1
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Plais L, Trachsel L, Scheuermann J. Asymmetry of Dual-Display DNA-Encoded Chemical Libraries. Bioconjug Chem 2024; 35:147-153. [PMID: 38266192 DOI: 10.1021/acs.bioconjchem.3c00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
While dual-display DNA-encoded chemical libraries (DELs) are increasingly employed for ligand discovery, some of their fundamental properties have not yet been studied in-depth. Aided with fluorescence polarization experiments, we demonstrate that dual-display DELs are intrinsically asymmetrical entities, and we deduce practical guidelines to perform better-informed on-DNA hit validation from these libraries.
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Affiliation(s)
- Louise Plais
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Louis Trachsel
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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2
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Bertran A, De Zotti M, Timmel CR, Di Valentin M, Bowen AM. Determining and controlling conformational information from orientationally selective light-induced triplet-triplet electron resonance spectroscopy for a set of bis-porphyrin rulers. Phys Chem Chem Phys 2024; 26:2589-2602. [PMID: 38170870 PMCID: PMC10793979 DOI: 10.1039/d3cp03454b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/31/2023] [Indexed: 01/05/2024]
Abstract
We recently reported a new technique, light-induced triplet-triplet electron resonance (LITTER) spectroscopy, which allows quantification of the dipolar interaction between the photogenerated triplet states of two chromophores. Here we carry out a systematic LITTER study, considering orientation selection by the detection pulses, of a series of bis-porphyrin model peptides with different porphyrin-porphyrin distances and relative orientations. Orientation-dependent analysis of the dipolar datasets yields conformational information of the molecules in frozen solution which is in good agreement with density functional theory predictions. Additionally, a fast partial orientational-averaging treatment produces distance distributions with minimized orientational artefacts. Finally, by direct comparison of LITTER data to double electron-electron resonance (DEER) measured on a system with Cu(II) coordinated into the porphyrins, we demonstrate the advantages of the LITTER technique over the standard DEER methodology. This is due to the remarkable spectroscopic properties of the photogenerated porphyrin triplet state. This work sets the basis for the use of LITTER in structural investigations of unmodified complex biological macromolecules, which could be combined with Förster resonance energy transfer and microscopy inside cells.
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Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Alice M Bowen
- The National Research Facility for Electron Paramagnetic Resonance, Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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3
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Lu YH, Jenkins MC, Richardson KG, Palui S, Islam MS, Tripathy J, Finn MG, Dickson RM. Sequential Two-Photon Delayed Fluorescence Anisotropy for Macromolecular Size Determination. J Phys Chem B 2023; 127:3861-3869. [PMID: 37096986 PMCID: PMC10165651 DOI: 10.1021/acs.jpcb.3c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Time-resolved fluorescence anisotropy (FA) uses the fluorophore depolarization rate to report on rotational diffusion, conformation changes, and intermolecular interactions in solution. Although FA is a rapid, sensitive, and nondestructive tool for biomolecular interaction studies, the short (∼ns) fluorescence lifetime of typical dyes largely prevents the application of FA on larger macromolecular species and complexes. By using triplet shelving and recovery of optical excitation, we introduce optically activated delayed fluorescence anisotropy (OADFA) measurements using sequential two-photon excitation, effectively stretching fluorescence anisotropy measurement times from the nanosecond scale to hundreds of microseconds. We demonstrate this scheme for measuring slow depolarization processes of large macromolecular complexes, derive a quantitative rate model, and perform Monte Carlo simulations to describe the depolarization process of OADFA at the molecular level. This setup has great potential to enable future biomacromolecular and colloidal studies.
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Affiliation(s)
- Yi-Han Lu
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Matthew C Jenkins
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Katherine G Richardson
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Sayan Palui
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Md Shariful Islam
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Jagnyaseni Tripathy
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Department of Physics, School of Applied Sciences, KIIT University, Bhubaneswar 751024, India
| | - M G Finn
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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4
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Nguyen TA, Puhl HL, Hines K, Liput DJ, Vogel SS. Binary-FRET reveals transient excited-state structure associated with activity-dependent CaMKII - NR2B binding and adaptation. Nat Commun 2022; 13:6335. [PMID: 36284097 PMCID: PMC9596428 DOI: 10.1038/s41467-022-33795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/03/2022] [Indexed: 12/25/2022] Open
Abstract
Synaptic functions are mediated and modulated by a coordinated choreography of protein conformational changes and interactions in response to intracellular calcium dynamics. Time-lapse Förster resonance energy transfer can be used to study the dynamics of both conformational changes and protein-protein interactions simultaneously under physiological conditions if two resonance energy transfer reactions can be multiplexed. Binary-FRET is a technique developed to independently monitor the dynamics of calcium-calmodulin dependent protein kinase-II catalytic-domain pair separation in the holoenzyme, and its role in establishing activity-dependent holoenzyme affinity for the NR2B binding fragment of the N-methyl-D-aspartate receptor. Here we show that a transient excited-state intermediate exists where paired catalytic-domains in the holoenzyme first separate prior to subsequent NR2B association. Additionally, at non-saturating free calcium concentrations, our multiplexed approach reveals that the holoenzyme exhibits a biochemical form of plasticity, calcium dependent adaptation of T-site ligand binding affinity.
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Affiliation(s)
- Tuan A Nguyen
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA
| | - Henry L Puhl
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA
| | - Kirk Hines
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA
| | - Daniel J Liput
- Laboratory for Integrative Neuroscience, NIAAA, NIH, Bethesda, USA
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA.
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5
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Mantovanelli L, Gaastra BF, Poolman B. Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell. CURRENT TOPICS IN MEMBRANES 2021; 88:1-54. [PMID: 34862023 DOI: 10.1016/bs.ctm.2021.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence-based sensors play a fundamental role in biological research. These sensors can be based on fluorescent proteins, fluorescent probes or they can be hybrid systems. The availability of a very large dataset of fluorescent molecules, both genetically encoded and synthetically produced, together with the structural insights on many sensing domains, allowed to rationally design a high variety of sensors, capable of monitoring both molecular and global changes in living cells or in in vitro systems. The advancements in the fluorescence-imaging field helped researchers to obtain a deeper understanding of how and where specific changes occur in a cell or in vitro by combining the readout of the fluorescent sensors with the spatial information provided by fluorescent microscopy techniques. In this review we give an overview of the state of the art in the field of fluorescent biosensors and fluorescence imaging techniques, and eventually guide the reader through the choice of the best combination of fluorescent tools and techniques to answer specific biological questions. We particularly focus on sensors for probing the bioenergetics and physicochemical status of the cell.
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Affiliation(s)
- Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands.
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6
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Díaz-García C, Renart ML, Poveda JA, Giudici AM, González-Ros JM, Prieto M, Coutinho A. Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements. Int J Mol Sci 2021; 22:ijms222111954. [PMID: 34769384 PMCID: PMC8584343 DOI: 10.3390/ijms222111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.
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Affiliation(s)
- Clara Díaz-García
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
- Correspondence: (M.L.R.); (A.C.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Manuel Prieto
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: (M.L.R.); (A.C.)
