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Petersen CE, Sun J, Silva K, Kosmach A, Balaban RS, Murphy E. Increased mitochondrial free Ca 2+ during ischemia is suppressed, but not eliminated by, germline deletion of the mitochondrial Ca 2+ uniporter. Cell Rep 2023; 42:112735. [PMID: 37421627 PMCID: PMC10529381 DOI: 10.1016/j.celrep.2023.112735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/20/2023] [Accepted: 06/18/2023] [Indexed: 07/10/2023] Open
Abstract
Mitochondrial Ca2+ overload is proposed to regulate cell death via opening of the mitochondrial permeability transition pore. It is hypothesized that inhibition of the mitochondrial Ca2+ uniporter (MCU) will prevent Ca2+ accumulation during ischemia/reperfusion and thereby reduce cell death. To address this, we evaluate mitochondrial Ca2+ in ex-vivo-perfused hearts from germline MCU-knockout (KO) and wild-type (WT) mice using transmural spectroscopy. Matrix Ca2+ levels are measured with a genetically encoded, red fluorescent Ca2+ indicator (R-GECO1) using an adeno-associated viral vector (AAV9) for delivery. Due to the pH sensitivity of R-GECO1 and the known fall in pH during ischemia, hearts are glycogen depleted to decrease the ischemic fall in pH. At 20 min of ischemia, there is significantly less mitochondrial Ca2+ in MCU-KO hearts compared with MCU-WT controls. However, an increase in mitochondrial Ca2+ is present in MCU-KO hearts, suggesting that mitochondrial Ca2+ overload during ischemia is not solely dependent on MCU.
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Affiliation(s)
- Courtney E Petersen
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Junhui Sun
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kavisha Silva
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Kosmach
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert S Balaban
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Murphy
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Wehler P, Armbruster D, Günter A, Schleicher E, Di Ventura B, Öztürk MA. Experimental Characterization of In Silico Red-Shift-Predicted iLOV L470T/Q489K and iLOV V392K/F410V/A426S Mutants. ACS OMEGA 2022; 7:19555-19560. [PMID: 35722011 PMCID: PMC9202016 DOI: 10.1021/acsomega.2c01283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
iLOV is a flavin mononucleotide-binding fluorescent protein used for in vivo cellular imaging similar to the green fluorescent protein. To expand the range of applications of iLOV, spectrally tuned red-shifted variants are desirable to reduce phototoxicity and allow for better tissue penetration. In this report, we experimentally tested two iLOV mutants, iLOVL470T/Q489K and iLOVV392K/F410V/A426S, which were previously computationally proposed by (KhrenovaJ. Phys. Chem. B2017, 121 ( (43), ), pp 10018-10025) to have red-shifted excitation and emission spectra. While iLOVL470T/Q489K is about 20% brighter compared to the WT in vitro, it exhibits a blue shift in contrast to quantum mechanics/molecular mechanics (QM/MM) predictions. Additional optical characterization of an iLOVV392K mutant revealed that V392 is essential for cofactor binding and, accordingly, variants with V392K mutation are unable to bind to FMN. iLOVL470T/Q489K and iLOVV392K/F410V/A426S are expressed at low levels and have no detectable fluorescence in living cells, preventing their utilization in imaging applications.
