1
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Kabir MP, Ghosh P, Gozem S. Electronic Structure Methods for Simulating Flavin's Spectroscopy and Photophysics: Comparison of Multi-reference, TD-DFT, and Single-Reference Wave Function Methods. J Phys Chem B 2024. [PMID: 39074870 DOI: 10.1021/acs.jpcb.4c03748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The use of flavins and flavoproteins in photocatalytic, sensing, and biotechnological applications has led to a growing interest in computationally modeling the excited-state electronic structure and photophysics of flavin. However, there is limited consensus regarding which computational methods are appropriate for modeling flavin's photophysics. We compare the energies of low-lying excited states of flavin computed with time-dependent density functional theory (TD-DFT), equation-of-motion coupled cluster (EOM-EE-CCSD), scaled opposite-spin configuration interaction [SOS-CIS(D)], multiconfiguration pair-density functional theory (MC-PDFT), and several multireference perturbation theory (MR-PT2) methods. In the first part, we focus on excitation energies of the first singlet excited state (S1) of five different redox and protonation states of flavin, with the goal of finding a suitable active space for MR-PT2 calculations. In the second part, we construct two sets of one-dimensional potential energy surfaces connecting the S0 and S1 equilibrium geometries (S0-S1 path) and the S1 (π,π*) and S2 (n,π*) equilibrium geometries (S1-S2 path). The first path therefore follows a Franck-Condon active mode of flavin while the second path maps crossings points between low-lying singlet and triplet states in flavin. We discuss the similarities and differences in the TD-DFT, EOM-EE-CCSD, SOS-CIS(D), MC-PDFT and MR-PT2 energy profiles along these paths. We find that (TD-)DFT methods are suitable for applications such as simulating the spectra of flavins but are inconsistent with several other methods when used for some geometry optimizations and when describing the energetics of dark (n,π*) states. MR-PT2 methods show promise for the simulation of flavin's low-lying excited states, but the selection of orbitals for the active space and the number of roots used for state averaging must be done carefully to avoid artifacts. Some properties, such as the intersystem crossing geometry and energy between the S1 (π,π*) and T2 (n,π*) states, may require additional benchmarking before they can be determined quantitatively.
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Affiliation(s)
- Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Paulami Ghosh
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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2
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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3
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Bracker M, Kubitz MK, Czekelius C, Marian CM, Kleinschmidt M. Computer‐Aided Design of Fluorinated Flavin Derivatives by Modulation of Intersystem Crossing and Fluorescence. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mario Bracker
- Institute of Theoretical and Computational Chemistry Heinrich-Heine-University Düsseldorf D-40204 Düsseldorf Germany
| | - Mira K. Kubitz
- Institute of Organic and Macromolecular Chemistry Heinrich-Heine-University Düsseldorf D-40204 Düsseldorf Germany
| | - Constantin Czekelius
- Institute of Organic and Macromolecular Chemistry Heinrich-Heine-University Düsseldorf D-40204 Düsseldorf Germany
| | - Christel M. Marian
- Institute of Theoretical and Computational Chemistry Heinrich-Heine-University Düsseldorf D-40204 Düsseldorf Germany
| | - Martin Kleinschmidt
- Institute of Theoretical and Computational Chemistry Heinrich-Heine-University Düsseldorf D-40204 Düsseldorf Germany
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4
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Comparing ultrafast excited state quenching of flavin 1,N 6-ethenoadenine dinucleotide and flavin adenine dinucleotide by optical spectroscopy and DFT calculations. Photochem Photobiol Sci 2022; 21:959-982. [PMID: 35218554 DOI: 10.1007/s43630-022-00187-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 02/01/2022] [Indexed: 10/19/2022]
Abstract
Flavins are photoenzymatic cofactors often exploiting the absorption of light to energize photoinduced redox chemistry in a variety of contexts. Both flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are used for this function. The study of these photoenzymes has been facilitated using flavin analogs. Most of these analogs involve modification of the flavin ring, and there is recent evidence that adenine (Ade)-modified FAD can affect enzyme turnover, but so far this has only been shown for enzymes where the adenine and flavin rings are close to each other in a stacked conformation. FAD is also stacked in aqueous solution, and its photodynamics are quite different from unstacked FAD or FMN. Oxidized photoexcited FAD decays rapidly, presumably through PET with Ade as donor and Fl* as acceptor. Definitive identification of the spectral signatures of Ade∙+ and Fl∙- radicals is elusive. Here we use the FAD analog Flavin 1,N6-Ethenoadenine Dinucleotide (εFAD) to study how different photochemical outcomes depend on the identity of the Ade moiety in stacked FAD and its analog εFAD. We have used UV-Vis transient absorption spectroscopy complemented by TD-DFT calculations to investigate the excited state evolution of the flavins. In FAD*, no radicals were observed, suggesting that FAD* does not undergo PET. εFAD* kinetics showed a broad absorption band that suggests a charge transfer state exists upon photoexcitation with evidence for radical pair formation. Surprisingly, significant triplet flavin was produced from εFAD* We hypothesize that the dipolar (ε)Ade moieties differentially modulate the singlet-triplet energy gap, resulting in different intersystem crossing rates. The additional electron density on the etheno group of εFAD supplies better orbital overlap with the flavin S1 state, accelerating charge transfer in that molecule.
