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dos Santos Rodrigues FH, Delgado GG, Santana da Costa T, Tasic L. Applications of fluorescence spectroscopy in protein conformational changes and intermolecular contacts. BBA ADVANCES 2023; 3:100091. [PMID: 37207090 PMCID: PMC10189374 DOI: 10.1016/j.bbadva.2023.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Emission fluorescence is one of the most versatile and powerful biophysical techniques used in several scientific subjects. It is extensively applied in the studies of proteins, their conformations, and intermolecular contacts, such as in protein-ligand and protein-protein interactions, allowing qualitative, quantitative, and structural data elucidation. This review, aimed to outline some of the most widely used fluorescence techniques in this area, illustrate their applications and display a few examples. At first, the data on the intrinsic fluorescence of proteins is disclosed, mainly on the tryptophan side chain. Predominantly, research to study protein conformational changes, protein interactions, and changes in intensities and shifts of the fluorescence emission maximums were discussed. Fluorescence anisotropy or fluorescence polarization is a measurement of the changing orientation of a molecule in space, concerning the time between the absorption and emission events. Absorption and emission indicate the spatial alignment of the molecule's dipoles relative to the electric vector of the electromagnetic wave of excitation and emitted light, respectively. In other words, if the fluorophore population is excited with vertically polarized light, the emitted light will retain some polarization based on how fast it rotates in solution. Therefore, fluorescence anisotropy can be successfully used in protein-protein interaction investigations. Then, green fluorescent proteins (GFPs), photo-transformable fluorescent proteins (FPs) such as photoswitchable and photoconvertible FPs, and those with Large Stokes Shift (LSS) are disclosed in more detail. FPs are potent tools for the study of biological systems. Their versatility and wide range of colours and properties allow many applications. Finally, the application of fluorescence in life sciences is exposed, especially the application of FPs in fluorescence microscopy techniques with super-resolution that enables precise in vivo photolabeling to monitor the movement and interactions of target proteins.
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Affiliation(s)
| | - Gonzalo Garcia Delgado
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
| | - Thyerre Santana da Costa
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
| | - Ljubica Tasic
- Chemical Biology Laboratory, Institute of Chemistry, Organic Chemistry Department, University of Campinas, P. O. Box 6154, Campinas 13083-970, SP, Brazil
- Corresponding author: Ljubica Tasic: IQ, UNICAMP, Rua Josué de Castro sn, 13083-970 Campinas, SP, Brazil
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2
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Mamontova AV, Shakhov AM, Lukyanov KA, Bogdanov AM. Deciphering the Role of Positions 145 and 165 in Fluorescence Lifetime Shortening in the EGFP Variants. Biomolecules 2020; 10:biom10111547. [PMID: 33202759 PMCID: PMC7696298 DOI: 10.3390/biom10111547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
The bright ultimately short lifetime enhanced emitter (BrUSLEE) green fluorescent protein, which differs from the enhanced green fluorescent protein (EGFP) in three mutations, exhibits an extremely short fluorescence lifetime at a relatively high brightness. An important contribution to shortening the BrUSLEE fluorescence lifetime compared to EGFP is provided by the T65G substitution of chromophore-forming residue and the Y145M mutation touching the chromophore environment. Although the influence of the T65G mutation was studied previously, the role of the 145th position in determining the GFPs physicochemical characteristics remains unclear. In this work, we show that the Y145M substitution, both alone and in combination with the F165Y mutation, does not shorten the fluorescence lifetime of EGFP-derived mutants. Thus, the unlocking of Y145M as an important determinant of lifetime tuning is possible only cooperatively with mutations at position 65. We also show here that the introduction of a T65G substitution into EGFP causes complex photobehavior of the respective mutants in the lifetime domain, namely, the appearance of two fluorescent states with different lifetimes, preserved in any combination with the Y145M and F165Y substitutions.
