1
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Ke HW, Sung K. 7-membered-ring effect on fluorescence quantum yield: does metal-complexation-induced twisting-inhibition of an amino GFP chromophore derivative enhance fluorescence? Phys Chem Chem Phys 2023; 25:14627-14634. [PMID: 37194347 DOI: 10.1039/d3cp00467h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To investigate two aspects, namely, (1) the 7-membered-ring effect on fluorescence quantum yield and (2) whether metal-complexation-induced twisting-inhibition of an amino green fluorescent protein (GFP) chromophore derivative is bound to enhance fluorescence, a novel GFP-chromophore-based triamine ligand, (Z)-o-PABDI, is designed and synthesized. Before complexation with metal ions, the S1 excited state of (Z)-o-PABDI undergoes τ-torsion relaxation (Z/E photoisomerization) with a Z/E photoisomerization quantum yield of 0.28, forming both ground-state (Z)- and (E)-o-PABDI isomers. Since (E)-o-PABDI is less stable than (Z)-o-PABDI, it is thermo-isomerized back to (Z)-o-PABDI at room temperature in acetonitrile with a first-order rate constant of (1.366 ± 0.082) × 10-6 s-1. After complexation with a Zn2+ ion, (Z)-o-PABDI as a tridentate ligand forms a 1 : 1 complex with the Zn2+ ion in acetonitrile and in the solid state, resulting in complete inhibition of the φ-torsion and τ-torsion relaxations, which does not enhance fluorescence but causes fluorescence quenching. (Z)-o-PABDI also forms complexes with other first-row transition metal ions Mn2+, Fe3+, Co2+, Ni2+ and Cu2+, generating almost the same fluorescence quenching effect. By comparison with the 2/Zn2+ complex, in which a 6-membered ring of Zn2+-complexation enhances fluorescence significantly (a positive 6-membered-ring effect on fluorescence quantum yield), we find that the flexible 7-membered rings of the (Z)-o-PABDI/Mn+ complexes trigger their S1 excited states to relax through internal conversion at a rate much faster than fluorescence (a negative 7-membered-ring effect on fluorescence quantum yield), leading to fluorescence quenching regardless of the type of transition metal that complexes with (Z)-o-PABDI.
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Affiliation(s)
- Hao-Wei Ke
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
| | - Kuangsen Sung
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.
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2
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Legault S, Fraser-Halberg DP, McAnelly RL, Eason MG, Thompson MC, Chica RA. Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing. Chem Sci 2022; 13:1408-1418. [PMID: 35222925 PMCID: PMC8809391 DOI: 10.1039/d1sc05088e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022] Open
Abstract
Red fluorescent proteins (RFPs) have found widespread application in chemical and biological research due to their longer emission wavelengths. Here, we use computational protein design to increase the quantum yield and thereby brightness of a dim monomeric RFP (mRojoA, quantum yield = 0.02) by optimizing chromophore packing with aliphatic residues, which we hypothesized would reduce torsional motions causing non-radiative decay. Experimental characterization of the top 10 designed sequences yielded mSandy1 (λ em = 609 nm, quantum yield = 0.26), a variant with equivalent brightness to mCherry, a widely used RFP. We next used directed evolution to further increase brightness, resulting in mSandy2 (λ em = 606 nm, quantum yield = 0.35), the brightest Discosoma sp. derived monomeric RFP with an emission maximum above 600 nm reported to date. Crystallographic analysis of mSandy2 showed that the chromophore p-hydroxybenzylidene moiety is sandwiched between the side chains of Leu63 and Ile197, a structural motif that has not previously been observed in RFPs, and confirms that aliphatic packing leads to chromophore rigidification. Our results demonstrate that computational protein design can be used to generate bright monomeric RFPs, which can serve as templates for the evolution of novel far-red fluorescent proteins.
