1
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Frederiksen A, Gerhards L, Reinholdt P, Kongsted J, Solov’yov IA. Importance of Polarizable Embedding for Absorption Spectrum Calculations of Arabidopsis thaliana Cryptochrome 1. J Phys Chem B 2024; 128:6283-6290. [PMID: 38913544 PMCID: PMC11228989 DOI: 10.1021/acs.jpcb.4c02168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/26/2024]
Abstract
Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD), a chromophore within cryptochromes, absorbs blue light, initiating electron transfer processes that lead to a biological signaling cascade. A key step in this cascade is the formation of the FAD semiquinone radical (FADH•), characterized through a specific red-light absorption. The absorption spectra of FADH• in cryptochromes are, however, significantly different from those recorded for the cofactor in solution, primarily due to protein-induced shifts in the absorption peaks. This study employs a multiscale approach, combining molecular dynamics (MD) simulations with quantum mechanical/molecular mechanical (QM/MM) methodologies, to investigate the influence of protein dynamics on embedded FADH• absorption. We emphasize the role of the protein's polarizable environment in the shaping of the absorption spectrum, crucial for accurate spectral predictions in cryptochromes. Our findings provide valuable insights into the absorption process, advancing our understanding of cryptochrome functioning.
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Affiliation(s)
- Anders Frederiksen
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Peter Reinholdt
- Department
of Physics, Chemistry, and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department
of Physics, Chemistry, and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26111 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
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2
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Aguida B, Babo J, Baouz S, Jourdan N, Procopio M, El-Esawi MA, Engle D, Mills S, Wenkel S, Huck A, Berg-Sørensen K, Kampranis SC, Link J, Ahmad M. 'Seeing' the electromagnetic spectrum: spotlight on the cryptochrome photocycle. FRONTIERS IN PLANT SCIENCE 2024; 15:1340304. [PMID: 38495372 PMCID: PMC10940379 DOI: 10.3389/fpls.2024.1340304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/12/2024] [Indexed: 03/19/2024]
Abstract
Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or 'lit' state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or 'resting' state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of 'magneto-genetics' for future applications in synthetic biology and medicine.
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Affiliation(s)
- Blanche Aguida
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Jonathan Babo
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Soria Baouz
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Nathalie Jourdan
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
| | - Maria Procopio
- Department of Biophysics, Faculty of Arts and Sciences, Johns Hopkins University, Baltimore, MD, United States
| | | | - Dorothy Engle
- Biology Department, Xavier University, Cincinnati, OH, United States
| | - Stephen Mills
- Chemistry Department, Xavier University, Cincinnati, OH, United States
| | - Stephan Wenkel
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Alexander Huck
- DTU Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Sotirios C. Kampranis
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Justin Link
- Physics and Engineering Department, Cincinnati, OH, United States
| | - Margaret Ahmad
- Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France
- Biology Department, Xavier University, Cincinnati, OH, United States
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3
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Hosokawa Y, Morita H, Nakamura M, Yamamoto J. A deazariboflavin chromophore kinetically stabilizes reduced FAD state in a bifunctional cryptochrome. Sci Rep 2023; 13:16682. [PMID: 37794070 PMCID: PMC10551024 DOI: 10.1038/s41598-023-43930-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
An animal-like cryptochrome derived from Chlamydomonas reinhardtii (CraCRY) is a bifunctional flavoenzyme harboring flavin adenine dinucleotide (FAD) as a photoreceptive/catalytic center and functions both in the regulation of gene transcription and the repair of UV-induced DNA lesions in a light-dependent manner, using different FAD redox states. To address how CraCRY stabilizes the physiologically relevant redox state of FAD, we investigated the thermodynamic and kinetic stability of the two-electron reduced anionic FAD state (FADH-) in CraCRY and related (6-4) photolyases. The thermodynamic stability of FADH- remained almost the same compared to that of all tested proteins. However, the kinetic stability of FADH- varied remarkably depending on the local structure of the secondary pocket, where an auxiliary chromophore, 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF), can be accommodated. The observed effect of 8-HDF uptake on the enhancement of the kinetic stability of FADH- suggests an essential role of 8-HDF in the bifunctionality of CraCRY.