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Affiliation(s)
- Pierre Wehler
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Daniel Armbruster
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Andreas Günter
- Institute
of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Erik Schleicher
- Institute
of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Barbara Di Ventura
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Mehmet Ali Öztürk
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
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3
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Tamayo-Nuñez J, de la Mora J, Padilla-Vaca F, Vargas-Maya NI, Rangel-Serrano Á, Anaya-Velázquez F, Páramo-Pérez I, Reyes-Martínez JE, España-Sánchez BL, Franco B. aeBlue Chromoprotein Color is Temperature Dependent. Protein Pept Lett 2019; 27:74-84. [PMID: 31385759 PMCID: PMC6978647 DOI: 10.2174/0929866526666190806145740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 11/23/2022]
Abstract
Background Marine sessile organisms display a color palette that is the result of the expression of fluorescent and non-fluorescent proteins. Fluorescent proteins have uncovered transcriptional regulation, subcellular localization of proteins, and the fate of cells during development. Chromoproteins have received less attention until recent years as bioreporters. Here, we studied the properties of aeBlue, a a 25.91 kDa protein from the anemone Actinia equina. Objective To assess the properties of aeBlue chromoprotein under different physicochemical conditions. Methods In this article, during the purification of aeBlue we uncovered that it suffered a color shift when frozen. We studied the color shift by different temperature incubation and physicochemical conditions and light spectroscopy. To assess the possible structural changes in the protein, circular dichroism analysis, size exclusion chromatography and native PAGE was performed. Results We uncover that aeBlue chromoprotein, when expressed from a synthetic construct in Escherichia coli, showed a temperature dependent color shift. Protein purified at 4 °C by metal affinity chromatography exhibited a pinkish color and shifts back at higher temperatures to its intense blue color. Circular dichroism analysis revealed that the structure in the pink form of the protein has reduced secondary structure at 4 °C, but at 35 °C and higher, the structure shifts to a native conformation and Far UV- vis CD spectra revealed the shift in an aromatic residue of the chromophore. Also, the chromophore retains its properties in a wide range of conditions (pH, denaturants, reducing and oxidants agents). Quaternary structure is also maintained as a tetrameric conformation as shown by native gel and size exclusion chromatography. Conclusion Our results suggest that the chromophore position in aeBlue is shifted from its native position rendering the pink color and the process to return it to its native blue conformation is temperature dependent.
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Affiliation(s)
- Jessica Tamayo-Nuñez
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Javier de la Mora
- Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico, Circuito Exterior S/N, Mexico City, 04510, Mexico
| | - Felipe Padilla-Vaca
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Fernando Anaya-Velázquez
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Itzel Páramo-Pérez
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Juana Elizabeth Reyes-Martínez
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
| | - Beatríz Liliana España-Sánchez
- CONACYT Centro de Investigacion y Desarrollo Tecnologico en Electroquimica SC. Parque Queretaro s/n Sanfandila, Pedro Escobedo Queretaro. C.P. 76703, Mexico
| | - Bernardo Franco
- Departamento de Biologia, Division de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto. 36050, Mexico
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4
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Tafoya-Ramírez MD, Padilla-Vaca F, Ramírez-Saldaña AP, Mora-Garduño JD, Rangel-Serrano Á, Vargas-Maya NI, Herrera-Gutiérrez LJ, Franco B. Replacing Standard Reporters from Molecular Cloning Plasmids with Chromoproteins for Positive Clone Selection. Molecules 2018; 23:molecules23061328. [PMID: 29857551 PMCID: PMC6099721 DOI: 10.3390/molecules23061328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 11/23/2022] Open
Abstract
Cloning and expression plasmids are the workhorses of modern molecular biology. Despite the pathway paved by synthetic biology, laboratories around the globe still relay on standard cloning techniques using plasmids with reporter proteins for positive clone selection, such as β-galactosidase alpha peptide complementation for blue/white screening or ccdB, which encodes for a toxic DNA gyrase. These reporters, when interrupted, serve as a positive clone detection system. In the present report, we show that molecular cloning plasmids bearing the coding sequence for a 25.4 kDa protein, AmilCP, encoded by a 685 bp gene, that is well expressed in Escherichia coli, render blue-purple colonies. Using this reporter protein, we developed and tested a cloning system based on the constitutive expression of the non-toxic AmilCP protein, that once interrupted, the loss of purple color serves to facilitate positive clone selection. The main advantage of this system is that is less expensive than other systems since media do not contain chromogenic markers such as X-gal, which is both expensive and cumbersome to prepare and use, or inductors such as IPTG. We also designed an inducible expression plasmid suitable for recombinant protein expression that also contains AmilCP cloning selection marker, a feature not commonly found in protein expression plasmids. The use of chromogenic reporters opens an important avenue for its application in other organisms besides E. coli for clone selection or even for mutant selection.
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Affiliation(s)
| | - Felipe Padilla-Vaca
- Departamento de Biología, Universidad de Guanajuato, Noria Alta, 36050 Guanajuato, Mexico.
| | | | | | - Ángeles Rangel-Serrano
- Departamento de Biología, Universidad de Guanajuato, Noria Alta, 36050 Guanajuato, Mexico.
| | | | | | - Bernardo Franco
- Departamento de Biología, Universidad de Guanajuato, Noria Alta, 36050 Guanajuato, Mexico.