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5
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Mogensen DJ, Westberg M, Breitenbach T, Etzerodt M, Ogilby PR. Stable Transfection of the Singlet Oxygen Photosensitizing Protein SOPP3: Examining Aspects of Intracellular Behavior †. Photochem Photobiol 2021; 97:1417-1430. [PMID: 33934354 DOI: 10.1111/php.13440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/26/2021] [Indexed: 01/28/2023]
Abstract
Protein-encased chromophores that photosensitize the production of reactive oxygen species, ROS, have been the center of recent activity in studies of oxidative stress. One potential attribute of such systems is that the local environment surrounding the chromophore, and that determines the chromophore's photophysics, ideally remains constant and independent of the global environment into which the system is placed. Therefore, a protein-encased sensitizer localized in the mitochondria would arguably have the same photophysics as that protein-encased sensitizer at the plasma membrane, for example. One thus obtains a useful tool to study processes modulated by spatially localized ROS. One ROS of interest is singlet oxygen, O2 (a1 Δg ). We recently developed a singlet oxygen photosensitizing protein, SOPP, in which flavin mononucleotide, FMN, is encased in a re-engineered light-oxygen-voltage protein. One goal was to ascertain how a version of this system, SOPP3, which selectively makes O2 (a1 Δg ), in vitro, behaves in a cell. We now demonstrate that SOPP3 undergoes exacerbated irradiation-mediated bleaching when expressed at either the plasma membrane or mitochondria in stable cell lines. We find that the environment around the SOPP3 system affects the bleaching rate, which argues against one of the key suppositions in support of a protein-encased chromophore.
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Affiliation(s)
| | | | | | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University, Aarhus, Denmark
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6
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Cardoso
Ramos F, Cupellini L, Mennucci B. Computational Investigation of Structural and Spectroscopic Properties of LOV-Based Proteins with Improved Fluorescence. J Phys Chem B 2021; 125:1768-1777. [PMID: 33566620 PMCID: PMC7917436 DOI: 10.1021/acs.jpcb.0c10834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/27/2021] [Indexed: 01/22/2023]
Abstract
Flavin-based fluorescent proteins are a class of fluorescent reporters derived from light, oxygen, and voltage (LOV) sensing proteins. Through mutagenesis, natural LOV proteins have been engineered to obtain improved fluorescence properties. In this study, we combined extended classical Molecular Dynamics simulations and multiscale Quantum Mechanics/Molecular Mechanics methods to clarify the relationship between structural and dynamic changes induced by specific mutations and the spectroscopic response. To reach this goal we compared two LOV variants, one obtained by the single mutation needed to photochemically inactivate the natural system, and the other (iLOV) obtained through additional mutations and characterized by a significantly improved fluorescence. Our simulations confirmed the "flipping and crowding" effect induced in iLOV by the additional mutations and revealed its mechanism of action. We also showed that these mutations, and the resulting differences in the composition and flexibility of the binding pockets, are not reflected in significant shifts of the excitation and emission energies, in agreement with the similarity of the spectra measured for the two systems. However, a small but consistent reduction was found in the Stokes shift of iLOV, suggesting a reduction of the intermolecular reorganization experienced by the chromophore after excitation, which could slow down its internal conversion to the ground state and improve the fluorescence.
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Affiliation(s)
- Felipe Cardoso
Ramos
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
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7
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Brisker-Klaiman D, Dreuw A. On the influence of dimerisation of lumiflavin in aqueous solution on its optical spectra – a quantum chemical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1616843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Daria Brisker-Klaiman
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
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8
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Bracker M, Dinkelbach F, Weingart O, Kleinschmidt M. Impact of fluorination on the photophysics of the flavin chromophore: a quantum chemical perspective. Phys Chem Chem Phys 2019; 21:9912-9923. [DOI: 10.1039/c9cp00805e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
10-Methylisoalloxazine (MIA) and its fluorinated derivatives (6-9F-MIA) were investigated by means of quantum chemistry, looking into the influence of fluorination on fluorescence, absorption and inter-system crossing (ISC) in vacuum and in aqueous solution.
