1
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Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci 2023; 32:e4633. [PMID: 36974585 PMCID: PMC10108435 DOI: 10.1002/pro.4633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Chloe M. Jones
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Kyle D. Shaffer
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Yarra Venkatesh
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Sam Giannakoulias
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Ryann M. Perez
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marshall G. Lougee
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Eshe Hummingbird
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Vinayak V. Pagar
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Christina M. Hurley
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Allen Li
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Robert H. Mach
- Department of RadiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Rahul M. Kohli
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of MedicinePerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - E. James Petersson
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
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2
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Meng Z, Zhao R, Li X, Ma C, Xie C. Synthesis of acridones through the ring expansion of isatins with arynes oxidated by O2 in air. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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3
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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4
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A theoretical and experimental analysis of the luminescent properties of Europium(III) complex sensitized by tryptophan. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Featherston ER, Issertell EJ, Cotruvo JA. Probing Lanmodulin's Lanthanide Recognition via Sensitized Luminescence Yields a Platform for Quantification of Terbium in Acid Mine Drainage. J Am Chem Soc 2021; 143:14287-14299. [PMID: 34432449 DOI: 10.1021/jacs.1c06360] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lanmodulin is the first natural, selective macrochelator for f elements-a protein that binds lanthanides with picomolar affinity at 3 EF hands, motifs that instead bind calcium in most other proteins. Here, we use sensitized terbium luminescence to probe the mechanism of lanthanide recognition by this protein as well as to develop a terbium-specific biosensor that can be applied directly in environmental samples. By incorporating tryptophan residues into specific EF hands, we infer the order of metal binding of these three sites. Despite lanmodulin's remarkable lanthanide binding properties, its coordination of approximately two solvent molecules per site (by luminescence lifetime) and metal dissociation kinetics (koff = 0.02-0.05 s-1, by stopped-flow fluorescence) are revealed to be rather ordinary among EF hands; what sets lanmodulin apart is that metal association is nearly diffusion limited (kon ≈ 109 M-1 s-1). Finally, we show that Trp-substituted lanmodulin can quantify 3 ppb (18 nM) terbium directly in acid mine drainage at pH 3.2 in the presence of a 100-fold excess of other rare earths and a 100 000-fold excess of other metals using a plate reader. These studies not only yield insight into lanmodulin's mechanism of lanthanide recognition and the structures of its metal binding sites but also show that this protein's unique combination of affinity and selectivity outperforms synthetic luminescence-based sensors, opening the door to rapid and inexpensive methods for selective sensing of individual lanthanides in the environment and in-line monitoring in industrial operations.
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Affiliation(s)
- Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Edward J Issertell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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6
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Gupta A, Garreffi BP, Guo M. Facile synthesis of a novel genetically encodable fluorescent α-amino acid emitting greenish blue light. Chem Commun (Camb) 2020; 56:12578-12581. [PMID: 32944728 PMCID: PMC7577945 DOI: 10.1039/d0cc03643a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report the facile synthesis and characterization of a novel fluorescent α-amino acid 4-phenanthracen-9-yl-l-phenylalanine (Phen-AA) (5) that emits greenish blue light in the visible region. This genetically encodable l-α-amino acid has excellent photostability with a 75% quantum yield. It readily gets into human cells, being clearly imaged upon 405 nm laser excitation. The synthetic procedure is resistant to racemization and only involves three simple steps which use mild conditions and generate the Phen-AA in reasonably good yield. It may find broad applications in research, biotechnology, and the pharmaceutical industry.
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Affiliation(s)
- Aakash Gupta
- Department of Chemistry and Biochemistry, UMass Cranberry Health Research Center, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA.
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7
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Cho U, Chen JK. Lanthanide-Based Optical Probes of Biological Systems. Cell Chem Biol 2020; 27:921-936. [PMID: 32735780 DOI: 10.1016/j.chembiol.2020.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/28/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
The unique photophysical properties of lanthanides, such as europium, terbium, and ytterbium, make them versatile molecular probes of biological systems. In particular, their long-lived photoluminescence, narrow bandwidth emissions, and large Stokes shifts enable experiments that are infeasible with organic fluorophores and fluorescent proteins. The ability of these metal ions to undergo luminescence resonance energy transfer, and photon upconversion further expands the capabilities of lanthanide probes. In this review, we describe recent advances in the design of lanthanide luminophores and their application in biological research. We also summarize the latest detection systems that have been developed to fully exploit the optical properties of lanthanide luminophores. We conclude with a discussion of remaining challenges and new frontiers in lanthanide technologies. The unprecedented levels of sensitivity and multiplexing afforded by rare-earth elements illustrate how chemistry can enable new approaches in biology.