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7
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Zago G, Saavedra PHV, Keshari KR, Perry JSA. Immunometabolism of Tissue-Resident Macrophages - An Appraisal of the Current Knowledge and Cutting-Edge Methods and Technologies. Front Immunol 2021; 12:665782. [PMID: 34025667 PMCID: PMC8138590 DOI: 10.3389/fimmu.2021.665782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
Tissue-resident macrophages exist in unique environments, or niches, that inform their identity and function. There is an emerging body of literature suggesting that the qualities of this environment, such as the types of cells and debris they eat, the intercellular interactions they form, and the length of time spent in residence, collectively what we call habitare, directly inform their metabolic state. In turn, a tissue-resident macrophage’s metabolic state can inform their function, including whether they resolve inflammation and protect the host from excessive perturbations of homeostasis. In this review, we summarize recent work that seeks to understand the metabolic requirements for tissue-resident macrophage identity and maintenance, for how they respond to inflammatory challenges, and for how they perform homeostatic functions or resolve inflammatory insults. We end with a discussion of the emerging technologies that are enabling, or will enable, in situ study of tissue-resident macrophage metabolism.
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Affiliation(s)
- Giulia Zago
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Pedro H V Saavedra
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Kayvan R Keshari
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Justin S A Perry
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, United States
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8
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Bertran A, Henbest KB, De Zotti M, Gobbo M, Timmel CR, Di Valentin M, Bowen AM. Light-Induced Triplet-Triplet Electron Resonance Spectroscopy. J Phys Chem Lett 2021; 12:80-85. [PMID: 33306382 PMCID: PMC8016185 DOI: 10.1021/acs.jpclett.0c02884] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
We present a new technique, light-induced triplet-triplet electron resonance spectroscopy (LITTER), which measures the dipolar interaction between two photoexcited triplet states, enabling both the distance and angular distributions between the two triplet moieties to be determined on a nanometer scale. This is demonstrated for a model bis-porphyrin peptide that renders dipolar traces with strong orientation selection effects. Using simulations and density functional theory calculations, we extract distance distributions and relative orientations of the porphyrin moieties, allowing the dominant conformation of the peptide in a frozen solution to be identified. LITTER removes the requirement of current light-induced electron spin resonance pulse dipolar spectroscopy techniques to have a permanent paramagnetic moiety, becoming more suitable for in-cell applications and facilitating access to distance determination in unmodified macromolecular systems containing photoexcitable moieties. LITTER also has the potential to enable direct comparison with Förster resonance energy transfer and combination with microscopy inside cells.
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Affiliation(s)
- Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kevin B. Henbest
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marta De Zotti
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marina Gobbo
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Alice M. Bowen
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
- Department
of Chemistry and Photon Science Institute, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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9
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Akamatsu K, Shikazono N, Saito T. Fluorescence anisotropy study of radiation-induced DNA damage clustering based on FRET. Anal Bioanal Chem 2020; 413:1185-1192. [PMID: 33245399 DOI: 10.1007/s00216-020-03082-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/01/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022]
Abstract
A clustered DNA damage site (cluster), in which two or more lesions exist within a few helical turns, is believed to be a key factor determining the fate of a living cell exposed to a DNA damaging agent such as ionizing radiation. However, the structural details of a cluster such as the number of included lesions and their proximity are unknown. Herein, we develop a method to characterize a cluster by fluorescence anisotropy measurements based on Förster resonance energy transfer (homo-FRET). Plasmid DNA (pUC19) was irradiated with 2.0 and 0.52 MeV/u 4He2+, or 0.37 MeV/u 12C5+ ion beams (linear energy transfer: ~ 70, ~ 150, ~ 760 keV/μm, respectively) and 60Co γ-rays as a standard (~ 0.2 keV/μm) in the solid state. The irradiated DNA was labeled with an aminooxyl fluorophore (Alexa Fluor 488) to the aldehyde/ketone moieties such as apurinic/apyrimidinic sites. Homo-FRET analyses provided the apparent base separation values between lesions in a cluster produced by each ion beam track as 21.1, 19.4, and 18.7 base pairs. The production frequency of a cluster increases with increasing linear energy transfer of radiation. Our results demonstrate that homo-FRET analysis has the potential to discover the qualitative and the quantitative differences of the clusters produced not only by a variety of ionizing radiation but also by other DNA damaging agents.
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Affiliation(s)
- Ken Akamatsu
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, 619-0215, Kyoto, Japan.
| | - Naoya Shikazono
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, 619-0215, Kyoto, Japan
| | - Takeshi Saito
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan, Osaka, 590-0494, Japan
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10
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Lou J, Priest DG, Solano A, Kerjouan A, Hinde E. Spatiotemporal dynamics of 53BP1 dimer recruitment to a DNA double strand break. Nat Commun 2020; 11:5776. [PMID: 33188174 PMCID: PMC7666136 DOI: 10.1038/s41467-020-19504-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 10/15/2020] [Indexed: 01/08/2023] Open
Abstract
Tumor suppressor p53-binding protein 1 (53BP1) is a DNA repair protein essential for the detection, assessment, and resolution of DNA double strand breaks (DSBs). The presence of a DSB is signaled to 53BP1 via a local histone modification cascade that triggers the binding of 53BP1 dimers to chromatin flanking this type of lesion. While biochemical studies have established that 53BP1 exists as a dimer, it has never been shown in a living cell when or where 53BP1 dimerizes upon recruitment to a DSB site, or upon arrival at this nuclear location, how the DSB histone code to which 53BP1 dimers bind regulates retention and self-association into higher-order oligomers. Thus, here in live-cell nuclear architecture we quantify the spatiotemporal dynamics of 53BP1 oligomerization during a DSB DNA damage response by coupling fluorescence fluctuation spectroscopy (FFS) with the DSB inducible via AsiSI cell system (DIvA). From adopting this multiplexed approach, we find that preformed 53BP1 dimers relocate from the nucleoplasm to DSB sites, where consecutive recognition of ubiquitinated lysine 15 of histone 2A (H2AK15ub) and di-methylated lysine 20 of histone 4 (H4K20me2), leads to the assembly of 53BP1 oligomers and a mature 53BP1 foci structure.
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Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - David G Priest
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashleigh Solano
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Adèle Kerjouan
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia. .,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
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11
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Howe ME, Barbour NA, Garcia RV, Garcia-Garibay MA. Fluorescence Anisotropy Decay of Molecular Rotors with Acene Rotators in Viscous Solution. J Org Chem 2020; 85:6872-6877. [DOI: 10.1021/acs.joc.9b03398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Morgan E. Howe
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Nicole A. Barbour
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Ronnie V. Garcia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Miguel A. Garcia-Garibay
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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12
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Althumairy D, Postal K, Barisas BG, Nunes GG, Roess DA, Crans DC. Polyoxometalates function as indirect activators of a G protein-coupled receptor. Metallomics 2020; 12:1044-1061. [DOI: 10.1039/d0mt00044b] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A series of multivalent polyoxovanadates were found to activate signaling of a G protein coupled receptor, the luteinizing hormone receptor.