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Affiliation(s)
- Sandrine Legault
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Derek P Fraser-Halberg
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Ralph L McAnelly
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Matthew G Eason
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
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3
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Khrenova MG, Mulashkin FD, Nemukhin AV. Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation. J Chem Inf Model 2021; 61:5125-5132. [PMID: 34601882 DOI: 10.1021/acs.jcim.1c00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a model for spectral tuning in red fluorescent proteins (RFPs) based on the relation between an electronic structure descriptor, the dipole moment variation upon excitation (DMV), and the excitation energy of a protein. This approach aims to overcome the problem of accurate prediction of excitation energies in RFPs, which span a very narrow window of band maxima. The latter roughly corresponds to the energy range of 0.1 eV, which is comparable with typical errors in calculations of the excitation energy by conventional quantum chemistry methods. In this work, we demonstrate a strong quantitative correlation between DMV values, obtained computationally with modest efforts, and excitation energies ΔEex at the experimental excitation band maxima for a series of RFPs with bands between 570 and 605 nm. Protein models are constructed by motifs of the relevant crystal structures, and atomic coordinates are optimized in quantum mechanics/molecular mechanics (QM/MM) calculations with QM-subsystems composed of large chromophore-containing regions. DMV values are evaluated with the electron density computed at the time-dependent density functional theory (TDDFT) level using several functionals and basis sets. We show that the results obtained with the CAM-B3LYP, BHHLYP, and M06-2X functionals demonstrate favorable correlations between DMV and ΔEex with the mean absolute error less than 0.01 eV. Taking into account the solid theoretical grounds of the relation between the DMV and the excitation energy in fluorescent proteins, the described modeling strategy presents a rational tool for spectral tuning in these efficient markers for in vivo imaging.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Fedor D Mulashkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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4
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Khrenova MG, Mulashkin FD, Bulavko ES, Zakharova TM, Nemukhin AV. Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores. J Chem Inf Model 2020; 60:6288-6297. [PMID: 33206518 DOI: 10.1021/acs.jcim.0c01028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a quantitative structure-property relationship (QSPR) model for prediction of spectral tuning in cyan, green, orange, and red fluorescent proteins, which are engineered by motifs of the green fluorescent protein. Protein variants, in which their chromophores are involved in the π-stacking interaction with amino acid residues tyrosine, phenylalanine, and histidine, are prospective markers useful in bioimaging and super-resolution microscopy. In this work, we constructed training sets of the π-stacked complexes of four fluorescent protein chromophores (of the green, orange, red, and cyan series) with various substituted benzenes and imidazoles and tested the use of dipole moment variation upon excitation (DMV) as a descriptor to evaluate the vertical excitation energies in these systems. To validate this approach, we computed and analyzed electron density distributions of the π-stacked complexes and correlated the QSPR predictions with the reference values of the transition energies obtained using the high-level ab initio quantum chemistry methods. According to our results, the use of the DMV descriptor allows one to predict excitation energies in the π-stacked complexes with errors not exceeding 0.1 eV, which makes this model a practically useful tool in the development of efficient fluorescent markers for in vivo imaging.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Fedor D Mulashkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Egor S Bulavko
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Tatiana M Zakharova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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5
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Sinha R, Shukla P. Current Trends in Protein Engineering: Updates and Progress. Curr Protein Pept Sci 2019; 20:398-407. [PMID: 30451109 DOI: 10.2174/1389203720666181119120120] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
Proteins are one of the most important and resourceful biomolecules that find applications in health, industry, medicine, research, and biotechnology. Given its tremendous relevance, protein engineering has emerged as significant biotechnological intervention in this area. Strategic utilization of protein engineering methods and approaches has enabled better enzymatic properties, better stability, increased catalytic activity and most importantly, interesting and wide range applicability of proteins. In fact, the commercialization of engineered proteins have manifested in economically beneficial and viable solutions for industry and healthcare sector. Protein engineering has also evolved to become a powerful tool contributing significantly to the developments in both synthetic biology and metabolic engineering. The present review revisits the current trends in protein engineering approaches such as rational design, directed evolution, de novo design, computational approaches etc. and encompasses the recent progresses made in this field over the last few years. The review also throws light on advanced or futuristic protein engineering aspects, which are being explored for design and development of novel proteins with improved properties or advanced applications.
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Affiliation(s)
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
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6
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Optimizing the fluorescent protein toolbox and its use. Curr Opin Biotechnol 2019; 58:183-191. [DOI: 10.1016/j.copbio.2019.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/24/2019] [Indexed: 01/07/2023]
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7
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Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. J Phys Chem B 2019; 123:6133-6149. [DOI: 10.1021/acs.jpcb.9b00591] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russian
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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8
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Canty L, Hariharan S, Liu Q, Haney SA, Andrews DW. Peak emission wavelength and fluorescence lifetime are coupled in far-red, GFP-like fluorescent proteins. PLoS One 2018; 13:e0208075. [PMID: 30485364 PMCID: PMC6261627 DOI: 10.1371/journal.pone.0208075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/12/2018] [Indexed: 11/25/2022] Open
Abstract
The discovery and use of fluorescent proteins revolutionized cell biology by allowing the visualization of proteins in living cells. Advances in fluorescent proteins, primarily through genetic engineering, have enabled more advanced analyses, including Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM) and the development of genetically encoded fluorescent biosensors. These fluorescence protein-based sensors are highly effective in cells grown in monolayer cultures. However, it is often desirable to use more complex models including tissue explants, organoids, xenografts, and whole animals. These types of samples have poor light penetration owing to high scattering and absorption of light by tissue. Far-red light with a wavelength between 650-900nm is less prone to scatter, and absorption by tissues and can thus penetrate more deeply. Unfortunately, there are few fluorescent proteins in this region of the spectrum, and they have sub-optimal fluorescent properties including low brightness and short fluorescence lifetimes. Understanding the relationships between the amino-acid sequences of far-red fluorescence proteins and their photophysical properties including peak emission wavelengths and fluorescence lifetimes would be useful in the design of new fluorescence proteins for this region of the spectrum. We used both site-directed mutagenesis and gene-shuffling between mScarlet and mCardinal fluorescence proteins to create new variants and assess their properties systematically. We discovered that for far-red, GFP-like proteins the emission maxima and fluorescence lifetime have a strong inverse correlation.
