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Sartor A, Dahlberg PD, Perez D, Moerner WE. Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms. J Phys Chem B 2023; 127:2690-2700. [PMID: 36943356 PMCID: PMC10069424 DOI: 10.1021/acs.jpcb.2c08995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/01/2023] [Indexed: 03/23/2023]
Abstract
Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.
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Affiliation(s)
- Annina
M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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2
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Nienhaus K, Nienhaus GU. Chromophore photophysics and dynamics in fluorescent proteins of the GFP family. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:443001. [PMID: 27604321 DOI: 10.1088/0953-8984/28/44/443001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Straße 1, 76131 Karlsruhe, Germany
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3
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Grigorenko BL, Nemukhin AV, Polyakov IV, Morozov DI, Krylov AI. First-Principles Characterization of the Energy Landscape and Optical Spectra of Green Fluorescent Protein along the A→I→B Proton Transfer Route. J Am Chem Soc 2013; 135:11541-9. [DOI: 10.1021/ja402472y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bella L. Grigorenko
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
- N.M. Emanuel Institute of Biochemical
Physics, Russian Academy of Sciences, Kosygina
4, Moscow, 119334, Russian Federation
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
- N.M. Emanuel Institute of Biochemical
Physics, Russian Academy of Sciences, Kosygina
4, Moscow, 119334, Russian Federation
| | - Igor V. Polyakov
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
| | - Dmitry I. Morozov
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie Gory
1/3, Moscow, 119991, Russian Federation
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
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García-Iriepa C, Marazzi M, Frutos LM, Sampedro D. E/Z Photochemical switches: syntheses, properties and applications. RSC Adv 2013. [DOI: 10.1039/c2ra22363e] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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5
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First principle study of proton transfer in the green fluorescent protein (GFP): Ab initio PES in a cluster model. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.02.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Wagie HE, Geissinger P. Hole-burning spectroscopy as a probe of nano-environments and processes in biomolecules: a review. APPLIED SPECTROSCOPY 2012; 66:609-627. [PMID: 22732531 DOI: 10.1366/12-06655] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Hole-burning spectroscopy, a high-resolution spectroscopic technique, allows details of heterogeneous nano-environments in biological systems to be obtained from broad absorption bands. Recently, this technique has been applied to proteins, nucleic acids, cells, and substructures of water to probe the electrostatic conditions created by macromolecules and the surrounding solvent. Starting with the factors that obscure the homogeneous linewidth of a chromophore within an inhomogeneously broadened absorption or emission band, we describe properties and processes in biological systems that are reflected in the measured hole spectra. The technique also lends itself to the resolution of perturbation experiments, such as temperature cycling to elucidate energy landscape barriers, applied external electric fields (Stark effect) to measure net internal electric fields, and applied hydrostatic pressure to find the volume compressibility of proteins.
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ZHANG HONG, SMITH SEANC. MODEL REAL-TIME QUANTUM DYNAMICAL SIMULATIONS OF PROTON TRANSFER IN THE GREEN FLUORESCENT PROTEIN (GFP). JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607003301] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, we present the results from model real-time quantum dynamical calculations of the proton transfer in green fluorescent protein (GFP) regarding four electronic states (labeled A, A*, I, I*). A coupled-states quantum wavepacket method has been used, which involves split-operator and fast FFT algorithms. The model potential energy surfaces are based upon data derived from experimental results with some modifications. Several important processes in GFP have been simulated, which include the photo-absorption and proton transfer in the excited state, the isotope effect and the recurrence time for proton motion in the excited state. The origin of the early-time (prompt) stimulated emission is tentatively explained in terms of off-resonance excitation as well as the contribution from the fastest component for proton transfer in GFP.
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Affiliation(s)
- HONG ZHANG
- Centre for Computational Molecular Science, Chemistry Building 68, The University of Queensland, Brisbane, Qld. 4072, Australia
| | - SEAN C. SMITH
- Centre for Computational Molecular Science, Chemistry Building 68, The University of Queensland, Brisbane, Qld. 4072, Australia
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Sun Q, Wang S, Zhang H, Li Z, Pifisterer C, Fischer S, Nanbu S, Smith SC. Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle. Aust J Chem 2010. [DOI: 10.1071/ch09509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.
