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Stepanenko OV, Stepanenko OV, Shcherbakova DM, Kuznetsova IM, Turoverov KK, Verkhusha VV. Modern fluorescent proteins: from chromophore formation to novel intracellular applications. Biotechniques 2012; 51:313-4, 316, 318 passim. [PMID: 22054544 DOI: 10.2144/000113765] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/29/2011] [Indexed: 01/24/2023] Open
Abstract
The diverse biochemical and photophysical properties of fluorescent proteins (FPs) have enabled the generation of a growing palette of colors, providing unique opportunities for their use in a variety of modern biology applications. Modulation of these FP characteristics is achieved through diversity in both the structure of the chromophore as well as the contacts between the chromophore and the surrounding protein barrel. Here we review our current knowledge of blue, green, and red chromophore formation in permanently emitting FPs, photoactivatable FPs, and fluorescent timers. Progress in understanding the interplay between FP structure and function has allowed the engineering of FPs with many desirable features, and enabled recent advances in microscopy techniques such as super-resolution imaging of single molecules, imaging of protein dynamics, photochromic FRET, deep-tissue imaging, and multicolor two-photon microscopy in live animals.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
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102
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González-González IM, Jaskolski F, Goldberg Y, Ashby MC, Henley JM. Measuring membrane protein dynamics in neurons using fluorescence recovery after photobleach. Methods Enzymol 2012; 504:127-46. [PMID: 22264532 PMCID: PMC3314508 DOI: 10.1016/b978-0-12-391857-4.00006-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The use of genetically encoded fluorescent tags such as green fluorescent protein (GFP) as reporters to monitor processes in living cells has transformed cell biology. One major application for these tools has been to analyze protein dynamics in neurons. In particular, fluorescence recovery after photobleach (FRAP) of surface expressed fluorophore-tagged proteins has been instrumental to addressing outstanding questions about how neurons orchestrate the synaptic delivery of proteins. Here, we provide an overview of the methodology, equipment, and analysis required to perform, analyze, and interpret these experiments.
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Affiliation(s)
- Inmaculada M González-González
- MRC Centre for Synaptic Plasticity, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, United Kingdom
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103
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Zuev D, Bravaya KB, Makarova MV, Krylov AI. Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins. J Chem Phys 2011; 135:194304. [DOI: 10.1063/1.3660350] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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104
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Di Donato M, van Wilderen LJGW, Van Stokkum IHM, Stuart TC, Kennis JTM, Hellingwerf KJ, van Grondelle R, Groot ML. Proton transfer events in GFP. Phys Chem Chem Phys 2011; 13:16295-305. [PMID: 21847481 DOI: 10.1039/c1cp20387h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proton transfer is one of the most important elementary processes in biology. Green fluorescent protein (GFP) serves as an important model system to elucidate the mechanistic details of this reaction, because in GFP proton transfer can be induced by light absorption. Illumination initiates proton transfer through a 'proton-wire', formed by the chromophore (the proton donor), water molecule W22, Ser205 and Glu222 (the acceptor), on a picosecond time scale. To obtain a more refined view of this process, we have used a combined approach of time resolved mid-infrared spectroscopy and visible pump-dump-probe spectroscopy to resolve with atomic resolution how and how fast protons move through this wire. Our results indicate that absorption of light by GFP induces in 3 ps (10 ps in D(2)O) a shift of the equilibrium positions of all protons in the H-bonded network, leading to a partial protonation of Glu222 and to a so-called low barrier hydrogen bond (LBHB) for the chromophore's proton, giving rise to dual emission at 475 and 508 nm. This state is followed by a repositioning of the protons on the wire in 10 ps (80 ps in D(2)O), ultimately forming the fully deprotonated chromophore and protonated Glu222.
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Affiliation(s)
- Mariangela Di Donato
- Department of Physics and Astronomy, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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105
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Uliczka F, Pisano F, Kochut A, Opitz W, Herbst K, Stolz T, Dersch P. Monitoring of gene expression in bacteria during infections using an adaptable set of bioluminescent, fluorescent and colorigenic fusion vectors. PLoS One 2011; 6:e20425. [PMID: 21673990 PMCID: PMC3108616 DOI: 10.1371/journal.pone.0020425] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/25/2011] [Indexed: 01/29/2023] Open
Abstract
A family of versatile promoter-probe plasmids for gene expression analysis was developed based on a modular expression plasmid system (pZ). The vectors contain different replicons with exchangeable antibiotic cassettes to allow compatibility and expression analysis on a low-, midi- and high-copy number basis. Suicide vector variants also permit chromosomal integration of the reporter fusion and stable vector derivatives can be used for in vivo or in situ expression studies under non-selective conditions. Transcriptional and translational fusions to the reporter genes gfpmut3.1, amCyan, dsRed2, luxCDABE, phoA or lacZ can be constructed, and presence of identical multiple cloning sites in the vector system facilitates the interchange of promoters or reporter genes between the plasmids of the series. The promoter of the constitutively expressed gapA gene of Escherichia coli was included to obtain fluorescent and bioluminescent expression constructs. A combination of the plasmids allows simultaneous detection and gene expression analysis in individual bacteria, e.g. in bacterial communities or during mouse infections. To test our vector system, we analyzed and quantified expression of Yersinia pseudotuberculosis virulence genes under laboratory conditions, in association with cells and during the infection process.