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Affiliation(s)
- Laura Canty
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Santosh Hariharan
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Qian Liu
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Steven A. Haney
- Department of Oncology and Translational Research, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - David W. Andrews
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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9
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Wannier TM, Gillespie SK, Hutchins N, McIsaac RS, Wu SY, Shen Y, Campbell RE, Brown KS, Mayo SL. Monomerization of far-red fluorescent proteins. Proc Natl Acad Sci U S A 2018; 115:E11294-E11301. [PMID: 30425172 PMCID: PMC6275547 DOI: 10.1073/pnas.1807449115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Anthozoa-class red fluorescent proteins (RFPs) are frequently used as biological markers, with far-red (λem ∼ 600-700 nm) emitting variants sought for whole-animal imaging because biological tissues are more permeable to light in this range. A barrier to the use of naturally occurring RFP variants as molecular markers is that all are tetrameric, which is not ideal for cell biological applications. Efforts to engineer monomeric RFPs have typically produced dimmer and blue-shifted variants because the chromophore is sensitive to small structural perturbations. In fact, despite much effort, only four native RFPs have been successfully monomerized, leaving the majority of RFP biodiversity untapped in biomarker development. Here we report the generation of monomeric variants of HcRed and mCardinal, both far-red dimers, and describe a comprehensive methodology for the monomerization of red-shifted oligomeric RFPs. Among the resultant variants is mKelly1 (emission maximum, λem = 656 nm), which, along with the recently reported mGarnet2 [Matela G, et al. (2017) Chem Commun (Camb) 53:979-982], forms a class of bright, monomeric, far-red FPs.
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Affiliation(s)
- Timothy M Wannier
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
| | - Sarah K Gillespie
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Nicholas Hutchins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - R Scott McIsaac
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Department of Chemistry, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Kevin S Brown
- Department of Chemical and Biomedical Engineering, University of Connecticut, Storrs, CT 06269
- Department of Physics, University of Connecticut, Storrs, CT 06269
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340
| | - Stephen L Mayo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
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10
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Campbell EC, Correy GJ, Mabbitt PD, Buckle AM, Tokuriki N, Jackson CJ. Laboratory evolution of protein conformational dynamics. Curr Opin Struct Biol 2018; 50:49-57. [DOI: 10.1016/j.sbi.2017.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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11
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Khrenova MG, Polyakov IV, Grigorenko BL, Krylov AI, Nemukhin AV. Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins. J Phys Chem B 2017; 121:10602-10609. [PMID: 29090574 DOI: 10.1021/acs.jpcb.7b07517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We characterize computationally a red fluorescent protein (RFP) with the chromophore (Chro) sandwiched between two aromatic tyrosine rings in a triple-decker motif. According to the original proposal [ J. Phys. Chem. Lett. 2013 , 4 , 1743 ], such a tyrosine-chromophore-tyrosine π-stacked construct can be accommodated in the green fluorescent protein (GFP). A recent study [ ACS Chem. Biol. 2016 , 11 , 508 ] attempted to realize the triple-decker motif and obtained an RFP variant called mRojoA-VYGV with two tyrosine residues surrounding the chromophore. The crystal structure showed that only a tyrosine-chromophore pair was involved in π-stacking, whereas the second tyrosine was oriented perpendicularly, edge-to-face with respect to the chromophore. We propose a more promising variant of this RFP with a perfect triple-decker unit achieved by introducing additional mutations in mRojoA-VYGV. The structures and optical properties of model proteins based on the structures of mCherry and mRojoA are characterized computationally by QM(DFT)/MM. The electronic transitions in the protein-bound chromophores are computed by high-level quantum chemical methods. According to our calculations, the triple-decker chromophore unit in the new RFP variant is stable within the protein and its optical bands are red-shifted with respect to the parent mCherry and mRojoA species.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, 119991, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, 119991, Russia
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12
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Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Nat Chem 2017; 10:31-37. [PMID: 29256511 DOI: 10.1038/nchem.2853] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 07/27/2017] [Indexed: 12/23/2022]
Abstract
Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.