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Affiliation(s)
- Yuhei Hosokawa
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Hiroyoshi Morita
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Mai Nakamura
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
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4
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Raics K, Pirisi K, Zhuang B, Fekete Z, Kis-Bicskei N, Pecsi I, Ujfalusi KP, Telek E, Li Y, Collado JT, Tonge PJ, Meech SR, Vos MH, Bodis E, Lukacs A. Photocycle alteration and increased enzymatic activity in genetically modified photoactivated adenylate cyclase OaPAC. J Biol Chem 2023; 299:105056. [PMID: 37468104 PMCID: PMC10448171 DOI: 10.1016/j.jbc.2023.105056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Photoactivated adenylate cyclases (PACs) are light activated enzymes that combine blue light sensing capacity with the ability to convert ATP to cAMP and pyrophosphate (PPi) in a light-dependent manner. In most of the known PACs blue light regulation is provided by a blue light sensing domain using flavin which undergoes a structural reorganization after blue-light absorption. This minor structural change then is translated toward the C-terminal of the protein, inducing a larger conformational change that results in the ATP conversion to cAMP. As cAMP is a key second messenger in numerous signal transduction pathways regulating various cellular functions, PACs are of great interest in optogenetic studies. The optimal optogenetic device must be "silent" in the dark and highly responsive upon light illumination. PAC from Oscillatoria acuminata is a very good candidate as its basal activity is very small in the dark and the conversion rates increase 20-fold upon light illumination. We studied the effect of replacing D67 to N, in the blue light using flavin domain. This mutation was found to accelerate the primary electron transfer process in the photosensing domain of the protein, as has been predicted. Furthermore, it resulted in a longer lived signaling state, which was formed with a lower quantum yield. Our studies show that the overall effects of the D67N mutation lead to a slightly higher conversion of ATP to cAMP, which points in the direction that by fine tuning the kinetic properties more responsive PACs and optogenetic devices can be generated.
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Affiliation(s)
- Katalin Raics
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Katalin Pirisi
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Bo Zhuang
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Palaiseau, France
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | | | - Ildiko Pecsi
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | | | - Elek Telek
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Yin Li
- Department of Physics, School of Physics and Materials Science, Nanchang University, Nanchang City, China
| | | | - Peter J Tonge
- Department of Chemistry, Stony Brook University, New York, USA
| | | | - Marten H Vos
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Palaiseau, France
| | - Emoke Bodis
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary.
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary.
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5
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Tateno A, Masuzawa K, Nagashima H, Maeda K. Anisotropic and Coherent Control of Radical Pairs by Optimized RF Fields. Int J Mol Sci 2023; 24:ijms24119700. [PMID: 37298651 DOI: 10.3390/ijms24119700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Radical pair kinetics is determined by the coherent and incoherent spin dynamics of spin pair and spin-selective chemical reactions. In a previous paper, reaction control and nuclear spin state selection by designed radiofrequency (RF) magnetic resonance was proposed. Here, we present two novel types of reaction control calculated by the local optimization method. One is anisotropic reaction control and the other is coherent path control. In both cases, the weighting parameters for the target states play an important role in the optimizing of the RF field. In the anisotropic control of radical pairs, the weighting parameters play an important role in the selection of the sub-ensemble. In coherent control, one can set the parameters for the intermediate states, and it is possible to specify the path to reach a final state by adjusting the weighting parameters. The global optimization of the weighting parameters for coherent control has been studied. These manifest calculations show the possibility of controlling the chemical reactions of radical pair intermediates in different ways.