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5
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Khrenova MG, Meteleshko YI, Nemukhin AV. Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers. J Phys Chem B 2017; 121:10018-10025. [DOI: 10.1021/acs.jpcb.7b07533] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yulia I. Meteleshko
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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6
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Pandelieva AT, Baran MJ, Calderini GF, McCann JL, Tremblay V, Sarvan S, Davey JA, Couture JF, Chica RA. Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif. ACS Chem Biol 2016; 11:508-17. [PMID: 26697759 DOI: 10.1021/acschembio.5b00774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Red fluorescent proteins (RFPs) are used extensively in chemical biology research as fluorophores for live cell imaging, as partners in FRET pairs, and as signal transducers in biosensors. For all of these applications, brighter RFP variants are desired. Here, we used rational design to increase the quantum yield of monomeric RFPs in order to improve their brightness. We postulated that we could increase quantum yield by restricting the conformational degrees of freedom of the RFP chromophore. To test our hypothesis, we introduced aromatic residues above the chromophore of mRojoA, a dim RFP containing a π-stacked Tyr residue directly beneath the chromophore, in order to reduce chromophore conformational flexibility via improved packing and steric complementarity. The best mutant identified displayed an absolute quantum yield increase of 0.07, representing an over 3-fold improvement relative to mRojoA. Remarkably, this variant was isolated following the screening of only 48 mutants, a library size that is several orders of magnitude smaller than those previously used to achieve equivalent gains in quantum yield in other RFPs. The crystal structure of the highest quantum yield mutant showed that the chromophore is sandwiched between two Tyr residues in a triple-decker motif of aromatic rings. Presence of this motif increases chromophore rigidity, as evidenced by the significantly reduced temperature factors compared to dim RFPs. Overall, the approach presented here paves the way for the rapid development of fluorescent proteins with higher quantum yield and overall brightness.
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Affiliation(s)
- Antonia T Pandelieva
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Miranda J Baran
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Guido F Calderini
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jenna L McCann
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - James A Davey
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa , 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa , 10 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa , 30 Marie-Curie, Ottawa, Ontario K1N 6N5, Canada
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7
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Don Paul C, Traore DAK, Olsen S, Devenish RJ, Close DW, Bell TDM, Bradbury A, Wilce MCJ, Prescott M. X-Ray Crystal Structure and Properties of Phanta, a Weakly Fluorescent Photochromic GFP-Like Protein. PLoS One 2015; 10:e0123338. [PMID: 25923520 PMCID: PMC4414407 DOI: 10.1371/journal.pone.0123338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/02/2015] [Indexed: 01/07/2023] Open
Abstract
Phanta is a reversibly photoswitching chromoprotein (ΦF, 0.003), useful for pcFRET, that was isolated from a mutagenesis screen of the bright green fluorescent eCGP123 (ΦF, 0.8). We have investigated the contribution of substitutions at positions His193, Thr69 and Gln62, individually and in combination, to the optical properties of Phanta. Single amino acid substitutions at position 193 resulted in proteins with very low ΦF, indicating the importance of this position in controlling the fluorescence efficiency of the variant proteins. The substitution Thr69Val in Phanta was important for supressing the formation of a protonated chromophore species observed in some His193 substituted variants, whereas the substitution Gln62Met did not significantly contribute to the useful optical properties of Phanta. X-ray crystal structures for Phanta (2.3 Å), eCGP123T69V (2.0 Å) and eCGP123H193Q (2.2 Å) in their non-photoswitched state were determined, revealing the presence of a cis-coplanar chromophore. We conclude that changes in the hydrogen-bonding network supporting the cis-chromophore, and its contacts with the surrounding protein matrix, are responsible for the low fluorescence emission of eCGP123 variants containing a His193 substitution.
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Affiliation(s)
- Craig Don Paul
- Department of Neuro- and Sensory Physiology, University Medicine, Göttingen, 37073, Göttingen, Germany
| | - Daouda A. K. Traore
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton campus, Victoria, 3800, Australia
| | - Seth Olsen
- School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Rodney J. Devenish
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton campus, Victoria, 3800, Australia
| | - Devin W. Close
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States of America
| | - Toby D. M. Bell
- School of Chemistry, Monash University, Clayton campus, Victoria, 3800, Australia
| | - Andrew Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States of America
| | - Matthew C. J. Wilce
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton campus, Victoria, 3800, Australia
- * E-mail: (MP); (MCJW)
| | - Mark Prescott
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton campus, Victoria, 3800, Australia
- * E-mail: (MP); (MCJW)
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8
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Akerboom J, Carreras Calderón N, Tian L, Wabnig S, Prigge M, Tolö J, Gordus A, Orger MB, Severi KE, Macklin JJ, Patel R, Pulver SR, Wardill TJ, Fischer E, Schüler C, Chen TW, Sarkisyan KS, Marvin JS, Bargmann CI, Kim DS, Kügler S, Lagnado L, Hegemann P, Gottschalk A, Schreiter ER, Looger LL. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front Mol Neurosci 2013; 6:2. [PMID: 23459413 PMCID: PMC3586699 DOI: 10.3389/fnmol.2013.00002] [Citation(s) in RCA: 498] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 02/11/2013] [Indexed: 12/17/2022] Open
Abstract
Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, “RCaMPs,” engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca2+-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca2+]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca2+ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.