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Affiliation(s)
- Duaa Althumairy
- Cell and Molecular Biology Program
- Colorado State University
- Fort Collins
- USA
- Department of Biological Sciences
| | - Kahoana Postal
- Department of Chemistry
- Colorado State University
- Fort Collins
- USA
- Department of Chemistry
| | - B. George Barisas
- Cell and Molecular Biology Program
- Colorado State University
- Fort Collins
- USA
- Department of Chemistry
| | - Giovana G. Nunes
- Department of Chemistry
- Universidade Federal do Paraná
- Curitiba
- Brazil
| | - Deborah A. Roess
- Cell and Molecular Biology Program
- Colorado State University
- Fort Collins
- USA
- Department of Biomedical Sciences, Colorado State University
| | - Debbie C. Crans
- Cell and Molecular Biology Program
- Colorado State University
- Fort Collins
- USA
- Department of Chemistry
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13
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Vinegoni C, Feruglio PF, Gryczynski I, Mazitschek R, Weissleder R. Fluorescence anisotropy imaging in drug discovery. Adv Drug Deliv Rev 2019; 151-152:262-288. [PMID: 29410158 PMCID: PMC6072632 DOI: 10.1016/j.addr.2018.01.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Non-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting has proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs.
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Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Ignacy Gryczynski
- University of North Texas Health Science Center, Institute for Molecular Medicine, Fort Worth, TX, United States
| | - Ralph Mazitschek
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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14
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Algar WR, Hildebrandt N, Vogel SS, Medintz IL. FRET as a biomolecular research tool — understanding its potential while avoiding pitfalls. Nat Methods 2019; 16:815-829. [DOI: 10.1038/s41592-019-0530-8] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 07/15/2019] [Indexed: 01/14/2023]
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15
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Hochreiter B, Kunze M, Moser B, Schmid JA. Advanced FRET normalization allows quantitative analysis of protein interactions including stoichiometries and relative affinities in living cells. Sci Rep 2019; 9:8233. [PMID: 31160659 PMCID: PMC6547726 DOI: 10.1038/s41598-019-44650-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
FRET (Fluorescence Resonance Energy Transfer) measurements are commonly applied to proof protein-protein interactions. However, standard methods of live cell FRET microscopy and signal normalization only allow a principle assessment of mutual binding and are unable to deduce quantitative information of the interaction. We present an evaluation and normalization procedure for 3-filter FRET measurements, which reflects the process of complex formation by plotting FRET-saturation curves. The advantage of this approach relative to traditional signal normalizations is demonstrated by mathematical simulations. Thereby, we also identify the contribution of critical parameters such as the total amount of donor and acceptor molecules and their molar ratio. When combined with a fitting procedure, this normalization facilitates the extraction of key properties of protein complexes such as the interaction stoichiometry or the apparent affinity of the binding partners. Finally, the feasibility of our method is verified by investigating three exemplary protein complexes. Altogether, our approach offers a novel method for a quantitative analysis of protein interactions by 3-filter FRET microscopy, as well as flow cytometry. To facilitate the application of this method, we created macros and routines for the programs ImageJ, R and MS-Excel, which we make publicly available.
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Affiliation(s)
- Bernhard Hochreiter
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Markus Kunze
- Medical University Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Vienna, Austria
| | - Bernhard Moser
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria
| | - Johannes A Schmid
- Medical University Vienna, Center for Physiology and Pharmacology, Institute for Vascular Biology and Thrombosis Research, Vienna, Austria.
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16
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Remmler D, Schwaar T, Pickhardt M, Donth C, Mandelkow E, Weller M, Börner H. On the way to precision formulation additives: 2D-screening to select solubilizers with tailored host and release capabilities. J Control Release 2018; 285:96-105. [DOI: 10.1016/j.jconrel.2018.06.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/14/2018] [Accepted: 06/26/2018] [Indexed: 02/04/2023]
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17
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Kim SY, Arai Y, Tani T, Takatsuka H, Saito Y, Kawashima T, Kawakami S, Miyawaki A, Nagai T. Simultaneous imaging of multiple cellular events using high-accuracy fluorescence polarization microscopy. Microscopy (Oxf) 2018; 66:110-119. [PMID: 28043995 DOI: 10.1093/jmicro/dfw110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/16/2016] [Indexed: 11/13/2022] Open
Abstract
Förster resonance energy transfer (FRET) has been widely used to design indicators for biomolecules. Conventional FRET-based indicators enable quantitative measurements of analyzes by calculating the ratio between donor and acceptor fluorophores. However, such 'hetero-FRET'-based indicators, which use multiple differently colored fluorophores, restrict the simultaneous use of other colors of fluorescent molecules. To overcome this problem, we developed a 'homo-FRET'-based Ca2+ indicator, W-Cameleon, composed of two identical yellow fluorescent proteins. The binding of Ca2+ to the indicator induces a change in FRET efficiency, which in turn transforms into changes in fluorescence anisotropy. Given that the fluorescence polarization is depolarized by light passing through a high numerical aperture lens and reflecting on a dichroic mirror, we also developed a microscopy technique that reliably detects fluorescence anisotropy with high precision. Our design is aided by photonic-crystal technology, to compensate for the fluorescence depolarization. We thereby succeeded in the simultaneous visualization of three individual intracellular events by using three different fluorescent indicators. Our system may contribute to an expansion of the number of events that can be observed, which will enable a more quantitative understanding of biological phenomena.
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Affiliation(s)
- Sang-Yeob Kim
- Laboratory for Nanosystems Physiology, Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Yoshiyuki Arai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tomomi Tani
- Laboratory for Nanosystems Physiology, Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Hirofumi Takatsuka
- Scientific Solutions Product Development Division, Product Development Department, Olympus Corporation, 2951 Ishikawa-cho, Hachijoji-shi, Tokyo 192-8507, Japan
| | - Yoshiharu Saito
- Scientific Solutions Product Development Division, Product Development Department, Olympus Corporation, 2951 Ishikawa-cho, Hachijoji-shi, Tokyo 192-8507, Japan
| | - Takayuki Kawashima
- Photonic Lattice, Inc., ICR 2F, 6-6-3 Minami-Yoshinari, Aoba, Sendai, Miyagi 989-3204, Japan
| | - Shojiro Kawakami
- Photonic Lattice, Inc., ICR 2F, 6-6-3 Minami-Yoshinari, Aoba, Sendai, Miyagi 989-3204, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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18
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Nolan R, Alvarez LA, Griffiths SC, Elegheert J, Siebold C, Padilla-Parra S. Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software. J Vis Exp 2018:58157. [PMID: 30080195 PMCID: PMC6126508 DOI: 10.3791/58157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be employed using a conventional confocal microscope equipped with digital detectors. A protocol for the use of the technique in vitro is shown by means of a use case where number and brightness can be seen to accurately quantify the oligomeric state of mVenus-labelled FKBP12F36V before and after the addition of the dimerizing drug AP20187. The importance of using the correct microscope acquisition parameters and the correct data preprocessing and analysis methods are discussed. In particular, the importance of the choice of photobleaching correction is stressed. This inexpensive method can be employed to study protein-protein interactions in many biological contexts.