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Affiliation(s)
- Akihiro Tateno
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kenta Masuzawa
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Hiroki Nagashima
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kiminori Maeda
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
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6
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Yang X, Ma L, Shao H, Zhou Z, Ling X, Yao M, Luo G, Scoditti S, Sicilia E, Mazzone G, Gao M, Tang BZ. Riboflavin-Promoted In Situ Photoactivation of Dihydroalkaloid Prodrugs for Cancer Therapy. J Med Chem 2022; 65:15738-15748. [PMID: 36410876 DOI: 10.1021/acs.jmedchem.2c01262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cancer therapies usually suffer from poor targeting ability and serious side effects. Photoactivatable cancer therapy has the significant advantage of a high spatiotemporal resolution, but most photoactivatable prodrugs require decoration with stoichiometric photocleavable groups, which are only responsive to ultraviolet irradiation and suffer from low reaction efficiency. To tackle these challenges, we herein propose a photoactivation strategy with biogenic riboflavin as the photosensitizer to promote the in situ transformation of noncytotoxic dihydroalkaloid prodrugs dihydrochelerythrine (DHCHE), dihydrosanguinarine (DHSAN), and dihydronitidine (DHNIT) into anticancer alkaloid drugs chelerythrine (CHE), sanguinarine (SAN), and nitidine (NIT), respectively, which can efficiently kill cancer cells and inhibit in vivo tumor growth. Meanwhile, the photoactivatable transformation can be in situ monitored by green-to-red fluorescence conversion, which will contribute to easy controlling of the therapeutic dose. The proposed photoactivatable transformation mechanism was also explored by density functional theory (DFT) calculations. We believe this riboflavin-promoted and imaging-guided photoactivation strategy is promising for precise cancer therapy.
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Affiliation(s)
- Xin Yang
- National Engineering Research Center for Tissue Restoration and Reconstruction, Key Laboratory of Biomedical Engineering of Guangdong Province, Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Limin Ma
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Hongwei Shao
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Zikai Zhou
- National Engineering Research Center for Tissue Restoration and Reconstruction, Key Laboratory of Biomedical Engineering of Guangdong Province, Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Xia Ling
- National Engineering Research Center for Tissue Restoration and Reconstruction, Key Laboratory of Biomedical Engineering of Guangdong Province, Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Mengyu Yao
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Guowen Luo
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Stefano Scoditti
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Emilia Sicilia
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Gloria Mazzone
- Department of Chemistry and Chemical Technologies, Università della Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Meng Gao
- National Engineering Research Center for Tissue Restoration and Reconstruction, Key Laboratory of Biomedical Engineering of Guangdong Province, Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Ben Zhong Tang
- Shenzhen Institute of Aggregate Science and Technology, School of Science and Engineering, The Chinese University of Hong Kong, 2001 Longxiang Boulevard, Longgang, Shenzhen, Guangdong 518172, China
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7
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Limited solvation of an electron donating tryptophan stabilizes a photoinduced charge-separated state in plant (6-4) photolyase. Sci Rep 2022; 12:5084. [PMID: 35332186 PMCID: PMC8948257 DOI: 10.1038/s41598-022-08928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/15/2022] [Indexed: 11/08/2022] Open
Abstract
(6-4) Photolyases ((6-4) PLs) are ubiquitous photoenzymes that use the energy of sunlight to catalyze the repair of carcinogenic UV-induced DNA lesions, pyrimidine(6-4)pyrimidone photoproducts. To repair DNA, (6-4) PLs must first undergo so-called photoactivation, in which their excited flavin adenine dinucleotide (FAD) cofactor is reduced in one or two steps to catalytically active FADH- via a chain of three or four conserved tryptophan residues, transiently forming FAD•-/FADH- ⋯ TrpH•+ pairs separated by distances of 15 to 20 Å. Photolyases and related photoreceptors cryptochromes use a plethora of tricks to prevent charge recombination of photoinduced donor-acceptor pairs, such as chain branching and elongation, rapid deprotonation of TrpH•+ or protonation of FAD•-. Here, we address Arabidopsis thaliana (6-4) PL (At64) photoactivation by combining molecular biology, in vivo survival assays, static and time-resolved spectroscopy and computational methods. We conclude that At64 photoactivation is astonishingly efficient compared to related proteins-due to two factors: exceptionally low losses of photoinduced radical pairs through ultrafast recombination and prevention of solvent access to the terminal Trp3H•+, which significantly extends its lifetime. We propose that a highly conserved histidine residue adjacent to the 3rd Trp plays a key role in Trp3H•+ stabilization.