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Affiliation(s)
- Jasper Akerboom
- Janelia Farm Research Campus, Howard Hughes Medical Institute Ashburn, VA, USA
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9
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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10
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Battad JM, Traore DAK, Byres E, Rossjohn J, Devenish RJ, Olsen S, Wilce MCJ, Prescott M. A green fluorescent protein containing a QFG tri-peptide chromophore: optical properties and X-ray crystal structure. PLoS One 2012; 7:e47331. [PMID: 23071789 PMCID: PMC3468514 DOI: 10.1371/journal.pone.0047331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/12/2012] [Indexed: 01/07/2023] Open
Abstract
Rtms5 is an deep blue weakly fluorescent GFP-like protein ([Formula: see text], 592 nm; [Formula: see text], 630nm; Φ(F), 0.004) that contains a (66)Gln-Tyr-Gly chromophore tripeptide sequence. We investigated the optical properties and structure of two variants, Rtms5(Y67F) and Rtms5(Y67F/H146S) in which the tyrosine at position 67 was substituted by a phenylalanine. Compared to the parent proteins the optical spectra for these new variants were significantly blue-shifted. Rtms5(Y67F) spectra were characterised by two absorbing species ([Formula: see text], 440 nm and 513 nm) and green fluorescence emission ([Formula: see text], 440 nm; [Formula: see text], 508 nm; Φ(F), 0.11), whilst Rtms5(Y67F/H146S) spectra were characterised by a single absorbing species ([Formula: see text], 440 nm) and a relatively high fluorescence quantum yield (Φ(F,) 0.75; [Formula: see text], 440 nm; [Formula: see text], 508 nm). The fluorescence emissions of each variant were remarkably stable over a wide range of pH (3-11). These are the first GFP-like proteins with green emissions (500-520 nm) that do not have a tyrosine at position 67. The X-ray crystal structure of each protein was determined to 2.2 Å resolution and showed that the benzylidine ring of the chromophore, similar to the 4-hydroxybenzylidine ring of the Rtms5 parent, is non-coplanar and in the trans conformation. The results of chemical quantum calculations together with the structural data suggested that the 513 nm absorbing species in Rtms5(Y67F) results from an unusual form of the chromophore protonated at the acylimine oxygen. These are the first X-ray crystal structures for fluorescent proteins with a functional chromophore containing a phenylalanine at position 67.
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Affiliation(s)
- Jion M. Battad
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Daouda A. K. Traore
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Emma Byres
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Rodney J. Devenish
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Seth Olsen
- School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew C. J. Wilce
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (MP); (MW)
| | - Mark Prescott
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (MP); (MW)
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11
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Sun Q, Li Z, Lan Z, Pfisterer C, Doerr M, Fischer S, Smith SC, Thiel W. Isomerization mechanism of the HcRed fluorescent protein chromophore. Phys Chem Chem Phys 2012; 14:11413-24. [PMID: 22801745 DOI: 10.1039/c2cp41217a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To understand how the protein achieves fluorescence, the isomerization mechanism of the HcRed chromophore is studied both under vacuum and in the solvated red fluorescent protein. Quantum mechanical (QM) and quantum mechanical/molecular mechanical (QM/MM) methods are applied both for the ground and the first excited state. The photoinduced processes in the chromophore mainly involve torsions around the imidazolinone-bridge bond (τ) and the phenoxy-bridge bond (φ). Under vacuum, the isomerization of the cis-trans chromophore essentially proceeds by τ twisting, while the radiationless decay requires φ torsion. By contrast, the isomerization of the cis-trans chromophore in HcRed occurs via simultaneous τ and φ twisting. The protein environment significantly reduces the barrier of this hula twist motion compared with vacuum. The excited-state isomerization barrier via the φ rotation of the cis-coplanar conformer in HcRed is computed to be significantly higher than that of the trans-non-coplanar conformer. This is consistent with the experimental observation that the cis-coplanar-conformation of the chromophore is related to the fluorescent properties of HcRed, while the trans-non-planar conformation is weakly fluorescent or non-fluorescent. Our study shows how the protein modifies the isomerization mechanism, notably by interactions involving the nearby residue Ile197, which keeps the chromophore coplanar and blocks the twisting motion that leads to photoinduced radiationless decay.
