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Cerezo J, García-Iriepa C, Santoro F, Navizet I, Prampolini G. Unraveling the contributions to the spectral shape of flexible dyes in solution: insights on the absorption spectrum of an oxyluciferin analogue. Phys Chem Chem Phys 2023; 25:5007-5020. [PMID: 36722876 DOI: 10.1039/d2cp05701h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We present a computational investigation of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH), an analogue of the emitter compound responsible for the bioluminescence in fireflies. Several factors participate in determining the 5,5-CprOxyLH's spectral shape: (i) the contribution of the four close-energy excited states, which show significant non-adiabatic couplings, (ii) the flexible molecular structure and (iii) the specific interactions established with the surrounding environment, which strongly couple the protic solvent dynamics with the dye's spectral response. To tackle the challenge to capture and dissect the role of all these effects we preliminarily investigate the role of non-adiabatic couplings with quantum dynamics simulations and a linear vibronic coupling model in the gas phase. Then, we account for both the molecular flexibility and solvent interactions by resorting to a mixed quantum classical protocol, named Adiabatic Molecular Dynamics generalized Vertical Gradient (Ad-MD|gVG), which is built on a method recently proposed by some of us. It is rooted in the partition between stiff degrees of freedom of the dye, accounted for at the vibronic level within the harmonic approximation, and flexible degrees of freedom of the solute (and of the solvent), described classically through a sampling based on Molecular Dynamics (MD). Ad-MD|gVG avoids spurious effects arising in the excited state Hessians due to non-adiabatic couplings, and can therefore be applied to account for the contributions of the first four excited states to the 5,5-CprOxyLH absorption spectrum. The final simulated spectrum is in very good agreement with the experiment, especially when the MD is driven by a refined quantum-mechanically derived force-field. More importantly, the origin of each separate contribution to the spectral shape is appropriately accounted for, paving the way to future applications of the method to more complex systems or alternative spectroscopies, as emission or circular dichroism.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Cristina García-Iriepa
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Grupo de Reactividad y Estructura Molecular (RESMOL), 28806 Alcalá de Henares (Madrid), Spain. .,Universidad de Alcalá, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28806 Alcalá de Henares (Madrid), Spain
| | - Fabrizio Santoro
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Isabelle Navizet
- Univ Gustave Eiffel, Univ Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Giacomo Prampolini
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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Sun Q, Li X, Guo Y, Qiu Y, Luo X, Liu G, Han Y. Coumarin-based turn-on fluorescence probe with a large Stokes shift for detection of endogenous neutrophil elastase in live cells and zebrafish. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121563. [PMID: 35810672 DOI: 10.1016/j.saa.2022.121563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Neutrophil elastase (NE), a serine proteinase, is a significant biomarker which is closely related to the progress of diseases. However, only few probes have been reported for detection of NE activity and cell imaging. And these probes have exhibited small Stokes shift, which leads to high fluorescence interferences. Furthermore, only one probe among them is able to image NE in vivo successfully. To overcome the above problems, we designed a novel coumarin-based fluorescent probe HNCOU-NE with large Stokes shift to visualize NE activity in living cells and zebrafish. The new probe HNCOU-NE for NE contains fluorophore HNCOU as the reporter and pentafluoroethyl as the enzyme-active trigger moiety. As expected, HNCOU-NE displays perfect detecting performance for sensing of NE, including good water solubility, large Stokes shift, high affinity and wide linear response concentration. In addition, HNCOU-NE has been successfully utilized for NE real-time detection and imaging in different living cells, exhibiting low cytotoxicity and excellent biocompatibility. Most importantly, endogenous NE fluorescence imaging experiments reveals that HNCOU-NE can distinguish liver cancer cells (HepG2) and other cells (293T, HeLa and SKOV3), illustrating its specific ability to diagnose liver cancer cells. Besides, probe HNCOU-NE also has the ability to specifically detect endogenous NE activity in living zebrafish. All the results indicate that HNCOU-NE is a valuable probe for qualitative and quantitative sensing of NE activity in vitro and in vivo.