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Affiliation(s)
- Frank Uliczka
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
- Department of Microbiology, Technical University Braunschweig, Braunschweig, Lower Saxony, Germany
| | - Fabio Pisano
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Annika Kochut
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Wiebke Opitz
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Katharina Herbst
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Tatjana Stolz
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Lower Saxony, Germany
- Department of Microbiology, Technical University Braunschweig, Braunschweig, Lower Saxony, Germany
- * E-mail:
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106
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Wang B, Gao Y, Li HW, Hu ZP, Wu Y. The switch-on luminescence sensing of histidine-rich proteins in solution: a further application of a Cu2+ ligand. Org Biomol Chem 2011; 9:4032-4. [PMID: 21541431 DOI: 10.1039/c1ob05372h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new probe/Cu(2+) complex for the detection of his-tagged protein has been developed, based on an improved probe, Dansyl-Gly-Py (1), by closely mimicing the structure of a peptide, ATCUN. In aqueous solution, 1/Cu(2+) has good selectivity to histidine and cysteine, and further can detect histidine-rich protein by releasing the quenched fluorescence of 1.
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Affiliation(s)
- Bin Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, No. 2699, Qianjin Street, Changchun, 130012, China
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107
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Pakhomov AA, Martynov VI. A method for the determination of the three-dimensional structure of fluorescent proteins based on homology modeling and mass spectrometry. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:429-32. [DOI: 10.1134/s1068162011030137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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108
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Losi A, Gärtner W. Old Chromophores, New Photoactivation Paradigms, Trendy Applications: Flavins in Blue Light-Sensing Photoreceptors†. Photochem Photobiol 2011; 87:491-510. [DOI: 10.1111/j.1751-1097.2011.00913.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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109
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Ivashkin PE, Lukyanov KA, Lukyanov S, Yampolsky IV. A Synthetic GFP-like Chromophore Undergoes Base-Catalyzed Autoxidation into Acylimine Red Form. J Org Chem 2011; 76:2782-91. [DOI: 10.1021/jo200150b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pavel E. Ivashkin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Konstantin A. Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Sergey Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ilia V. Yampolsky
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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110
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Pakhomov AA, Martynov VI. Probing the structural determinants of yellow fluorescence of a protein from Phialidium sp. Biochem Biophys Res Commun 2011; 407:230-5. [PMID: 21382348 DOI: 10.1016/j.bbrc.2011.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 03/02/2011] [Indexed: 10/18/2022]
Abstract
Fluorescent proteins homologous to green fluorescent protein (avGFP) display pronounced spectral variability due to different chromophore structures and variable chromophore interactions with the surrounding amino acids. To gain insight into the structural basis for yellow emission, the 3D structure of phiYFP (λ(em)=537 nm), a protein from the sea medusa Phialidium sp., was built by a combined homology modeling - mass spectrometry approach. Mass spectrometry of the isolated chromophore-bearing peptide reveals that the chromophore of phiYFP is chemically identical to that of avGFP (λ(em)=508 nm). The experimentally acquired chromophore structure was combined with the homology-based model of phiYFP, and the proposed 3D structure was used as a starting point for identification of the structural features responsible for yellow fluorescence. Mutagenesis of residues in the local chromophore environment of phiYFP suggests that multiple factors cooperate to establish the longest-wavelength emission maximum among fluorescent proteins with an unmodified GFP-like chromophore.
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Affiliation(s)
- Alexey A Pakhomov
- Chromoproteins Chemistry Research Group, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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111
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Razgulin A, Ma N, Rao J. Strategies for in vivo imaging of enzyme activity: an overview and recent advances. Chem Soc Rev 2011; 40:4186-216. [DOI: 10.1039/c1cs15035a] [Citation(s) in RCA: 226] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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112
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Absorption tuning of the green fluorescent protein chromophore: synthesis and studies of model compounds. MONATSHEFTE FUR CHEMIE 2010. [DOI: 10.1007/s00706-010-0430-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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113
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Lukyanov KA, Serebrovskaya EO, Lukyanov S, Chudakov DM. Fluorescent proteins as light-inducible photochemical partners. Photochem Photobiol Sci 2010; 9:1301-6. [PMID: 20672171 DOI: 10.1039/c0pp00114g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 07/14/2010] [Indexed: 01/19/2023]
Abstract
Green Fluorescent Protein (GFP) and other related fluorescent proteins are generally used as genetically encoded, chemically inert labels in vivo. This review focuses on the emerging application of fluorescent proteins as light-inducible intracellular photochemical partners. The first example of a chemically active GFP-like protein was the phototoxic red fluorescent protein KillerRed, which can be used for precise light-induced killing of cells, protein inactivation, and studying reactive oxygen species signaling in different cellular compartments. Moreover, recent studies revealed that various GFPs can act as light-induced electron donors in photochemical reactions with biologically relevant electron acceptors. These findings have important implications for practical uses of fluorescent proteins as well as for our understanding of the evolution and biology of this protein family.