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Affiliation(s)
- Ukrae Cho
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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8
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Kovacs D, Mathieu E, Kiraev SR, Wells JAL, Demeyere E, Sipos A, Borbas KE. Coordination Environment-Controlled Photoinduced Electron Transfer Quenching in Luminescent Europium Complexes. J Am Chem Soc 2020; 142:13190-13200. [DOI: 10.1021/jacs.0c05518] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniel Kovacs
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Emilie Mathieu
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Salauat R. Kiraev
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Jordann A. L. Wells
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Ellen Demeyere
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Agnès Sipos
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - K. Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
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9
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Victor TW, O'Toole KH, Easthon LM, Ge M, Smith RJ, Huang X, Yan H, Chu YS, Chen S, Gursoy D, Ralle M, Imperiali B, Allen KN, Miller LM. Lanthanide-Binding Tags for 3D X-ray Imaging of Proteins in Cells at Nanoscale Resolution. J Am Chem Soc 2020; 142:2145-2149. [PMID: 31923358 DOI: 10.1021/jacs.9b11571] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the application of lanthanide-binding tags (LBTs) for two- and three-dimensional X-ray imaging of individual proteins in cells with a sub-15 nm beam. The method combines encoded LBTs, which are tags of minimal size (ca. 15-20 amino acids) affording high-affinity lanthanide ion binding, and X-ray fluorescence microscopy (XFM). This approach enables visualization of LBT-tagged proteins while simultaneously measuring the elemental distribution in cells at a spatial resolution necessary for visualizing cell membranes and eukaryotic subcellular organelles.
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Affiliation(s)
- Tiffany W Victor
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Katherine H O'Toole
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Lindsey M Easthon
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Mingyuan Ge
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Randy J Smith
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Xiaojing Huang
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Hanfei Yan
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Yong S Chu
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Si Chen
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Doga Gursoy
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States.,Department of Electrical Engineering and Computer Science , Northwestern University , Evanston , Illinois 60298 , United States
| | - Martina Ralle
- Department of Molecular and Medical Genetics , Oregon Health Science University , Portland , Oregon 97239 , United States
| | - Barbara Imperiali
- Department of Biology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Karen N Allen
- Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Lisa M Miller
- National Synchrotron Light Source II , Brookhaven National Laboratory , Upton , New York 11973 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
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10
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Gao F, Thornley BS, Tressler CM, Naduthambi D, Zondlo NJ. Phosphorylation-dependent protein design: design of a minimal protein kinase-inducible domain. Org Biomol Chem 2019; 17:3984-3995. [PMID: 30942803 PMCID: PMC6668337 DOI: 10.1039/c9ob00502a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinases and phosphatases modulate protein structure and function, which in turn regulate cellular activities. The development of novel proteins and protein motifs that are responsive to protein phosphorylation provides new ways to probe the functions of individual protein kinases and the intracellular effects of their activation and downregulation. Herein we develop a minimal motif that is responsive to protein phosphorylation, termed a minimal protein kinase-inducible domain. The encodable protein motif comprises a 7- or 8-residue sequence (DKDADXW or DKDADXXW), derived from EF-Hand calcium-binding domains, that is necessary but not sufficient for binding terbium, combined with a protein phosphorylation site (Ser or Thr at residue 9) that, upon phosphorylation, completes the metal-binding motif. Thus, the motif binds metal poorly and exhibits weak terbium luminescence when not phosphorylated. Upon phosphorylation, the peptide binds metal with significantly higher affinity and exhibits robust terbium luminescence. Phosphorylation results in up to a 23× increase in terbium luminescence. Minimal phosphorylation-dependent motifs as small as 9 residues (DKDADGWIS) were developed. NMR spectroscopy on this lanthanum(iii)·phosphopeptide complex confirmed that binding occurs in a manner similar to that in an EF-Hand, despite the absence of the conserved Glu12 typically present in an EF-Hand. By combining molecular design with known protein kinase recognition sequences, minimal protein kinase-inducible domains were developed that were responsive to phosphorylation by Protein Kinase A (PKA: DKDADRRW(S/pS)IIAK), Protein Kinase C (PKC: DKDADGWI(T/pT)FRRKA), and Casein Kinase 1 (CK1: DKDADDWA(S/pS)I). Phosphorylation by PKA was quantified in HeLa cell extracts, with a 4.4× increase in fluorescence (terbium luminescence) observed at 544 nm. The optimized minimal motif includes alternating aspartate residues at positions 1, 3, and 5, plus binding through the main-chain carbonyl at position 7; a lysine at position 2 to provide electrostatic balance and reduce binding in the absence of phosphorylation; an alanine at residue 4 to promote the αL conformation observed at that position of the EF Hand; a tryptophan at residue 7 or 8 to sensitize terbium luminescence; and a phosphorylation site with serine or threonine at residue 9. Residues at positions 6; 7 or 8; and 10 or later may be changed to provide kinase specificity. In the CK1-responsive peptide, the acidic residues in the proto-terbium-binding motif are employed as part of the kinase recognition sequence. This work thus presents fundamental rules for the design of compact phosphorylation-responsive terbium-binding motifs, with potential further application to motifs responsive to other protein post-translational modifications.