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Affiliation(s)
- Qiao Sun
- Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Qld 4072, Brisbane, Australia.
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Pettikiriarachchi A, Gong L, Perugini MA, Devenish RJ, Prescott M. Ultramarine, a chromoprotein acceptor for Förster resonance energy transfer. PLoS One 2012; 7:e41028. [PMID: 22815901 PMCID: PMC3397996 DOI: 10.1371/journal.pone.0041028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/17/2012] [Indexed: 11/29/2022] Open
Abstract
We have engineered a monomeric blue non-fluorescent chromoprotein called Ultramarine (fluorescence quantum yield, 0.001; ε 585nm, 64,000 M−1. cm−1) for use as a Förster resonance energy transfer acceptor for a number of different donor fluorescent proteins. We show its use for monitoring activation of caspase 3 in live cells using fluorescence lifetime imaging. Ultramarine has the potential to increase the number of cellular parameters that can be imaged simultaneously.
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Affiliation(s)
- Anne Pettikiriarachchi
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Victoria, Australia
| | - Lan Gong
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Victoria, Australia
- ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Clayton Campus, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Rodney J. Devenish
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Victoria, Australia
- ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Clayton Campus, Victoria, Australia
| | - Mark Prescott
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Victoria, Australia
- * E-mail:
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Affiliation(s)
- Fedor V. Subach
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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14
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Rusanov AL, Mironov VA, Goryashenko AS, Grigorenko BL, Nemukhin AV, Savitsky AP. Conformational Partitioning in pH-Induced Fluorescence of the Kindling Fluorescent Protein (KFP). J Phys Chem B 2011; 115:9195-201. [DOI: 10.1021/jp1094245] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander L. Rusanov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991 Russian Federation
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospekt, 33, Moscow, 119071 Russian Federation
| | - Vladimir A. Mironov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991 Russian Federation
| | - Alexander S. Goryashenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991 Russian Federation
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospekt, 33, Moscow, 119071 Russian Federation
| | - Bella L. Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991 Russian Federation
| | - Alexander V. Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991 Russian Federation
| | - Alexander P. Savitsky
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/3, Moscow, 119991 Russian Federation
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospekt, 33, Moscow, 119071 Russian Federation
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15
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Mudalige K, Habuchi S, Goodwin PM, Pai RK, De Schryver F, Cotlet M. Photophysics of the Red Chromophore of HcRed: Evidence for Cis−Trans Isomerization and Protonation-State Changes. J Phys Chem B 2010; 114:4678-85. [DOI: 10.1021/jp9102146] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kumara Mudalige
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Mail Stop 735, Upton New York 11973, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee Leuven B-3001, Belgium, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545
| | - Satoshi Habuchi
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Mail Stop 735, Upton New York 11973, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee Leuven B-3001, Belgium, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545
| | - Peter M. Goodwin
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Mail Stop 735, Upton New York 11973, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee Leuven B-3001, Belgium, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545
| | - Ranjith K. Pai
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Mail Stop 735, Upton New York 11973, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee Leuven B-3001, Belgium, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545
| | - Frans De Schryver
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Mail Stop 735, Upton New York 11973, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee Leuven B-3001, Belgium, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545
| | - Mircea Cotlet
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Mail Stop 735, Upton New York 11973, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Heverlee Leuven B-3001, Belgium, and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545
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Sun Q, Doerr M, Li Z, Smith SC, Thiel W. QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed. Phys Chem Chem Phys 2010; 12:2450-8. [PMID: 20449359 DOI: 10.1039/b918523b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The far-red fluorescent protein HcRed was investigated using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three models of HcRed (anionic chromophore) were considered, differing in the protonation states of nearby Glu residues (A: Glu214 and Glu146 both protonated; B: Glu214 protonated and Glu146 deprotonated; C: Glu214 and Glu146 both deprotonated). SCC-DFTB/MM MD simulations of model B yield good agreement with the available crystallographic data at ambient pH. Bond lengths in the QM region are well reproduced, with a root mean square (rms) deviation between experimental and average MD data of 0.079 A; the chromophore is almost co-planar, which is consistent with experimental observation; and the five hydrogen bonds involving the chromophore are conserved. QM/MM geometry optimizations were performed on representative snapshot structures from the MD simulations for each model. They confirm the structural features observed in the MD simulations. According to the DFT(B3LYP)/MM results, the cis-conformation of the chromophore is more stable than the trans-form by 9.1-12.9 kcal mol(-1) in model B, and by 12.4-19.9 kcal mol(-1) in model C, consistent with the experimental preference for the cis-isomer. However, in model A when both Glu214 and Glu146 are protonated, the stability is inverted with the trans-form being favored. The different protonation states of the titratable active-site residues Glu214 and Glu146 thus critically influence the manner in which the relative stability and degree of planarity of the cis- and trans-conformers vary with pH. Coupled with the known correlation of chromophore conformation with fluorescence efficiency, this work provides a detailed structural basis for the observed phenomenon that red fluorescent proteins such as HcRed, mKate and Rtms5 show bright fluorescence at high pH.