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Affiliation(s)
- Qi Sun
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, Key Laboratory of Novel Biomass-based Environmental and Energy Materials in Petroleum and Chemical Industry and School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Xiang Li
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, Key Laboratory of Novel Biomass-based Environmental and Energy Materials in Petroleum and Chemical Industry and School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Yun Guo
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, Key Laboratory of Novel Biomass-based Environmental and Energy Materials in Petroleum and Chemical Industry and School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Yuan Qiu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, Key Laboratory of Novel Biomass-based Environmental and Energy Materials in Petroleum and Chemical Industry and School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Xiaogang Luo
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, Key Laboratory of Novel Biomass-based Environmental and Energy Materials in Petroleum and Chemical Industry and School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, China; School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, China
| | - Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, Key Laboratory of Novel Biomass-based Environmental and Energy Materials in Petroleum and Chemical Industry and School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, China.
| | - Yunfeng Han
- Department of Nuclear Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Al-Handawi MB, Polavaram S, Kurlevskaya A, Commins P, Schramm S, Carrasco-López C, Lui NM, Solntsev KM, Laptenok SP, Navizet I, Naumov P. Spectrochemistry of Firefly Bioluminescence. Chem Rev 2022; 122:13207-13234. [PMID: 35926147 DOI: 10.1021/acs.chemrev.1c01047] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.
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Affiliation(s)
- Marieh B Al-Handawi
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Srujana Polavaram
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Anastasiya Kurlevskaya
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Patrick Commins
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stefan Schramm
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Nathan M Lui
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sergey P Laptenok
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Isabelle Navizet
- Univ. Gustave Eiffel, Univ. Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Panče Naumov
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Molecular Design Institute, Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing. BIOSENSORS 2022; 12:bios12060400. [PMID: 35735548 PMCID: PMC9221268 DOI: 10.3390/bios12060400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Firefly luciferases catalyze the efficient production of yellow-green light under normal physiological conditions, having been extensively used for bioanalytical purposes for over 5 decades. Under acidic conditions, high temperatures and the presence of heavy metals, they produce red light, a property that is called pH-sensitivity or pH-dependency. Despite the demand for physiological intracellular biosensors for pH and heavy metals, firefly luciferase pH and metal sensitivities were considered drawbacks in analytical assays. We first demonstrated that firefly luciferases and their pH and metal sensitivities can be harnessed to estimate intracellular pH variations and toxic metal concentrations through ratiometric analysis. Using Macrolampis sp2 firefly luciferase, the intracellular pH could be ratiometrically estimated in bacteria and then in mammalian cells. The luciferases of Macrolampis sp2 and Cratomorphus distinctus fireflies were also harnessed to ratiometrically estimate zinc, mercury and other toxic metal concentrations in the micromolar range. The temperature was also ratiometrically estimated using firefly luciferases. The identification and engineering of metal-binding sites have allowed the development of novel luciferases that are more specific to certain metals. The luciferase of the Amydetes viviani firefly was selected for its special sensitivity to cadmium and mercury, and for its stability at higher temperatures. These color-tuning luciferases can potentially be used with smartphones for hands-on field analysis of water contamination and biochemistry teaching assays. Thus, firefly luciferases are novel color-tuning sensors for intracellular pH and toxic metals. Furthermore, a single luciferase gene is potentially useful as a dual bioluminescent reporter to simultaneously report intracellular ATP and/or luciferase concentrations luminometrically, and pH or metal concentrations ratiometrically, providing a useful tool for real-time imaging of intracellular dynamics and stress.
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de Almeida Barbosa NM, Gosset P, Réal E, Ledentu V, Didier P, Ferré N. pH-Dependent absorption spectrum of oxyluciferin analogues in the active site of firefly luciferase. Phys Chem Chem Phys 2020; 22:21731-21740. [PMID: 32985625 DOI: 10.1039/d0cp02514c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quest for the identification of the light emitter(s) responsible for the firefly bioluminescence, the study of oxyluciferin analogues with controlled chemical and electronic structures is of particular importance. In this article, we report the results of our experimental and computational investigation of the pH-dependent absorption spectra characterizing three analogues bound into the luciferase cavity, together with adenosine-monophosphate (AMP). While the analogue microscopic pKa values do not differ much from their reference values, it turns out that the AMP protonation state is analogue-dependent and never doubly-deprotonated. A careful analysis of the interactions evidences the main role of E344 glutamic acid, as well as the flexibility of the cavity which can accommodate any oxyluciferin analogue. The consideration of the absorption spectra suggests that the oxyluciferin enolate form has to be excluded from the list of the bioluminescence reaction products.