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Affiliation(s)
- Feng Gao
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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11
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Hewitt SH, Butler SJ. Application of lanthanide luminescence in probing enzyme activity. Chem Commun (Camb) 2018; 54:6635-6647. [PMID: 29790500 DOI: 10.1039/c8cc02824a] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
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12
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Kovacs D, Phipps D, Orthaber A, Borbas KE. Highly luminescent lanthanide complexes sensitised by tertiary amide-linked carbostyril antennae. Dalton Trans 2018; 47:10702-10714. [DOI: 10.1039/c8dt01270a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The replacement of the secondary amide linker that carries the sensitizing carbostyril antenna with a tertiary amide in luminescent Eu and Tb complexes dramatically increases the lanthanide emission quantum yields.
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Affiliation(s)
- Daniel Kovacs
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
| | - Dulcie Phipps
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
| | - Andreas Orthaber
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
| | - K. Eszter Borbas
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
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13
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Barthelmes D, Barthelmes K, Schnorr K, Jonker HRA, Bodmer B, Allen KN, Imperiali B, Schwalbe H. Conformational dynamics and alignment properties of loop lanthanide-binding-tags (LBTs) studied in interleukin-1β. JOURNAL OF BIOMOLECULAR NMR 2017; 68:187-194. [PMID: 28534082 DOI: 10.1007/s10858-017-0118-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Encodable lanthanide binding tags (LBTs) have become an attractive tool in modern structural biology as they can be expressed as fusion proteins of targets of choice. Previously, we have demonstrated the feasibility of inserting encodable LBTs into loop positions of interleukin-1β (Barthelmes et al. in J Am Chem Soc 133:808-819, 2011). Here, we investigate the differences in fast dynamics of selected loop-LBT interleukin-1β constructs by measuring 15N nuclear spin relaxation experiments. We show that the loop-LBT does not significantly alter the dynamic motions of the host protein in the sub-τc-timescale and that the loop-LBT adopts a rigid conformation with significantly reduced dynamics compared to the terminally attached encodable LBT leading to increased paramagnetic alignment strength. We further analyze residual dipolar couplings (RDCs) obtained by loop-LBTs and additional liquid crystalline media to assess the applicability of the loop-LBT approach for RDC-based methods to determine structure and dynamics of proteins, including supra-τc dynamics. Using orthogonalized linear combinations (OLCs) of RDCs and Saupe matrices, we show that the combined use of encodable LBTs and external alignment media yields up to five linear independent alignments.
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Affiliation(s)
- Dominic Barthelmes
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Katja Barthelmes
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Kai Schnorr
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Hendrik R A Jonker
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Bianca Bodmer
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Barbara Imperiali
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany.
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14
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Kovacs D, Lu X, Mészáros LS, Ott M, Andres J, Borbas KE. Photophysics of Coumarin and Carbostyril-Sensitized Luminescent Lanthanide Complexes: Implications for Complex Design in Multiplex Detection. J Am Chem Soc 2017; 139:5756-5767. [PMID: 28388066 DOI: 10.1021/jacs.6b11274] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Luminescent lanthanide (Ln(III)) complexes with coumarin or carbostyril antennae were synthesized and their photophysical properties evaluated using steady-state and time-resolved UV-vis spectroscopy. Ligands bearing distant hydroxycoumarin-derived antennae attached through triazole linkers were modest sensitizers for Eu(III) and Tb(III), whereas ligands with 7-amidocarbostyrils directly linked to the coordination site could reach good quantum yields for multiple Ln(III), including the visible emitters Sm(III) and Dy(III), and the near-infrared emitters Nd(III) and Yb(III). The highest lanthanide-centered luminescence quantum yields were 35% (Tb), 7.9% (Eu), 0.67% (Dy), and 0.18% (Sm). Antennae providing similar luminescence intensities with 2-4 Ln-emitters were identified. Photoredox quenching of the carbostyril antenna excited states was observed for all Eu(III)-complexes and should be sensitizing in the case of Yb(III); the scope of the process extends to Ln(III) for which it has not been seen previously, specifically Dy(III) and Sm(III). The proposed process is supported by photophysical and electrochemical data. A FRET-type mechanism was identified in architectures with both distant and close antennae for all of the Lns. This mechanism seems to be the only sensitizing one at long distance and probably contributes to the sensitization at shorter distances along with the triplet pathway. The complexes were nontoxic to either bacterial or mammalian cells. Complexes of an ester-functionalized ligand were taken up by bacteria in a concentration-dependent manner. Our results suggest that the effects of FRET and photoredox quenching should be taken into consideration when designing luminescent Ln complexes. These results also establish these Ln(III)-complexes for multiplex detection beyond the available two-color systems.