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8
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Abstract
Light activated proteins are at the heart of photobiology and optogenetics, so there is wide interest in understanding the mechanisms coupling optical excitation to protein function. In addition, such light activated proteins provide unique insights into the real-time dynamics of protein function. Using pump-probe spectroscopy, the function of a photoactive protein can be initiated by a sub-100 fs pulse of light, allowing subsequent protein dynamics to be probed from femtoseconds to milliseconds and beyond. Among the most interesting photoactive proteins are the blue light using flavin (BLUF) domain proteins, which regulate the response to light of a wide range of bacterial and some euglenoid processes. The photosensing mechanism of BLUF domains has long been a subject of debate. In contrast to other photoactive proteins, the electronic and nuclear structure of the chromophore (flavin) is the same in dark- and light-adapted states. Thus, the driving force for photoactivity is unclear.To address this question requires real-time observation of both chromophore excited state processes and their effect on the structure and dynamics of the surrounding protein matrix. In this Account we describe how time-resolved infrared (IR) experiments, coupled with chemical biology, provide important new insights into the signaling mechanism of BLUF domains. IR measurements are sensitive to changes in both chromophore electronic structure and protein hydrogen bonding interactions. These contributions are resolved by isotope labeling of the chromophore and protein separately. Further, a degree of control over BLUF photochemistry is achieved through mutagenesis, while unnatural amino acid substitution allows us to both fine-tune the photochemistry and time resolve protein dynamics with spatial resolution.Ultrafast studies of BLUF domains reveal non-single-exponential relaxation of the flavin excited state. That relaxation leads within one nanosecond to the original flavin ground state bound in a modified hydrogen-bonding network, as seen in transient and steady-state IR spectroscopy. The change in H-bond configuration arises from formation of an unusual enol (imine) form of a critical glutamine residue. The dynamics observed, complemented by quantum mechanical calculations, suggest a unique sequential electron then double proton transfer reaction as the driving force, followed by rapid reorganization in the binding site and charge recombination. Importantly, studies of several BLUF domains reveal an unexpected diversity in their dynamics, although the underlying structure appears highly conserved. It is suggested that this diversity reflects structural dynamics in the ground state at standard temperature, leading to a distribution of structures and photochemical outcomes. Time resolved IR measurements were extended to the millisecond regime for one BLUF domain, revealing signaling state formation on the microsecond time scale. The mechanism involves reorganization of a β-sheet connected to the chromophore binding pocket via a tryptophan residue. The potential of site-specific labeling amino acids with IR labels as a tool for probing protein structural dynamics was demonstrated.In summary, time-resolved IR studies of BLUF domains (along with related studies at visible wavelengths and quantum and molecular dynamics calculations) have resolved the photoactivation mechanism and real-time dynamics of signaling state formation. These measurements provide new insights into protein structural dynamics and will be important in optimizing the potential of BLUF domains in optobiology.