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13
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Eason MG, Damry AM, Chica RA. Structure-guided rational design of red fluorescent proteins: towards designer genetically-encoded fluorophores. Curr Opin Struct Biol 2017; 45:91-99. [PMID: 28038355 DOI: 10.1016/j.sbi.2016.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 01/26/2023]
Abstract
Red fluorescent proteins (RFPs) have become an integral part of modern biological research due to their longer excitation and emission wavelengths. Protein engineering efforts have improved many key properties of RFPs for their practical use in imaging. Even so, continued engineering is required to overcome the shortcomings of the red chromophore and create RFPs with photophysical properties rivalling those of their optimized green and yellow counterparts. Here, we highlight recent examples of structure-guided rational design of RFPs to improve brightness, monomerization, maturation, and photostability, and discuss possible pathways for the future engineering of designer RFPs tailored to specific applications.
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Affiliation(s)
- Matthew G Eason
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - Adam M Damry
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada.
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14
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Jurgielewicz P, Harmsen S, Wei E, Bachmann MH, Ting R, Aras O. New imaging probes to track cell fate: reporter genes in stem cell research. Cell Mol Life Sci 2017; 74:4455-4469. [PMID: 28674728 DOI: 10.1007/s00018-017-2584-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/06/2017] [Accepted: 06/26/2017] [Indexed: 01/09/2023]
Abstract
Cell fate is a concept used to describe the differentiation and development of a cell in its organismal context over time. It is important in the field of regenerative medicine, where stem cell therapy holds much promise but is limited by our ability to assess its efficacy, which is mainly due to the inability to monitor what happens to the cells upon engraftment to the damaged tissue. Currently, several imaging modalities can be used to track cells in the clinical setting; however, they do not satisfy many of the criteria necessary to accurately assess several aspects of cell fate. In recent years, reporter genes have become a popular option for tracking transplanted cells, via various imaging modalities in small mammalian animal models. This review article examines the reporter gene strategies used in imaging modalities such as MRI, SPECT/PET, Optoacoustic and Bioluminescence Imaging. Strengths and limitations of the use of reporter genes in each modality are discussed.
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Affiliation(s)
- Piotr Jurgielewicz
- Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Stefan Harmsen
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | | | | | - Richard Ting
- Department of Radiology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Omer Aras
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, Suite 1511, New York, NY, 10065, USA.
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15
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Abstract
Influenza virus vaccine production is currently limited by the ability to grow circulating human strains in chicken eggs or in cell culture. To facilitate cost-effective growth, vaccine strains are serially passaged under production conditions, which frequently results in mutations of the major antigenic protein, the viral hemagglutinin (HA). Human vaccination with an antigenically drifted strain is known to contribute to poor vaccine efficacy. To address this problem, we developed a replication-competent influenza A virus (IAV) with an artificial genomic organization that allowed the incorporation of two independent and functional HA proteins with different growth requirements onto the same virion. Vaccination with these viruses induced protective immunity against both strains from which the HA proteins were derived, and the magnitude of the response was as high as or higher than vaccination with either of the monovalent parental strains alone. Dual-HA viruses also displayed remarkable antigenic stability; even when using an HA protein known to be highly unstable during growth in eggs, we observed high-titer virus amplification without a single adaptive mutation. Thus, the viral genomic design described in this work can be used to grow influenza virus vaccines to high titers without introducing antigenic mutations.IMPORTANCE Influenza A virus (IAV) is a major public health threat, and vaccination is currently the best available strategy to prevent infection. While there have been many advances in influenza vaccine production, the fact that we cannot predict the growth characteristics of a given strain under vaccine production conditions a priori introduces fundamental uncertainty into the process. Clinically relevant IAV strains frequently grow poorly under vaccine conditions, and this poor growth can result in the delay of vaccine production or the exchange of the recommended strain for one with favorable growth properties. Even in strains that grow to high titers, adaptive mutations in the antigenic protein hemagglutinin (HA) that make it antigenically dissimilar to the circulating strain are common. The genomic restructuring of the influenza virus described in this work offers a solution to the problem of uncertain or unstable growth of IAV during vaccine production.
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16
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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