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114
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Kyrychenko A, Wu F, Thummel RP, Waluk J, Ladokhin AS. Partitioning and localization of environment-sensitive 2-(2'-pyridyl)- and 2-(2'-pyrimidyl)-indoles in lipid membranes: a joint refinement using fluorescence measurements and molecular dynamics simulations. J Phys Chem B 2010; 114:13574-84. [PMID: 20925327 PMCID: PMC4470561 DOI: 10.1021/jp106981c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence of environment-sensitive dyes is widely applied to monitor local structure and solvation dynamics of biomolecules. It has been shown that, in comparison with a parent indole fluorophore, fluorescence of 2-(2'-pyridyl)-5-methylindole (5M-PyIn-0) and 2-[2'-(4',6'-dimethylpyrimidyl)]-indole (DMPmIn-0) is remarkably sensitive to hydrogen bonding with protic partners. Strong fluorescence, observed for these compounds in nonpolar and polar aprotic solvents, is efficiently quenched in aqueous solution. This study demonstrates that 5M-PyIn-0 and DMPmIn-0, which are almost nonemitting in aqueous solution, become highly fluorescent upon titrating with phospholipid vesicles. The fluorescence enhancement is accompanied by a significant blue shift of emission maximum. The Gibbs free energy of membrane partitioning, measured by the increase in the steady-state fluorescence intensities during transfer from an aqueous environment to a lipid bilayer, is very favorable for both compounds, being in a range from -7.1 to -8.0 kcal/mol and depending only slightly on lipid composition of the membrane. The fluorescence enhancement upon membrane partitioning is indicative of the loss of the specific hydrogen-bonding interactions between the excited fluorophore and water molecules, causing efficient fluorescence quenching in bulk water. This conclusion is supported by atomistic molecular dynamics (MD) simulations, demonstrating that both 5M-PyIn-0 and DMPmIn-0 bind rapidly and partition deeply into a lipid bilayer. MD simulations also show a rapid, nanosecond-scale decrease in the probability of solute-solvent hydrogen bonding during passive diffusion of the probe molecules from bulk water into a lipid bilayer. At equilibrium conditions, both 5M-PyIn-0 and DMPmIn-0 prefer deep localization within the hydrophobic, water-free region of the bilayer. A free energy profile of penetration across a bilayer estimated using MD umbrella sampling shows that both indole derivatives favor residence in a rather wide potential energy well located 10-15 Å from the bilayer center.
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Affiliation(s)
- Alexander Kyrychenko
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
| | | | | | - Jacek Waluk
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
| | - Alexey S. Ladokhin
- Corresponding authors. (A.K.) Phone: (+38)-057-707-5335. . (J.W.) Fax: (+48)-22-343-3333. . (A.S.L.) Fax: (+1)-913-588-7440.
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115
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Abstract
According to World Health Organization estimates, infectious organisms are responsible for approximately one in four deaths worldwide. Animal models play an essential role in the development of vaccines and therapeutic agents but large numbers of animals are required to obtain quantitative microbiological data by tissue sampling. Biophotonic imaging (BPI) is a highly sensitive, nontoxic technique based on the detection of visible light, produced by luciferase-catalysed reactions (bioluminescence) or by excitation of fluorescent molecules, using sensitive photon detectors. The development of bioluminescent/fluorescent microorganisms therefore allows the real-time noninvasive detection of microorganisms within intact living animals. Multiple imaging of the same animal throughout an experiment allows disease progression to be followed with extreme accuracy, reducing the number of animals required to yield statistically meaningful data. In the study of infectious disease, the use of BPI is becoming widespread due to the novel insights it can provide into established models, as well as the impact of the technique on two of the guiding principles of using animals in research, namely reduction and refinement. Here, we review the technology of BPI, from the instrumentation through to the generation of a photonic signal, and illustrate how the technique is shedding light on infection dynamics in vivo.