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Affiliation(s)
- Rory Nolan
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford
| | - Luis A Alvarez
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford
| | - Samuel C Griffiths
- Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford
| | - Jonathan Elegheert
- Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford
| | - Sergi Padilla-Parra
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford; Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford; Dynamic Structural Virology Group, Biocruces Health Research Centre; IKERBASQUE, Basque Foundation for Science;
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19
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Nguyen TA, Puhl HL, Pham AK, Vogel SS. Auto-FPFA: An Automated Microscope for Characterizing Genetically Encoded Biosensors. Sci Rep 2018; 8:7374. [PMID: 29743504 PMCID: PMC5943267 DOI: 10.1038/s41598-018-25689-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/26/2018] [Indexed: 12/14/2022] Open
Abstract
Genetically encoded biosensors function by linking structural change in a protein construct, typically tagged with one or more fluorescent proteins, to changes in a biological parameter of interest (such as calcium concentration, pH, phosphorylation-state, etc.). Typically, the structural change triggered by alterations in the bio-parameter is monitored as a change in either fluorescent intensity, or lifetime. Potentially, other photo-physical properties of fluorophores, such as fluorescence anisotropy, molecular brightness, concentration, and lateral and/or rotational diffusion could also be used. Furthermore, while it is likely that multiple photo-physical attributes of a biosensor might be altered as a function of the bio-parameter, standard measurements monitor only a single photo-physical trait. This limits how biosensors are designed, as well as the accuracy and interpretation of biosensor measurements. Here we describe the design and construction of an automated multimodal-microscope. This system can autonomously analyze 96 samples in a micro-titer dish and for each sample simultaneously measure intensity (photon count), fluorescence lifetime, time-resolved anisotropy, molecular brightness, lateral diffusion time, and concentration. We characterize the accuracy and precision of this instrument, and then demonstrate its utility by characterizing three types of genetically encoded calcium sensors as well as a negative control.
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Affiliation(s)
- Tuan A Nguyen
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - Henry L Puhl
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - An K Pham
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - Steven S Vogel
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA.
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20
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Saha S, Majhi D, Bhattacharyya K, Preeyanka N, Datta A, Sarkar M. Evidence of homo-FRET in quantum dot–dye heterostructured assembly. Phys Chem Chem Phys 2018; 20:9523-9535. [DOI: 10.1039/c7cp07233c] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evidence of homo-FRET in inorganic–organic hybrid hetero-structured assembly is demonstrated
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Affiliation(s)
- Samyabrata Saha
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar
- India
| | - Debashis Majhi
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar
- India
| | | | - Naupada Preeyanka
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar
- India
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Moloy Sarkar
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar
- India
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21
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Influenza A Virus Virulence Depends on Two Amino Acids in the N-Terminal Domain of Its NS1 Protein To Facilitate Inhibition of the RNA-Dependent Protein Kinase PKR. J Virol 2017; 91:JVI.00198-17. [PMID: 28250123 DOI: 10.1128/jvi.00198-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/20/2017] [Indexed: 12/22/2022] Open
Abstract
The RNA-dependent protein kinase (PKR) has broad antiviral activity inducing translational shutdown of viral and cellular genes and is therefore targeted by various viral proteins to facilitate pathogen propagation. The pleiotropic NS1 protein of influenza A virus acts as silencer of PKR activation and ensures high-level viral replication and virulence. However, the exact manner of this inhibition remains controversial. To elucidate the structural requirements within the NS1 protein for PKR inhibition, we generated a set of mutant viruses, identifying highly conserved arginine residues 35 and 46 within the NS1 N terminus as being most critical not only for binding to and blocking activation of PKR but also for efficient virus propagation. Biochemical and Förster resonance energy transfer (FRET)-based interaction studies showed that mutation of R35 or R46 allowed formation of NS1 dimers but eliminated any detectable binding to PKR as well as to double-stranded RNA (dsRNA). Using in vitro and in vivo approaches to phenotypic restoration, we demonstrated the essential role of the NS1 N terminus for blocking PKR. The strong attenuation conferred by NS1 mutation R35A or R46A was substantially alleviated by stable knockdown of PKR in human cells. Intriguingly, both NS1 mutant viruses did not trigger any signs of disease in PKR+/+ mice, but replicated to high titers in lungs of PKR-/- mice and caused lethal infections. These data not only establish the NS1 N terminus as highly critical for neutralization of PKR's antiviral activity but also identify this blockade as an indispensable contribution of NS1 to the viral life cycle.IMPORTANCE Influenza A virus inhibits activation of the RNA-dependent protein kinase (PKR) by means of its nonstructural NS1 protein, but the underlying mode of inhibition is debated. Using mutational analysis, we identified arginine residues 35 and 46 within the N-terminal NS1 domain as highly critical for binding to and functional silencing of PKR. In addition, our data show that this is a main activity of amino acids 35 and 46, as the strong attenuation of corresponding mutant viruses in human cells was rescued to a large extent by lowering of PKR expression levels. Significantly, this corresponded with restoration of viral virulence for NS1 R35A and R46A mutant viruses in PKR-/- mice. Therefore, our data establish a model in which the NS1 N-terminal domain engages in a binding interaction to inhibit activation of PKR and ensure efficient viral propagation and virulence.
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22
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Haney CM, Cleveland CL, Wissner RF, Owei L, Robustelli J, Daniels M, Canyurt M, Rodriguez P, Ischiropoulos H, Baumgart T, Petersson EJ. Site-Specific Fluorescence Polarization for Studying the Disaggregation of α-Synuclein Fibrils by Small Molecules. Biochemistry 2017; 56:683-691. [PMID: 28045494 PMCID: PMC5520965 DOI: 10.1021/acs.biochem.6b01060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fibrillar aggregates of the protein α-synuclein (αS) are one of the hallmarks of Parkinson's disease. Here, we show that measuring the fluorescence polarization (FP) of labels at several sites on αS allows one to monitor changes in the local dynamics of the protein after binding to micelles or vesicles, and during fibril formation. Most significantly, these site-specific FP measurements provide insight into structural remodeling of αS fibrils by small molecules and have the potential for use in moderate-throughput screens to identify small molecules that could be used to treat Parkinson's disease.
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Affiliation(s)
- Conor M. Haney
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
| | - Christina L. Cleveland
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
| | - Rebecca F. Wissner
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
| | - Lily Owei
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
| | - Jaclyn Robustelli
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
| | - Malcolm Daniels
- Pharmacology Graduate Group; University of Pennsylvania; 3400 Civic Center Blvd, Philadelphia, PA 19104
| | | | | | - Harry Ischiropoulos
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104
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23
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Soleimaninejad H, Chen MZ, Lou X, Smith TA, Hong Y. Measuring macromolecular crowding in cells through fluorescence anisotropy imaging with an AIE fluorogen. Chem Commun (Camb) 2017; 53:2874-2877. [DOI: 10.1039/c6cc09916e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report a new strategy that allows spatiotemporal visualization of the macromolecular crowding effect in cells.