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Affiliation(s)
- Qiao Sun
- Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Qld 4072, Brisbane, Australia
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17
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Photophysics and Spectroscopy of Fluorophores in the Green Fluorescent Protein Family. SPRINGER SERIES ON FLUORESCENCE 2010. [DOI: 10.1007/978-3-642-04702-2_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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18
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Vallverdu G, Demachy I, Mérola F, Pasquier H, Ridard J, Lévy B. Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations. Proteins 2009; 78:1040-54. [DOI: 10.1002/prot.22628] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Taguchi N, Mochizuki Y, Nakano T, Amari S, Fukuzawa K, Ishikawa T, Sakurai M, Tanaka S. Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits). J Phys Chem B 2009; 113:1153-61. [PMID: 19127982 DOI: 10.1021/jp808151c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion.
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Affiliation(s)
- Naoki Taguchi
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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21
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Pakhomov AA, Martynov VI. GFP Family: Structural Insights into Spectral Tuning. ACTA ACUST UNITED AC 2008; 15:755-64. [DOI: 10.1016/j.chembiol.2008.07.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/02/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
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22
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Olsen S, Smith SC. Bond Selection in the Photoisomerization Reaction of Anionic Green Fluorescent Protein and Kindling Fluorescent Protein Chromophore Models. J Am Chem Soc 2008; 130:8677-89. [DOI: 10.1021/ja078193e] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Seth Olsen
- Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Sean C. Smith
- Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072 Australia
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Hendrix J, Flors C, Dedecker P, Hofkens J, Engelborghs Y. Dark states in monomeric red fluorescent proteins studied by fluorescence correlation and single molecule spectroscopy. Biophys J 2008; 94:4103-13. [PMID: 18234806 PMCID: PMC2367191 DOI: 10.1529/biophysj.107.123596] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 12/21/2007] [Indexed: 11/18/2022] Open
Abstract
Monomeric red fluorescent proteins (mRFPs) have become indispensable tools for studying protein dynamics, interactions and functions in the cellular environment. Their emission spectrum can be well separated from other fluorescent proteins, and their monomeric structure preserves the natural function of fusion proteins. However, previous photophysical studies of some RFPs have shown the presence of light-induced dark states that can complicate the interpretation of cellular experiments. In this article, we extend these studies to mRFP1, mCherry, and mStrawberry by means of fluorescence correlation spectroscopy and prove that this light-driven intensity flickering also occurs in these proteins. Furthermore, we show that the flickering in these proteins is pH-dependent. Single molecule spectroscopy revealed reversible transitions from a bright to a dark state in several timescales, even up to seconds. Time-resolved fluorescence spectroscopy showed multiexponential decays, consistent with a "loose" conformation. We offer a structural basis for the fluorescence flickering using known crystal structures and point out that the environment of Glu-215 is critical for the pH dependence of the flickering in RFPs. We apply dual-color fluorescence correlation spectroscopy inside live cells to prove that this flickering can seriously hamper cellular measurements if the timescales of the flickering and diffusion are not well separated.
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Affiliation(s)
- Jelle Hendrix
- Laboratory of Biomolecular Dynamics, Department of Chemistry, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
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