Protocol, we include a detailed guide for implementing the VIPER technology for imaging receptors on live cells and intracellular targets in fixed cells. This protocol is complemented by two other Bio-Protocols outlining the use of VIPER (Doh et al., 2019a and 2019b).
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Affiliation(s)
- Julia K. Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Caroline A. Enns
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Kimberly E. Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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10
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Enzymatically Catalyzed Radiofluorination of Biomolecules. Methods Mol Biol 2019. [PMID: 31332755 DOI: 10.1007/978-1-4939-9654-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
There has been significant and rapid growth in the development of amino acid-based molecular imaging agents (e.g., peptides, proteins, and antibody constructs) largely due to facile library preparation and high throughput screening. Positron-emitting fluorine-18 (half-life = 109.7 min) has a unique set of properties that match well with the pharmacokinetics of smaller sized constructs. Several indirect fluorine-18 labeling approaches have been developed yet only a few have advanced to human trials. Enzymatically catalyzed radiofluorination utilizing lipoic acid ligase shows promise as a mild site-specific method for coupling fluorine-18-labeled carboxylate substrates with biomolecules. Methods for preparation of two [18F]fluorocarboxylates and their ligation to a specific peptide sequence (LAP peptide) are presented herein.
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11
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Thornlow DN, Cox EC, Walker JA, Sorkin M, Plesset JB, DeLisa MP, Alabi CA. Dual Site-Specific Antibody Conjugates for Sequential and Orthogonal Cargo Release. Bioconjug Chem 2019; 30:1702-1710. [PMID: 31083974 DOI: 10.1021/acs.bioconjchem.9b00244] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibody-drug conjugates utilize the antigen specificity of antibodies and the potency of chemotherapeutic and antibiotic drugs for targeted therapy. However, as cancers and bacteria evolve to resist the action of drugs, innovative controlled release methods must be engineered to deliver multidrug cocktails. In this work, we engineer lipoate-acid ligase A (LplA) acceptor peptide (LAP) tags into the constant heavy and light chain of a humanized Her2 targeted antibody, trastuzumab. These engineered LAP tags, along with the glutamine 295 (Q295) residue in the heavy chain, were used to generate orthogonally cleavable site-specific antibody conjugates via a one-pot chemoenzymatic ligation with microbial transglutaminase (mTG) and LplA. We demonstrate orthogonal cargo release from these dual-labeled antibody bioconjugates via matrix metalloproteinase-2 and cathepsin-B-mediated bond cleavage. To the best of our knowledge, this is the first demonstration of temporal control on dual-labeled antibody conjugates, and we believe this platform will allow for sequential release and cooperative drug combinations on a single antibody bioconjugate.
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Affiliation(s)
- Dana N Thornlow
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Emily C Cox
- Biological and Biomedical Sciences , Cornell University College of Veterinary Medicine , Ithaca , New York 14853 , United States
| | - Joshua A Walker
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Michelle Sorkin
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Jacqueline B Plesset
- Meinig School of Biomedical Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
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12
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Chan HCS, Pan L, Li Y, Yuan S. Rationalization of stereoselectivity in enzyme reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- H. C. Stephen Chan
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
- Faculty of Life Sciences University of Bradford Bradford UK
| | - Lu Pan
- Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai China
| | - Yi Li
- Department of Neurology University of Southern California Los Angeles California
| | - Shuguang Yuan
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
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13
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Fluorescent Labeling of Protein Using Blue-Emitting 8-Amino-BODIPY Derivatives. J Fluoresc 2017; 27:2231-2238. [DOI: 10.1007/s10895-017-2164-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/10/2017] [Indexed: 01/27/2023]
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14
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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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15
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Lee M, Peterson BR. Quantification of Small Molecule-Protein Interactions using FRET between Tryptophan and the Pacific Blue Fluorophore. ACS OMEGA 2016; 1:1266-1276. [PMID: 28058293 PMCID: PMC5204206 DOI: 10.1021/acsomega.6b00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/06/2016] [Indexed: 05/14/2023]
Abstract
We report a new method to quantify the affinity of small molecules for proteins. This method is based on Förster resonance energy transfer (FRET) between endogenous tryptophan (Trp) residues and the coumarin-derived fluorophore Pacific Blue (PB). Tryptophan residues are frequently found in proteins near ligand-binding sites, making this approach potentially applicable to a wide range of systems. To improve access to PB, we developed a scalable multigram synthesis of this fluorophore, starting with inexpensive 2,3,4,5-tetrafluorobenzoic acid. This route was used to synthesize fluorescent derivatives of biotin, as well as lower affinity thiobiotin, iminobiotin, and imidazolidinethione analogues that bind the protein streptavidin. Compared with previously published FRET acceptors for tryptophan, PB proved to be superior in both sensitivity and efficiency. These unique properties of PB enabled direct quantification of dissociation constants (Kd) as well as competitive inhibition constants (Ki) in the micromolar to nanomolar range. In comparison to analogous binding studies using fluorescence polarization, fluorescence quenching, or fluorescence enhancement, affinities determined using Trp-FRET were more precise and accurate as validated using independent isothermal titration calorimetry studies. FRET between tryptophan and PB represents a new tool for the characterization of protein-ligand complexes.