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Affiliation(s)
- Andras Lukacs
- Department of Biophysics, Medical School, University of Pécs, Szigeti str 12, 7624 Pécs, Hungary
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794-3400, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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9
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Kang X, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Ding B, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiu‐Wen Kang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zijing Chen
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Siwei Tang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tianyi Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Bei Ding
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Department of Physics Department of Chemistry and Biochemistry and Programs of Biophysics Chemical Physics, and Biochemistry The Ohio State University Columbus OH 43210 USA
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10
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Cellini A, Shankar MK, Wahlgren WY, Nimmrich A, Furrer A, James D, Wranik M, Aumonier S, Beale EV, Dworkowski F, Standfuss J, Weinert T, Westenhoff S. Structural basis of the radical pair state in photolyases and cryptochromes. Chem Commun (Camb) 2022; 58:4889-4892. [PMID: 35352724 PMCID: PMC9008703 DOI: 10.1039/d2cc00376g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the structure of a photoactivated animal (6-4) photolyase in its radical pair state, captured by serial crystallography. We observe how a conserved asparigine moves towards the semiquinone FAD chromophore and stabilizes it by hydrogen bonding. Several amino acids around the final tryptophan radical rearrange, opening it up to the solvent. The structure explains how the protein environment stabilizes the radical pair state, which is crucial for function of (6-4) photolyases and cryptochromes. The structural response of the drosophila (6-4) photolyase to photoinduced electron transfer along a chain of tryptophans is revealed using a serial crystallographic snapshot of the protein in its radical pair state.![]()
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sylvain Aumonier
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Emma V Beale
- Photon Science Division - Laboratory for Synchrotron Radiation and Femtochemistry (LSF), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Florian Dworkowski
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
- Department of Chemistry-BMC, University of Uppsala, Husargatan 3, 75237 Uppsala, Sweden
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11
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Ding B, Kang XW, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2021; 61:e202114423. [PMID: 34927328 DOI: 10.1002/anie.202114423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 11/10/2022]
Abstract
We present direct observation of ultrafast proton rocking in the central motif of a BLUF domain protein scaffold. The mutant design has taken considerations of modulating the proton-coupled electron transfer (PCET) driving forces by replacing Tyr in the original motif with Trp, as well as of removing the interference of a competing electron transfer pathway. Using femtosecond pump-probe spectroscopy and detailed kinetics analysis, we resolved an electron-transfer-coupled Grotthuss-type forward and reversed proton rocking along the FMN-Gln-Trp proton relay chain. The rates of forward and reversed proton transfer are determined to be very close, namely 51 ps vs 52 ps. The kinetic isotope effect (KIE) constants associated with the forward and reversed proton transfer are 3.9 and 5.3, respectively. The observation of ultrafast proton rocking is not only a crucial step towards revealing the nature of proton relay in BLUF domain, but also provides a new paradigm of proton transfer in proteins for theoretical investigations.
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Affiliation(s)
- Bei Ding
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, 800 Dongchuan Road, 200240, Shanghai, CHINA
| | - Xiu-Wen Kang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zijing Chen
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zhongneng Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yalin Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Siwei Tang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yifei Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Tianyi Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Dongping Zhong
- The Ohio State University, Department of Chemical and Biomolecular Engineering, CHINA
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12
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Goett-Zink L, Kottke T. Plant Cryptochromes Illuminated: A Spectroscopic Perspective on the Mechanism. Front Chem 2021; 9:780199. [PMID: 34900940 PMCID: PMC8653763 DOI: 10.3389/fchem.2021.780199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Plant cryptochromes are central blue light receptors for the control of land plant and algal development including the circadian clock and the cell cycle. Cryptochromes share a photolyase homology region with about 500 amino acids and bind the chromophore flavin adenine dinucleotide. Characteristic for plant cryptochromes is a conserved aspartic acid close to flavin and an exceptionally long C-terminal extension. The mechanism of activation by excitation and reduction of the chromophore flavin adenine dinucleotide has been controversially discussed for many years. Various spectroscopic techniques have contributed to our understanding of plant cryptochromes by providing high time resolution, ambient conditions and even in-cell approaches. As a result, unifying and differing aspects of photoreaction and signal propagation have been revealed in comparison to members from other cryptochrome subfamilies. Here, we review the insight from spectroscopy on the flavin photoreaction in plant cryptochromes and present the current models on the signal propagation from flavin reduction to dissociation of the C-terminal extension.
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Affiliation(s)
- Lukas Goett-Zink
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany.,Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
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13
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Karki N, Vergish S, Zoltowski BD. Cryptochromes: Photochemical and structural insight into magnetoreception. Protein Sci 2021; 30:1521-1534. [PMID: 33993574 DOI: 10.1002/pro.4124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Cryptochromes (CRYs) function as blue light photoreceptors in diverse physiological processes in nearly all kingdoms of life. Over the past several decades, they have emerged as the most likely candidates for light-dependent magnetoreception in animals, however, a long history of conflicts between in vitro photochemistry and in vivo behavioral data complicate validation of CRYs as a magnetosensor. In this review, we highlight the origins of conflicts regarding CRY photochemistry and signal transduction, and identify recent data that provides clarity on potential mechanisms of signal transduction in magnetoreception. The review primarily focuses on examining differences in photochemistry and signal transduction in plant and animal CRYs, and identifies potential modes of convergent evolution within these independent lineages that may identify conserved signaling pathways.