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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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11
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12
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van Thor JJ, Zanetti G, Ronayne KL, Towrie M. Structural events in the photocycle of green fluorescent protein. J Phys Chem B 2007; 109:16099-108. [PMID: 16853046 DOI: 10.1021/jp051315+] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picosecond time-resolved mid-infrared absorption changes of the wild type green fluorescent protein from Aequorea victoria are reported on structural events during the photocycle. Concomitant with rapid H/D transfer following excitation of the neutral A state at 400 nm, a transient signal at 1721/1711 cm(-1) (H/D) developed belonging to protonated glutamate 222, which was definitively assigned using the E222D mutant from the altered proton-transfer kinetics to aspartate in addition to the altered band position and intensity in the spectra. A transient at 1697 cm(-1), assigned to a structural perturbation of glutamine 69, had a H/D kinetic isotope effect of >32, showing the conformational dynamics to be sensitive to the active site H/D vibrations. The kinetic data up to 2 ns after excitation in the 1250-1800 cm(-1) region in D2O provided 10 and 75 ps time constants for the excited-state deuteron transfer and the associated A1* - A1 and A2* - A2 difference spectra and showed the radiative intermediate I state vibrations and the transient accumulation of the long-lived ground-state intermediate I2. Assignments of chromophore modes for the A1, A2, and I2 ground states are proposed on the basis of published model compound studies (Esposito, A. P.; Schellenberg, P.; Parson, W. W.; Reid, P. J. J. Mol. Struct. 2001, 569, 25 and He, X.; Bell, A. F.; Tonge, P. J. J. Phys. Chem. B 2002, 106, 6056). Tentative assignments for the singlet-state intermediates A1*, A2*, and I* are discussed. An unexpected and unassigned band that may be a C=C chromophore vibration was observed in the ground state (1665 cm(-1)) as well as in all photocycle intermediates. Optical dumping of the transient I population was achieved using an additional 532 nm pulse and the directly obtained I2 - I* difference spectrum was highly similar to the I2 - I* photocycle spectrum. The pump-dump-probe spectrum differed from the pump-probe photocycle difference spectrum with respect to the intensity of the phenol 1 mode at 1578 cm(-1), suggesting stronger delocalization of the negative charge onto the phenolic ring of the anionic chromophore in the dumped I2 state. Indication for structural heterogeneity of the chromophore, Glu 222, and the chromophore environment was found in the two parallel proton-transfer reactions and their distinct associated ground- and intermediate-state vibrations. Vibrational spectral markers at 1695 cm(-1) assigned to Gln 69, at 1631 cm(-1) belonging to a C=C mode, and at 1354 cm(-1) belonging to a phenolate vibration further indicated the I2 and I* states to be unrelaxed.
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Affiliation(s)
- Jasper J van Thor
- Laboratory of Molecular Biophysics, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, United Kingdom.
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13
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Nienhaus K, Renzi F, Vallone B, Wiedenmann J, Nienhaus GU. Chromophore-protein interactions in the anthozoan green fluorescent protein asFP499. Biophys J 2006; 91:4210-20. [PMID: 16980366 PMCID: PMC1635683 DOI: 10.1529/biophysj.106.087411] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 08/30/2006] [Indexed: 11/18/2022] Open
Abstract
Despite their similar fold topologies, anthozoan fluorescent proteins (FPs) can exhibit widely different optical properties, arising either from chemical modification of the chromophore itself or from specific interactions of the chromophore with the surrounding protein moiety. Here we present a structural and spectroscopic investigation of the green FP asFP499 from the sea anemone Anemonia sulcata var. rufescens to explore the effects of the protein environment on the chromophore. The optical absorption and fluorescence spectra reveal two discrete species populated in significant proportions over a wide pH range. Moreover, multiple protonation reactions are evident from the observed pH-dependent spectral changes. The x-ray structure of asFP499, determined by molecular replacement at a resolution of 1.85 A, shows the typical beta-barrel fold of the green FP from Aequorea victoria (avGFP). In its center, the chromophore, formed from the tripeptide Gln(63)-Tyr(64)-Gly(65), is tightly held by multiple hydrogen bonds in a polar cage that is structurally quite dissimilar to that of avGFP. The x-ray structure provides interesting clues as to how the spectroscopic properties are fine tuned by the chromophore environment.