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Affiliation(s)
| | - Moore Z. Chen
- School of Chemistry
- The University of Melbourne
- Parkville VIC 3010
- Australia
| | - Xiaoding Lou
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
| | - Trevor A. Smith
- School of Chemistry
- The University of Melbourne
- Parkville VIC 3010
- Australia
| | - Yuning Hong
- School of Chemistry
- The University of Melbourne
- Parkville VIC 3010
- Australia
- Department of Chemistry and Physics
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24
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Visser AJWG, Westphal AH, Skakun VV, Borst JW. GFP as potential cellular viscosimeter. Methods Appl Fluoresc 2016; 4:035002. [PMID: 28355162 DOI: 10.1088/2050-6120/4/3/035002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The molecular dimensions of proteins such as green fluorescent protein (GFP) are large as compared to the ones of solvents like water or glycerol. The microscopic viscosity, which determines the resistance to diffusion of, e.g. GFP, is then the same as that determined from the resistance of the solvent to flow, which is known as macroscopic viscosity. GFP in water/glycerol mixtures senses this macroscopic viscosity, because the translational and rotational diffusion coefficients are proportional to the reciprocal value of the viscosity as predicted by the Stokes-Einstein equations. To test this hypothesis, we have performed time-resolved fluorescence anisotropy (reporting on rotational diffusion) and fluorescence correlation spectroscopy (reporting on translational diffusion) experiments of GFP in water/glycerol mixtures. When the solvent also contains macromolecules of similar or larger dimensions as GFP, the microscopic and macroscopic viscosities can be markedly different and the Stokes-Einstein relations must be adapted. It was established from previous dynamic fluorescence spectroscopy observations of diffusing proteins with dextran polysaccharides as co-solvents (Lavalette et al 2006 Eur. Biophys. J. 35 517-22), that rotation and translation sense a different microscopic viscosity, in which the one arising from rotation is always less than that from translation. A microscopic viscosity parameter is defined that depends on scaling factors between GFP and its immediate environment. The direct consequence is discussed for two reported diffusion coefficients of GFP in living cells.
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Affiliation(s)
- Antonie J W G Visser
- Laboratory of Biochemistry, Microspectroscopy Centre, Wageningen University, PO Box 8128, 6700 ET Wageningen, The Netherlands
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25
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Orrego AH, García C, Mancheño JM, Guisán JM, Lillo MP, López-Gallego F. Two-Photon Fluorescence Anisotropy Imaging to Elucidate the Dynamics and the Stability of Immobilized Proteins. J Phys Chem B 2016; 120:485-91. [DOI: 10.1021/acs.jpcb.5b12385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Alejandro H. Orrego
- Enzymatic
Engineering Group, Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Carolina García
- Fluorescence
Molecular Biophysics Group, Instituto Química Física
“Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - José M. Mancheño
- Crystallography
and Structural Biology Group, Instituto Química Física
“Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Jose M. Guisán
- Enzymatic
Engineering Group, Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - M. Pilar Lillo
- Fluorescence
Molecular Biophysics Group, Instituto Química Física
“Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Fernando López-Gallego
- Heterogeneus
Biocatalysis Group, CIC BiomaGUNE, Pase Miramon 182, 20009 San Sebastian-Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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26
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Sahasrabudhe A, Ghate K, Mutalik S, Jacob A, Ghose A. Formin 2 regulates the stabilization of filopodial tip adhesions in growth cones and affects neuronal outgrowth and pathfinding in vivo. Development 2015; 143:449-60. [PMID: 26718007 DOI: 10.1242/dev.130104] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/23/2015] [Indexed: 12/28/2022]
Abstract
Growth cone filopodia are actin-based mechanosensory structures that are essential for chemoreception and the generation of contractile forces necessary for directional motility. However, little is known about the influence of filopodial actin structures on substrate adhesion and filopodial contractility. Formin 2 (Fmn2) localizes along filopodial actin bundles and its depletion does not affect filopodia initiation or elongation. However, Fmn2 activity is required for filopodial tip adhesion maturation and the ability of filopodia to generate traction forces. Dysregulation of filopodia in Fmn2-depleted neurons leads to compromised growth cone motility. Additionally, in mouse fibroblasts, Fmn2 regulates ventral stress fiber assembly and affects the stability of focal adhesions. In the developing chick spinal cord, Fmn2 activity is required cell-autonomously for the outgrowth and pathfinding of spinal commissural neurons. Our results reveal an unanticipated function for Fmn2 in neural development. Fmn2 regulates structurally diverse bundled actin structures, parallel filopodial bundles in growth cones and anti-parallel stress fibers in fibroblasts, in turn modulating the stability of substrate adhesions. We propose Fmn2 as a mediator of actin bundle integrity, enabling efficient force transmission to the adhesion sites.
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Affiliation(s)
- Abhishek Sahasrabudhe
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhaba Road, Pune 411008, India
| | - Ketakee Ghate
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhaba Road, Pune 411008, India
| | - Sampada Mutalik
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhaba Road, Pune 411008, India
| | - Ajesh Jacob
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhaba Road, Pune 411008, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhaba Road, Pune 411008, India
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27
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Yi NY, He Q, Caligan TB, Smith GR, Forsberg LJ, Brenman JE, Sexton JZ. Development of a Cell-Based Fluorescence Polarization Biosensor Using Preproinsulin to Identify Compounds That Alter Insulin Granule Dynamics. Assay Drug Dev Technol 2015; 13:558-69. [PMID: 26505612 PMCID: PMC4955689 DOI: 10.1089/adt.2015.665] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Diabetes currently affects 9.3% of the U.S. population totaling $245 billion annually in U.S. direct and indirect healthcare costs. Current therapies for diabetes are limited in their ability to control blood glucose and/or enhance insulin sensitivity. Therefore, innovative and efficacious therapies for diabetes are urgently needed. Herein we describe a fluorescent insulin reporter system (preproinsulin-mCherry, PPI-mCherry) that tracks live-cell insulin dynamics and secretion in pancreatic β-cells with utility for high-content assessment of real-time insulin dynamics. Additionally, we report a new modality for sensing insulin granule packaging in conventional high-throughput screening (HTS), using a hybrid cell-based fluorescence polarization (FP)/internal FRET biosensor using the PPI-mCherry reporter system. We observed that bafilomycin, a vacuolar H(+) ATPase inhibitor and inhibitor of insulin granule formation, significantly increased mCherry FP in INS-1 cells with PPI-mCherry. Partial least squares regression analysis demonstrated that an increase of FP by bafilomycin is significantly correlated with a decrease in granularity of PPI-mCherry signal in the cells. The increased FP by bafilomycin is due to inhibition of self-Förster resonant energy transfer (homo-FRET) caused by the increased mCherry intermolecular distance. FP substantially decreases when insulin is tightly packaged in the granules, and the homo-FRET decreases when insulin granule packaging is inhibited, resulting in increased FP. We performed pilot HTS of 1782 FDA-approved small molecules and natural products from Prestwick and Enzo chemical libraries resulting in an overall Z'-factor of 0.52 ± 0.03, indicating the suitability of this biosensor for HTS. This novel biosensor enables live-cell assessment of protein-protein interaction/protein aggregation in live cells and is compatible with conventional FP plate readers.