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Affiliation(s)
- Mario Bracker
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Fabian Dinkelbach
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Martin Kleinschmidt
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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9
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Applications of molecular modeling to flavoproteins: Insights and challenges. Methods Enzymol 2019; 620:277-314. [DOI: 10.1016/bs.mie.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Marian CM, Heil A, Kleinschmidt M. The DFT/MRCI method. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1394] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Christel M. Marian
- Institute of Theoretical and Computational Chemistry Heinrich Heine Universität Düsseldorf Düsseldorf
| | - Adrian Heil
- Institute of Theoretical and Computational Chemistry Heinrich Heine Universität Düsseldorf Düsseldorf
| | - Martin Kleinschmidt
- Institute of Theoretical and Computational Chemistry Heinrich Heine Universität Düsseldorf Düsseldorf
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11
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Initial excited state structural dynamics of lumiflavin upon ultraviolet excitation. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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12
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Penfold TJ, Gindensperger E, Daniel C, Marian CM. Spin-Vibronic Mechanism for Intersystem Crossing. Chem Rev 2018; 118:6975-7025. [DOI: 10.1021/acs.chemrev.7b00617] [Citation(s) in RCA: 401] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Thomas J. Penfold
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon-Tyne NE1 7RU, United Kingdom
| | - Etienne Gindensperger
- Laboratoire de Chimie Quantique, Institut de Chimie UMR-7177, CNRS - Université de Strasbourg, 1 Rue Blaise Pascal 67008 Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie UMR-7177, CNRS - Université de Strasbourg, 1 Rue Blaise Pascal 67008 Strasbourg, France
| | - Christel M. Marian
- Institut für Theoretische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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13
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Khrenova MG, Meteleshko YI, Nemukhin AV. Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers. J Phys Chem B 2017; 121:10018-10025. [DOI: 10.1021/acs.jpcb.7b07533] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yulia I. Meteleshko
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - 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
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14
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Nakagawa S, Weingart O, Marian CM. Dual Photochemical Reaction Pathway in Flavin-Based Photoreceptor LOV Domain: A Combined Quantum-Mechanics/Molecular-Mechanics Investigation. J Phys Chem B 2017; 121:9583-9596. [PMID: 28926259 DOI: 10.1021/acs.jpcb.7b09207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The primary photochemical reaction of the light, oxygen, and voltage (LOV) domain of the blue-light photosensor YtvA of Bacillus subtilis were investigated using high-level QM(DFT/MRCI)/MM methods. After blue-light excitation, the Sγ atom of the reactive cysteine forms a covalent bond with the C4a of the flavin mononucleotide (FMN) ring. Two conformations for the side chain of reactive cysteine with occupancies of 70% (conf A) and 30% (conf B) are observed in the X-ray crystallographic structures of the YtvA-LOV ( Möglich , A. ; Moffat , K. J. Mol. Biol. 2007 , 373 , 112 - 126 ). In conf A, the thiol group is directed toward the dimethylbenzene moiety of the FMN ring whereas it is placed directly above the N5 atom of the FMN ring in conf B. Starting from both conformations, the singlet and triplet excited pathways were evaluated. The singlet states excited from conf A decay nonradiatively to the triplet states by intersystem crossing (ISC). After the formation of a neutral biradical, the triplet states cross over to the electronic ground state by a second ISC and the adducts are efficiently formed. The singlet states excited from conf B are located near the S1/S0 conical intersection (CIn). A major fraction returns to the initial states through the CIn. The rest may directly reach the adduct state. Thus, the photoexcitation has a dual reaction pathway. In YtvA-LOV, it is inferred that the efficient triplet excitation from conf A was chosen by bypassing the less efficient singlet excitation from conf B.
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Affiliation(s)
- Setsuko Nakagawa
- Department of Human Life and Environment, Kinjo Gakuin University , Omori, Moriyama-ku, Nagoya 463-8521, Japan
| | - Oliver Weingart
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Christel M Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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15
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Chang XP, Gao YJ, Fang WH, Cui G, Thiel W. Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor. Angew Chem Int Ed Engl 2017. [PMID: 28632317 DOI: 10.1002/anie.201703487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The dark- and light-adapted states of YtvA LOV domains exhibit distinct excited-state behavior. We have employed high-level QM(MS-CASPT2)/MM calculations to study the photochemical reactions of the dark- and light-adapted states. The photoreaction from the dark-adapted state starts with an S1 →T1 intersystem crossing followed by a triplet-state hydrogen transfer from the thiol to the flavin moiety that produces a diradical intermediate, and a subsequent internal conversion that triggers a barrierless C-S bond formation in the S0 state. The energy profiles for these transformations are different for the four conformers of the dark-adapted state considered. The photochemistry of the light-adapted state does not involve the triplet state: photoexcitation to the S1 state triggers C-S bond cleavage followed by recombination in the S0 state; both these processes are essentially barrierless and thus ultrafast. The present work offers new mechanistic insights into the photoresponse of flavin-containing blue-light photoreceptors.