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Affiliation(s)
- Karin Nienhaus
- Department of Biophysics, University of Ulm, 89069 Ulm, Germany.
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14
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Wang S, Smith SC. Mechanistic Aspects of Proton Chain Transfer: A Computational Study for the Green Fluorescent Protein Chromophore. J Phys Chem B 2006; 110:5084-93. [PMID: 16526751 DOI: 10.1021/jp056966k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205--for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging "water" that already has substantial negative charge.
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Affiliation(s)
- Sufan Wang
- Centre for Computational Molecular Science, Chemistry Building #68, The University of Queensland, Brisbane, Queensland 4072, Australia
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15
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Habuchi S, Dedecker P, Hotta JI, Flors C, Ando R, Mizuno H, Miyawaki A, Hofkens J. Photo-induced protonation/deprotonation in the GFP-like fluorescent protein Dronpa: mechanism responsible for the reversible photoswitching. Photochem Photobiol Sci 2006; 5:567-76. [PMID: 16761085 DOI: 10.1039/b516339k] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, reversible photoswitching in bulk samples or in individual molecules of Dronpa, a mutant of a green fluorescent protein (GFP)-like fluorescent protein, has been demonstrated. Intense irradiation at 488 nm changed Dronpa in a dim protonated form, and weak irradiation at 405 nm restored it to the bright deprotonated form. Here, we report on the mechanism of photoswitching of Dronpa by means of ensemble and single-molecule spectroscopy. Ensemble spectroscopy shows that the photoswitching can be described, in first approximation, by a three-state model including a deprotonated (B), a protonated (A1), and a photoswitched protonated (A2) forms of the chromophore. While the B and the A1 forms are in a ground state acid-base equilibrium, the B and the A2 forms are reversibly photoswitched upon irradiation with 488 and 405 nm light. At the single-molecule level, the on-times in fluorescence intensity trajectories excited at 488 nm decrease with increasing the excitation power, consistent with the photoswitching from the B to A2 form. The on-times agree well with expected values, which are calculated based on the ensemble spectroscopic properties of Dronpa. The fluorescence trajectory obtained with simultaneous dual-color excitation at 488 and 405 nm demonstrates reversible photoswitching between the B and the A2 forms at the single-molecule level. The efficiency of the photoswitching from the A2 to B form increased with increasing the excitation power of the 405 nm light. Our results demonstrate that Dronpa holds its outstanding photoswitching properties, based on a photo-induced protonation/deprotonation process, even at the single-molecule level.
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Affiliation(s)
- Satoshi Habuchi
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium.
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16
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Bonsma S, Purchase R, Jezowski S, Gallus J, Könz F, Völker S. Green and red fluorescent proteins: photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning. Chemphyschem 2005; 6:838-49. [PMID: 15884066 DOI: 10.1002/cphc.200500005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Indexed: 11/12/2022]
Abstract
The cloning and expression of autofluorescent proteins in living matter, combined with modern imaging techniques, have thoroughly changed the world of bioscience. In particular, such proteins are widely used as genetically encoded labels to track the movement of proteins as reporters of cellular signals and to study protein-protein interactions by fluorescence resonance energy transfer (FRET). Their optical properties, however, are complex and it is important to understand these for the correct interpretation of imaging data and for the design of new fluorescent mutants. In this Minireview we start with a short survey of the field and then focus on the photo- and thermally induced dynamics of green and red fluorescent proteins. In particular, we show how fluorescence line narrowing and high-resolution spectral hole burning at low temperatures can be used to unravel the photophysics and photochemistry and shed light on the intricate electronic structure of these proteins.
