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Graßl F, Konrad MMB, Krüll J, Pezerovic A, Zähnle L, Burkovski A, Heinrich MR. Tuning the Polarity of Antibiotic-Cy5 Conjugates Enables Highly Selective Labeling of Binding Sites. Chemistry 2023; 29:e202301208. [PMID: 37247408 DOI: 10.1002/chem.202301208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
Multidrug-resistant bacteria pose a major threat to global health, even as newly introduced antibiotics continue to lose their therapeutic value. Against this background, deeper insights into bacterial interaction with antibiotic drugs are urgently required, whereas fluorescently labeled drug conjugates can serve as highly valuable tools. Herein, the preparation and biological evaluation of 13 new fluorescent antibiotic-Cy5 dye conjugates is described, in which the tuning of the polarity of the Cy5 dye proved to be a key element to achieve highly favorable properties for various fields of application.
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Affiliation(s)
- Fabian Graßl
- Department of Chemistry and Pharmacy, Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Maike M B Konrad
- Department of Biology, Microbiology Division, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Jasmin Krüll
- Department of Chemistry and Pharmacy, Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Azra Pezerovic
- Department of Chemistry and Pharmacy, Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Leon Zähnle
- Department of Chemistry and Pharmacy, Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Andreas Burkovski
- Department of Biology, Microbiology Division, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
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2
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Baek I, Le SN, Jeon J, Chun Y, Reed C, Buratowski S. A set of Saccharomyces cerevisiae integration vectors for fluorescent dye labeling of proteins. G3 (BETHESDA, MD.) 2022; 12:6659097. [PMID: 35944214 PMCID: PMC9526040 DOI: 10.1093/g3journal/jkac201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 01/05/2023]
Abstract
Protein fusions are frequently used for fluorescence imaging of individual molecules, both in vivo and in vitro. The SNAP, CLIP, HALO (aka HaloTag7), and DHFR protein tags can be linked to small molecule dyes that provide brightness and photo-stability superior to fluorescent proteins. To facilitate fluorescent dye tagging of proteins in the yeast Saccharomyces cerevisiae, we constructed a modular set of vectors with various combinations of labeling protein tags and selectable markers. These vectors can be used in combination to create strains where multiple proteins labeled with different colored dyes can be simultaneously observed.
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Affiliation(s)
- Inwha Baek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah N Le
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jongcheol Jeon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte Reed
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen Buratowski
- Corresponding author: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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3
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Martynov VI, Pakhomov AA. BODIPY derivatives as fluorescent reporters of molecular activities in living cells. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
Fluorescent compounds have become indispensable tools for imaging molecular activities in the living cell. 4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) is currently one of the most popular fluorescent reporters due to its unique photophysical properties. This review provides a general survey and presents a summary of recent advances in the development of new BODIPY-based cellular biomarkers and biosensors. The review starts with the consideration of the properties of BODIPY derivatives required for their application as cellular reporters. Then review provides examples of the design of sensors for different biologically important molecules, ions, membrane potential, temperature and viscosity defining the live cell status. Special attention is payed to BODPY-based phototransformable reporters.
The bibliography includes 339 references.
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4
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Morris MA, Malek M, Hashemian MH, Nguyen BT, Manuse S, Lewis K, Nowick JS. A Fluorescent Teixobactin Analogue. ACS Chem Biol 2020; 15:1222-1231. [PMID: 32045203 DOI: 10.1021/acschembio.9b00908] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This report describes the first synthesis and application of a fluorescent teixobactin analogue that exhibits antibiotic activity and binds to the cell walls of Gram-positive bacteria. The teixobactin analogue, Lys(Rhod)9,Arg10-teixobactin, has a fluorescent tag at position 9 and an arginine in place of the natural allo-enduracididine residue at position 10. The fluorescent teixobactin analogue retains partial antibiotic activity, with minimum inhibitory concentrations of 4-8 μg/mL across a panel of Gram-positive bacteria, as compared to 1-4 μg/mL for the unlabeled Arg10-teixobactin analogue. Lys(Rhod)9,Arg10-teixobactin is prepared by a regioselective labeling strategy that labels Lys9 with an amine-reactive rhodamine fluorophore during solid-phase peptide synthesis, with the resulting conjugate tolerating subsequent solid-phase peptide synthesis reactions. Treatment of Gram-positive bacteria with Lys(Rhod)9,Arg10-teixobactin results in septal and lateral staining, which is consistent with an antibiotic targeting cell wall precursors. Concurrent treatment of Lys(Rhod)9,Arg10-teixobactin and BODIPY FL vancomycin results in septal colocalization, providing further evidence that Lys(Rhod)9,Arg10-teixobactin binds to cell wall precursors. Controls with either Gram-negative bacteria, or an inactive fluorescent homologue with Gram-positive bacteria, showed little or no staining in fluorescence micrographic studies. Lys(Rhod)9,Arg10-teixobactin can thus serve as a functional probe to study Gram-positive bacteria and their interactions with teixobactin.