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Affiliation(s)
- Na Young Yi
- Biomanufacturing Research Institute and Technology Enterprise, Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina
| | - Qingping He
- Biomanufacturing Research Institute and Technology Enterprise, Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina
| | - Thomas B. Caligan
- Biomanufacturing Research Institute and Technology Enterprise, Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina
| | - Ginger R. Smith
- Biomanufacturing Research Institute and Technology Enterprise, Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina
| | - Lawrence J. Forsberg
- The Neuroscience Center and Department of Cell Biology & Physiology, UNC Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jay E. Brenman
- The Neuroscience Center and Department of Cell Biology & Physiology, UNC Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jonathan Z. Sexton
- Biomanufacturing Research Institute and Technology Enterprise, Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina
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28
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Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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Warren SC, Margineanu A, Katan M, Dunsby C, French PMW. Homo-FRET Based Biosensors and Their Application to Multiplexed Imaging of Signalling Events in Live Cells. Int J Mol Sci 2015; 16:14695-716. [PMID: 26133241 PMCID: PMC4519867 DOI: 10.3390/ijms160714695] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/20/2022] Open
Abstract
Multiplexed imaging of Förster Resonance Energy Transfer (FRET)-based biosensors potentially presents a powerful approach to monitoring the spatio-temporal correlation of signalling pathways within a single live cell. Here, we discuss the potential of homo-FRET based biosensors to facilitate multiplexed imaging. We demonstrate that the homo-FRET between pleckstrin homology domains of Akt (Akt-PH) labelled with mCherry may be used to monitor 3'-phosphoinositide accumulation in live cells and show how global analysis of time resolved fluorescence anisotropy measurements can be used to quantify this accumulation. We further present multiplexed imaging readouts of calcium concentration, using fluorescence lifetime measurements of TN-L15-a CFP/YFP based hetero-FRET calcium biosensor-with 3'-phosphoinositide accumulation.
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Affiliation(s)
- Sean C Warren
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Anca Margineanu
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Matilda Katan
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
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Devauges V, Matthews DR, Aluko J, Nedbal J, Levitt JA, Poland SP, Coban O, Weitsman G, Monypenny J, Ng T, Ameer-Beg SM. Steady-state acceptor fluorescence anisotropy imaging under evanescent excitation for visualisation of FRET at the plasma membrane. PLoS One 2014; 9:e110695. [PMID: 25360776 PMCID: PMC4215982 DOI: 10.1371/journal.pone.0110695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/15/2014] [Indexed: 11/22/2022] Open
Abstract
We present a novel imaging system combining total internal reflection fluorescence (TIRF) microscopy with measurement of steady-state acceptor fluorescence anisotropy in order to perform live cell Förster Resonance Energy Transfer (FRET) imaging at the plasma membrane. We compare directly the imaging performance of fluorescence anisotropy resolved TIRF with epifluorescence illumination. The use of high numerical aperture objective for TIRF required correction for induced depolarization factors. This arrangement enabled visualisation of conformational changes of a Raichu-Cdc42 FRET biosensor by measurement of intramolecular FRET between eGFP and mRFP1. Higher activity of the probe was found at the cell plasma membrane compared to intracellularly. Imaging fluorescence anisotropy in TIRF allowed clear differentiation of the Raichu-Cdc42 biosensor from negative control mutants. Finally, inhibition of Cdc42 was imaged dynamically in live cells, where we show temporal changes of the activity of the Raichu-Cdc42 biosensor.
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Affiliation(s)
- Viviane Devauges
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Daniel R. Matthews
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Justin Aluko
- Department of Physics, King's College London, London, United Kingdom
| | - Jakub Nedbal
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James A. Levitt
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Simon P. Poland
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Oana Coban
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Gregory Weitsman
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James Monypenny
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Tony Ng
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Simon M. Ameer-Beg
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
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Jiang L, Saavedra AN, Way G, Alanis J, Kung R, Li J, Xiang W, Liao J. Specific substrate recognition and thioester intermediate determinations in ubiquitin and SUMO conjugation cascades revealed by a high-sensitive FRET assay. MOLECULAR BIOSYSTEMS 2014; 10:778-86. [DOI: 10.1039/c3mb70155g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Kim SE, Huang H, Zhao M, Zhang X, Zhang A, Semonov MV, MacDonald BT, Zhang X, Garcia Abreu J, Peng L, He X. Wnt stabilization of β-catenin reveals principles for morphogen receptor-scaffold assemblies. Science 2013; 340:867-70. [PMID: 23579495 DOI: 10.1126/science.1232389] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Wnt signaling stabilizes β-catenin through the LRP6 receptor signaling complex, which antagonizes the β-catenin destruction complex. The Axin scaffold and associated glycogen synthase kinase-3 (GSK3) have central roles in both assemblies, but the transduction mechanism from the receptor to the destruction complex is contentious. We report that Wnt signaling is governed by phosphorylation regulation of the Axin scaffolding function. Phosphorylation by GSK3 kept Axin activated ("open") for β-catenin interaction and poised for engagement of LRP6. Formation of the Wnt-induced LRP6-Axin signaling complex promoted Axin dephosphorylation by protein phosphatase-1 and inactivated ("closed") Axin through an intramolecular interaction. Inactivation of Axin diminished its association with β-catenin and LRP6, thereby inhibiting β-catenin phosphorylation and enabling activated LRP6 to selectively recruit active Axin for inactivation reiteratively. Our findings reveal mechanisms for scaffold regulation and morphogen signaling.
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Affiliation(s)
- Sung-Eun Kim
- F. M. Kirby Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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34
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Blakeley BD, DePorter SM, Mohan U, Burai R, Tolbert BS, McNaughton BR. Methods for identifying and characterizing interactions involving RNA. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Cambi A, Lidke DS. Nanoscale membrane organization: where biochemistry meets advanced microscopy. ACS Chem Biol 2012; 7:139-49. [PMID: 22004174 DOI: 10.1021/cb200326g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Understanding the molecular mechanisms that shape an effective cellular response is a fundamental question in biology. Biochemical measurements have revealed critical information about the order of protein-protein interactions along signaling cascades but lack the resolution to determine kinetics and localization of interactions on the plasma membrane. Furthermore, the local membrane environment influences membrane receptor distributions and dynamics, which in turn influences signal transduction. To measure dynamic protein interactions and elucidate the consequences of membrane architecture interplay, direct measurements at high spatiotemporal resolution are needed. In this review, we discuss the biochemical principles regulating membrane nanodomain formation and protein function, ranging from the lipid nanoenvironment to the cortical cytoskeleton. We also discuss recent advances in fluorescence microscopy that are making it possible to quantify protein organization and biochemical events at the nanoscale in the living cell membrane.