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Affiliation(s)
- Nuria Andreu
- Department of Medicine, Imperial College London, London, UK
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116
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Bettati S, Pasqualetto E, Lolli G, Campanini B, Battistutta R. Structure and single crystal spectroscopy of Green Fluorescent Proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:824-33. [PMID: 20940063 DOI: 10.1016/j.bbapap.2010.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 10/01/2010] [Accepted: 10/04/2010] [Indexed: 11/15/2022]
Abstract
Usually, spectroscopic data on proteins in solution are interpreted at molecular level on the basis of the three-dimensional structures determined in the crystalline state. While it is widely recognized that the protein crystal structures are reliable models for the solution 3D structures, nevertheless it is also clear that sometimes the crystallization process can introduce some "artifacts" that can make difficult or even flaw the attempt to correlate the properties in solution with those in the crystalline state. In general, therefore, it would be desirable to identify some sort of control. In the case of the spectroscopic properties of proteins, the most straightforward check is to acquire data not only in solution but also on the crystals. In this regard, the Green Fluorescent Protein (GFP) is an interesting case in that a massive quantity of data correlating the spectroscopic properties in solution with the structural information in the crystalline state is available in literature. Despite that, a relatively limited amount of spectroscopic studies on single crystals of GFP or related FPs have been described. Here we review and discuss the main spectroscopic (in solution) and structural (in crystals) studies performed on the GFP and related fluorescent proteins, together with the spectroscopic analyses on various FPs members in the crystalline state. One main conclusion is that "in cristallo" spectroscopic studies are useful in providing new opportunities for gathering information not available in solution and are highly recommended to reliably correlate solution properties with structural features. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Stefano Bettati
- Department of Biochemistry and Molecular Biology, University of Parma, Viale Usberti 23/A, 43124 Parma, Italy
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117
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Wachter RM, Watkins JL, Kim H. Mechanistic diversity of red fluorescence acquisition by GFP-like proteins. Biochemistry 2010; 49:7417-27. [PMID: 20666493 DOI: 10.1021/bi100901h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review aims to summarize our current state of knowledge of several post-translational modification mechanisms known to yield red fluorescence in the family of GFP-like (green fluorescent protein-like) proteins. We begin with a brief review of the maturation mechanism that leads to green fluorescence in GFPs. The main body of this article is focused on a series of main chain redox and beta-elimination reactions mediated by light and O(2), ultimately yielding a red-emitting chromophore. In all GFP-like proteins, a tyrosine-derived phenolic group constitutes an essential building block of the chromophore's skeleton. Two major classes of red-emitting species have been identified in naturally occurring fluorescent proteins. In the DsRed type, an acylimine moiety is found to be conjugated to the GFP-like chromophore. Recent evidence has suggested that two mechanistic pathways, a green branch and a red branch, diverge from an early cyclic intermediate that bears a standard tyrosine side chain. Therefore, the long-standing notion that all FP colors originate from modifications of the GFP-like chromophore may need to be revised. In the Kaede-type green-to-red photoconvertible class of FPs, a light-mediated main chain elimination reaction partakes in the formation of a three-ring chromophore that involves the incorporation of a histidine residue into the conjugated system. A mechanistic role for photoexcitation of the GFP-like chromophore is undisputed; however, the nature of associated proton transfer steps and the charge state of the critical imidazole group remain controversial. In addition to the two major classes of red fluorescent proteins, we briefly describe yellow fluorescence arising from modifications of DsRed-type intermediates, and the less well understood photoactivated oxidative redding phenomenon.
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Affiliation(s)
- Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA.
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118
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Ikmi A, Gibson MC. Identification and in vivo characterization of NvFP-7R, a developmentally regulated red fluorescent protein of Nematostella vectensis. PLoS One 2010; 5:e11807. [PMID: 20668556 PMCID: PMC2910727 DOI: 10.1371/journal.pone.0011807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 06/30/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In recent years, the sea anemone Nematostella vectensis has emerged as a critical model organism for comparative genomics and developmental biology. Although Nematostella is a member of the anthozoan cnidarians (known for producing an abundance of diverse fluorescent proteins (FPs)), endogenous patterns of Nematostella fluorescence have not been described and putative FPs encoded by the genome have not been characterized. METHODOLOGY/PRINCIPAL FINDINGS We described the spatiotemporal expression of endogenous red fluorescence during Nematostella development. Spatially, there are two patterns of red fluorescence, both restricted to the oral endoderm in developing polyps. One pattern is found in long fluorescent domains associated with the eight mesenteries and the other is found in short fluorescent domains situated between tentacles. Temporally, the long domains appear simultaneously at the 12-tentacle stage. In contrast, the short domains arise progressively between the 12- and 16-tentacle stage. To determine the source of the red fluorescence, we used bioinformatic approaches to identify all possible putative Nematostella FPs and a Drosophila S2 cell culture assay to validate NvFP-7R, a novel red fluorescent protein. We report that both the mRNA expression pattern and spectral signature of purified NvFP-7R closely match that of the endogenous red fluorescence. Strikingly, the red fluorescent pattern of NvFP-7R exhibits asymmetric expression along the directive axis, indicating that the nvfp-7r locus senses the positional information of the body plan. At the tissue level, NvFP-7R exhibits an unexpected subcellular localization and a complex complementary expression pattern in apposed epithelia sheets comprising each endodermal mesentery. CONCLUSIONS/SIGNIFICANCE These experiments not only identify NvFP-7R as a novel red fluorescent protein that could be employed as a research tool; they also uncover an unexpected spatio-temporal complexity of gene expression in an adult cnidarian. Perhaps most importantly, our results define Nematostella as a new model organism for understanding the biological function of fluorescent proteins in vivo.