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Affiliation(s)
- Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | | | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Correspondence:
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3
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Williams DE, Dolgopolova EA, Pellechia PJ, Palukoshka A, Wilson TJ, Tan R, Maier JM, Greytak AB, Smith MD, Krause JA, Shustova NB. Mimic of the Green Fluorescent Protein β-Barrel: Photophysics and Dynamics of Confined Chromophores Defined by a Rigid Porous Scaffold. J Am Chem Soc 2015; 137:2223-6. [DOI: 10.1021/ja5131269] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Derek E. Williams
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ekaterina A. Dolgopolova
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Andrei Palukoshka
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Thomas J. Wilson
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Rui Tan
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Josef M. Maier
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Andrew B. Greytak
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jeanette A. Krause
- Department
of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Natalia B. Shustova
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Sendersky E, Kozer N, Levi M, Garini Y, Shav-Tal Y, Schwarz R. The proteolysis adaptor, NblA, initiates protein pigment degradation by interacting with the cyanobacterial light-harvesting complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:118-126. [PMID: 24798071 DOI: 10.1111/tpj.12543] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/03/2014] [Accepted: 04/25/2014] [Indexed: 06/03/2023]
Abstract
Degradation of the cyanobacterial protein pigment complexes, the phycobilisomes, is a central acclimation response that controls light energy capture. The small protein, NblA, is essential for proteolysis of these large complexes, which may reach a molecular mass of up to 4 MDa. Interactions of NblA in vitro supported the suggestion that NblA is a proteolysis adaptor that labels the pigment proteins for degradation. The mode of operation of NblA in situ, however, remained unresolved. Particularly, it was unclear whether NblA interacts with phycobilisome proteins while part of the large complex, or alternatively interaction with NblA, necessitates dissociation of pigment subunits from the assembly. Fluorescence intensity profiles demonstrated the preferential presence of NblA::GFP (green fluorescent protein) at the photosynthetic membranes, indicating co-localization with phycobilisomes. Furthermore, fluorescence lifetime imaging microscopy provided in situ evidence for interaction of NblA with phycobilisome protein pigments. Additionally, we demonstrated the role of NblA in vivo as a proteolysis tag based on the rapid degradation of the fusion protein NblA::GFP compared with free GFP. Taken together, these observations demonstrated in vivo the role of NblA as a proteolysis adaptor. Additionally, the interaction of NblA with phycobilisomes indicates that the dissociation of protein pigment subunits from the large complex is not a prerequisite for interaction with this adaptor and, furthermore, implicates NblA in the disassembly of the protein pigment complex. Thus, we suggest that, in the case of proteolysis of the phycobilisome, the adaptor serves a dual function: undermining the complex stability and designating the dissociated pigments for degradation.
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Affiliation(s)
- Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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Wingen M, Potzkei J, Endres S, Casini G, Rupprecht C, Fahlke C, Krauss U, Jaeger KE, Drepper T, Gensch T. The photophysics of LOV-based fluorescent proteins – new tools for cell biology. Photochem Photobiol Sci 2014; 13:875-83. [DOI: 10.1039/c3pp50414j] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this study photophysical characteristics of LOV-based fluorescent proteins which are essential for analytic methods as well as imaging approaches have been comparatively analyzed in detail.