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Affiliation(s)
- S Bonsma
- Huygens and Gorlaeus Laboratories, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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17
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Jung G, Wiehler J, Zumbusch A. The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222. Biophys J 2004; 88:1932-47. [PMID: 15613627 PMCID: PMC1305246 DOI: 10.1529/biophysj.104.044412] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The three amino acids S65, T203, and E222 crucially determine the photophysical behavior of wild-type green fluorescent protein. We investigate the impact of four point mutations at these positions and their respective combinations on green fluorescent protein's photophysics using absorption spectroscopy, as well as steady-state and time-resolved fluorescence spectroscopy. Our results highlight the influence of the protein's hydrogen-bonding network on the equilibrium between the different chromophore states and on the efficiency of the excited-state proton transfer. The mutagenic approach allows us to separate different mechanisms responsible for fluorescence quenching, some of which were previously discussed theoretically. Our results will be useful for the development of new strategies for the generation of autofluorescent proteins with specific photophysical properties. One example presented here is a variant exhibiting uncommon blue fluorescence.
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Affiliation(s)
- Gregor Jung
- Department Chemie and Center for Nanoscience, LMU Munich, Munich, Germany
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18
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Wiehler J, Jung G, Seebacher C, Zumbusch A, Steipe B. Mutagenic stabilization of the photocycle intermediate of green fluorescent protein (GFP). Chembiochem 2004; 4:1164-71. [PMID: 14613107 DOI: 10.1002/cbic.200300595] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The optical spectra of the Aequorea victoria green fluorescent protein (GFP) are governed by an equilibrium between three different chromophore states. Mutants that predominantly show either the protonated (A) or the deprotonated (B) form of the chromophore have previously been described. In contrast, the I form, which is formed by rapid excited-state deprotonation of the A form of the chromophore, has only been described as an obligatory photochemical intermediate. We report the design of a new GFP mutant with a stabilized I form. For this purpose, we introduced two isosteric point mutations, Thr203Val and Glu222Gln, that selectively raise the potential energy of both the A and the B form. Knowledge of the absorption spectrum of the I form at room temperature allows the detailed analysis of concentration dependent changes in bulk wild-type(wt)-GFP spectra, as well as the determination of the dimerization constant of GFP. This information expands the use of GFP to that of a spectral probe for protein concentration. We determined energy differences between the chromophore ground states in the monomer and the dimer and reconstructed part of the potential energy surface.
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Affiliation(s)
- Jens Wiehler
- Genzentrum der Ludwig-Maximilians-Universität, Feodor-Lynen Strasse 25, 81377 Münich, Germany
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19
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Mandal D, Tahara T, Meech SR. Excited-State Dynamics in the Green Fluorescent Protein Chromophore. J Phys Chem B 2003. [DOI: 10.1021/jp035816b] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debabrata Mandal
- Molecular Spectroscopy Laboratory, The Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako 351-0198, Japan, and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, The Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako 351-0198, Japan, and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Stephen R. Meech
- Molecular Spectroscopy Laboratory, The Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako 351-0198, Japan, and School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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20
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Stübner M, Schellenberg P. Low-Temperature Photochemistry and Photodynamics of the Chromophore of Green Fluorescent Protein (GFP). J Phys Chem A 2003. [DOI: 10.1021/jp027038d] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Markus Stübner
- Lehrstuhl für Physik Weihenstephan, Physik-Department E14, TU München, D-85350 Freising, Germany, and Institut für Physikalische und Theoretische Chemie, TU München, D-85747 Garching, Germany
| | - Peter Schellenberg
- Lehrstuhl für Physik Weihenstephan, Physik-Department E14, TU München, D-85350 Freising, Germany, and Institut für Physikalische und Theoretische Chemie, TU München, D-85747 Garching, Germany
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22
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Lill MA, Helms V. Proton shuttle in green fluorescent protein studied by dynamic simulations. Proc Natl Acad Sci U S A 2002; 99:2778-81. [PMID: 11880630 PMCID: PMC122424 DOI: 10.1073/pnas.052520799] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As a direct simulation of a multistep proton transfer reaction involving protein residues, the proton relay shuttle between A and I forms of green fluorescent protein (GFP) is simulated in atomic detail by using a special molecular dynamics simulation technique. Electronic excitation of neutral chromophore in wild-type GFP is generally followed by excited-state proton transfer to a nearby glutamic acid residue via a water molecule and a serine residue. Here we show that the second and third transfer steps occur ultrafast on time scales of several tens of femtoseconds. Proton back-shuttle in the ground state is slower and occurs in a different sequence of events. The simulations provide atomic models of various intermediates and yield realistic rate constants for proton transfer events. In particular, we argue that the I form observed spectroscopically under equilibrium conditions may differ from the I form observed as a fast intermediate by an anti to syn rotation of the carboxyl proton of neutral Glu-222.