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Affiliation(s)
- Xue-Ping Chang
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Yuan-Jun Gao
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Ganglong Cui
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
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16
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Chang XP, Gao YJ, Fang WH, Cui G, Thiel W. Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xue-Ping Chang
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Yuan-Jun Gao
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Wei-Hai Fang
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Ganglong Cui
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung; 45470 Mülheim an der Ruhr Germany
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17
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Westberg M, Bregnhøj M, Etzerodt M, Ogilby PR. Temperature Sensitive Singlet Oxygen Photosensitization by LOV-Derived Fluorescent Flavoproteins. J Phys Chem B 2017; 121:2561-2574. [PMID: 28257211 DOI: 10.1021/acs.jpcb.7b00561] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Optogenetic sensitizers that selectively produce a given reactive oxygen species (ROS) constitute a promising tool for studying cell signaling processes with high levels of spatiotemporal control. However, to harness the full potential of this tool for live cell studies, the photophysics of currently available systems need to be explored further and optimized. Of particular interest in this regard, are the flavoproteins miniSOG and SOPP, both of which (1) contain the chromophore flavin mononucleotide, FMN, in a LOV-derived protein enclosure, and (2) photosensitize the production of singlet oxygen, O2(a1Δg). Here we present an extensive experimental study of the singlet and triplet state photophysics of FMN in SOPP and miniSOG over a physiologically relevant temperature range. Although changes in temperature only affect the singlet excited state photophysics slightly, the processes that influence the deactivation of the triplet excited state are more sensitive to temperature. Most notably, for both proteins, the rate constant for quenching of 3FMN by ground state oxygen, O2(X3Σg-), increases ∼10-fold upon increasing the temperature from 10 to 43 °C, while the oxygen-independent channels of triplet state deactivation are less affected. As a consequence, this increase in temperature results in higher yields of O2(a1Δg) formation for both SOPP and miniSOG. We also show that the quantum yields of O2(a1Δg) production by both miniSOG and SOPP are mainly limited by the fraction of FMN triplet states quenched by O2(X3Σg-). The results presented herein provide a much-needed quantitative framework that will facilitate the future development of optogenetic ROS sensitizers.
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Affiliation(s)
- Michael Westberg
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
| | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University , DK-8000 Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University , DK-8000 Aarhus, Denmark
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18
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Davari MD, Kopka B, Wingen M, Bocola M, Drepper T, Jaeger KE, Schwaneberg U, Krauss U. Photophysics of the LOV-Based Fluorescent Protein Variant iLOV-Q489K Determined by Simulation and Experiment. J Phys Chem B 2016; 120:3344-52. [DOI: 10.1021/acs.jpcb.6b01512] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehdi D. Davari
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
| | - Benita Kopka
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Marcus Wingen
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Marco Bocola
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
| | - Thomas Drepper
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
- Institut
für Bio- und Geowissenschaften, IBG-1, Biotechnologie, Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Ulrich Krauss
- Institut
für Molekulare Enzymtechnologie, Heinrich Heine University
Düsseldorf, Forschungszentrum Jülich, 52426 Jülich, Germany
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19
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Karasulu B, Götze JP, Thiel W. Assessment of Franck-Condon Methods for Computing Vibrationally Broadened UV-vis Absorption Spectra of Flavin Derivatives: Riboflavin, Roseoflavin, and 5-Thioflavin. J Chem Theory Comput 2015; 10:5549-66. [PMID: 26583238 DOI: 10.1021/ct500830a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We address the performance of the vertical and adiabatic Franck-Condon (VFC/AFC) approaches combined with time-independent or time-dependent (TI/TD) formalisms in simulating the one-photon absorption spectra of three flavin compounds with distinct structural features. Calculations were done in the gas phase and in two solvents (water, benzene) for which experimental reference measurements are available. We utilized the independent mode displaced harmonic oscillator model without or with frequency alteration (IMDHO/IMDHO-FA) and also accounted for Duschinsky mixing effects. In the initial validation on the first excited singlet state of riboflavin, the range-separated functionals, CAM-B3LYP and ωB97xD, showed the best performance, but B3LYP also gave a good compromise between peak positions and spectral topology. Large basis sets were not mandatory to obtain high-quality spectra for the selected systems. The presence of a symmetry plane facilitated the computation of vibrationally broadened spectra, since different FC variants yield similar results and the harmonic approximation holds rather well. Compared with the AFC approach, the VFC approach performed equally well or even better for all three flavins while offering several advantages, such as avoiding error-prone geometry optimization procedures on excited-state surfaces. We also explored the advantages of curvilinear displacements and of a Duschinsky treatment for the AFC spectra in cases when a rotatable group is present on the chromophore. Taken together, our findings indicate that the combination of the VFC approach with the TD formalism and the IMDHO-FA model offers the best overall performance.