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Affiliation(s)
- Daniel Kovacs
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University , Uppsala 75120, Sweden
| | - Xi Lu
- Department of Engineering Sciences, Ångström Laboratory, Box 534, Uppsala University , Uppsala 75121, Sweden
| | - Lívia S Mészáros
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University , Uppsala 75120, Sweden
| | - Marjam Ott
- Department of Engineering Sciences, Ångström Laboratory, Box 534, Uppsala University , Uppsala 75121, Sweden
| | - Julien Andres
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University , Uppsala 75120, Sweden
| | - K Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Box 523, Uppsala University , Uppsala 75120, Sweden
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15
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Raibaut L, Vasseur W, Shimberg GD, Saint-Pierre C, Ravanat JL, Michel SLJ, Sénèque O. Design of a synthetic luminescent probe from a biomolecule binding domain: selective detection of AU-rich mRNA sequences. Chem Sci 2016; 8:1658-1664. [PMID: 28451295 PMCID: PMC5364516 DOI: 10.1039/c6sc04086a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/02/2016] [Indexed: 12/12/2022] Open
Abstract
We report the design of a luminescent sensor based upon the zinc finger protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA.
We report the design of a luminescent sensor based upon the zinc finger (ZF) protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA. This sensor is composed of the tandem ZF RNA binding domain of TIS11d functionalized with a luminescent Tb3+ complex on one of the ZFs and a sensitizing antenna on the other. This work provides the proof of principle that an RNA binding protein can be re-engineered as an RNA sensor and, more generally, that tunable synthetic luminescent probes for biomolecules can be obtained by modifying biomolecule-binding domains.
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Affiliation(s)
- Laurent Raibaut
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
| | - William Vasseur
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
| | - Geoffrey D Shimberg
- Department of Pharmaceutical Sciences , School of Pharmacy , University of Maryland , Baltimore , Maryland 21201-1180 , USA .
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences , School of Pharmacy , University of Maryland , Baltimore , Maryland 21201-1180 , USA .
| | - Olivier Sénèque
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
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Jadhav PD, Shen J, Sammynaiken R, Reaney MJT. Site Covalent Modification of Methionyl Peptides for the Production of FRET Complexes. Chemistry 2015; 21:17023-34. [DOI: 10.1002/chem.201502699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 11/05/2022]
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The best and the brightest: exploiting tryptophan-sensitized Tb(3+) luminescence to engineer lanthanide-binding tags. Methods Mol Biol 2015; 1248:201-20. [PMID: 25616335 DOI: 10.1007/978-1-4939-2020-4_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Consider the lanthanide metals, comprising lanthanum through lutetium. Lanthanides form stable cations with a +3 charge, and these ions exhibit a variety of useful physical properties (long-lifetime luminescence, paramagnetism, anomalous X-ray scattering) that are amenable to studies of biomolecules. The absence of lanthanide ions in living systems means that background signals are generally a nonissue; however, to exploit the advantageous properties it is necessary to engineer a robust lanthanide-binding sequence that can be appended to any macromolecules of interest. To this end, the luminescence produced by tryptophan-sensitized Tb(3+) has been used as a selection marker for peptide sequences that avidly chelate these ions. A combinatorial split-and-pool library that uses two orthogonal linkers-one that is cleaved for selection and one that is cleaved for sequencing and characterization-has been used to develop lanthanide-binding tags (LBTs): peptides of 15-20 amino acids with low-nM affinity for Tb(3+). Further validating the success of this screen, knowledge about LBTs has enabled the introduction of a lanthanide-binding loop in place of one of the four native calcium-binding loops within the protein calcineurin B.