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Affiliation(s)
- Alessandra Cambi
- Department of Tumor Immunology,
Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Diane S. Lidke
- Department of Pathology and
Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States
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Storti B, Bizzarri R, Cardarelli F, Beltram F. Intact microtubules preserve transient receptor potential vanilloid 1 (TRPV1) functionality through receptor binding. J Biol Chem 2012; 287:7803-11. [PMID: 22262838 DOI: 10.1074/jbc.m111.332296] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transient receptor potential cation channel subfamily V member 1 (TRPV1) is a protein currently under scrutiny as a pharmacological target for pain management therapies. Recently, the role of TRPV1-microtubule interaction in transducing nociception stimuli to cells by cytoskeletal rearrangement was proposed. In this work, we investigate TRPV1-microtubule interaction in living cells under the resting or activated state of TRPV1, as well as in presence of structurally intact or depolymerized cytoskeletal microtubules. We combined a toolbox of high resolution/high sensitivity fluorescence imaging techniques (such as FRET, correlation spectroscopy, and fluorescence anisotropy) to monitor TRPV1 aggregation status, membrane mobility, and interaction with microtubules. We found that TRPV1 is a dimeric membrane protein characterized by two populations with different diffusion properties in basal condition. After stimulation with resiniferatoxin, TRPV1 dimers tetramerize. The tetramers and the slower population of TRPV1 dimers bind dynamically to intact microtubules but not to tubulin dimers. Upon microtubule disassembly, the interaction with TRPV1 is lost thereby inducing receptor self-aggregation with partial loss of functionality. Intact microtubules play an essential role in maintaining TRPV1 functionality toward activation stimuli. This previously undisclosed property mirrors the recently reported role of TRPV1 in modulating microtubule assembly/disassembly and suggests the participation of these two players in a feedback cycle linking nociception and cytoskeletal remodeling.
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Affiliation(s)
- Barbara Storti
- National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza S. Silvestro 12, 56127 Pisa, Italy.
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37
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Loura LMS, Prieto M. FRET in Membrane Biophysics: An Overview. Front Physiol 2011; 2:82. [PMID: 22110442 PMCID: PMC3216123 DOI: 10.3389/fphys.2011.00082] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/26/2011] [Indexed: 12/31/2022] Open
Abstract
Förster resonance energy transfer (FRET), in most applications used as a “spectroscopic ruler,” allows an easy determination of the donor-acceptor intermolecular distance. However, the situation becomes complex in membranes, since around each donor there is an ensemble of acceptors at non-correlated distances. In this review, state-of-the-art methodologies for this situation are presented, usually involving time-resolved data and model fitting. This powerful approach can be used to study the occurrence of phase separation (“rafts” or other type of domains), allowing their detection as well as size evaluation. Formalisms for studying lipid–protein and protein–protein interactions according to specific topologies are also addressed. The advantages and added complexity of a specific type of FRET (energy homotransfer or energy migration) are described, as well as applications of FRET under the microscope.
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Affiliation(s)
- Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra Coimbra, Portugal
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38
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Kozer N, Henderson C, Jackson JT, Nice EC, Burgess AW, Clayton AHA. Evidence for extended YFP-EGFR dimers in the absence of ligand on the surface of living cells. Phys Biol 2011; 8:066002. [PMID: 21946082 DOI: 10.1088/1478-3975/8/6/066002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a member of the erbB tyrosine kinase family of receptors. Structural studies have revealed two distinct conformations of the ectodomain of the EGFR: a compact, tethered, conformation and an untethered extended conformation. In the context of a monomer-dimer transition model, ligand binding is thought to untether the monomeric receptor leading to exposure of a dimerization arm which then facilitates receptor dimerization, kinase activation and signaling. For receptors directed orthogonal to the local plane of the membrane surface, this would lead to a large change in the distance of the receptor N-terminus from the membrane surface. To investigate this experimentally, we produced stable BaF/3 cell lines expressing a biochemically functional yellow fluorescent protein (YFP)-EGFR chimera and determined the vertical separation of the N-terminal YFP tag from the membrane using fluorescence resonance energy transfer (FRET) techniques. Homo-FRET/rFLIM was employed to determine the presence of unliganded dimers and to measure the average distance between the N-terminal tags in those dimers. The results suggest that EGF-induced activation occurs within or between pre-formed and extended dimers with very little change in the extension of the N-terminii from the membrane surface. These results provide constraints on possible models for EGFR activation.
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Affiliation(s)
- Noga Kozer
- Centre for Microphotonics, Swinburne University of Technology, Victoria, Australia
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39
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Miyawaki A. Development of Probes for Cellular Functions Using Fluorescent Proteins and Fluorescence Resonance Energy Transfer. Annu Rev Biochem 2011; 80:357-73. [DOI: 10.1146/annurev-biochem-072909-094736] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Atsushi Miyawaki
- Laboratory for Cell Function and Dynamics, Brain Science Institute, RIKEN, Wako-city, Saitama 351-0198, Japan;
- Life Function and Dynamics, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Wako-city, Saitama 351-0198, Japan
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40
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Characterization of Förster resonance energy transfer in a botulinum neurotoxin protease assay. Anal Biochem 2011; 413:43-9. [DOI: 10.1016/j.ab.2011.01.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/28/2011] [Accepted: 01/29/2011] [Indexed: 11/22/2022]
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41
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Kozer N, Kelly MP, Orchard S, Burgess AW, Scott AM, Clayton AHA. Differential and synergistic effects of epidermal growth factor receptor antibodies on unliganded ErbB dimers and oligomers. Biochemistry 2011; 50:3581-90. [PMID: 21495621 DOI: 10.1021/bi101785h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibodies directed against the epidermal growth factor receptor (EGFR) offer a potentially powerful therapeutic approach against cancers driven by the EGFR pathway. EGFR antibodies are believed to halt cell surface activation by blocking ligand-induced receptor tyrosine kinase activation, i.e., ligand binding, a change in conformation, or the monomer-dimer transition. In this work, we demonstrate that wild-type EGFR and the truncated de2-7-EGFR (tumor-associated mutant) formed unliganded homo-oligomers and examined the effects of two clinically relevant antibodies on the conformation and quaternary state of these ligand-free EGFR oligomers on the surface of cells. The EGFR antibodies were mAb528, a ligand-blocking antibody that binds domain III, and mAb806, a conformationally sensitive antibody that binds near the dimer interface in domain II. We used a model cellular system, BaF/3 cells, with GFP-tagged receptors in the absence of interference from secreted ligands or other erbB receptor members. Different antibody-mediated effects (conformational transition, receptor cross-linking, or receptor dissociation) were distinguished by combining two complementary biophysical techniques: image correlation spectroscopy (submicrometer scale clustering) and homo-Forster resonance energy transfer (association and/or conformation on a 1-10 nm scale). mAb528 cross-linked EGFR into an inactive EGFR dimer of dimers but had no effect when added to de2-7-EGFR oligomers. mAb806 had a minor effect on EGFR dimers as expected from its poor binding to a conformationally shielded epitope on wtEGFR but bound de2-7-EGFR oligomers, causing a conformational change in the intracellular C-terminal GFP-tagged tail. The combination of the two antibodies had synergistic effects, increasing the level of cross-linking of de2-7-EGFR, but did not lead to enhanced cross-linking of EGFR. The results reveal new modes of receptor-antibody interactions for EGFR and de2-7-EGFR.