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Affiliation(s)
- Aissam Ikmi
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Matthew C. Gibson
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, Kansas University Medical School, Kansas City, Kansas, United States of America
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119
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Zhang L, Gurskaia NG, Kopantseva EE, Mudrik NN, Vagner LL, Luk'ianov KA, Chudakov DM. [Identification of the amino acid residues responsible for the reversible photoconversion of the monomeric red fluorescent protein TagRFP protein]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:187-92. [PMID: 20531476 DOI: 10.1134/s1068162010020068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The site-directed mutagenesis of the monomeric red fluorescent protein TagRFP and its variants was performed with the goal of generating reversibly photoactivatable fluorescent proteins. Amino acids at positions 69, 148, 165, 179, and 181 (enumeration according to the green fluorescent protein GFP) were shown to play a key role in the manifestation of the photoactivatable properties. A reversibly photoactivatable red fluorescent protein KFP-HC with excitation and emission maxima at 585 and 615 nm, respectively, was generated. The KFP-HC fluorescent intensity was decreased by 5-10 times under green light (530-560 nm) irradiation (due to the fall of the fluorescence quantum yield) and restored under irradiation with blue light (450-490 nm) or after incubation in the dark (time of half reconstruction of 30 min).
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Affiliation(s)
- L Zhang
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997 Russia
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120
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Isarankura-Na-Ayudhya C, Tantimongcolwat T, Galla HJ, Prachayasittikul V. Fluorescent protein-based optical biosensor for copper ion quantitation. Biol Trace Elem Res 2010; 134:352-63. [PMID: 19649570 DOI: 10.1007/s12011-009-8476-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Accepted: 07/17/2009] [Indexed: 10/20/2022]
Abstract
In the present study, spectroscopic determinations of copper ions using chimeric metal-binding green fluorescent protein (His6GFP) as an active indicator have been explored. Supplementation of copper ions to the GFP solution led to a remarkable decrease of fluorescent intensity corresponding to metal concentrations. For circumstances, rapid declining of fluorescence up to 60% was detected in the presence of 500 microM copper. This is in contrast to those observed in the case of zinc and calcium ions, in which approximately 10-20% of fluorescence was affected. Recovery of its original fluorescence up to 80% was mediated by the addition of ethylenediamine tetraacetic acid. More importantly, in the presence of metal ions, the emission wavelength maximum remains unchanged while reduction of the optical density of the absorption spectrum has been observed. This indicates that the chromophore's ground state was possibly affected by the static quenching process. Results from circular dichroism measurements revealed that the overall patterns of circular dichroism spectra after exposure to copper ions were not significantly different from that of the control, where the majority of sharp positive band around 195-196 nm in combination with a broad negative deflection around 215-216 nm was obtained. Taken together, it can be presumed that copper ions exerted their static quenching on the fluorescence rather than structural or conformational alteration. However, notification has to be made that some peptide rearrangements may also occur in the presence of metal ions. Further studies were conducted to investigate the feasibility of using the His6GFP as a sensing unit for copper ions. The His6GFP was encapsulated in Sol-gel and immobilized onto the optical fiber connected with a fluorescence detecting device. The Sol-gel was doped into the metal solution where the quenching of fluorescence could be monitored in real time. The sensing unit provided a high sensitivity of detection in the range of 0.5 microM to 50 mM with high selectivity for copper ions. All these findings open up a high potential to apply the fluorescent protein-based bioanalytical tool for copper determination in the future.
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121
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 665] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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122
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Rajput J, Rahbek DB, Aravind G, Andersen LH. Spectral tuning of the photoactive yellow protein chromophore by H-bonding. Biophys J 2010; 98:488-92. [PMID: 20141763 DOI: 10.1016/j.bpj.2009.10.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 10/19/2009] [Accepted: 10/19/2009] [Indexed: 11/24/2022] Open
Abstract
Spectral tuning in the photoactive yellow protein (PYP) is investigated by performing gas-phase absorption measurements on a PYP-model chromophore with two water molecules hydrogen-bonded to it. The photoabsorption maximum shows an unusually large blue shift of 0.71 eV in going from the bare to the hydrogen-bonded chromophore. It is concluded that several interactions within the PYP protein are mutually cancelling each other, yielding an absorption maximum that is close to the absorption maximum of the bare chromophore. The system breaks apart upon photoexcitation in the gas phase by releasing the two water molecules, leaving the chromophore itself intact. The hydrogen-bonding interactions thus play an important role in stabilizing the gas phase chromophore against photofragmentation. The relaxation dynamics for the breakup process was also studied, and the timescale of relaxation via fragmentation was found to be < 25 ns.
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Affiliation(s)
- J Rajput
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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123
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Ivashkin PE, Iampol'skiĭ IV, Luk'ianov KA. [Synthesis and properties of chromophores of fluorescent proteins]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 35:726-43. [PMID: 20208574 DOI: 10.1134/s1068162009060028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We describe the existing approaches to the synthesis of 5-arylidene-3,5-dihydro-4H-imidazol-4-ones - model chromophores of fluorescent proteins and their nonnatural analogs. We discuss in detail the chemical (acid-base and redox reactions, cis-trans isomery, etc.) and spectral properties of the chromophores and the influence of substitutes and the environment. The study of synthetic chromophores allows for modeling of the photophysical characteristics of fluorescent proteins.