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Lipchik AM, Perez M, Bolton S, Dumrongprechachan V, Ouellette SB, Cui W, Parker LL. KINATEST-ID: a pipeline to develop phosphorylation-dependent terbium sensitizing kinase assays. J Am Chem Soc 2015; 137:2484-94. [PMID: 25689372 DOI: 10.1021/ja507164a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nonreceptor protein tyrosine kinases (NRTKs) are essential for cellular homeostasis and thus are a major focus of current drug discovery efforts. Peptide substrates that can enhance lanthanide ion luminescence upon tyrosine phosphorylation enable rapid, sensitive screening of kinase activity, however design of suitable substrates that can distinguish between tyrosine kinase families is a huge challenge. Despite their different substrate preferences, many NRTKs are structurally similar even between families. Furthermore, the development of lanthanide-based kinase assays is hampered by incomplete understanding of how to integrate sequence selectivity with metal ion binding, necessitating laborious iterative substrate optimization. We used curated proteomic data from endogenous kinase substrates and known Tb(3+)-binding sequences to build a generalizable in silico pipeline with tools to generate, screen, align, and select potential phosphorylation-dependent Tb(3+)-sensitizing substrates that are most likely to be kinase specific. We demonstrated the approach by developing several substrates that are selective within kinase families and amenable to high-throughput screening (HTS) applications. Overall, this strategy represents a pipeline for developing efficient and specific assays for virtually any tyrosine kinase that use HTS-compatible lanthanide-based detection. The tools provided in the pipeline also have the potential to be adapted to identify peptides for other purposes, including other enzyme assays or protein-binding ligands.
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Affiliation(s)
- Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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21
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Speight LC, Muthusamy AK, Goldberg JM, Warner JB, Wissner RF, Willi TS, Woodman BF, Mehl RA, Petersson EJ. Efficient synthesis and in vivo incorporation of acridon-2-ylalanine, a fluorescent amino acid for lifetime and Förster resonance energy transfer/luminescence resonance energy transfer studies. J Am Chem Soc 2013; 135:18806-14. [PMID: 24303933 DOI: 10.1021/ja403247j] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein conformational change because it is a long lifetime, visible wavelength fluorophore that is small enough to be incorporated during ribosomal biosynthesis. Incorporation of Acd into proteins expressed in Escherichia coli requires efficient chemical synthesis to produce large quantities of the amino acid and the generation of a mutant aminoacyl tRNA synthetase that can selectively charge the amino acid onto a tRNA. Here, we report the synthesis of Acd in 87% yield over five steps from Tyr and the identification of an Acd synthetase by screening candidate enzymes previously evolved from Methanococcus janaschii Tyr synthetase for unnatural amino acid incorporation. Furthermore, we characterize the photophysical properties of Acd, including quenching interactions with select natural amino acids and Förster resonance energy transfer (FRET) interactions with common fluorophores such as methoxycoumarin (Mcm). Finally, we demonstrate the value of incorporation of Acd into proteins, using changes in Acd fluorescence lifetimes, Mcm/Acd FRET, or energy transfer to Eu(3+) to monitor protein folding and binding interactions.
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Affiliation(s)
- Lee C Speight
- University of Pennsylvania , Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323, United States
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Selivanova N, Vasilieva K, Galyametdinov Y. Luminescent complexes of terbium ion for molecular recognition of ibuprofen. LUMINESCENCE 2013; 29:202-10. [DOI: 10.1002/bio.2526] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/15/2013] [Accepted: 03/25/2013] [Indexed: 01/19/2023]
Affiliation(s)
- Natalia Selivanova
- Kazan National Research Technological University; Department Physical and Colloid Chemistry; K. Marks 68 Kazan 420015 Russia
| | - Kristina Vasilieva
- Kazan National Research Technological University; Department Physical and Colloid Chemistry; K. Marks 68 Kazan 420015 Russia
| | - Yury Galyametdinov
- Kazan National Research Technological University; Department Physical and Colloid Chemistry; K. Marks 68 Kazan 420015 Russia
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Krueger AT, Imperiali B. Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology. Chembiochem 2013; 14:788-99. [DOI: 10.1002/cbic.201300079] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 12/16/2022]
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Szíjjártó C, Pershagen E, Ilchenko NO, Borbas KE. A versatile long-wavelength-absorbing scaffold for Eu-based responsive probes. Chemistry 2013; 19:3099-109. [PMID: 23307197 DOI: 10.1002/chem.201203957] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Indexed: 12/27/2022]
Abstract
Coumarin-sensitized, long-wavelength-absorbing luminescent Eu(III)-complexes have been synthesized and characterized. The lanthanide binding site consists of a cyclen-based chelating framework that is attached through a short linker to a 7-hydroxycoumarin, a 7-B(OH)(2)-coumarin, a 7-O-(4-pinacolatoboronbenzyl)-coumarin or a 7-O-(4-methoxybenzyl)-coumarin. The syntheses are straightforward, use readily available building blocks, and proceed through a small number of high-yielding steps. The sensitivity of coumarin photophysics to the 7-substituent enables modulation of the antenna-absorption properties, and thus the lanthanide excitation spectrum. Reactions of the boronate-based functionalities (cages) with H(2)O(2) yielded the corresponding 7-hydroxycoumarin species. The same species was produced with peroxynitrite in a ×10(6)-10(7)-fold faster reaction. Both reactions resulted in the emergence of a strong ≈407 nm excitation band, with concomitant decrease of the 366 nm band of the caged probe. In aqueous solution the methoxybenzyl caged Eu-complex was quenched by ONOO(-). We have shown that preliminary screening of simple coumarin-based antennae through UV/Vis absorption spectroscopy is possible as the changes in absorption profile translate with good fidelity to changes in Eu(III)-excitation profile in the fully elaborated complex. Taken together, our results show that the 7-hydroxycoumarin antenna is a viable scaffold for the construction of turn-on and ratiometric luminescent probes.