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Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Jan Philipp Götze
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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20
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Falklöf O, Durbeej B, Norman P. Inter-Excited-State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin. J Phys Chem A 2015; 119:11911-21. [DOI: 10.1021/acs.jpca.5b08908] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Olle Falklöf
- Division of Theoretical
Chemistry, IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - Bo Durbeej
- Division of Theoretical
Chemistry, IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - Patrick Norman
- Division of Theoretical
Chemistry, IFM, Linköping University, SE-581 83 Linköping, Sweden
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21
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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22
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Khrenova MG, Nemukhin AV, Domratcheva T. Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant. J Phys Chem B 2015; 119:5176-83. [DOI: 10.1021/acs.jpcb.5b01299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
| | - Tatiana Domratcheva
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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23
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Karasulu B, Thiel W. Photoinduced Intramolecular Charge Transfer in an Electronically Modified Flavin Derivative: Roseoflavin. J Phys Chem B 2014; 119:928-43. [DOI: 10.1021/jp506101x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470, Mülheim, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470, Mülheim, Germany
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24
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Hou C, Liu YJ, Ferré N, Fang WH. Understanding Bacterial Bioluminescence: A Theoretical Study of the Entire Process, from Reduced Flavin to Light Emission. Chemistry 2014; 20:7979-86. [DOI: 10.1002/chem.201400253] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Indexed: 11/08/2022]
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25
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Marian CM, Nakagawa S, Rai-Constapel V, Karasulu B, Thiel W. Photophysics of flavin derivatives absorbing in the blue-green region: thioflavins as potential cofactors of photoswitches. J Phys Chem B 2014; 118:1743-53. [PMID: 24479961 DOI: 10.1021/jp4098233] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The purpose of this study was to find flavin derivatives with absorption maxima in the blue-green region of the visible spectrum that might be used as alternative cofactors in blue-light photoreceptors. To this end, the vertical absorption spectra of eight lumiflavin-related compounds were calculated by means of quantum chemical methods. The compounds differ from lumiflavin by the subsitution of an S atom for an O atom at the 2- and/or 4-positions of the isoalloxazine core, the substitution of an N atom for a CH group in the 6- and/or 9-positions, or an extension of the π system at the 7- and 8-positions. For the three most promising compounds, 2-thio-lumiflavin, 4-thio-lumiflavin, and 2,4-dithio-lumiflavin, the quantum chemical investigations were extended to include geometry relaxations in the excited states, rates for spin-forbidden transitions and an estimate of spectral shifts brought about by polar protic environments. We find these thiocarbonyl compounds to have very promising excited-state properties. They absorb in the blue-green wavelength regime around 500 nm, i.e., substantially red-shifted with respect to lumiflavin that is the cofactor of natural blue-light photoreceptors. Their triplet quantum yields are predicted to be close to unity while their triplet lifetimes are long enough to enable bimolecular photochemical reactions. The combination of these properties makes the thioflavins potentially suitable candidates as cofactors in biomimetic photoswitches.
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Affiliation(s)
- Christel M Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstr. 1, D-40225 Düsseldorf, Germany
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26
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List NH, Pimenta FM, Holmegaard L, Jensen RL, Etzerodt M, Schwabe T, Kongsted J, Ogilby PR, Christiansen O. Effect of chromophore encapsulation on linear and nonlinear optical properties: the case of “miniSOG”, a protein-encased flavin. Phys Chem Chem Phys 2014; 16:9950-9. [DOI: 10.1039/c3cp54470b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Domratcheva T, Udvarhelyi A, Shahi ARM. Computational spectroscopy, dynamics, and photochemistry of photosensory flavoproteins. Methods Mol Biol 2014; 1146:191-228. [PMID: 24764094 DOI: 10.1007/978-1-4939-0452-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Extensive interest in photosensory proteins stimulated computational studies of flavins and flavoproteins in the past decade. This review is dedicated to the three central topics of these studies: calculations of flavin UV-visible and IR spectra, simulated dynamics of photoreceptor proteins, and flavin photochemistry. Accordingly, this chapter is divided into three parts; each part describes corresponding computational protocols, summarizes computational results, and discusses the emerging mechanistic picture.
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Affiliation(s)
- Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany,
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28
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Silva MR, Mansurova M, Gärtner W, Thiel W. Photophysics of structurally modified flavin derivatives in the blue-light photoreceptor YtvA: a combined experimental and theoretical study. Chembiochem 2013; 14:1648-61. [PMID: 23940057 DOI: 10.1002/cbic.201300217] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Indexed: 11/10/2022]
Abstract
The light-induced processes of two flavin mononucleotide derivatives (1- and 5-deaza flavin mononucleotide, 1DFMN and 5DFMN), incorporated into the LOV domain of YtvA protein from Bacillus subtilis, were studied by a combination of experimental and computational methods. Quantum mechanics/molecular mechanics (QM/MM) calculations were carried out in which the QM part was treated by density functional theory (DFT) using the B3LYP functional for geometry optimizations and the DFT/MRCI method for spectroscopic properties, whereas the MM part was described by the CHARMM force field. 1DFMN is incorporated into the protein binding site, yielding a red-shifted absorption band (λ(max) =530 nm compared to YtvA wild-type λ(max) =445 nm), but does not undergo any LOV-typical photoreactions such as triplet and photoadduct formation. QM/MM computations confirmed the absence of a channel for triplet formation and located a radiation-free channel (through an S₁/S₀ conical intersection) along a hydrogen transfer path that might allow for fast deactivation. By contrast, 5DFMN-YtvA-LOV shows a blue-shifted absorption (λ(max) =410 nm) and undergoes similar photochemical processes to FMN in the wild-type protein, both with regard to the photophysics and the formation of a photoadduct with a flavin-cysteinyl covalent bond. The QM/MM calculations predict a mechanism that involves hydrogen transfer in the T₁ state, followed by intersystem crossing and adduct formation in the S₀ state for the forward reaction. Experimentally, in contrast to wild-type YtvA, dark-state recovery in 5DFMN-YtvA-LOV is not thermally driven but can only be accomplished after absorption of a second photon by the photoadduct, again via the triplet state. The QM/MM calculations suggest a photochemical mechanism for dark-state recovery that is accessible only for the adduct with a C4a--S bond but not for alternative adducts with a C5--S bond.
