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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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Paul BK, Guchhait N. Looking at the Green Fluorescent Protein (GFP) chromophore from a different perspective: a computational insight. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 103:295-303. [PMID: 23261626 DOI: 10.1016/j.saa.2012.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 06/01/2023]
Abstract
In the present contribution Density Functional Theory (DFT) has been applied to explore molecular dipole moment, frontier molecular orbital (FMO) features, chemical hardness, and the molecular electrostatic potential surface (MEPS) characteristics for optimized molecular geometry of the Green Fluorescent Protein (GFP) chromophore p-hydroxybenzylideneimidazolinone (HBDI) both in its protonated (neutral) and deprotonated (anion) forms. The distribution of atomic charges over the entire molecular framework as obtained from Natural Bond Orbital (NBO) analysis is found to faithfully replicate the predictions from the MEP map in respect of reactivity map of HBDI (neutral and anion) and possible sites for hydrogen bonding interactions etc. The three dimensional MEP map encompassing the entire molecule yields a reliable reactivity map of HBDI molecule also displaying the most probable regions for non-covalent interactions. The differential distribution of the electrostatic potential over the neutral and anionic species of HBDI is authentically reflected on MEP map and NBO charge distribution analysis. Thermodynamic properties such as heat capacity, thermal energy, enthalpy, entropy have been calculated and the correlation of the various thermodynamic functions with temperature has been established for neutral molecule. More importantly, however, the computational approach has been employed to unveil the nonlinear optical (NLO) properties of protonated (neutral) and deprotonated (anion) HBDI. Also in an endeavor to achieve a fuller understanding on this aspect the effect of basis set on the NLO properties of the title molecule has been investigated. Our computations delineate the discernible differences in NLO properties between the neutral and anionic species of HBDI whereby indicating the possibility of development of photoswitchable NLO device.
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Affiliation(s)
- Bijan Kumar Paul
- Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700 009, India
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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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Tolbert LM, Baldridge A, Kowalik J, Solntsev KM. Collapse and recovery of green fluorescent protein chromophore emission through topological effects. Acc Chem Res 2012; 45:171-81. [PMID: 21861536 DOI: 10.1021/ar2000925] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Housed within the 11-stranded β-barrel of the green fluorescent protein (GFP) is the arylideneimidazolidinone (AMI) chromophore, the component responsible for fluorescence. This class of small-molecule chromophore has drawn significant attention for its remarkable photophysical and photochemical properties, both within the intact protein and after its denaturation. All of the proteins so far isolated that have visible light fluorescence have been found to contain an AMI chromophore. These proteins comprise an extensive rainbow, ranging from GFP, which contains the simplest chromophore, p-hydroxybenzylideneimidazolidinone (p-HOBDI), to proteins having molecules with longer conjugation lengths and a variety of intraprotein interactions. The fluorescence invariably almost vanishes upon removal of the protective β-barrel. The role of the barrel in hindering internal conversion has been the subject of numerous studies, especially in our laboratories and those of our collaborators. A better understanding of these chromophores has been facilitated by the development of numerous synthetic protocols. These syntheses, which commonly use the Erlenmeyer azlactone method, have evolved in recent years with the development of a [2 + 3] cycloaddition exploited in our laboratory. The synthetic AMI chromophores have allowed delineation of the complex photophysics of GFP and its derivatives. Upon denaturation, AMI chromophores are marked by 4 orders of magnitude of diminution in emission quantum yield (EQY). This result is attributed to internal conversion resulting from conformational freedom in the released chromophore, which is not allowed within the restrictive β-barrel. To date, the photophysical properties of the AMI chromophore remain elusive and have been attributed to a variety of mechanisms, including cis-trans isomerization, triplet formation, hula twisting, and proton transfer. Advanced studies involving gas-phase behavior, solvent effects, and protonation states have significantly increased our understanding of the chromophore photophysics, but a comprehensive picture is only slowly emerging. Most importantly, mechanisms in structurally defined chromophores may provide clues as to the origin of the "blinking" behavior of the fluorescent proteins themselves. One approach to examining the effect of conformational freedom on rapid internal conversion of the chromophores is to restrict the molecules, both through structural modifications and through adjustments of the supramolecular systems. We thus include here a discussion of studies involving the crystalline state, inclusion within natural protein-binding pockets, complexation with metal ions, and sequestration within synthetic cavities; all of this research affirms the role of restricting conformational freedom in partially restoring the EQY. Additionally, new photochemistry is observed within these restricted systems. Many of the studies carried out in our laboratories show promise for these molecules to be adapted as molecular probes, wherein inclusion turns on the fluorescence and provides a signaling mechanism. In this Account, we present an overview of the AMI chromophores, including synthesis, overall photophysics, and supramolecular behavior. A significant amount of work remains for researchers to fully understand the properties of these chromophores, but important progress achieved thus far in photophysics and photochemistry is underscored here.
