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Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0
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Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 20 December 2024 | Viewed by 6897

Special Issue Editor

Dr. Eugene S. Vysotski

E-Mail Website
Guest Editor
Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences, Institute of Biophysics SB RAS, Krasnoyarsk 660036, Russia
Interests: bioluminescent and fluorescent proteins; molecular mechanism of bioluminescence; structure of bioluminescent proteins; bioluminescent analysis and imaging; BRET technologies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bioluminescence, a natural phenomenon of visible light emission by living organisms, has been found in numerous terrestrial and marine organisms. The study of bioluminescent reactions in organisms has revealed a specific feature—the mechanisms underlying light emission considerably differ in species of different taxa. Both the substrates and cofactors involved in bioluminescence reactions as well as the enzymes catalyzing these reactions have turned out to be peculiar. In addition to luciferases, many bioluminescence systems contain “antenna” proteins, such as Green fluorescent protein (GFP), which e.g., modulate the bioluminescence color by means of energy transfer. Although investigation of bioluminescence and fluorescence proteins is undoubtedly of fundamental interest, the main driving force that has attracted researchers to this topic is the broad analytical potential of bioluminescent proteins. Currently, there are no fields of biology or medicine where bioluminescence could not be widely used. This Special Issue of the International Journal of Molecular Science is devoted to experimental and theoretical studies on functioning mechanisms of bioluminescent proteins from various organisms, the proteins involved in bioluminescence (the lumazine protein, GFP and GPF-like proteins, and the enzymes participating in the synthesis of substrates), novel assays with the use of these proteins, and applications of these proteins in experimental biology and medicine. We invite authors to present their latest research in related fields.

Dr. Eugene S. Vysotski
Guest Editor

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Keywords

  • bioluminescence
  • luciferase
  • photoprotein
  • luciferin
  • coelenterazine
  • GFP
  • GFP-like proteins
  • immuno and hybridization assays
  • BRET and FRET assays
  • imaging

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Published Papers (5 papers)