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16
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Specht EA, Braselmann E, Palmer AE. A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging. Annu Rev Physiol 2016; 79:93-117. [PMID: 27860833 DOI: 10.1146/annurev-physiol-022516-034055] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescent tools have revolutionized our ability to probe biological dynamics, particularly at the cellular level. Fluorescent sensors have been developed on several platforms, utilizing either small-molecule dyes or fluorescent proteins, to monitor proteins, RNA, DNA, small molecules, and even cellular properties, such as pH and membrane potential. We briefly summarize the impressive history of tool development for these various applications and then discuss the most recent noteworthy developments in more detail. Particular emphasis is placed on tools suitable for single-cell analysis and especially live-cell imaging applications. Finally, we discuss prominent areas of need in future fluorescent tool development-specifically, advancing our capability to analyze and integrate the plethora of high-content data generated by fluorescence imaging.
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Affiliation(s)
- Elizabeth A Specht
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
| | - Esther Braselmann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
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17
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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18
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Drake CR, Sevillano N, Truillet C, Craik CS, VanBrocklin HF, Evans MJ. Site-Specific Radiofluorination of Biomolecules with 8-[(18)F]-Fluorooctanoic Acid Catalyzed by Lipoic Acid Ligase. ACS Chem Biol 2016; 11:1587-94. [PMID: 27008570 DOI: 10.1021/acschembio.6b00172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
New methodologies for site-specifically radiolabeling proteins with (18)F are required to generate high quality radiotracers for preclinical and clinical applications with positron emission tomography. Herein, we report an approach by which we use lipoic acid ligase (LplA) to conjugate [(18)F]-fluorooctanoic acid to an antibody fragment bearing the peptide substrate of LplA. The mild conditions of the reaction preserve antibody immunoreactivity, and the efficiency of LplA allows for >90% yield even with very small amounts of peptidic precursor (1-10 nmol). These features are advantageous compared to the current gold standard in the field. Moreover, the methodology introduces a new application for an important tool in chemical biology.
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Affiliation(s)
- Christopher R. Drake
- Department
of Radiology and Biomedical Imaging, University of California San Francisco, Suite 350, 185 Berry Street, San Francisco, California 94107, United States
| | - Natalia Sevillano
- Department
of Pharmaceutical Chemistry, University of California San Francisco, Genentech Hall, S-514, 600 16th Street, San
Francisco, California 94158, United States
| | - Charles Truillet
- Department
of Radiology and Biomedical Imaging, University of California San Francisco, Suite 350, 185 Berry Street, San Francisco, California 94107, United States
| | - Charles S. Craik
- Department
of Pharmaceutical Chemistry, University of California San Francisco, Genentech Hall, S-514, 600 16th Street, San
Francisco, California 94158, United States
| | - Henry F. VanBrocklin
- Department
of Radiology and Biomedical Imaging, University of California San Francisco, Suite 350, 185 Berry Street, San Francisco, California 94107, United States
| | - Michael J. Evans
- Department
of Radiology and Biomedical Imaging, University of California San Francisco, Suite 350, 185 Berry Street, San Francisco, California 94107, United States
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19
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Naganbabu M, Perkins LA, Wang Y, Kurish J, Schmidt BF, Bruchez MP. Multiexcitation Fluorogenic Labeling of Surface, Intracellular, and Total Protein Pools in Living Cells. Bioconjug Chem 2016; 27:1525-31. [PMID: 27159569 PMCID: PMC4911959 DOI: 10.1021/acs.bioconjchem.6b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Malachite
green (MG) is a fluorogenic dye that shows fluorescence enhancement
upon binding to its engineered cognate protein, a fluorogen activating
protein (FAP). Energy transfer donors such as cyanine and rhodamine
dyes have been conjugated with MG to modify the spectral properties
of the fluorescent complexes, where the donor dyes transfer energy
through Förster resonance energy transfer to the MG complex
resulting in binding-conditional fluorescence emission in the far-red
region. In this article, we use a violet-excitable dye as a donor
to sensitize the far-red emission of the MG-FAP complex. Two blue
emitting fluorescent coumarin dyes were coupled to MG and evaluated
for energy transfer to the MG-FAP complex via its secondary excitation
band. 6,8-Difluoro-7-hydroxycoumarin-3-carboxylic acid (Pacific blue,
PB) showed the most efficient energy transfer and maximum brightness
in the far-red region upon violet (405 nm) excitation. These blue-red
(BluR) tandem dyes are spectrally varied from other tandem dyes and
are able to produce fluorescence images of the MG-FAP complex with
a large Stokes shift (>250 nm). These dyes are cell-permeable and
are used to label intracellular proteins. Used together with a cell-impermeable
hexa-Cy3-MG (HCM) dye that labels extracellular proteins, we are able
to visualize extracellular, intracellular, and total pools of cellular
protein using one fluorogenic tag that combines with distinct dyes
to effect different spectral characteristics.