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Affiliation(s)
- Mario R Silva
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
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29
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Hedegård ED, List NH, Jensen HJA, Kongsted J. The multi-configuration self-consistent field method within a polarizable embedded framework. J Chem Phys 2013; 139:044101. [DOI: 10.1063/1.4811835] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Metz S, Kästner J, Sokol AA, Keal TW, Sherwood P. C
hem
S
hell—a modular software package for
QM
/
MM
simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1163] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Metz
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Johannes Kästner
- Institute of Theoretical ChemistryUniversity of StuttgartStuttgartGermany
| | | | - Thomas W. Keal
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Paul Sherwood
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
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31
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Udvarhelyi A, Domratcheva T. Glutamine Rotamers in BLUF Photoreceptors: A Mechanistic Reappraisal. J Phys Chem B 2013; 117:2888-97. [DOI: 10.1021/jp400437x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anikó Udvarhelyi
- Department of Biomolecular
Mechanisms, Max Planck Institute for Medical Research, Jahnstraße
29, 69120 Heidelberg, Germany
| | - Tatiana Domratcheva
- Department of Biomolecular
Mechanisms, Max Planck Institute for Medical Research, Jahnstraße
29, 69120 Heidelberg, Germany
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32
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Mansurova M, Simon J, Salzmann S, Marian CM, Gärtner W. Spectroscopic and Theoretical Study on Electronically Modified Chromophores in LOV Domains: 8-Bromo- and 8-Trifluoromethyl-Substituted Flavins. Chembiochem 2013; 14:645-54. [DOI: 10.1002/cbic.201200670] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Indexed: 11/11/2022]
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33
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Falklöf O, Durbeej B. Modeling of phytochrome absorption spectra. J Comput Chem 2013; 34:1363-74. [DOI: 10.1002/jcc.23265] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Olle Falklöf
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
| | - Bo Durbeej
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
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34
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Solov’yov IA, Domratcheva T, Shahi ARM, Schulten K. Decrypting cryptochrome: revealing the molecular identity of the photoactivation reaction. J Am Chem Soc 2012; 134:18046-52. [PMID: 23009093 PMCID: PMC3500783 DOI: 10.1021/ja3074819] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Migrating birds fly thousands of miles or more, often without visual cues and in treacherous winds, yet keep direction. They employ for this purpose, apparently as a powerful navigational tool, the photoreceptor protein cryptochrome to sense the geomagnetic field. The unique biological function of cryptochrome supposedly arises from a photoactivation reaction involving radical pair formation through electron transfer. Radical pairs, indeed, can act as a magnetic compass; however, the cryptochrome photoreaction pathway is not fully resolved yet. To reveal this pathway and underlying photochemical mechanisms, we carried out a combination of quantum chemical calculations and molecular dynamics simulations on plant ( Arabidopsis thaliana ) cryptochrome. The results demonstrate that after photoexcitation a radical pair forms, becomes stabilized through proton transfer, and decays back to the protein's resting state on time scales allowing the protein, in principle, to act as a radical pair-based magnetic sensor. We briefly relate our findings on A. thaliana cryptochrome to photoreaction pathways in animal cryptochromes.
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35
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Pohler L, Kleinschmidt M, Etinski M, Marian CM. In search of the dark state of 5-methyl-2-hydroxypyrimidine using a numerical DFT/MRCI gradient. Mol Phys 2012. [DOI: 10.1080/00268976.2012.695030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Larissa Pohler
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
| | - Martin Kleinschmidt
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
| | - Mihajlo Etinski
- b Faculty of Physical Chemistry , University of Belgrade , Studentski Trg 12-16, 11000 Belgrade , Serbia
| | - Christel M. Marian
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
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36
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Spin-orbit coupling and intersystem crossing in molecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.83] [Citation(s) in RCA: 412] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Etinski M, Tatchen J, Marian CM. Time-dependent approaches for the calculation of intersystem crossing rates. J Chem Phys 2011; 134:154105. [DOI: 10.1063/1.3575582] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Raffelberg S, Mansurova M, Gärtner W, Losi A. Modulation of the photocycle of a LOV domain photoreceptor by the hydrogen-bonding network. J Am Chem Soc 2011; 133:5346-56. [PMID: 21410163 DOI: 10.1021/ja1097379] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An extended hydrogen-bonding (HB) network stabilizes the isoalloxazine ring of the flavin mononucleotide (FMN) chromophore within the photosensing LOV domain of blue-light protein receptors, via interactions between the C(2)═O, N(3)H, C(4)═O, and N(5) groups and conserved glutamine and asparagine residues. In this work we studied the influence of the HB network on the efficiency, kinetics, and energetics of a LOV protein photocycle, involving the reversible formation of a FMN-cysteine covalent adduct. The following results were found for mutations of the conserved amino acids N94, N104, and Q123 in the Bacillus subtilis LOV protein YtvA: (i) Increased (N104D, N94D) or strongly reduced (N94A) rate of adduct formation; this latter mutation extends the lifetime of the flavin triplet state, i.e., adduct formation, more than 60-fold, from 2 μs for the wild-type (WT) protein to 129 μs. (ii) Acceleration of the overall photocycle for N94S, N94A, and Q123N, with recovery lifetimes 20, 45, and 85 times faster than for YtvA-WT, respectively. (iii) Slight modifications of FMN spectral features, correlated with the polarization of low-energy transitions. (iv) Strongly reduced (N94S) or suppressed (Q123N) structural volume changes accompanying adduct formation, as determined by optoacoustic spectroscopy. (v) Minor effects on the quantum yield, with the exception of a considerable reduction for Q123N, i.e., 0.22 vs 0.49 for YtvA-WT. The data stress the importance of the HB network in modulating the photocycle of LOV domains, while at the same time establishing a link with functional responses.