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124
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Formation of Schiff-base for photoreaction mechanism of red shift of GFP spectra. Biophys Chem 2010; 147:140-5. [DOI: 10.1016/j.bpc.2010.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/16/2010] [Accepted: 01/20/2010] [Indexed: 11/19/2022]
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125
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Ilagan RP, Rhoades E, Gruber DF, Kao HT, Pieribone VA, Regan L. A new bright green-emitting fluorescent protein--engineered monomeric and dimeric forms. FEBS J 2010; 277:1967-78. [PMID: 20345907 PMCID: PMC2855763 DOI: 10.1111/j.1742-4658.2010.07618.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent proteins have become essential tools in molecular and biological applications. Here, we present a novel fluorescent protein isolated from warm water coral, Cyphastrea microphthalma. The protein, which we named vivid Verde fluorescent protein (VFP), matures readily at 37 degrees C and emits bright green light. Further characterizations revealed that VFP has a tendency to form dimers. By creating a homology model of VFP, based on the structure of the red fluorescent protein, DsRed, we were able to make mutations that alter the protein's oligomerization state. We present two proteins, mVFP and mVFP1, that are both exclusively monomeric, and one protein, dVFP, which is dimeric. We characterized the spectroscopic properties of VFP and its variants in comparison with enhanced green fluorescent protein (EGFP), a widely used variant of GFP. All the VFP variants are at least twice as bright as EGFP. Finally, we demonstrated the effectiveness of the VFP variants in both in vitro and in vivo detection applications.
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Affiliation(s)
- Robielyn P. Ilagan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Elizabeth Rhoades
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - David F. Gruber
- Department of Natural Sciences, Baruch College and The Graduate Center, City University of New York, New York, NY 10010
| | - Hung-Teh Kao
- Department of Psychiatry and Human Behavior, Brown University, Providence, RI
| | | | - Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
- Department of Chemistry, Yale University, New Haven, CT 06520
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126
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Olsen S. A Modified Resonance-Theoretic Framework for Structure−Property Relationships in a Halochromic Oxonol Dye. J Chem Theory Comput 2010. [DOI: 10.1021/ct100001b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Seth Olsen
- Centre for Organic Photonics and Electronics, School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072 Australia
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127
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Pakhomov AA, Tretyakova YA, Martynov VI. Posttranslational reactions that shift spectra of asFP595, a Protein from Anemonia sulcata, towards the long-wavelength region. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:117-21. [DOI: 10.1134/s1068162010010127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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128
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Wang H, Nakata E, Hamachi I. Recent progress in strategies for the creation of protein-based fluorescent biosensors. Chembiochem 2010; 10:2560-77. [PMID: 19693761 DOI: 10.1002/cbic.200900249] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The creation of novel bioanalytical tools for the detection and monitoring of a range of important target substances and biological events in vivo and in vitro is a great challenge in chemical biology and biotechnology. Protein-based fluorescent biosensors--integrated devices that convert a molecular-recognition event to a fluorescent signal--have recently emerged as a powerful tool. As the recognition units various proteins that can specifically recognize and bind a variety of molecules of biological significance with high affinity are employed. For the transducer, fluorescent proteins, such as green fluorescent protein (GFP) or synthetic fluorophores, are mostly adopted. Recent progress in protein engineering and organic synthesis allows us to manipulate proteins genetically and/or chemically, and a library of such protein scaffolds has been significantly expanded by genome projects. In this review, we briefly describe the recent progress of protein-based fluorescent biosensors on the basis of their platform and construction strategy, which are primarily divided into the genetically encoded fluorescent biosensors and chemically constructed biosensors.
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Affiliation(s)
- Hangxiang Wang
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
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129
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Li Y, Li HW, Ma LJ, Dang YQ, Wu Y. A unique protein labeling system based on melittin and the non-covalent binding-induced pyrene excimer. Chem Commun (Camb) 2010; 46:3768-70. [DOI: 10.1039/b925401c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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130
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Abstract
Understanding how cells are assembled in three dimensions to generate an organ, or a whole organism, is a pivotal question in developmental biology. Similarly, it is critical to understand how adult stem cells integrate into an existing organ during regeneration or in response to injury. Key to discovering the answers to these questions is being able to study the various behaviors of distinct cell types during development or regeneration. Fate mapping techniques are fundamental to studying cell behaviors such as proliferation, movement, and lineage segregation, as the techniques allow precursor cells to be marked and their descendants followed and characterized over time. The generation of transgenic mice, combined with the use of site-specific recombinases (SSR) in the mouse genome, has provided a means to develop powerful genetic fate mapping approaches. A key advantage of genetic fate mapping is that it allows cells to be genetically marked, and therefore the mark is transmitted to all the descendants of the initially marked cells. By making modifications to the SSRs that render their enzymatic activity inducible, and the development of an assortment of reporter alleles for marking cells, increasingly sophisticated genetic fate mapping studies can be performed. In this chapter, we review the four main genetic fate mapping methods that utilize intrachromosomal recombination to mark cells (cumulative, inducible, clonal, and intersectional) and one interchromosomal method, the tools required to carry out each approach, and the practical considerations that have to be taken into account before embarking on each type of genetic fate mapping study.