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Affiliation(s)
- Matharishwan Naganbabu
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Lydia A Perkins
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Yi Wang
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Jeffery Kurish
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Brigitte F Schmidt
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Marcel P Bruchez
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
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20
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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21
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Best M, Degen A, Baalmann M, Schmidt TT, Wombacher R. Two-step protein labeling by using lipoic acid ligase with norbornene substrates and subsequent inverse-electron demand Diels-Alder reaction. Chembiochem 2015; 16:1158-62. [PMID: 25900689 DOI: 10.1002/cbic.201500042] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 12/24/2022]
Abstract
Inverse-electron-demand Diels-Alder cycloaddition (DAinv ) between strained alkenes and tetrazines is a highly bio-orthogonal reaction that has been applied in the specific labeling of biomolecules. In this work we present a two-step labeling protocol for the site-specific labeling of proteins based on attachment of a highly stable norbornene derivative to a specific peptide sequence by using a mutant of the enzyme lipoic acid ligase A (LplA(W37V) ), followed by the covalent attachment of tetrazine-modified fluorophores to the norbornene moiety through the bio-orthogonal DAinv . We investigated 15 different norbornene derivatives for their selective enzymatic attachment to a 13-residue lipoic acid acceptor peptide (LAP) by using a standardized HPLC protocol. Finally, we used this two-step labeling strategy to label proteins in cell lysates in a site-specific manner and performed cell-surface labeling on living cells.
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Affiliation(s)
- Marcel Best
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Anna Degen
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Mathis Baalmann
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Tobias T Schmidt
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Richard Wombacher
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany).
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22
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Rashidian M, Dozier JK, Distefano MD. Enzymatic labeling of proteins: techniques and approaches. Bioconjug Chem 2014; 24:1277-94. [PMID: 23837885 DOI: 10.1021/bc400102w] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Site-specific modification of proteins is a major challenge in modern chemical biology due to the large number of reactive functional groups typically present in polypeptides. Because of its importance in biology and medicine, the development of methods for site-specific modification of proteins is an area of intense research. Selective protein modification procedures have been useful for oriented protein immobilization, for studies of naturally occurring post-translational modifications, for creating antibody–drug conjugates, for the introduction of fluorophores and other small molecules on to proteins, for examining protein structure, folding, dynamics, and protein–protein interactions, and for the preparation of protein–polymer conjugates. One of the most important approaches for protein labeling is to incorporate bioorthogonal functionalities into proteins at specific sites via enzymatic reactions. The incorporated tags then enable reactions that are chemoselective, whose functional groups not only are inert in biological media, but also do not occur natively in proteins or other macromolecules. This review article summarizes the enzymatic strategies, which enable site-specific functionalization of proteins with a variety of different functional groups. The enzymes covered in this review include formylglycine generating enzyme, sialyltransferases, phosphopantetheinyltransferases, O-GlcNAc post-translational modification, sortagging, transglutaminase, farnesyltransferase, biotin ligase, lipoic acid ligase, and N-myristoyltransferase.
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23
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Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proc Natl Acad Sci U S A 2014; 111:E4551-9. [PMID: 25313043 PMCID: PMC4217414 DOI: 10.1073/pnas.1404736111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.