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Affiliation(s)
- Csongor Szíjjártó
- Department of Chemistry, BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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Zherdeva VV, Savitsky AP. Using lanthanide-based resonance energy transfer for in vitro and in vivo studies of biological processes. BIOCHEMISTRY (MOSCOW) 2013; 77:1553-74. [DOI: 10.1134/s0006297912130111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Ancel L, Gateau C, Lebrun C, Delangle P. DNA Sensing by a Eu-Binding Peptide Containing a Proflavine Unit. Inorg Chem 2013; 52:552-4. [DOI: 10.1021/ic302456q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Laetitia Ancel
- INAC, Service de
Chimie Inorganique et Biologique (UMR_E 3 CEA UJF), Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble cedex,
France
| | - Christelle Gateau
- INAC, Service de
Chimie Inorganique et Biologique (UMR_E 3 CEA UJF), Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble cedex,
France
| | - Colette Lebrun
- INAC, Service de
Chimie Inorganique et Biologique (UMR_E 3 CEA UJF), Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble cedex,
France
| | - Pascale Delangle
- INAC, Service de
Chimie Inorganique et Biologique (UMR_E 3 CEA UJF), Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble cedex,
France
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Niedźwiecka A, Cisnetti F, Lebrun C, Delangle P. Femtomolar Ln(III) Affinity in Peptide-Based Ligands Containing Unnatural Chelating Amino Acids. Inorg Chem 2012; 51:5458-64. [DOI: 10.1021/ic300448y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Agnieszka Niedźwiecka
- Service de Chimie Inorganique et Biologique (UMR_E
3 CEA UJF), INAC, Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble Cedex,
France
| | - Federico Cisnetti
- Service de Chimie Inorganique et Biologique (UMR_E
3 CEA UJF), INAC, Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble Cedex,
France
| | - Colette Lebrun
- Service de Chimie Inorganique et Biologique (UMR_E
3 CEA UJF), INAC, Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble Cedex,
France
| | - Pascale Delangle
- Service de Chimie Inorganique et Biologique (UMR_E
3 CEA UJF), INAC, Commissariat à
l′Energie Atomique, 17 rue des martyrs, 38054 Grenoble Cedex,
France
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Bonnet CS, Devocelle M, Gunnlaugsson T. Luminescent lanthanide-binding peptides: sensitising the excited states of Eu(iii) and Tb(iii) with a 1,8-naphthalimide-based antenna. Org Biomol Chem 2012; 10:126-33. [DOI: 10.1039/c1ob06567j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Arslanbaeva LR, Zherdeva VV, Ivashina TV, Vinokurov LM, Morozov VB, Olenin AN, Savitskii AP. Induction-resonance energy transfer between the terbium-binding peptide and the red fluorescent proteins DsRed2 and TagRFP. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911030043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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am Ende CW, Meng HY, Ye M, Pandey AK, Zondlo NJ. Design of lanthanide fingers: compact lanthanide-binding metalloproteins. Chembiochem 2010; 11:1738-47. [PMID: 20623571 DOI: 10.1002/cbic.201000056] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lanthanides have interesting chemical properties; these include luminescent, magnetic, and catalytic functions. Toward the development of proteins incorporating novel functions, we have designed a new lanthanide-binding motif, lanthanide fingers. These were designed based on the Zif268 zinc finger, which exhibits a beta beta alpha structural motif. Lanthanide fingers utilize an Asp(2)Glu(2) metal-coordination environment to bind lanthanides through a tetracarboxylate peptide ligand. The iterative design of a general lanthanide-binding peptide incorporated the following key elements: 1) residues with high alpha-helix and beta-sheet propensities in the respective secondary structures; 2) an optimized big box alpha-helix N-cap; 3) a Schellman alpha-helix C-cap motif; and 4) an optional D-Pro-Ser type II' beta-turn in the beta-hairpin. The peptides were characterized for lanthanide binding by circular dichroism (CD), NMR, and fluorescence spectroscopy. In all instances, stabilization of the peptide secondary