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Affiliation(s)
- Noga Kozer
- Ludwig Institute for Cancer Research, Melbourne-Parkville Branch, Royal Melbourne Hospital, Victoria 3050, Australia
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42
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Sahoo H. Förster resonance energy transfer – A spectroscopic nanoruler: Principle and applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2011. [DOI: 10.1016/j.jphotochemrev.2011.05.001] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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43
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Levitt JA, Chung PH, Kuimova MK, Yahioglu G, Wang Y, Qu J, Suhling K. Fluorescence anisotropy of molecular rotors. Chemphyschem 2011; 12:662-72. [PMID: 21328515 DOI: 10.1002/cphc.201000782] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 01/10/2011] [Indexed: 12/12/2022]
Abstract
We present polarization-resolved fluorescence measurements of fluorescent molecular rotors 9-(2-carboxy-2-cyanovinyl)julolidine (CCVJ), 9-(2,2-dicyanovinyl)julolidine (DCVJ), and a meso-substituted boron dipyrromethene (BODIPY-C(12)). The photophysical properties of these molecules are highly dependent on the viscosity of the surrounding solvent. The relationship between their quantum yields and the viscosity of the surrounding medium is given by an equation first described and presented by Förster and Hoffmann and can be used to determine the microviscosity of the environment around a fluorophore. Herein we evaluate the applicability of molecular rotors as probes of apparent viscosity on a microscopic scale based on their viscosity dependent fluorescence depolarization. We develop a theoretical framework, combining the Förster-Hoffmann equation with the Perrin equation and compare the dynamic ranges and usable working regimes for these dyes in terms of utilising fluorescence anisotropy as a measure of viscosity. We present polarization-resolved fluorescence spectra and steady-state fluorescence anisotropy imaging data for measurements of intracellular viscosity. We find that the dynamic range for fluorescence anisotropy for CCVJ and DCVJ is significantly lower than that of BODIPY-C(12) in the viscosity range 0.6<η<600 cP. Moreover, using steady-state anisotropy measurements to probe microviscosity in the low (<3 cP) viscosity regime, the molecular rotors can offer a better dynamic range in anisotropy compared with a rigid dye as a probe of microviscosity, and a higher total working dynamic range in terms of viscosity.
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Affiliation(s)
- James A Levitt
- Department of Physics, King's College London, Strand, London, WC2R 2LS, UK
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Bader AN, Hoetzl S, Hofman EG, Voortman J, van Bergen en Henegouwen PMP, van Meer G, Gerritsen HC. Homo‐FRET Imaging as a Tool to Quantify Protein and Lipid Clustering. Chemphyschem 2010; 12:475-83. [DOI: 10.1002/cphc.201000801] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Indexed: 11/11/2022]
Affiliation(s)
- Arjen N. Bader
- Department of Molecular Biophysics, Universiteit Utrecht, Princetonplein 1, 3584 CC Utrecht (The Netherlands), Fax: (+31) 30 253 2706
| | - Sandra Hoetzl
- Department of Membrane Enzymology, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
| | - Erik G. Hofman
- Department of Cellular Dynamics, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
| | - Jarno Voortman
- Department of Cellular Dynamics, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
| | | | - Gerrit van Meer
- Department of Membrane Enzymology, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
| | - Hans C. Gerritsen
- Department of Molecular Biophysics, Universiteit Utrecht, Princetonplein 1, 3584 CC Utrecht (The Netherlands), Fax: (+31) 30 253 2706
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45
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46
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Affiliation(s)
- Mikhail Y. Berezin
- Department of Radiology, Washington University School of Medicine, 4525 Scott Ave, St. Louis, USA, Tel. 314-747-0701, 314-362-8599, fax 314-747-5191
| | - Samuel Achilefu
- Department of Radiology, Washington University School of Medicine, 4525 Scott Ave, St. Louis, USA, Tel. 314-747-0701, 314-362-8599, fax 314-747-5191
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47
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Comparative Analysis of Fluorescence Reporter Signals Based on Intensity, Anisotropy, Time-Resolution, and Wavelength-Ratiometry. SPRINGER SERIES ON FLUORESCENCE 2010. [DOI: 10.1007/978-3-642-04702-2_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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48
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Opanasyuk O, Johansson LBÅ. Extended Förster theory: a quantitative approach to the determination of inter-chromophore distances in biomacromolecules. Phys Chem Chem Phys 2010; 12:7758-67. [DOI: 10.1039/b924113b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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van Ham TJ, Esposito A, Kumita JR, Hsu STD, Kaminski Schierle GS, Kaminski CF, Dobson CM, Nollen EAA, Bertoncini CW. Towards multiparametric fluorescent imaging of amyloid formation: studies of a YFP model of alpha-synuclein aggregation. J Mol Biol 2009; 395:627-42. [PMID: 19891973 DOI: 10.1016/j.jmb.2009.10.066] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/04/2009] [Accepted: 10/27/2009] [Indexed: 12/16/2022]
Abstract
Misfolding and aggregation of proteins are characteristics of a range of increasingly prevalent neurodegenerative disorders including Alzheimer's and Parkinson's diseases. In Parkinson's disease and several closely related syndromes, the protein alpha-synuclein (AS) aggregates and forms amyloid-like deposits in specific regions of the brain. Fluorescence microscopy using fluorescent proteins, for instance the yellow fluorescent protein (YFP), is the method of choice to image molecular events such as protein aggregation in living organisms. The presence of a bulky fluorescent protein tag, however, may potentially affect significantly the properties of the protein of interest; for AS in particular, its relative small size and, as an intrinsically unfolded protein, its lack of defined secondary structure could challenge the usefulness of fluorescent-protein-based derivatives. Here, we subject a YFP fusion of AS to exhaustive studies in vitro designed to determine its potential as a means of probing amyloid formation in vivo. By employing a combination of biophysical and biochemical studies, we demonstrate that the conjugation of YFP does not significantly perturb the structure of AS in solution and find that the AS-YFP protein forms amyloid deposits in vitro that are essentially identical with those observed for wild-type AS, except that they are fluorescent. Of the several fluorescent properties of the YFP chimera that were assayed, we find that fluorescence anisotropy is a particularly useful parameter to follow the aggregation of AS-YFP, because of energy migration Förster resonance energy transfer (emFRET or homoFRET) between closely positioned YFP moieties occurring as a result of the high density of the fluorophore within the amyloid species. Fluorescence anisotropy imaging microscopy further demonstrates the ability of homoFRET to distinguish between soluble, pre-fibrillar aggregates and amyloid fibrils of AS-YFP. Our results validate the use of fluorescent protein chimeras of AS as representative models for studying protein aggregation and offer new opportunities for the investigation of amyloid aggregation in vivo using YFP-tagged proteins.
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Affiliation(s)
- Tjakko J van Ham
- Department of Genetics, University of Groningen, Groningen, The Netherlands
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50
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Lidke DS, Wilson BS. Caught in the act: quantifying protein behaviour in living cells. Trends Cell Biol 2009; 19:566-74. [PMID: 19801189 DOI: 10.1016/j.tcb.2009.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/14/2009] [Accepted: 08/20/2009] [Indexed: 01/23/2023]
Abstract
Protein localization and dynamics both have important roles in cell signal transduction. Biochemical studies have elucidated many details about the chain of events in signal cascades, but the poor temporal resolution and absence of spatial localization in these conventional techniques make it difficult to determine the "where and when" of protein interactions. Over the past decade, imaging technologies and biological tools have developed to a point where many fundamental questions about protein activity can be addressed at the molecular level in living cells, revealing spatio-temporal information that is not provided by traditional biochemical assays. In this review, we illustrate the power of emerging fluorescence microscopy techniques to capture and quantify protein dynamics.
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Affiliation(s)
- Diane S Lidke
- Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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