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Affiliation(s)
| | | | - Florian Richter
- Department of Biochemistry, Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems and
| | | | - Douglas Richardson
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093; and
| | - Catherine L Drennan
- Departments of Chemistry and Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David Baker
- Department of Biochemistry, Howard Hughes Medical Institute, and
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24
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Hauke S, Best M, Schmidt TT, Baalmann M, Krause A, Wombacher R. Two-step protein labeling utilizing lipoic acid ligase and Sonogashira cross-coupling. Bioconjug Chem 2014; 25:1632-7. [PMID: 25152073 DOI: 10.1021/bc500349h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Labeling proteins in their natural settings with fluorescent proteins or protein tags often leads to problems. Despite the high specificity, these methods influence the natural functions due to the rather large size of the proteins used. Here we present a two-step labeling procedure for the attachment of various fluorescent probes to a small peptide sequence (13 amino acids) using enzyme-mediated peptide labeling in combination with palladium-catalyzed Sonogashira cross-coupling. We identified p-iodophenyl derivatives from a small library that can be covalently attached to a lysine residue within a specific 13-amino-acid peptide sequence by Escherichia coli lipoic acid ligase A (LplA). The derivatization with p-iodophenyl subsequently served as a reactive handle for bioorthogonal transition metal-catalyzed Sonogashira cross-coupling with alkyne-functionalized fluorophores on both the peptide as well as on the protein level. Our two-step labeling strategy combines high selectivity of enzyme-mediated labeling with the chemoselectivity of palladium-catalyzed Sonogashira cross-coupling.
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Affiliation(s)
- Sebastian Hauke
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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25
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van Vught R, Pieters RJ, Breukink E. Site-specific functionalization of proteins and their applications to therapeutic antibodies. Comput Struct Biotechnol J 2014; 9:e201402001. [PMID: 24757499 PMCID: PMC3995230 DOI: 10.5936/csbj.201402001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/28/2014] [Accepted: 02/04/2014] [Indexed: 12/19/2022] Open
Abstract
Protein modifications are often required to study structure and function relationships. Instead of the random labeling of lysine residues, methods have been developed to (sequence) specific label proteins. Next to chemical modifications, tools to integrate new chemical groups for bioorthogonal reactions have been applied. Alternatively, proteins can also be selectively modified by enzymes. Herein we review the methods available for site-specific modification of proteins and their applications for therapeutic antibodies.
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Affiliation(s)
- Remko van Vught
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Roland J Pieters
- Department of Medicinal Chemistry and Chemical Biology. Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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26
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Abstract
This protocol describes an efficient method to site-specifically label cell-surface or purified proteins with chemical probes in two steps: probe incorporation mediated by enzymes (PRIME) followed by chelation-assisted copper-catalyzed azide-alkyne cycloaddition (CuAAC). In the PRIME step, Escherichia coli lipoic acid ligase (LplA) site-specifically attaches a picolyl azide (pAz) derivative to a 13-aa recognition sequence that has been genetically fused onto the protein of interest. Proteins bearing pAz are chemoselectively derivatized with an alkyne-probe conjugate by chelation-assisted CuAAC in the second step. We describe herein the optimized protocols to synthesize pAz to perform PRIME labeling and to achieve CuAAC derivatization of pAz on live cells, fixed cells and purified proteins. Reagent preparations, including synthesis of pAz probes and expression of LplA, take 12 d, whereas the procedure for performing site-specific pAz ligation and CuAAC on cells or on purified proteins takes 40 min-3 h.
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27
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White KA, Zegelbone PM. Directed evolution of a probe ligase with activity in the secretory pathway and application to imaging intercellular protein-protein interactions. Biochemistry 2013; 52:3728-39. [PMID: 23614685 DOI: 10.1021/bi400268m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, we reported a new method for intracellular protein labeling in living cells called PRIME (probe incorporation mediated by enzymes). PRIME uses a mutant of Escherichia coli lipoic acid ligase (LplA) to catalyze covalent probe ligation onto a 13-amino acid peptide recognition sequence. While our first demonstration labeled proteins with a coumarin fluorophore, subsequent engineering produced alkyl azide and trans-cyclooctene ligases as well as an interaction-dependent form of the coumarin PRIME method (ID-PRIME). One major limitation of the PRIME methodologies is that LplA mutants have very low activity in the secretory pathway. Here, we extend PRIME labeling to oxidizing compartments such as the endoplasmic reticulum and the cell surface. We used yeast-display evolution and four rounds of selection to isolate LplA mutants with improved picolyl azide ligation activity. Then we compared the ligation activities of the evolved mutants both in vitro and on the mammalian cell surface. We characterized the picolyl azide ligation activity of the most active LplA variant in vitro, in the endoplasmic reticulum, and at the mammalian cell surface. Finally, we used the optimized LplA variant to label neurexin and neuroligin interactions at the mammalian cell surface in just 5 min. Compared to another method for imaging these protein-protein interactions (GFP recomplementation across synapses), our optimized ID-PRIME ligase is faster, more sensitive, and does not trap interacting proteins in a complex (nontrapping).