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Affiliation(s)
- Marcus Wingen
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Janko Potzkei
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Stephan Endres
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Giorgia Casini
- Institute of Complex Systems 4 (ICS-4
- Cellular Biophysics)
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Christian Rupprecht
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Christoph Fahlke
- Institute of Complex Systems 4 (ICS-4
- Cellular Biophysics)
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- Forschungszentrum Jülich
- 52425 Jülich, Germany
| | - Thomas Gensch
- Institute of Complex Systems 4 (ICS-4
- Cellular Biophysics)
- Forschungszentrum Jülich
- 52425 Jülich, Germany
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Fernandez-Lima FA, Eller MJ, DeBord JD, Levy MJ, Verkhoturov SV, Della-Negra S, Schweikert EA. Analysis of Fluorescent Proteins with a Nanoparticle Probe. J Phys Chem Lett 2012; 3:337-341. [PMID: 22308203 PMCID: PMC3270945 DOI: 10.1021/jz201547x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This letter presents the first application of high energy, single nanoparticle probes (e.g., 520 keV Au(400) 2nm NP) in the characterization of surfaces containing fluorescent proteins (e.g., GFP variants) by their co-emitted photon, electron and secondary ion signals. NP induced protein luminescence increases with the NP incident energy, is originated by the NP impact and is transferred to the protein fluorophor via electronic energy transfer. Multi-electron emission is observed per single NP impacts and their distributions are specific to the target morphology and composition. Fragment ions of protein sub-units consisting of 2-7 amino acid peptides are observed under individual NP impacts that can be correlated to the random protein orientation relative to the impact site (e.g., outer layer or "skin" of the protein).
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Affiliation(s)
| | - Michael J. Eller
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - J. Daniel DeBord
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - Michaella J. Levy
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | | | | | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
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7
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Nakabayashi T, Kinjo M, Ohta N. Electric field effects on fluorescence of the green fluorescent protein. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Quantitative lifetime unmixing of multiexponentially decaying fluorophores using single-frequency fluorescence lifetime imaging microscopy. Biophys J 2008; 95:378-89. [PMID: 18359789 DOI: 10.1529/biophysj.107.125229] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a quantitative microscopy technique for imaging nanosecond decay times of fluorophores. In the case of frequency-domain FLIM, several methods have been described to resolve the relative abundance of two fluorescent species with different fluorescence decay times. Thus far, single-frequency FLIM methods generally have been limited to quantifying two species with monoexponential decay. However, multiexponential decays are the norm rather than the exception, especially for fluorescent proteins and biological samples. Here, we describe a novel method for determining the fractional contribution in each pixel of an image of a sample containing two (multiexponentially) decaying species using single-frequency FLIM. We demonstrate that this technique allows the unmixing of binary mixtures of two spectrally identical cyan or green fluorescent proteins, each with multiexponential decay. Furthermore, because of their spectral identity, quantitative images of the relative molecular abundance of these fluorescent proteins can be generated that are independent of the microscope light path. The method is rigorously tested using samples of known composition and applied to live cell microscopy using cells expressing multiple (multiexponentially decaying) fluorescent proteins.
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9
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Tam JM, Upadhyay R, Pittet MJ, Weissleder R, Mahmood U. Improved in Vivo Whole-Animal Detection Limits of Green Fluorescent Protein–Expressing Tumor Lines by Spectral Fluorescence Imaging. Mol Imaging 2007. [DOI: 10.2310/7290.2007.00023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Green fluorescent protein (GFP) has been used for cell tracking and imaging gene expression in superficial or surgically exposed structures. However, in vivo murine imaging is often limited by several factors, including scatter and attenuation with depth and overlapping autofluorescence. The autofluorescence signals have spectral profiles that are markedly different from the GFP emission spectral profile. The use of spectral imaging allows separation and quantitation of these contributions to the total fluorescence signal seen in vivo by weighting known pure component profiles. Separation of relative GFP and autofluorescence signals is not readily possible using epifluorescent continuous-wave single excitation and emission bandpass imaging (EFI). To evaluate detection thresholds using these two methods, nude mice were subcutaneously injected with a series of GFP-expressing cells. For EFI, optimized excitation and emission bandpass filters were used. Owing to the ability to separate autofluorescence contributions from the emission signal using spectral imaging compared with the mixed contributions of GFP and autofluorescence in the emission signal recorded by the EFI system, we achieved a 300-fold improvement in the cellular detection limit. The detection limit was 3 × 103 cells for spectral imaging versus 1 × 106 cells for EFI. Despite contributions to image stacks from autofluorescence, a 100-fold dynamic range of cell number in the same image was readily visualized. Finally, spectral imaging was able to separate signal interference of red fluorescent protein from GFP images and vice versa. These findings demonstrate the utility of the approach in detecting low levels of multiple fluorescent markers for whole-animal in vivo applications.
