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Carvalho J, Cruz C. Forster resonance energy transfer for studying nucleic acids denaturation: A chemical and biological sciences laboratory experiment. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:329-336. [PMID: 32268010 DOI: 10.1002/bmb.21353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/25/2020] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
The Förster resonance energy transfer (FRET) melting assay intends to evaluate the unfolding, denaturation process of DNA secondary structures, and its stabilization using compounds known as DNA binders, some of which are highly specific for G-quadruplex DNAs versus duplex DNAs. First, students determined the melting temperature (Tm ) of DNA sequences double labeled with 5'-FAM (fluorescein) and 3'-TAMRA (tetramethylrhodamine) in the absence of DNA binders. Second, they determined the melting temperature of the DNAs in the presence of DNA binders by monitoring fluorescence. After completing this experiment, students understood that this method allows a semiquantitative analysis to test a variety of DNA binders against DNA secondary structures, and it can be used to rapidly identify the most promising drug candidates in the drug development stages at the basic research level.
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Affiliation(s)
- Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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2
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Detection of misfolded rhodopsin aggregates in cells by Förster resonance energy transfer. Methods Cell Biol 2018; 149:87-105. [PMID: 30616829 DOI: 10.1016/bs.mcb.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells of the retina that plays a central role in phototransduction and rod photoreceptor cell health. Rhodopsin mutations are the leading known cause of autosomal dominant retinitis pigmentosa, a retinal degenerative disease. A majority of rhodopsin mutations cause misfolding and aggregation of the apoprotein opsin. The nature of aggregates formed by misfolded rhodopsin mutants and the associated cell toxicity is poorly understood. Misfolding rhodopsin mutants have been characterized biochemically, and categorized as either partial or complete misfolding mutants. This classification is incomplete and does not provide sufficient information to fully understand rhodopsin aggregation, disease pathogenesis, and evaluate therapeutic strategies. To better understand the aggregation of misfolded rhodopsin mutants, a Förster resonance energy transfer assay has been developed to monitor the aggregation of fluorescently tagged mutant rhodopsins expressed in live cells.
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Gragg M, Park PSH. Misfolded rhodopsin mutants display variable aggregation properties. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2938-2948. [PMID: 29890221 PMCID: PMC6066411 DOI: 10.1016/j.bbadis.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 11/20/2022]
Abstract
The largest class of rhodopsin mutations causing autosomal dominant retinitis pigmentosa (adRP) is mutations that lead to misfolding and aggregation of the receptor. The misfolding mutants have been characterized biochemically, and categorized as either partial or complete misfolding mutants. This classification is incomplete and does not provide sufficient information to fully understand the disease pathogenesis and evaluate therapeutic strategies. A Förster resonance energy transfer (FRET) method was utilized to directly assess the aggregation properties of misfolding rhodopsin mutants within the cell. Partial (P23H and P267L) and complete (G188R, H211P, and P267R) misfolding mutants were characterized to reveal variability in aggregation properties. The complete misfolding mutants all behaved similarly, forming aggregates when expressed alone, minimally interacting with the wild-type receptor when coexpressed, and were unresponsive to treatment with the pharmacological chaperone 9-cis retinal. In contrast, variability was observed between the partial misfolding mutants. In the opsin form, the P23H mutant behaved similarly as the complete misfolding mutants. In contrast, the opsin form of the P267L mutant existed as both aggregates and oligomers when expressed alone and formed mostly oligomers with the wild-type receptor when coexpressed. The partial misfolding mutants both reacted similarly to the pharmacological chaperone 9-cis retinal, displaying improved folding and oligomerization when expressed alone but aggregating with wild-type receptor when coexpressed. The observed differences in aggregation properties and effect of 9-cis retinal predict different outcomes in disease pathophysiology and suggest that retinoid-based chaperones will be ineffective or even detrimental.
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Affiliation(s)
- Megan Gragg
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
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Becirovic E, Böhm S, Nguyen ONP, Riedmayr LM, Hammelmann V, Schön C, Butz ES, Wahl-Schott C, Biel M, Michalakis S. AAV Vectors for FRET-Based Analysis of Protein-Protein Interactions in Photoreceptor Outer Segments. Front Neurosci 2016; 10:356. [PMID: 27516733 PMCID: PMC4963399 DOI: 10.3389/fnins.2016.00356] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/14/2016] [Indexed: 11/18/2022] Open
Abstract
Fluorescence resonance energy transfer (FRET) is a powerful method for the detection and quantification of stationary and dynamic protein-protein interactions. Technical limitations have hampered systematic in vivo FRET experiments to study protein-protein interactions in their native environment. Here, we describe a rapid and robust protocol that combines adeno-associated virus (AAV) vector-mediated in vivo delivery of genetically encoded FRET partners with ex vivo FRET measurements. The method was established on acutely isolated outer segments of murine rod and cone photoreceptors and relies on the high co-transduction efficiency of retinal photoreceptors by co-delivered AAV vectors. The procedure can be used for the systematic analysis of protein-protein interactions of wild type or mutant outer segment proteins in their native environment. Conclusively, our protocol can help to characterize the physiological and pathophysiological relevance of photoreceptor specific proteins and, in principle, should also be transferable to other cell types.