structures resulted in an increase in metal affinity. The optimized protein design was a 25-residue peptide that was a general lanthanide-binding motif; this binds all lanthanides examined in a competitive aqueous environment, with a dissociation constant of 9.3 microM for binding Er(3+). CD spectra of the peptide-lanthanide complexes are similar to those of zinc fingers and other beta beta alpha proteins. Metal binding involves residues from the N-terminal beta-hairpin and the C terminal alpha-helical segments of the peptide. NMR data indicated that metal binding induced a global change in the peptide structure. The D-Pro-Ser type II' beta-turn motif could be replaced by Thr-Ile to generate genetically encodable lanthanide fingers. Replacement of the central Phe with Trp generated genetically encodable lanthanide fingers that exhibited terbium luminescence greater than that of an EF-hand peptide.
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Affiliation(s)
- Christopher W am Ende
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Chaisemartin L, Chinestra P, Favre G, Blonski C, Faye JC. Synthesis and application of a N-1' fluorescent biotinyl derivative inducing the specific carboxy-terminal dual labeling of a novel RhoB-selective scFv. Bioconjug Chem 2010; 20:847-55. [PMID: 19348471 DOI: 10.1021/bc800272r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The fluorescent site-specific labeling of protein would provide a new, easy-to-use alternative to biochemical and immunochemical methods. We used an intein-mediated strategy for covalent labeling of the carboxy-terminal amino acid of a RhoB-selective scFv previously isolated from a phage display library (a human synthetic V(H) + V(L) scFv phage library). The scFv fused to the Mxe intein was produced in E. coli and purified and was then labeled with a newly synthesized fluorescent biotinyl cysteine derivative capable of inducing scFv-Mxe intein splicing. In this study, we investigated the splicing and labeling properties of various amino acids in the hinge domain between scFv and Mxe under thiol activation. In this dual labeling system, the fluorescein is used for antibody detection and biotin is used for purification, resulting in a high specific activity for fluorescence. We then checked that the purified biotinylated fluorescent scFv retained its selectivity for RhoB without modification of its affinity.
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Affiliation(s)
- L Chaisemartin
- INSERM U563, Departement Oncogenese, Signalisation et Innovation Therapeutique, Institut Claudius Regaud, 31052 Toulouse, France
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Su Y, Nykanen M, Jahn KA, Whan R, Cantrill L, Soon LL, Ratinac KR, Braet F. Multi-dimensional correlative imaging of subcellular events: combining the strengths of light and electron microscopy. Biophys Rev 2010; 2:121-135. [PMID: 28510069 DOI: 10.1007/s12551-010-0035-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 07/02/2010] [Indexed: 01/26/2023] Open
Abstract
To genuinely understand how complex biological structures function, we must integrate knowledge of their dynamic behavior and of their molecular machinery. The combined use of light or laser microscopy and electron microscopy has become increasingly important to our understanding of the structure and function of cells and tissues at the molecular level. Such a combination of two or more different microscopy techniques, preferably with different spatial- and temporal-resolution limits, is often referred to as 'correlative microscopy'. Correlative imaging allows researchers to gain additional novel structure-function information, and such information provides a greater degree of confidence about the structures of interest because observations from one method can be compared to those from the other method(s). This is the strength of correlative (or 'combined') microscopy, especially when it is combined with combinatorial or non-combinatorial labeling approaches. In this topical review, we provide a brief historical perspective of correlative microscopy and an in-depth overview of correlative sample-preparation and imaging methods presently available, including future perspectives on the trend towards integrative microscopy and microanalysis.