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Affiliation(s)
- Emilie Legué
- Memorial Sloan-Kettering Cancer Center, New York, USA
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131
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Abstract
Fluorescence imaging is an important tool for molecular biology research. There is a wide array of fluorescent labels and activatable probes available for investigation of biochemical processes at a molecular level in living cells. Given the large number of potential imaging agents and numerous variables that can impact the utility of these fluorescent materials for imaging, selection of the appropriate probes can be a difficult task. In this report an overview of fluorescent imaging agents and details on their optical and physical properties that can impact their function are presented.
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Affiliation(s)
- Scott A Hilderbrand
- Center for Molecular Imaging Research, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA, USA
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132
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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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133
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Lincke K, Sølling T, Andersen LH, Klærke B, Rahbek DB, Rajput J, Oehlenschlæger CB, Petersen MÅ, Nielsen MB. On the absorption of the phenolatechromophore in the green fluorescent protein—role of individual interactions. Chem Commun (Camb) 2010; 46:734-6. [DOI: 10.1039/b920378h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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134
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Perron A, Mutoh H, Launey T, Knöpfel T. Red-shifted voltage-sensitive fluorescent proteins. CHEMISTRY & BIOLOGY 2009; 16:1268-77. [PMID: 20064437 PMCID: PMC2818747 DOI: 10.1016/j.chembiol.2009.11.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/12/2009] [Accepted: 11/19/2009] [Indexed: 10/20/2022]
Abstract
Electrical signals generated by nerve cells provide the basis of brain function. Whereas single or small numbers of cells are easily accessible using microelectrode recording techniques, less invasive optogenetic methods with spectral properties optimized for in vivo imaging are required for elucidating the operation mechanisms of neuronal circuits composed of large numbers of neurons originating from heterogeneous populations. To this end, we generated and characterized a series of genetically encoded voltage-sensitive fluorescent proteins by molecular fusion of the voltage-sensing domain of Ci-VSP (Ciona intestinalis voltage sensor-containing phosphatase) to red-shifted fluorescent protein operands. We show how these indicator proteins convert voltage-dependent structural rearrangements into a modulation of fluorescence output and demonstrate their applicability for optical recording of individual or simultaneous electrical signals in cultured hippocampal neurons at single-cell resolution without temporal averaging.
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Affiliation(s)
- Amelie Perron
- Laboratory for Neuronal Circuit Dynamics, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
| | - Hiroki Mutoh
- Laboratory for Neuronal Circuit Dynamics, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
| | - Thomas Launey
- Launey Research Unit, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
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135
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Gassensmith JJ, Baumes JM, Smith BD. Discovery and early development of squaraine rotaxanes. Chem Commun (Camb) 2009:6329-38. [PMID: 19841772 PMCID: PMC2854661 DOI: 10.1039/b911064j] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemical and photophysical properties of a fluorescent squaraine dye are greatly enhanced when it is mechanically encapsulated inside a tetralactam macrocycle. This feature article describes the synthesis, structure, and photophysical performance of first-generation squaraine rotaxanes, and shows how they can be used as fluorescent imaging probes and chemosensors.
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Affiliation(s)
- Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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136
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Hori Y, Ueno H, Mizukami S, Kikuchi K. Photoactive Yellow Protein-Based Protein Labeling System with Turn-On Fluorescence Intensity. J Am Chem Soc 2009; 131:16610-1. [DOI: 10.1021/ja904800k] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yuichiro Hori
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hideki Ueno
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shin Mizukami
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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137
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Can the fluorescence of green fluorescent protein chromophore be related directly to the nativity of protein structure? Biochem Biophys Res Commun 2009; 390:1167-70. [PMID: 19861120 DOI: 10.1016/j.bbrc.2009.10.109] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 10/20/2009] [Indexed: 11/21/2022]
Abstract
In studies of green fluorescence protein (GFP) or other proteins with the use of GFP as a marker, the fluorescence of GFP is for the most part related directly to the nativity of its structure. Naturally, such a relation does exist since the chromophore of this protein is formed autocatalytically only just after GFP acquires its native structure. However, the fluorescence method may not yield reliable information on protein structure when studying renaturation and denaturation of this protein (with the formed chromophore). Using proteolysis, denaturant gradient gel electrophoresis and circular dichroism, we demonstrate herein that at major disturbances of the native structure of protein GFP-cycle3 the intensity of fluorescence of its chromophore can change insignificantly. In other words, the chromophore fluorescence does not reliably mirror alterations in protein structure. Since the main conclusions of this study are especially qualitative, it can be suggested that during renaturation/denaturation of wild-type GFP and its "multicolored" mutants their fluorescence is also not always associated with the changes in the structure of these proteins.