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Affiliation(s)
- Sarah Raffelberg
- Max-Planck-Institute for Bioinorganic Chemistry, Stiftstrasse 34-36, 45470 Mülheim, Germany
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39
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Sneskov K, Schwabe T, Kongsted J, Christiansen O. The polarizable embedding coupled cluster method. J Chem Phys 2011; 134:104108. [DOI: 10.1063/1.3560034] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Peter E, Dick B, Baeurle SA. Effect of computational methodology on the conformational dynamics of the protein photosensor LOV1 from Chlamydomonas reinhardtii. J Chem Biol 2011; 4:167-84. [PMID: 22408688 DOI: 10.1007/s12154-011-0060-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 02/17/2011] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED LOV domains are the light-sensitive protein domains of plant phototropins and bacteria. They photochemically form a covalent bond between a flavin mononucleotide (FMN) chromophore and a cysteine, attached to the apo-protein, upon irradiation with blue light, which triggers a signal in the adjacent kinase. Although their signaling state has been well characterized through experimental means, their signal transduction pathway as well as dark-state activity are generally only poorly understood. Here we show results from molecular dynamics simulations where we investigated the effect of thermostating and long-range electrostatics on the solution structure and dynamical behavior of the wild-type LOV1 domain from the green algae Chlamydomonas reinhardtii in the dark. We demonstrate that these computational issues can dramatically affect the conformational fluctuations of such protein domains by suppressing configurations far from equilibrium or destabilizing local configurations, leading to artificial changes of the protein secondary structure as well as the H-bond network formed by the amino acids and the FMN. By comparing our calculation results with recent experimental data, we show that the non-invasive thermostating strategy, where the protein solute is only indirectly coupled to the thermostat via the solvent, in conjunction with the particle-mesh Ewald technique, provides dark-state conformers, which are in consistency with experimental observations. Moreover, our calculations indicate that the LOV1 domains can alter the intersystem crossing rate and rate of adduct formation by adjusting the population distribution of these dark-state conformers. This might permit them to function as a modulator of the signal intensity under low light conditions. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s12154-011-0060-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuel Peter
- Department of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
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41
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Moyon NS, Mitra S. Fluorescence solvatochromism in lumichrome and excited-state tautomerization: a combined experimental and DFT study. J Phys Chem A 2011; 115:2456-64. [PMID: 21388154 DOI: 10.1021/jp1102687] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence solvatochromism of lumichrome (LC) was studied by steady-state and time-resolved fluorescence spectroscopy. The excited-state properties of LC do not show any correlation with solvent polarity, however, reasonably good correlation with solvent E(T)(30) parameter was observed. A quantitative estimation of contribution from different solvatochromic parameters, like solvent polarizability (π*), hydrogen bond donor (α), and hydrogen bond acceptor (β) ability of the solvent, was made using linear free energy relationship on the basis of Kamlet-Taft equation. The analysis reveals that hydrogen bond donating ability (acidity) of the solvent is the most important parameter that characterizes the excited-state behavior of lumichrome. Quantum mechanical calculations using density functional theory (DFT) were done to study the most stable structure and excited-state tautomerization process of LC toward the formation of isoalloxazines. Charge localization in the excited state and formation of hydrogen-bonded cluster through solvent hydrogen bond donation on the N10 atom of alloxazine moiety were predicted to be the key step toward this water-catalyzed tautomerization process.
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42
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Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site. Biochemistry 2011; 50:2411-23. [PMID: 21323358 DOI: 10.1021/bi200198x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Phototropins, a class of light-activated protein kinases, are essential for several blue light responses in plants and algae, including phototropism. These proteins contain two internal light, oxygen, and voltage sensitive (LOV) domains, which bind flavin chromophores and undergo a reversible photochemical formation of a cysteinyl-flavin adduct as part of the light sensing process. While the photodynamic properties of such photosensory domains are dictated by interactions between the chromophore and surrounding protein, more distant residues can play a significant role as well. Here we explore the role of the Phe434 residue in the photosensory response of the second LOV domain of Avena sativa phototropin 1 (AsLOV2), a model photochemical system for these LOV domains. Phe434 is more than 6 Å from the FMN chromophore in AsLOV2; nevertheless, an F434Y point mutation is likely to change several structural features of the chromophore binding site, as we demonstrate using molecular dynamics simulations. Transient absorption signals spanning 15 decades in time were compared for wild-type AsLOV2 and the F434Y mutant, showing that the latter has significantly altered photodynamics, including (i) a faster intersystem crossing leading to triplet formation on a nanosecond time scale, (ii) biphasic formation of adduct-state kinetics on the microsecond time scale, and (iii) greatly accelerated ground-state recovery kinetics on a second time scale. We present mechanistic models that link these spectroscopic differences to changes in the configuration of the critical cysteine residue and in the chromophore's accessibility to solvent and oxygen according to MD trajectories and purging experiments. Taken together, these results demonstrate the importance of residues outside the chromophore-binding pocket in modulating LOV domain photodynamics.