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Affiliation(s)
- Michael A. Morris
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Melody Malek
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mohammad H. Hashemian
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Betty T. Nguyen
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Sylvie Manuse
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
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5
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Fluorescent Antibiotics: New Research Tools to Fight Antibiotic Resistance. Trends Biotechnol 2018; 36:523-536. [PMID: 29478675 DOI: 10.1016/j.tibtech.2018.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 01/02/2023]
Abstract
Better understanding how multidrug-resistant (MDR) bacteria can evade current and novel antibiotics requires a better understanding of the chemical biology of antibiotic action. This necessitates using new tools and techniques to advance our knowledge of bacterial responses to antibiotics, ideally in live cells in real time, to selectively investigate bacterial growth, division, metabolism, and resistance in response to antibiotic challenge. In this review, we discuss the preparation and biological evaluation of fluorescent antibiotics, focussing on how these reporters and assay methods can help elucidate resistance mechanisms. We also examine the potential utility of such probes for real-time in vivo diagnosis of infections.
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6
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Rogawski R, Sergeyev IV, Zhang Y, Tran TH, Li Y, Tong L, McDermott AE. NMR Signal Quenching from Bound Biradical Affinity Reagents in DNP Samples. J Phys Chem B 2017; 121:10770-10781. [PMID: 29116793 PMCID: PMC5842680 DOI: 10.1021/acs.jpcb.7b08274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We characterize the effect of specifically bound biradicals on the NMR spectra of dihydrofolate reductase from E. coli. Dynamic nuclear polarization methods enhance the signal-to-noise of solid state NMR experiments by transferring polarization from unpaired electrons of biradicals to nuclei. There has been recent interest in colocalizing the paramagnetic polarizing agents with the analyte of interest through covalent or noncovalent specific interactions. This experimental approach broadens the scope of dynamic nuclear polarization methods by offering the possibility of selective signal enhancements and the potential to work in a broad range of environments. Paramagnetic compounds can have other effects on the NMR spectroscopy of nearby nuclei, including broadening of nuclear resonances due to the proximity of the paramagnetic agent. Understanding the distance dependence of these interactions is important for the success of the technique. Here we explore paramagnetic signal quenching due to a bound biradical, specifically a biradical-derivatized trimethoprim ligand of E. coli dihydrofolate reductase. Biradical-derivatized trimethoprim has nanomolar affinity for its target, and affords strong and selective signal enhancements in dynamic nuclear polarization experiments. In this work, we show that, although the trimethoprim fragment is well ordered, the biradical (TOTAPOL) moiety is disordered when bound to the protein. The distance dependence in bleaching of NMR signal intensity allows us to detect numerous NMR signals in the protein. We present the possibility that static disorder and electron spin diffusion play roles in this observation, among other contributions. The fact that the majority of signals are observed strengthens the case for the use of high affinity or covalent radicals in dynamic nuclear polarization solid state NMR enhancement.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yinglu Zhang
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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7