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Affiliation(s)
| | - Pauline Gosset
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
| | - Eléonore Réal
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
| | | | - Pascal Didier
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
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Manuel de Almeida Barbosa N, Zemmouche M, Gosset P, García‐Iriepa C, Ledentu V, Navizet I, Didier P, Ferré N. pH‐Dependent Absorption Spectrum of Oxyluciferin Analogues in the Presence of Adenosine Monophosphate. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Madjid Zemmouche
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi ÉchelleMSME UMR 8208 CNRS, UPEM 5 bd Descartes 77454 Marne-la-Vallée France
| | - Pauline Gosset
- Université de Strasbourg, CNRSLaboratoire de Bioimagerie et Pathologies UMR 7021 67034 Strasbourg France
| | - Cristina García‐Iriepa
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi ÉchelleMSME UMR 8208 CNRS, UPEM 5 bd Descartes 77454 Marne-la-Vallée France
- Departmento de Química Analítica, Química Física e Ingeniería QuímicaUniversidad de Alcalá, Ctra. Madrid-Barcelona Km 33,600 28871 Alcalá de Henares Spain
| | | | - Isabelle Navizet
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi ÉchelleMSME UMR 8208 CNRS, UPEM 5 bd Descartes 77454 Marne-la-Vallée France
| | - Pascal Didier
- Université de Strasbourg, CNRSLaboratoire de Bioimagerie et Pathologies UMR 7021 67034 Strasbourg France
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR 13013 Marseille France
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Goswami A, Phukan P, Barua AG. Manifestation of Peaks in a Live Firefly Flash. J Fluoresc 2019; 29:505-513. [DOI: 10.1007/s10895-019-02364-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/10/2019] [Indexed: 11/28/2022]
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Lui NM, Schramm S, Naumov P. pH-Dependent fluorescence from firefly oxyluciferin in agarose thin films. NEW J CHEM 2019. [DOI: 10.1039/c8nj05469j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emitter of the firefly bioluminescence, oxyluciferin, and its derivatives were incorporated in agarose matrix to obtain self-supporting, lightweight fluorescent acidochromic thin films. This study demonstrates an alternative approach to investigating environmental effects on bioluminescent molecules.
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Affiliation(s)
- Nathan M. Lui
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
- Department of Chemistry and Chemical Biology, Baker Laboratory
- Cornell University
| | - Stefan Schramm
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - Panče Naumov
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
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Min CG, Liu QB, Leng Y, Huang SJ, Liu CX, Yang XK, Ren AM, Pinto da Silva L. Development of firefly oxyluciferin derivatives as pH sensitive fluorescent Probes: A DFT/TDDFT study. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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García-Iriepa C, Gosset P, Berraud-Pache R, Zemmouche M, Taupier G, Dorkenoo KD, Didier P, Léonard J, Ferré N, Navizet I. Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water. J Chem Theory Comput 2018; 14:2117-2126. [DOI: 10.1021/acs.jctc.7b01240] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Cristina García-Iriepa
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Pauline Gosset
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg UMR 7504 and Labex NIE, 67034 Strasbourg, France
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, 67034 Strasbourg, France
| | - Romain Berraud-Pache
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Madjid Zemmouche
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Grégory Taupier
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg UMR 7504 and Labex NIE, 67034 Strasbourg, France
| | - Kokou Dodzi Dorkenoo
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg UMR 7504 and Labex NIE, 67034 Strasbourg, France
| | - Pascal Didier
- Université de Strasbourg, CNRS, Laboratoire de Bioimagerie et Pathologies UMR 7021, 67034 Strasbourg, France
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg UMR 7504 and Labex NIE, 67034 Strasbourg, France
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Isabelle Navizet
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France
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