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Affiliation(s)
- Markus A Lill
- Max Planck Institute of Biophysics, Kennedyallee 70, 60596 Frankfurt, Germany
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23
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Zimmer M. Green fluorescent protein (GFP): applications, structure, and related photophysical behavior. Chem Rev 2002; 102:759-81. [PMID: 11890756 DOI: 10.1021/cr010142r] [Citation(s) in RCA: 823] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marc Zimmer
- Department of Chemistry, Connecticut College, New London, Connecticut 06320, USA.
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24
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Vibrational spectroscopy and mode assignments for an analog of the green fluorescent protein chromophore. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00825-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Schellenberg P, Johnson E, Esposito AP, Reid PJ, Parson WW. Resonance Raman Scattering by the Green Fluorescent Protein and an Analogue of Its Chromophore. J Phys Chem B 2001. [DOI: 10.1021/jp0046243] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Schellenberg
- Departments of Biochemistry and Chemistry, University of Washington, Seattle, Washington
| | - Ethan Johnson
- Departments of Biochemistry and Chemistry, University of Washington, Seattle, Washington
| | - Anthony P. Esposito
- Departments of Biochemistry and Chemistry, University of Washington, Seattle, Washington
| | - Philip J. Reid
- Departments of Biochemistry and Chemistry, University of Washington, Seattle, Washington
| | - William W. Parson
- Departments of Biochemistry and Chemistry, University of Washington, Seattle, Washington
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Yoo HY, Boatz JA, Helms V, McCammon JA, Langhoff PW. Chromophore Protonation States and the Proton Shuttle Mechanism in Green Fluorescent Protein: Inferences Drawn from ab Initio Theoretical Studies of Chemical Structures and Vibrational Spectra. J Phys Chem B 2001. [DOI: 10.1021/jp003683d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hi-Young Yoo
- Department of Chemistry, University of California, Irvine, California 92619-2025, Air Force Research Laboratory (AFRL/PRS), 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, Max-Planck-Institute of Biophysics, Kennedyallee 70, 60596 Frankfurt, Germany, Department of Chemistry and Biochemistry and Department of Pharmacology, University of CaliforniaSan Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, and
| | - J. A. Boatz
- Department of Chemistry, University of California, Irvine, California 92619-2025, Air Force Research Laboratory (AFRL/PRS), 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, Max-Planck-Institute of Biophysics, Kennedyallee 70, 60596 Frankfurt, Germany, Department of Chemistry and Biochemistry and Department of Pharmacology, University of CaliforniaSan Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, and
| | - Volkhard Helms
- Department of Chemistry, University of California, Irvine, California 92619-2025, Air Force Research Laboratory (AFRL/PRS), 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, Max-Planck-Institute of Biophysics, Kennedyallee 70, 60596 Frankfurt, Germany, Department of Chemistry and Biochemistry and Department of Pharmacology, University of CaliforniaSan Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, and
| | - J. Andrew McCammon
- Department of Chemistry, University of California, Irvine, California 92619-2025, Air Force Research Laboratory (AFRL/PRS), 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, Max-Planck-Institute of Biophysics, Kennedyallee 70, 60596 Frankfurt, Germany, Department of Chemistry and Biochemistry and Department of Pharmacology, University of CaliforniaSan Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, and
| | - Peter W. Langhoff
- Department of Chemistry, University of California, Irvine, California 92619-2025, Air Force Research Laboratory (AFRL/PRS), 10 East Saturn Boulevard, Edwards AFB, California 93524-7680, Max-Planck-Institute of Biophysics, Kennedyallee 70, 60596 Frankfurt, Germany, Department of Chemistry and Biochemistry and Department of Pharmacology, University of CaliforniaSan Diego, 9500 Gilman Drive, La Jolla, California 92093-0365, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, and
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Jung G, Bräuchle C, Zumbusch A. Two-color fluorescence correlation spectroscopy of one chromophore: Application to the E222Q mutant of the green fluorescent protein. J Chem Phys 2001. [DOI: 10.1063/1.1342014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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