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Rogawski R, Sergeyev IV, Li Y, Ottaviani MF, Cornish V, McDermott AE. Dynamic Nuclear Polarization Signal Enhancement with High-Affinity Biradical Tags. J Phys Chem B 2017; 121:1169-1175. [PMID: 28099013 DOI: 10.1021/acs.jpcb.6b09021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dynamic nuclear polarization is an emerging technique for sensitizing solid-state NMR experiments by transferring polarization from electrons to nuclei. Stable biradicals, the polarization source for the cross effect mechanism, are typically codissolved at millimolar concentrations with proteins of interest. Here we describe the high-affinity biradical tag TMP-T, created by covalently linking trimethoprim, a nanomolar affinity ligand of dihydrofolate reductase (DHFR), to the biradical polarizing agent TOTAPOL. With TMP-T bound to DHFR, large enhancements of the protein spectrum are observed, comparable to when TOTAPOL is codissolved with the protein. In contrast to TOTAPOL, the tight binding TMP-T can be added stoichiometrically at radical concentrations orders of magnitude lower than in previously described preparations. Benefits of the reduced radical concentration include reduced spectral bleaching, reduced chemical perturbation of the sample, and the ability to selectively enhance signals for the protein of interest.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - M Francesca Ottaviani
- Department of Pure and Applied Sciences, University of Urbino , Loc. Crocicchia, 61029 Urbino, Italy
| | - Virginia Cornish
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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8
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Phetsang W, Pelingon R, Butler MS, KC S, Pitt ME, Kaeslin G, Cooper MA, Blaskovich MAT. Fluorescent Trimethoprim Conjugate Probes To Assess Drug Accumulation in Wild Type and Mutant Escherichia coli. ACS Infect Dis 2016; 2:688-701. [PMID: 27737551 PMCID: PMC5067704 DOI: 10.1021/acsinfecdis.6b00080] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Reduced
susceptibility to antimicrobials in Gram-negative bacteria may result
from multiple resistance mechanisms, including increased efflux pump
activity or reduced porin protein expression. Up-regulation of the
efflux pump system is closely associated with multidrug resistance
(MDR). To help investigate the role of efflux pumps on compound accumulation,
a fluorescence-based assay was developed using fluorescent derivatives
of trimethoprim (TMP), a broad-spectrum synthetic antibiotic that
inhibits an intracellular target, dihydrofolate reductase (DHFR).
Novel fluorescent TMP probes inhibited eDHFR activity
with comparable potency to TMP, but did not kill or inhibit growth
of wild type Escherichia coli. However,
bactericidal activity was observed against an efflux pump deficient E. coli mutant strain (ΔtolC). A simple and quick fluorescence assay was developed to measure
cellular accumulation of the TMP probe using either fluorescence spectroscopy
or flow cytometry, with validation by LC-MS/MS. This fluorescence
assay may provide a simple method to assess efflux pump activity with
standard laboratory equipment.
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Affiliation(s)
- Wanida Phetsang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ruby Pelingon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark S. Butler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sanjaya KC
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Miranda E. Pitt
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geraldine Kaeslin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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9
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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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10
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Martynov VI, Pakhomov AA, Popova NV, Deyev IE, Petrenko AG. Synthetic Fluorophores for Visualizing Biomolecules in Living Systems. Acta Naturae 2016; 8:33-46. [PMID: 28050265 PMCID: PMC5199205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The last decade has witnessed significant advance in the imaging of living systems using fluorescent markers. This progress has been primarily associated with the discovery of different spectral variants of fluorescent proteins. However, the fluorescent protein technology has its own limitations and, in some cases, the use of low-molecular-weight fluorophores is preferable. In this review, we describe the arsenal of synthetic fluorescent tools that are currently in researchers' hands and span virtually the entire spectrum, from the UV to visible and, further, to the near-infrared region. An overview of recent advances in site-directed introduction of synthetic fluorophores into target cellular objects is provided. Application of these fluorescent probes to the solution of a wide range of biological problems, in particular, to the determination of local ion concentrations and pH in living systems, is discussed.