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Affiliation(s)
- Katharine A White
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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28
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Liu DS, Phipps WS, Loh KH, Howarth M, Ting AY. Quantum dot targeting with lipoic acid ligase and HaloTag for single-molecule imaging on living cells. ACS NANO 2012; 6:11080-11087. [PMID: 23181687 PMCID: PMC3528850 DOI: 10.1021/nn304793z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present a methodology for targeting quantum dots to specific proteins on living cells in two steps. In the first step, Escherichia coli lipoic acid ligase (LplA) site-specifically attaches 10-bromodecanoic acid onto a 13 amino acid recognition sequence that is genetically fused to a protein of interest. In the second step, quantum dots derivatized with HaloTag, a modified haloalkane dehalogenase, react with the ligated bromodecanoic acid to form a covalent adduct. We found this targeting method to be specific, fast, and fully orthogonal to a previously reported and analogous quantum dot targeting method using E. coli biotin ligase and streptavidin. We used these two methods in combination for two-color quantum dot visualization of different proteins expressed on the same cell or on neighboring cells. Both methods were also used to track single molecules of neurexin, a synaptic adhesion protein, to measure its lateral diffusion in the presence of neuroligin, its trans-synaptic adhesion partner.
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29
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Huynh TH, Abrahamsen B, Madsen KK, Gonzalez-Franquesa A, Jensen AA, Bunch L. Design, synthesis and pharmacological characterization of coumarin-based fluorescent analogs of excitatory amino acid transporter subtype 1 selective inhibitors, UCPH-101 and UCPH-102. Bioorg Med Chem 2012; 20:6831-9. [DOI: 10.1016/j.bmc.2012.09.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 11/30/2022]
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30
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Cohen JD, Zou P, Ting AY. Site-specific protein modification using lipoic acid ligase and bis-aryl hydrazone formation. Chembiochem 2012; 13:888-94. [PMID: 22492621 PMCID: PMC4758125 DOI: 10.1002/cbic.201100764] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Indexed: 12/17/2022]
Abstract
A screen of Trp37 mutants of Escherichia coli lipoic acid ligase (LplA) revealed enzymes capable of ligating an aryl-aldehyde or aryl-hydrazine substrate to LplA's 13-residue acceptor peptide. Once site-specifically attached to recombinant proteins fused to this peptide, aryl-aldehydes could be chemoselectively derivatized with hydrazine-probe conjugates, and aryl-hydrazines could be derivatized in an analogous manner with aldehyde-probe conjugates. Such two-step labeling was demonstrated for AlexaFluor568 targeting to monovalent streptavidin in vitro, and to neurexin-1β on the surface of living mammalian cells. To further highlight this technique, we labeled the low-density lipoprotein receptor on the surface of live cells with fluorescent phycoerythrin protein to allow single-molecule imaging and tracking over time.
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Affiliation(s)
- Justin D. Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA, 02139 (USA), Fax: (+1) 617-253-7929
| | - Peng Zou
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA, 02139 (USA), Fax: (+1) 617-253-7929
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA, 02139 (USA), Fax: (+1) 617-253-7929
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31
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Yao JZ, Uttamapinant C, Poloukhtine A, Baskin JM, Codelli JA, Sletten EM, Bertozzi CR, Popik VV, Ting AY. Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition. J Am Chem Soc 2012; 134:3720-8. [PMID: 22239252 PMCID: PMC3306817 DOI: 10.1021/ja208090p] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methods for targeting of small molecules to cellular proteins can allow imaging with fluorophores that are smaller, brighter, and more photostable than fluorescent proteins. Previously, we reported targeting of the blue fluorophore coumarin to cellular proteins fused to a 13-amino acid recognition sequence (LAP), catalyzed by a mutant of the Escherichia coli enzyme lipoic acid ligase (LplA). Here, we extend LplA-based labeling to green- and red-emitting fluorophores by employing a two-step targeting scheme. First, we found that the W37I mutant of LplA catalyzes site-specific ligation of 10-azidodecanoic acid to LAP in cells, in nearly quantitative yield after 30 min. Second, we evaluated a panel of five different cyclooctyne structures and found that fluorophore conjugates to aza-dibenzocyclooctyne (ADIBO) gave the highest and most specific derivatization of azide-conjugated LAP in cells. However, for targeting of hydrophobic fluorophores such as ATTO 647N, the hydrophobicity of ADIBO was detrimental, and superior targeting was achieved by conjugation to the less hydrophobic monofluorinated cyclooctyne (MOFO). Our optimized two-step enzymatic/chemical labeling scheme was used to tag and image a variety of LAP fusion proteins in multiple mammalian cell lines with diverse fluorophores including fluorescein, rhodamine, Alexa Fluor 568, ATTO 647N, and ATTO 655.
