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Belousov A, Maslov I, Orekhov P, Khorn P, Kuzmichev P, Baleeva N, Motov V, Bogorodskiy A, Krasnova S, Mineev K, Zinchenko D, Zernii E, Ivanovich V, Permyakov S, Hofkens J, Hendrix J, Cherezov V, Gensch T, Mishin A, Baranov M, Mishin A, Borshchevskiy V. Monitoring GPCR conformation with GFP-inspired dyes. iScience 2024; 27:110466. [PMID: 39156645 PMCID: PMC11326922 DOI: 10.1016/j.isci.2024.110466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/15/2024] [Accepted: 07/02/2024] [Indexed: 08/20/2024] Open
Abstract
Solvatochromic compounds have emerged as valuable environment-sensitive probes for biological research. Here we used thiol-reactive solvatochromic analogs of the green fluorescent protein (GFP) chromophore to track conformational changes in two proteins, recoverin and the A2A adenosine receptor (A2AAR). Two dyes showed Ca2+-induced fluorescence changes when attached to recoverin. Our best-performing dye, DyeC, exhibited agonist-induced changes in both intensity and shape of its fluorescence spectrum when attached to A2AAR; none of these effects were observed with other common environment-sensitive dyes. Molecular dynamics simulations showed that activation of the A2AAR led to a more confined and hydrophilic environment for DyeC. Additionally, an allosteric modulator of A2AAR induced distinct fluorescence changes in the DyeC spectrum, indicating a unique receptor conformation. Our study demonstrated that GFP-inspired dyes are effective for detecting structural changes in G protein-coupled receptors (GPCRs), offering advantages such as intensity-based and ratiometric tracking, redshifted fluorescence spectra, and sensitivity to allosteric modulation.
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Affiliation(s)
- Anatoliy Belousov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Sechenov University, Moscow 119146, Russia
| | - Polina Khorn
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Pavel Kuzmichev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nadezhda Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vladislav Motov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Svetlana Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- National Research University Higher School of Economics, Moscow 101000, Russia
| | - Konstantin Mineev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitry Zinchenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Evgeni Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | | | - Sergei Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142292, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Alexander Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Mikhail Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Joint Institute for Nuclear Research, Dubna 141980, Russian Federation
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Bogdanova YA, Solovyev ID, Baleeva NS, Myasnyanko IN, Gorshkova AA, Gorbachev DA, Gilvanov AR, Goncharuk SA, Goncharuk MV, Mineev KS, Arseniev AS, Bogdanov AM, Savitsky AP, Baranov MS. Fluorescence lifetime multiplexing with fluorogen activating protein FAST variants. Commun Biol 2024; 7:799. [PMID: 38956304 PMCID: PMC11219735 DOI: 10.1038/s42003-024-06501-1] [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: 08/28/2023] [Accepted: 06/24/2024] [Indexed: 07/04/2024] Open
Abstract
In this paper, we propose a fluorescence-lifetime imaging microscopy (FLIM) multiplexing system based on the fluorogen-activating protein FAST. This genetically encoded fluorescent labeling platform employs FAST mutants that activate the same fluorogen but provide different fluorescence lifetimes for each specific protein-dye pair. All the proposed probes with varying lifetimes possess nearly identical and the smallest-in-class size, along with quite similar steady-state optical properties. In live mammalian cells, we target these chemogenetic tags to two intracellular structures simultaneously, where their fluorescence signals are clearly distinguished by FLIM. Due to the unique structure of certain fluorogens under study, their complexes with FAST mutants display a monophasic fluorescence decay, which may facilitate enhanced multiplexing efficiency by reducing signal cross-talks and providing optimal prerequisites for signal separation upon co-localized and/or spatially overlapped labeling.
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Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ilya D Solovyev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Anastasia A Gorshkova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Goethe University Frankfurt, Frankfurt am Main, 60433, Germany
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Department of Photonics, İzmir Institute of Technology, 35430, İzmir, Turkey
| | - Alexander P Savitsky
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, 119991 Russia, 121205, Moscow, Russia.
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Devos J, Van Dijck P, Van Genechten W. A multi-colour fluorogenic tag and its application in Candida albicans. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001451. [PMID: 38535895 PMCID: PMC10995450 DOI: 10.1099/mic.0.001451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Fluorescent proteins (FPs) have always been a crucial part of molecular research in life sciences, including the research into the human fungal pathogen Candida albicans, but have obvious shortcomings such as their relatively large size and long maturation time. However, the next generation of FPs overcome these issues and rely on the binding of a fluorogen for the protein to become fluorescently active. This generation of FPs includes the improved version of Fluorescence activating and Absorption Shifting Tag (iFAST). The binding between the fluorogen and the iFAST protein is reversible, thus resulting in reversible fluorescence. The fluorogens of iFAST are analogues of 4-hydroxylbenzylidene-rhodanine (HBR). These HBR analogues differ in spectral properties depending on functional group substitutions, which gives the iFAST system flexibility in terms of absorbance and emission maxima. In this work we describe and illustrate the application of iFAST as a protein tag and its reversible multi-colour characteristics in C. albicans.
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Affiliation(s)
- Jonas Devos
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium
| | - Wouter Van Genechten
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, 3001 Leuven, Belgium
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Lushpa VA, Baleeva NS, Goncharuk SA, Goncharuk MV, Arseniev AS, Baranov MS, Mineev KS. Spatial Structure of nanoFAST in the Apo State and in Complex with its Fluorogen HBR-DOM2. Int J Mol Sci 2022; 23:ijms231911361. [PMID: 36232662 PMCID: PMC9570328 DOI: 10.3390/ijms231911361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
NanoFAST is a fluorogen-activating protein and can be considered one of the smallest encodable fluorescent tags. Being a shortened variant of another fluorescent tag, FAST, nanoFAST works nicely only with one out of all known FAST ligands. This substantially limits the applicability of this protein. To find the reason for such a behavior, we investigated the spatial structure and dynamics of nanoFAST, both in the apo state and in the complex with its fluorogen molecule, using the solution NMR spectroscopy. We showed that the truncation of FAST did not affect the structure of the remaining part of the protein. Our data suggest that the deleted N-terminus of FAST destabilizes the C-terminal domain in the apo state. While it does not contact the fluorogen directly, it serves as a free energy reservoir that enhances the ligand binding propensity of the protein. The structure of nanoFAST/HBR-DOM2 complex reveals the atomistic details of nanoFAST interactions with the rhodanine-based ligands and explains the ligand specificity. NanoFAST selects ligands with the lowest dissociation constants, 2,5-disubstituted 4-hydroxybenzyldienerhodainines, which allow the non-canonical intermolecular CH–N hydrogen bonding and provide the optimal packing of the ligand within the hydrophobic cavity of the protein.
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Affiliation(s)
- Vladislav A. Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
| | - Nadezhda S. Baleeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
| | - Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | | | - Mikhail S. Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Correspondence: (M.S.B.); (K.S.M.)
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
- Correspondence: (M.S.B.); (K.S.M.)
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