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Affiliation(s)
- Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Satyam Vergish
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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14
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Einholz C, Nohr D, Rodriguez R, Topitsch A, Kern M, Goldmann J, Chileshe E, Okasha M, Weber S, Schleicher E. pH-dependence of signaling-state formation in Drosophila cryptochrome. Arch Biochem Biophys 2021; 700:108787. [PMID: 33545100 DOI: 10.1016/j.abb.2021.108787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/30/2022]
Abstract
Cryptochromes, FAD-dependent blue light photoreceptors, undergo a series of electron transfer reactions after light excitation. Time-resolved optical spectroscopy was employed to investigate the pH dependence of all light-dependent reactions in the cryptochrome from fruit flies. Signal state formation experiments on a time scale of seconds were found to be strongly pH dependent, and formation of both anionic and neutral FAD radicals could be detected, with reaction rates increasing by a factor of ~2.5 from basic to neutral pH values. Additionally, the influence of the amino acid His378 was investigated in further detail: Two protein variants, DmCry H378A and H378Q, showed significantly reduced rate constants for signal state formation, which again differed at neutral and alkaline pH values. Hence, His378 was identified as an amino acid responsible for the pronounced pH dependence; however, this amino acid can be excluded as a proton donor for the protonation of the anionic FAD radical. Other conserved amino acids appear to alter the overall polarity of the binding pocket and thus to be responsible for the pronounced pH dependence. Furthermore, the influence of pH and other experimental parameters, such as temperature, glycerol or ferricyanide concentrations, on the intermediately formed FAD-tryptophan radical pair was explored, which deprotonates on a microsecond time scale with a clear pH dependence, and subsequently recombines within milliseconds. Surprisingly, the latter reaction showed no pH dependence; potential reasons are discussed. All results are reviewed in terms of the photoreceptor and potential magnetoreceptor functions of Drosophila cryptochrome.
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Affiliation(s)
- Christopher Einholz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Ryan Rodriguez
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Annika Topitsch
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Maria Kern
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Jacqueline Goldmann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Emma Chileshe
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Moustafa Okasha
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany.
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15
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Ma L, Guan Z, Wang Q, Yan X, Wang J, Wang Z, Cao J, Zhang D, Gong X, Yin P. Structural insights into the photoactivation of Arabidopsis CRY2. NATURE PLANTS 2020; 6:1432-1438. [PMID: 33199893 DOI: 10.1038/s41477-020-00800-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
The blue-light receptor cryptochrome (CRY) in plants undergoes oligomerization to transduce blue-light signals after irradiation, but the corresponding molecular mechanism remains poorly understood. Here, we report the cryogenic electron microscopy structure of a blue-light-activated CRY2 tetramer at a resolution of 3.1 Å, which shows how the CRY2 tetramer assembles. Our study provides insights into blue-light-mediated activation of CRY2 and a theoretical basis for developing regulators of CRYs for optogenetic manipulation.
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Affiliation(s)
- Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Kobilka Institute of Innovative Drug Discovery, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xuhui Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Zhizheng Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P. R. China
| | - Jianbo Cao
- Public Laboratory of Electron Microscopy, Huazhong Agricultural University, Wuhan, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xin Gong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.
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16
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Regulatory Impact of the C-Terminal Tail on Charge Transfer Pathways in Drosophila Cryptochrome. Molecules 2020; 25:molecules25204810. [PMID: 33086760 PMCID: PMC7587983 DOI: 10.3390/molecules25204810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 01/02/2023] Open
Abstract
Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains.