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Affiliation(s)
- Jenny M. Tam
- From the Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Rabi Upadhyay
- From the Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Mikael J. Pittet
- From the Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Ralph Weissleder
- From the Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Umar Mahmood
- From the Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA
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10
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Barakat NH, Love JJ. Molecular diversity in engineered protein libraries. Curr Opin Chem Biol 2007; 11:335-41. [PMID: 17548238 DOI: 10.1016/j.cbpa.2007.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 05/17/2007] [Indexed: 11/26/2022]
Abstract
Engineered protein libraries, defined here as a collection of different mutant variants of a single specific protein, are intentionally designed to be rich in molecular diversity and can span ranges from as little as 400 different variants to greater than 10(12) members per library. The goal of engineering libraries is to generate new protein variants, identified upon screening, that possess desired novel properties. Exploitation of the natural organization of the genetic code has led to 'focused' libraries that are lower in overall complexity yet biased towards variants with preferred biophysical properties. An emerging trend, in which computational algorithms are blended with in vivo screens, is also leading towards greater and more rapid success in the field of protein design.
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Affiliation(s)
- Nora H Barakat
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
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Kukolka F, Müller BK, Paternoster S, Arndt A, Niemeyer CM, Bräuchle C, Lamb DC. A single-molecule Förster resonance energy transfer analysis of fluorescent DNA-protein conjugates for nanobiotechnology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2006; 2:1083-9. [PMID: 17193172 DOI: 10.1002/smll.200600202] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The development of nanobiotechnological devices requires the ability to build various components with nanometer accuracy. DNA is a well-established nanoscale building block that self assembles due to specific interactions that are encoded in its sequence. Recently, it has become possible to couple proteins to DNA, thereby expanding the capabilities of DNA for use with molecular photonics and bioelectronics. Here, we present the design and characterization of a supramolecular Förster resonance energy transfer (FRET) system by using a fluorescent protein bound to single-stranded DNA (ssDNA), a fluorophore attached to a second ssDNA molecule, and a complementary strand for hybridizing the two fluorophores together. The FRET efficiency was studied by using both ensemble and single-pair FRET measurements. The distance between the two fluorophores was determined from the single-pair FRET efficiency and could be described by a simple cylindrical model for the DNA. Hence, DNA can be used as a scaffold for positioning fluorescent proteins, as well as traditional fluorophores, with nanometer accuracy and shows great potential for use in the future of nanobiotechnology.
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Affiliation(s)
- Florian Kukolka
- Fachbereich Chemie Biologisch-Chemische Mikrostrukturtechnik, Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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12
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Wachter RM. The family of GFP-like proteins: structure, function, photophysics and biosensor applications. Introduction and perspective. Photochem Photobiol 2006; 82:339-44. [PMID: 16223340 DOI: 10.1562/2005-10-02-ir-708] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In this issue, we offer a symposium-in-print that is focused on several new advancements in fundamental research related to the family of GFP (green fluorescent protein)-like proteins. A few applied aspects are also included to illustrate the impact this amazing set of colored proteins has made on our understanding of cell biology at the molecular level. The six articles presented here cut across several disciplines ranging from biological function to protein structure to photophysical aspects. These highly original pieces of work include both experimental and computational approaches, and will provide the reader with significant insight into current, state-of-the-art research activities in this very dynamic and fast-paced field. In the first part of this perspective, I will give a brief overview of the history and salient features of GFPs, cite some examples that illustrate their impact on biotechnology, and provide a brief review of the structural and chemical features that lend these proteins their fascinating appearance. In the second part, I will introduce each of the peer-reviewed contributions of the participating authors.
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Affiliation(s)
- Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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