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43
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Udvarhelyi A, Domratcheva T. Photoreaction in BLUF Receptors: Proton-coupled Electron Transfer in the Flavin-Gln-Tyr System†. Photochem Photobiol 2011; 87:554-63. [DOI: 10.1111/j.1751-1097.2010.00884.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mansurova M, Scheercousse P, Simon J, Kluth M, Gärtner W. Chromophore exchange in the blue light-sensitive photoreceptor YtvA from Bacillus subtilis. Chembiochem 2011; 12:641-6. [PMID: 21259411 DOI: 10.1002/cbic.201000515] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Indexed: 11/08/2022]
Abstract
YtvA from Bacillus subtilis was found as the first prokaryotic phototropin-like blue-light-responsive photoreceptor. It is composed of two domains, the photoactive LOV (light, oxygen, voltage) domain, which binds a flavin mononucleotide (FMN) as a chromophore and a STAS (sulfate transporter/anti-sigma-factor antagonist) domain, which generates a physiological signal. Here we present a routine chromophore-exchange protocol that allows chemically synthesized, structurally modified chromophores instead of the naturally present flavin mononucleotide (FMN) chromophore to be introduced. FMN was exchanged for riboflavin (RF), flavin adenine dinucleotide (FAD), 7,8-didemethyl flavin mononucleotide (DMFMN), and 8-isopropyl flavin mononucleotide (iprFMN). LOV domains reconstituted with new flavins undergo the same photocycle as native YtvA LOV, consisting of triplet formation and covalent binding of the chromophore followed by a thermal recovery of the parent state, albeit with different kinetics and photophysical properties. Interestingly, the iprFMN chromophore, inducing steric hindrances to the protein, exhibits a very fast light-to-dark-conversion and shows a high fluorescence quantum yield (0.4). Incorporation of FAD causes an increase of its fluorescence quantum yield from 0.04 (H(2)O) to 0.2.
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Affiliation(s)
- Madina Mansurova
- Max Planck Institute for Bioinorganic Chemistry, Postfach 10135, 45410 Mülheim an der Ruhr, Germany.
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Pauwels E, Declerck R, Verstraelen T, De Sterck B, Kay CWM, Van Speybroeck V, Waroquier M. Influence of Protein Environment on the Electron Paramagnetic Resonance Properties of Flavoprotein Radicals: A QM/MM Study. J Phys Chem B 2010; 114:16655-65. [DOI: 10.1021/jp109763t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ewald Pauwels
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Reinout Declerck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Bart De Sterck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Christopher W. M. Kay
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Michel Waroquier
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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Alexandre MT, Purcell EB, van Grondelle R, Robert B, Kennis JT, Crosson S. Electronic and protein structural dynamics of a photosensory histidine kinase. Biochemistry 2010; 49:4752-9. [PMID: 20459101 PMCID: PMC2882989 DOI: 10.1021/bi100527a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The bacterium Caulobacter crescentus encodes a two-component signaling protein, LovK, that contains an N-terminal photosensory LOV domain coupled to a C-terminal histidine kinase. LovK binds a flavin cofactor, undergoes a reversible photocycle, and displays regulated ATPase and autophosphorylation activity in response to visible light. Femtosecond to nanosecond visible absorption spectroscopy demonstrates congruence between full-length LovK and isolated LOV domains in the mechanism and kinetics of light-dependent cysteinyl-C4(a) adduct formation and rupture, while steady-state absorption and fluorescence line narrowing (FLN) spectroscopies reveal unique features in the electronic structure of the LovK flavin cofactor. In agreement with other sensor histidine kinases, ATP binds specifically to LovK with micromolar affinity. However, ATP binding to the histidine kinase domain of LovK has no apparent effect on global protein structure as assessed by differential Fourier transform infrared (FTIR) spectroscopy. Cysteinyl adduct formation results in only minor changes in the structure of LovK as determined by differential FTIR. This study provides insight into the structural underpinnings of LOV-mediated signal transduction in the context of a full-length histidine kinase. In particular, the data provide evidence for a model in which small changes in the tertiary/quaternary structure of LovK, as triggered by photon detection in the N-terminal LOV sensory domain, are sufficient to regulate histidine kinase activity.
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Affiliation(s)
- Maxime T.A. Alexandre
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Erin B. Purcell
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Rienk van Grondelle
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Bruno Robert
- Commissariat à l’Énergie Atomique, Institut de Biologie et de Technologie de Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - John T.M. Kennis
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- The Committee on Microbiology, University of Chicago, Chicago, IL, USA
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Sadeghian K, Bocola M, Schütz M. A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form. Phys Chem Chem Phys 2010; 12:8840-6. [DOI: 10.1039/b925908b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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