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Affiliation(s)
- Yingying Su
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Madsen Building F09, Sydney, NSW, 2006, Australia
| | - Marko Nykanen
- Kids Research Institute, Children's Hospital Westmead, Westmead, Locked Bag 4001, NSW, 2145, Australia
| | - Kristina A Jahn
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Madsen Building F09, Sydney, NSW, 2006, Australia
| | - Renee Whan
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Madsen Building F09, Sydney, NSW, 2006, Australia
| | - Laurence Cantrill
- Kids Research Institute, Children's Hospital Westmead, Westmead, Locked Bag 4001, NSW, 2145, Australia
| | - Lilian L Soon
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Madsen Building F09, Sydney, NSW, 2006, Australia
| | - Kyle R Ratinac
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Madsen Building F09, Sydney, NSW, 2006, Australia
| | - Filip Braet
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Madsen Building F09, Sydney, NSW, 2006, Australia.
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Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure. Chemistry 2010; 16:6651-9. [DOI: 10.1002/chem.200903092] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Arslanbaeva LR, Zherdeva VV, Ivashina TV, Vinokurov LM, Rusanov AL, Savitsky AP. Genetically encoded FRET-pair on the basis of terbium-binding peptide and red fluorescent protein. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810020055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Affiliation(s)
- Jean-Claude G. Bünzli
- Laboratory of Lanthanide Supramolecular Chemistry, École Polytechnique Fédérale de Lausanne (EPFL), BCH 1402, CH-1015 Lausanne, Switzerland, and Department of Advanced Materials Chemistry, WCU Center for Next Generation Photovoltaic Systems, Korea University, Sejong Campus, 208 Seochang, Jochiwon, Chung Nam 339-700, Republic of Korea
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Mathis G, Bazin H. Stable Luminescent Chelates and Macrocyclic Compounds. LANTHANIDE LUMINESCENCE 2010. [DOI: 10.1007/4243_2010_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Eliseeva SV, Bünzli JCG. Lanthanide luminescence for functional materials and bio-sciences. Chem Soc Rev 2010; 39:189-227. [PMID: 20023849 DOI: 10.1039/b905604c] [Citation(s) in RCA: 2126] [Impact Index Per Article: 151.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Svetlana V Eliseeva
- Laboratory of Lanthanide Supramolecular Chemistry, Swiss Federal Institute of Technology, Lausanne (EPFL)
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Andrews M, Ward B, Laye R, Kariuki B, Pope S. Sensitized Lanthanide-Ion Luminescence with Aryl-SubstitutedN-(2-Nitrophenyl)acetamide-Derived Chromophores. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zucchi G, Maury O, Thuéry P, Gumy F, Bünzli JC, Ephritikhine M. 2,2′-Bipyrimidine as Efficient Sensitizer of the Solid-State Luminescence of Lanthanide and Uranyl Ions from Visible to Near-Infrared. Chemistry 2009; 15:9686-96. [DOI: 10.1002/chem.200901517] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Cisnetti F, Gateau C, Lebrun C, Delangle P. Lanthanide(III) Complexes with Two Hexapeptides Incorporating Unnatural Chelating Amino Acids: Secondary Structure and Stability. Chemistry 2009; 15:7456-69. [DOI: 10.1002/chem.200900747] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Bonnet C, Fries P, Crouzy S, Sénèque O, Cisnetti F, Boturyn D, Dumy P, Delangle P. A Gadolinium-Binding Cyclodecapeptide with a Large High-Field Relaxivity Involving Second-Sphere Water. Chemistry 2009; 15:7083-93. [DOI: 10.1002/chem.200900636] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Song B, Vandevyver CDB, Chauvin AS, Bünzli JCG. Time-resolved luminescence microscopy of bimetallic lanthanide helicates in living cells. Org Biomol Chem 2008; 6:4125-33. [PMID: 18972043 DOI: 10.1039/b811427g] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cellular uptake mechanism and intracellular distribution of emissive lanthanide helicates have been elucidated by time-resolved luminescence microscopy (TRLM). The helicates are non-cytotoxic and taken up by normal (HaCat) and cancer (HeLa, MCF-7) cells by endocytosis and show a late endosomal-lysosomal cellular distribution. The lysosomes predominantly localize around the nucleus and co-localize with the endoplasmatic reticulum. The egress is slow and limited, around 30% after 24 h. The first bright luminescent images can be observed with an external concentration gradient of 5 microM of the Eu(III) helicate [Q = 0.21, tau = 2.43 ms], compared to >10 microM when using conventional luminescence microscopy. Furthermore, multiplex labeling could be achieved with the Tb(III) [Q = 0.11, tau = 0.65 ms], and Sm(III) [Q = 0.0038, tau = 0.030 ms] analogues.
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Affiliation(s)
- Bo Song
- Laboratory of Lanthanide Supramolecular Chemistry, Ecole Polytechnique Fédérale de Lausanne, BCH 1404, 1015 Lausanne, Switzerland
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