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Research

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10 pages, 1699 KiB  
Article
Development of Malate Biosensor-Containing Hydrogels and Living Cell-Based Sensors
by Nathan J. Ricks, Monica Brachi, Kevin McFadden, Rohit G. Jadhav, Shelley D. Minteer and Ming C. Hammond
Int. J. Mol. Sci. 2024, 25(20), 11098; https://doi.org/10.3390/ijms252011098 - 16 Oct 2024
Viewed by 287
Abstract
Malate is a key intermediate in the citric acid cycle, an enzymatic cascade that is central to cellular energy metabolism and that has been applied to make biofuel cells. To enable real-time sensing of malate levels, we have engineered a genetically encoded, protein-based [...] Read more.
Malate is a key intermediate in the citric acid cycle, an enzymatic cascade that is central to cellular energy metabolism and that has been applied to make biofuel cells. To enable real-time sensing of malate levels, we have engineered a genetically encoded, protein-based fluorescent biosensor called Malon specifically responsive to malate by performing structure-based mutagenesis of the Cache-binding domain of the Citron GFP-based biosensor. Malon demonstrates high specificity and fluorescence activation in response to malate, and has been applied to monitor enzymatic reactions in vitro. Furthermore, we successfully incorporated Malon into redox polymer hydrogels and bacterial cells, enabling analysis of malate levels in these materials and living systems. These results show the potential for fluorescent biosensors in enzymatic cascade monitoring within biomaterials and present Malon as a novel tool for bioelectronic devices. Full article
(This article belongs to the Special Issue Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0)
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15 pages, 2751 KiB  
Article
Bioluminescence of (R)-Cypridina Luciferin with Cypridina Luciferase
by Shusei Kanie, Chun Wu, Kiyohito Kihira, Rie Yasuno, Yasuo Mitani and Yoshihiro Ohmiya
Int. J. Mol. Sci. 2024, 25(5), 2699; https://doi.org/10.3390/ijms25052699 - 26 Feb 2024
Cited by 1 | Viewed by 1477
Abstract
Cypridina luciferin (CypL) is a marine natural product that functions as the luminous substrate for the enzyme Cypridina luciferase (CypLase). CypL has two enantiomers, (R)- and (S)-CypL, due to its one chiral center at the sec-butyl moiety. Previous [...] Read more.
Cypridina luciferin (CypL) is a marine natural product that functions as the luminous substrate for the enzyme Cypridina luciferase (CypLase). CypL has two enantiomers, (R)- and (S)-CypL, due to its one chiral center at the sec-butyl moiety. Previous studies reported that (S)-CypL or racemic CypL with CypLase produced light, but the luminescence of (R)-CypL with CypLase has not been investigated. Here, we examined the luminescence of (R)-CypL, which had undergone chiral separation from the enantiomeric mixture, with a recombinant CypLase. Our luminescence measurements demonstrated that (R)-CypL with CypLase produced light, indicating that (R)-CypL must be considered as the luminous substrate for CypLase, as in the case of (S)-CypL, rather than a competitive inhibitor for CypLase. Additionally, we found that the maximum luminescence intensity from the reaction of (R)-CypL with CypLase was approximately 10 fold lower than that of (S)-CypL with CypLase, but our kinetic analysis of CypLase showed that the Km value of CypLase for (R)-CypL was approximately 3 fold lower than that for (S)-CypL. Furthermore, the chiral high-performance liquid chromatography (HPLC) analysis of the reaction mixture of racemic CypL with CypLase showed that (R)-CypL was consumed more slowly than (S)-CypL. These results indicate that the turnover rate of CypLase for (R)-CypL was lower than that for (S)-CypL, which caused the less efficient luminescence of (R)-CypL with CypLase. Full article
(This article belongs to the Special Issue Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0)
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25 pages, 4413 KiB  
Article
The Role of Tyr-His-Trp Triad and Water Molecule Near the N1-Atom of 2-Hydroperoxycoelenterazine in Bioluminescence of Hydromedusan Photoproteins: Structural and Mutagenesis Study
by Pavel V. Natashin, Ludmila P. Burakova, Margarita I. Kovaleva, Mikhail B. Shevtsov, Daria A. Dmitrieva, Elena V. Eremeeva, Svetlana V. Markova, Alexey V. Mishin, Valentin I. Borshchevskiy and Eugene S. Vysotski
Int. J. Mol. Sci. 2023, 24(7), 6869; https://doi.org/10.3390/ijms24076869 - 6 Apr 2023
Cited by 2 | Viewed by 2264
Abstract
Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of [...] Read more.
Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction. Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed, many features of their functioning are yet unclear. In particular, which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role of the water molecule residing in a proximity to the N1 atom of 2-hydroperoxycoelenterazine in the bioluminescence reaction are still under discussion. With the aim to elucidate the function of this water molecule as well as to pinpoint the amino acid residues presumably involved in the protonation of the primarily formed dioxetanone anion, we constructed a set of single and double obelin and aequorin mutants with substitutions of His, Trp, Tyr, and Ser to residues with different properties of side chains and investigated their bioluminescence properties (specific activity, bioluminescence spectra, stopped-flow kinetics, and fluorescence spectra of Ca2+-discharged photoproteins). Moreover, we determined the spatial structure of the obelin mutant with a substitution of His64, the key residue of the presumable proton transfer, to Phe. On the ground of the bioluminescence properties of the obelin and aequorin mutants as well as the spatial structures of the obelin mutants with the replacements of His64 and Tyr138, the conclusion was made that, in fact, His residue of the Tyr-His-Trp triad and the water molecule perform the “catalytic function” by transferring the proton from solvent to the dioxetanone anion to generate its neutral ionic state in complex with water, as only the decomposition of this form of dioxetanone can provide the highest light output in the light-emitting reaction of the hydromedusan photoproteins. Full article
(This article belongs to the Special Issue Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0)
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15 pages, 2505 KiB  
Review
Recombinant Influenza A Viruses Expressing Reporter Genes from the Viral NS Segment
by Luis Martinez-Sobrido and Aitor Nogales
Int. J. Mol. Sci. 2024, 25(19), 10584; https://doi.org/10.3390/ijms251910584 - 1 Oct 2024
Viewed by 475
Abstract
Studying influenza A viruses (IAVs) requires secondary experimental procedures to detect the presence of the virus in infected cells or animals. The ability to generate recombinant (r)IAV using reverse genetics techniques has allowed investigators to generate viruses expressing foreign genes, including fluorescent and [...] Read more.
Studying influenza A viruses (IAVs) requires secondary experimental procedures to detect the presence of the virus in infected cells or animals. The ability to generate recombinant (r)IAV using reverse genetics techniques has allowed investigators to generate viruses expressing foreign genes, including fluorescent and luciferase proteins. These rIAVs expressing reporter genes have allowed for easily tracking viral infections in cultured cells and animal models of infection without the need for secondary approaches, representing an excellent option to study different aspects in the biology of IAV where expression of reporter genes can be used as a readout of viral replication and spread. Likewise, these reporter-expressing rIAVs provide an excellent opportunity for the rapid identification and characterization of prophylactic and/or therapeutic approaches. To date, rIAV expressing reporter genes from different viral segments have been described in the literature. Among those, rIAV expressing reporter genes from the viral NS segment have been shown to represent an excellent option to track IAV infection in vitro and in vivo, eliminating the need for secondary approaches to identify the presence of the virus. Here, we summarize the status on rIAV expressing traceable reporter genes from the viral NS segment and their applications for in vitro and in vivo influenza research. Full article
(This article belongs to the Special Issue Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0)
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21 pages, 5473 KiB  
Review
Fluorescence of the Retinal Chromophore in Microbial and Animal Rhodopsins
by Dmitrii M. Nikolaev, Andrey A. Shtyrov, Sergey Yu. Vyazmin, Andrey V. Vasin, Maxim S. Panov and Mikhail N. Ryazantsev
Int. J. Mol. Sci. 2023, 24(24), 17269; https://doi.org/10.3390/ijms242417269 - 8 Dec 2023
Cited by 1 | Viewed by 1292
Abstract
Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low, in accordance with their functions that depend on efficient transduction of absorbed light energy. However, several recently proposed classes of engineered rhodopsins with enhanced fluorescence, along with the discovery of [...] Read more.
Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low, in accordance with their functions that depend on efficient transduction of absorbed light energy. However, several recently proposed classes of engineered rhodopsins with enhanced fluorescence, along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsin property. Here, we review the available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates, as well as different isomers of the protonated retinal Schiff base in various solvents and the gas phase. Full article
(This article belongs to the Special Issue Bioluminescent and Fluorescent Proteins: Molecular Mechanisms and Modern Applications 4.0)
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