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Affiliation(s)
- Laren M. Tolbert
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony Baldridge
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Janusz Kowalik
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Kyril M. Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
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Leiderman P, Gepshtein R, Tsimberov I, Huppert D. Effect of Temperature on Excited-State Proton Tunneling in wt-Green Fluorescent Protein. J Phys Chem B 2008; 112:1232-9. [DOI: 10.1021/jp077642u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Leiderman
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and the Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - R. Gepshtein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and the Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - I. Tsimberov
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and the Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dan Huppert
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel, and the Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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Vendrell O, Gelabert R, Moreno M, Lluch JM. Potential Energy Landscape of the Photoinduced Multiple Proton-Transfer Process in the Green Fluorescent Protein: Classical Molecular Dynamics and Multiconfigurational Electronic Structure Calculations. J Am Chem Soc 2006; 128:3564-74. [PMID: 16536529 DOI: 10.1021/ja0549998] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The green fluorescent protein proton wire operating upon photoexcitation of the internally caged chromophore is investigated by means of classical molecular dynamics and multiconfigurational electronic structure calculations. The structure of the proton wire is studied for the solvated protein, showing that the wire is likely to be found in a configuration ready to operate as soon as the chromophore is photoexcited, and leading to a total of three proton translocations in the vicinity of the chromophore. Multiconfigurational CASSCF and CASPT2 calculations provide a detailed overview of the energy landscape of the proton wire for the ground electronic state S0, the photoactive 1pi pi* state, and the charge-transfer 1pi sigma* state. The results allow discussion of the operation of the wire in terms of the sequence of proton-transfer events and the participation of each electronic state.
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Affiliation(s)
- Oriol Vendrell
- Departament de Química, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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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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Vendrell O, Gelabert R, Moreno M, Lluch JM. Photoinduced proton transfer from the green fluorescent protein chromophore to a water molecule: analysis of the transfer coordinate. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.08.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Martin ME, Negri F, Olivucci M. Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution. J Am Chem Soc 2004; 126:5452-64. [PMID: 15113217 DOI: 10.1021/ja037278m] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio CASPT2//CASSCF relaxation path computations are employed to determine the intrinsic (e.g., in vacuo) mechanism underlying the rise and decay of the luminescence of the anionic form of the green fluorescent protein (GFP) fluorophore. Production and decay of the fluorescent state occur via a two-mode reaction coordinate. Relaxation along the first (totally symmetric) mode leads to production of the fluorescent state that corresponds to a planar species. The second (out-of-plane) mode controls the fluorescent state decay and mainly corresponds to a barrierless twisting of the fluorophore phenyl moiety. While a "space-saving" hula-twist conical intersection decay channel is found to lie only 5 kcal mol(-1) above the fluorescent state, the direct involvement of a hula-twist deformation in the decay is not supported by our data. The above results indicate that the ultrafast fluorescence decay observed for the GFP chromophore in solution is likely to have an intrinsic origin. The possible effects of the GFP protein cavity on the fluorescence lifetime of the investigated chromophore model are discussed.
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Affiliation(s)
- María Elena Martin
- Dipartimento di Chimica, Università di Siena, via Aldo Moro I-53100 Siena, Italy
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Glasbeek M, Zhang H. Femtosecond Studies of Solvation and Intramolecular Configurational Dynamics of Fluorophores in Liquid Solution. Chem Rev 2004; 104:1929-54. [PMID: 15080717 DOI: 10.1021/cr0206723] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Max Glasbeek
- Laboratory for Physical Chemistry, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands.
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Relationship between structure and optical properties in green fluorescent proteins: a quantum mechanical study of the chromophore environment. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2003.10.040] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Scharnagl C, Raupp-Kossmann RA. Solution pKa Values of the Green Fluorescent Protein Chromophore from Hybrid Quantum-Classical Calculations. J Phys Chem B 2003. [DOI: 10.1021/jp036411u] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christina Scharnagl
- Physik-Department, E14 Lehrstuhl für Physik Weihenstephan, Technische Universität München, D-85350 Freising, Germany, and Institut für Theoretische Physik T38, Technische Universität München, D-85747 Garching, Germany
| | - Robert A. Raupp-Kossmann
- Physik-Department, E14 Lehrstuhl für Physik Weihenstephan, Technische Universität München, D-85350 Freising, Germany, and Institut für Theoretische Physik T38, Technische Universität München, D-85747 Garching, Germany
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Litvinenko KL, Webber NM, Meech SR. Internal Conversion in the Chromophore of the Green Fluorescent Protein: Temperature Dependence and Isoviscosity Analysis. J Phys Chem A 2003. [DOI: 10.1021/jp027376e] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Naomi M. Webber
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Stephen R. Meech
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
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