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Affiliation(s)
- V. I. Martynov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - A. A. Pakhomov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - N. V. Popova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - I. E. Deyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - A. G. Petrenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
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11
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Bosch PJ, Corrêa IR, Sonntag MH, Ibach J, Brunsveld L, Kanger JS, Subramaniam V. Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells. Biophys J 2015; 107:803-14. [PMID: 25140415 DOI: 10.1016/j.bpj.2014.06.040] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/22/2014] [Accepted: 06/10/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule tracking has become a widely used technique for studying protein dynamics and their organization in the complex environment of the cell. In particular, the spatiotemporal distribution of membrane receptors is an active field of study due to its putative role in the regulation of signal transduction. The SNAP-tag is an intrinsically monovalent and highly specific genetic tag for attaching a fluorescent label to a protein of interest. Little information is currently available on the choice of optimal fluorescent dyes for single-molecule microscopy utilizing the SNAP-tag labeling system. We surveyed 6 green and 16 red excitable dyes for their suitability in single-molecule microscopy of SNAP-tag fusion proteins in live cells. We determined the nonspecific binding levels and photostability of these dye conjugates when bound to a SNAP-tag fused membrane protein in live cells. We found that only a limited subset of the dyes tested is suitable for single-molecule tracking microscopy. The results show that a careful choice of the dye to conjugate to the SNAP-substrate to label SNAP-tag fusion proteins is very important, as many dyes suffer from either rapid photobleaching or high nonspecific staining. These characteristics appear to be unpredictable, which motivated the need to perform the systematic survey presented here. We have developed a protocol for evaluating the best dyes, and for the conditions that we evaluated, we find that Dy 549 and CF 640 are the best choices tested for single-molecule tracking. Using an optimal dye pair, we also demonstrate the possibility of dual-color single-molecule imaging of SNAP-tag fusion proteins. This survey provides an overview of the photophysical and imaging properties of a range of SNAP-tag fluorescent substrates, enabling the selection of optimal dyes and conditions for single-molecule imaging of SNAP-tagged fusion proteins in eukaryotic cell lines.
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Affiliation(s)
- Peter J Bosch
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | | | - Michael H Sonntag
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jenny Ibach
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Johannes S Kanger
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.
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12
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A theoretical justification for single molecule peptide sequencing. PLoS Comput Biol 2015; 11:e1004080. [PMID: 25714988 PMCID: PMC4341059 DOI: 10.1371/journal.pcbi.1004080] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/10/2014] [Indexed: 11/19/2022] Open
Abstract
The proteomes of cells, tissues, and organisms reflect active cellular processes and change continuously in response to intracellular and extracellular cues. Deep, quantitative profiling of the proteome, especially if combined with mRNA and metabolite measurements, should provide an unprecedented view of cell state, better revealing functions and interactions of cell components. Molecular diagnostics and biomarker discovery should benefit particularly from the accurate quantification of proteomes, since complex diseases like cancer change protein abundances and modifications. Currently, shotgun mass spectrometry is the primary technology for high-throughput protein identification and quantification; while powerful, it lacks high sensitivity and coverage. We draw parallels with next-generation DNA sequencing and propose a strategy, termed fluorosequencing, for sequencing peptides in a complex protein sample at the level of single molecules. In the proposed approach, millions of individual fluorescently labeled peptides are visualized in parallel, monitoring changing patterns of fluorescence intensity as N-terminal amino acids are sequentially removed, and using the resulting fluorescence signatures (fluorosequences) to uniquely identify individual peptides. We introduce a theoretical foundation for fluorosequencing and, by using Monte Carlo computer simulations, we explore its feasibility, anticipate the most likely experimental errors, quantify their potential impact, and discuss the broad potential utility offered by a high-throughput peptide sequencing technology. The development of next-generation DNA and RNA sequencing methods has transformed biology, with current platforms generating >1 billion sequencing reads per run. Unfortunately, no method of similar scale and throughput exists to identify and quantify specific proteins in complex mixtures, representing a critical bottleneck in many biochemical and molecular diagnostic assays. What is urgently needed is a massively parallel method, akin to next-gen DNA sequencing, for identifying and quantifying peptides or proteins in a sample. In principle, single-molecule peptide sequencing could achieve this goal, allowing billions of distinct peptides to be sequenced in parallel and thereby identifying proteins composing the sample and digitally quantifying them by direct counting of peptides. Here, we discuss theoretical considerations of single molecule peptide sequencing, suggest one possible experimental strategy, and, using computer simulations, characterize the potential utility and unusual properties of this future proteomics technology.
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