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138
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Yampolsky IV, Balashova TA, Lukyanov KA. Synthesis and spectral and chemical properties of the yellow fluorescent protein zFP538 chromophore. Biochemistry 2009; 48:8077-82. [PMID: 19610669 DOI: 10.1021/bi900719x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of the green fluorescent protein (GFP) family become chromophoric through a unique pathway based on autocatalytic modifications of their amino acid residues. The yellow fluorescent protein zFP538 from the button polyp Zoanthus possesses unique spectral characteristics that are intermediate between those of the green and orange-red fluorescent proteins. In this study, we used chemical synthesis to resolve conflicting data from crystallographic and biochemical analyses of the zFP538 chromophore structure. We synthesized 2-(5-amino-1-oxopentyl)-5-(4-hydroxybenzylidene)-3-methyl-3,5-dihydro-4H-imidazol-4-one (5), which can spontaneously react intramolecularly to form cyclic imine (7). Compound 7 represents the native chromophore structure reported in the crystallographic study. We have also discovered an unusual isomerization of a 2-acylimidazolone to a 2,6-diketopiperazine derivative. The zFP538 chromophore is a complex system with intriguing chemical and spectral behavior, properties that have led to discrepancies in the interpretation of its structure. Our study supports the findings of previous crystallographic work, which postulated a cyclic imine chromophore structure within the native zFP538 protein, and also provides an explanation for experimental results obtained in the biochemical characterization of zFP538-derived chromopeptides.
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Affiliation(s)
- Ilia V Yampolsky
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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139
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Nienhaus GU, Wiedenmann J. Structure, dynamics and optical properties of fluorescent proteins: perspectives for marker development. Chemphyschem 2009; 10:1369-79. [PMID: 19229892 DOI: 10.1002/cphc.200800839] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Indexed: 01/02/2023]
Abstract
GFP-like proteins, originally cloned from marine animals, are genetically encoded fluorescence markers that have become indispensable tools for the life sciences. The search for GFP-like proteins with novel and improved properties is still ongoing, however, driven by the persistent need for advanced and specialized fluorescence labels for cellular imaging. Overall, the structures of these proteins are similar, but considerable variations have been found in the covalent structures and stereochemistry of the fluorophore, which govern essential optical properties such as the absorption/emission wavelengths. Moreover, as the fluorophore-enclosing cavity forms its solvation shell, it can also have a significant effect on the absorption/emission wavelengths and the brightness of the fluorophore. Most exciting are recent developments of photoactivatable fluorescence markers which change their color and/or intensity upon irradiation with light of specific wavelengths. A detailed understanding of the structure and dynamics of GFP-like proteins greatly aids in the rational engineering of advanced fluorescence marker proteins. Herein, we review our present knowledge of the structural diversity of GFP-like proteins and discuss how structure and dynamics govern their optical properties, with an emphasis on red fluorescent proteins.
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Affiliation(s)
- G Ulrich Nienhaus
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
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140
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Bogdanov AM, Mishin AS, Yampolsky IV, Belousov VV, Chudakov DM, Subach FV, Verkhusha VV, Lukyanov S, Lukyanov KA. Green fluorescent proteins are light-induced electron donors. Nat Chem Biol 2009; 5:459-61. [PMID: 19396176 PMCID: PMC2784199 DOI: 10.1038/nchembio.174] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proteins of the green fluorescent protein (GFP) family are well known owing to their unique biochemistry and extensive use as in vivo markers. We discovered that GFPs of diverse origins can act as light-induced electron donors in photochemical reactions with various electron acceptors, including biologically relevant ones. Moreover, via green-to-red GFP photoconversion, this process can be observed in living cells without additional treatment.
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Affiliation(s)
- Alexey M Bogdanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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141
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142
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Pakhomov AA, Martynov VI. Posttranslational chemistry of proteins of the GFP family. BIOCHEMISTRY (MOSCOW) 2009; 74:250-9. [DOI: 10.1134/s000629790903002x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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143
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Abstract
Autofluorescent proteins have become indispensable in our quest to visualize molecular events in living cells. Further progress in the visualization and quantification of all biochemical activities of the cell will require the introduction of additional and complementary methods for sensing and probing biomolecules. Here I highlight some of the areas where the development of new probes and labeling methods is eagerly awaited and where chemical biologists could make important contributions.
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Affiliation(s)
- Kai Johnsson
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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144
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Rajput J, Rahbek DB, Andersen LH, Rocha-Rinza T, Christiansen O, Bravaya KB, Erokhin AV, Bochenkova AV, Solntsev KM, Dong J, Kowalik J, Tolbert LM, Åxman Petersen M, Brøndsted Nielsen M. Photoabsorption studies of neutral green fluorescent protein model chromophores in vacuo. Phys Chem Chem Phys 2009; 11:9996-10002. [DOI: 10.1039/b914276b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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145
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Sample V, Newman RH, Zhang J. The structure and function of fluorescent proteins. Chem Soc Rev 2009; 38:2852-64. [DOI: 10.1039/b913033k] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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146
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van Thor JJ. Photoreactions and dynamics of the green fluorescent protein. Chem Soc Rev 2009; 38:2935-50. [DOI: 10.1039/b820275n] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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147
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148
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De Meulenaere E, Asselberghs I, de Wergifosse M, Botek E, Spaepen S, Champagne B, Vanderleyden J, Clays K. Second-order nonlinear optical properties of fluorescent proteins for second-harmonic imaging. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b907789h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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149
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Lefort CT, Kim M. Chapter 12 Fluorescence Resonance Energy Transfer in the Studies of Integrin Activation. CURRENT TOPICS IN MEMBRANES 2009. [DOI: 10.1016/s1063-5823(09)64012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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