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Affiliation(s)
- Elvir Becirovic
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Sybille Böhm
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Ong N P Nguyen
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Lisa M Riedmayr
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Verena Hammelmann
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Christian Schön
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Elisabeth S Butz
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Christian Wahl-Schott
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Martin Biel
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
| | - Stylianos Michalakis
- Department of Pharmacy - Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität MünchenMunich, Germany; Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenMunich, Germany
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Gragg M, Kim TG, Howell S, Park PSH. Wild-type opsin does not aggregate with a misfolded opsin mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1850-9. [PMID: 27117643 DOI: 10.1016/j.bbamem.2016.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/06/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Megan Gragg
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tae Gyun Kim
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Scott Howell
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - P S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
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Han X, Tang J, Wang J, Ren F, Zheng J, Gragg M, Kiser P, Park PSH, Palczewski K, Yao X, Zhang Y. Conformational Change of Human Checkpoint Kinase 1 (Chk1) Induced by DNA Damage. J Biol Chem 2016; 291:12951-9. [PMID: 27129240 DOI: 10.1074/jbc.m115.713248] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 01/05/2023] Open
Abstract
Phosphorylation of Chk1 by ataxia telangiectasia-mutated and Rad3-related (ATR) is critical for checkpoint activation upon DNA damage. However, how phosphorylation activates Chk1 remains unclear. Many studies suggest a conformational change model of Chk1 activation in which phosphorylation shifts Chk1 from a closed inactive conformation to an open active conformation during the DNA damage response. However, no structural study has been reported to support this Chk1 activation model. Here we used FRET and bimolecular fluorescence complementary techniques to show that Chk1 indeed maintains a closed conformation in the absence of DNA damage through an intramolecular interaction between a region (residues 31-87) at the N-terminal kinase domain and the distal C terminus. A highly conserved Leu-449 at the C terminus is important for this intramolecular interaction. We further showed that abolishing the intramolecular interaction by a Leu-449 to Arg mutation or inducing ATR-dependent Chk1 phosphorylation by DNA damage disrupts the closed conformation, leading to an open and activated conformation of Chk1. These data provide significant insight into the mechanisms of Chk1 activation during the DNA damage response.
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Affiliation(s)
- Xiangzi Han
- From the Department of Pharmacology, Case Comprehensive Cancer Center, and
| | - Jinshan Tang
- the Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jingna Wang
- From the Department of Pharmacology, Case Comprehensive Cancer Center, and
| | - Feng Ren
- From the Department of Pharmacology, Case Comprehensive Cancer Center, and
| | - Jinhua Zheng
- From the Department of Pharmacology, Case Comprehensive Cancer Center, and
| | - Megan Gragg
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio 44106 and
| | - Philip Kiser
- From the Department of Pharmacology, Case Comprehensive Cancer Center, and
| | - Paul S H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio 44106 and
| | | | - Xinsheng Yao
- the Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Youwei Zhang
- From the Department of Pharmacology, Case Comprehensive Cancer Center, and
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Miller LM, Gragg M, Kim TG, Park PSH. Misfolded opsin mutants display elevated β-sheet structure. FEBS Lett 2015; 589:3119-25. [PMID: 26358292 DOI: 10.1016/j.febslet.2015.08.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/31/2015] [Indexed: 01/04/2023]
Abstract
Mutations in rhodopsin can cause misfolding and aggregation of the receptor, which leads to retinitis pigmentosa, a progressive retinal degenerative disease. The structure adopted by misfolded opsin mutants and the associated cell toxicity is poorly understood. Förster resonance energy transfer (FRET) and Fourier transform infrared (FTIR) microspectroscopy were utilized to probe within cells the structures formed by G188R and P23H opsins, which are misfolding mutants that cause autosomal dominant retinitis pigmentosa. Both mutants formed aggregates in the endoplasmic reticulum and exhibited altered secondary structure with elevated β-sheet and reduced α-helical content. The newly formed β-sheet structure may facilitate the aggregation of misfolded opsin mutants. The effects observed for the mutants were unrelated to retention of opsin molecules in the endoplasmic reticulum itself.
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Affiliation(s)
- Lisa M Miller
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.
| | - Megan Gragg
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Tae Gyun Kim
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA.
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Alexiev U, Farrens DL. Fluorescence spectroscopy of rhodopsins: insights and approaches. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:694-709. [PMID: 24183695 DOI: 10.1016/j.bbabio.2013.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Ulrike Alexiev
- Physics Department, Freie Universität Berlin, Berlin, Germany.
| | - David L Farrens
- Departments of Biochemistry and Molecular Biology, Oregon Health Sciences University, USA
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