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Affiliation(s)
- Jennifer Z. Yao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue. Cambridge, Massachusetts 02139
| | - Chayasith Uttamapinant
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue. Cambridge, Massachusetts 02139
| | - Andrei Poloukhtine
- Bioconjugate Technologies, LLC, 7850 E. Evans Road, Ste 107, Scottsdale, Arizona, 85260
| | - Jeremy M. Baskin
- Department of Chemistry, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Julian A. Codelli
- Department of Chemistry, California Institute of Technology, 1200 East California Boulevard. Pasadena, California 91125
| | - Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Vladimir V. Popik
- Department of Chemistry, Complex Carbohydrate Research Center, University of Georgia, Athens, 30602
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue. Cambridge, Massachusetts 02139
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Liu DS, Tangpeerachaikul A, Selvaraj R, Taylor MT, Fox JM, Ting AY. Diels-Alder cycloaddition for fluorophore targeting to specific proteins inside living cells. J Am Chem Soc 2012; 134:792-5. [PMID: 22176354 PMCID: PMC3381951 DOI: 10.1021/ja209325n] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The inverse-electron-demand Diels-Alder cycloaddition between trans-cyclooctenes and tetrazines is biocompatible and exceptionally fast. We utilized this chemistry for site-specific fluorescence labeling of proteins on the cell surface and inside living mammalian cells by a two-step protocol. Escherichia coli lipoic acid ligase site-specifically ligates a trans-cyclooctene derivative onto a protein of interest in the first step, followed by chemoselective derivatization with a tetrazine-fluorophore conjugate in the second step. On the cell surface, this labeling was fluorogenic and highly sensitive. Inside the cell, we achieved specific labeling of cytoskeletal proteins with green and red fluorophores. By incorporating the Diels-Alder cycloaddition, we have broadened the panel of fluorophores that can be targeted by lipoic acid ligase.
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Affiliation(s)
- Daniel S Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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Gnaccarini C, Ben-Tahar W, Mulani A, Roy I, Lubell WD, Pelletier JN, Keillor JW. Site-specific protein propargylation using tissue transglutaminase. Org Biomol Chem 2012; 10:5258-65. [DOI: 10.1039/c2ob25752a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Lowder MA, Appelbaum JS, Hobert EM, Schepartz A. Visualizing protein partnerships in living cells and organisms. Curr Opin Chem Biol 2011; 15:781-8. [PMID: 22104179 DOI: 10.1016/j.cbpa.2011.10.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 10/25/2011] [Accepted: 10/25/2011] [Indexed: 11/25/2022]
Abstract
In recent years, scientists have expanded their focus from cataloging genes to characterizing the multiple states of their translated products. One anticipated result is a dynamic map of the protein association networks and activities that occur within the cellular environment. While in vitro-derived network maps can illustrate which of a multitude of possible protein-protein associations could exist, they supply a falsely static picture lacking the subtleties of subcellular location (where) or cellular state (when). Generating protein association network maps that are informed by both subcellular location and cell state requires novel approaches that accurately characterize the state of protein associations in living cells and provide precise spatiotemporal resolution. In this review, we highlight recent advances in visualizing protein associations and networks under increasingly native conditions. These advances include second generation protein complementation assays (PCAs), chemical and photo-crosslinking techniques, and proximity-induced ligation approaches. The advances described focus on background reduction, signal optimization, rapid and reversible reporter assembly, decreased cytotoxicity, and minimal functional perturbation. Key breakthroughs have addressed many challenges and should expand the repertoire of tools useful for generating maps of protein interactions resolved in both time and space.
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Affiliation(s)
- Melissa A Lowder
- Yale University, Department of Molecular Biophysics and Biochemistry, 60 Whitney Ave., New Haven, CT 06520-8114, USA
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