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17
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Liu H, Su T, He W, Wang Q, Lin C. The Universally Conserved Residues Are Not Universally Required for Stable Protein Expression or Functions of Cryptochromes. Mol Biol Evol 2020; 37:327-340. [PMID: 31550045 DOI: 10.1093/molbev/msz217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Universally conserved residues (UCRs) are invariable amino acids evolutionarily conserved among members of a protein family across diverse kingdoms of life. UCRs are considered important for stability and/or function of protein families, but it has not been experimentally examined systematically. Cryptochromes are photoreceptors in plants or light-independent components of the circadian clocks in mammals. We experimentally analyzed 51 UCRs of Arabidopsis cryptochrome 2 (CRY2) that are universally conserved in eukaryotic cryptochromes from Arabidopsis to human. Surprisingly, we found that UCRs required for stable protein expression of CRY2 in plants are not similarly required for stable protein expression of human hCRY1 in human cells. Moreover, 74% of the stably expressed CRY2 proteins mutated in UCRs retained wild-type-like activities for at least one photoresponses analyzed. Our finding suggests that the evolutionary mechanisms underlying conservation of UCRs or that distinguish UCRs from non-UCRs determining the same functions of individual cryptochromes remain to be investigated.
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Affiliation(s)
- Huachun Liu
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
| | - Tiantian Su
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA.,UCLA-FAFU Joint Research Center on Plant Proteomics, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjin He
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA.,College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qin Wang
- UCLA-FAFU Joint Research Center on Plant Proteomics, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA
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18
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Cloning, expression, and characterization of a novel plant type cryptochrome gene from the green alga Haematococcus pluvialis. Protein Expr Purif 2020; 172:105633. [PMID: 32259580 DOI: 10.1016/j.pep.2020.105633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/30/2020] [Indexed: 11/20/2022]
Abstract
A full-length cDNA sequence of plant type CRY (designated Hae-P-CRY) was cloned from the green alga Haematococcus pluvialis. The cDNA sequence was 3608 base pairs (bp) in length, which contained a 2988-bp open reading frame encoding 995 amino acids with molecular mass of 107.7 kDa and isoelectric point of 6.19. Multiple alignment analysis revealed that the deduced amino acid sequence of Hae-P-CRY shared high identity of 47-66% with corresponding plant type CRYs from other eukaryotes. The catalytic motifs of plant type CRYs were detected in the amino acid sequence of Hae-P-CRY including the typical PHR and CTE domains. Phylogenetic analysis showed that the Hae-P-CRY was grouped together with other plant type CRYs from green algae and higher plants, which distinguished from other distinct groups. The transcriptional level of Hae-P-CRY was strongly decreased after 0-4 h under HL stress. In addition, the Hae-P-CRY gene was heterologously expressed in Escherichia coli BL21 (DE3) and successfully purified. The typical spectroscopic characteristics of plant type CRYs were present in Hae-P-CRY indicated that it may be an active enzyme, which provided valuable clue for further functional investigation in the green alga H. pluvialis. These results lay the foundation for further function and interaction protein identification involved in CRYs mediated signal pathway under HL stress in H. pluvialis.
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19
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Goings JJ, Hammes-Schiffer S. Early Photocycle of Slr1694 Blue-Light Using Flavin Photoreceptor Unraveled through Adiabatic Excited-State Quantum Mechanical/Molecular Mechanical Dynamics. J Am Chem Soc 2019; 141:20470-20479. [DOI: 10.1021/jacs.9b11196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua J. Goings
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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20
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21
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Nass Kovacs G, Colletier JP, Grünbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, Schlichting I. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Nat Commun 2019; 10:3177. [PMID: 31320619 PMCID: PMC6639342 DOI: 10.1038/s41467-019-10758-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2019] [Indexed: 11/10/2022] Open
Abstract
Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins. Bacteriorhodopsin (bR) is a light-driven proton pump. Here the authors combine time-resolved crystallography at a free-electron laser, ultrafast spectroscopy and quantum chemistry to study the structural changes following multiphoton photoexcitation of bR and find that they occur within 300 fs not only in the light-absorbing chromophore but also in the surrounding protein.
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Affiliation(s)
- Gabriela Nass Kovacs
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Jacques-Philippe Colletier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Marie Luise Grünbein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Yang Yang
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Till Stensitzki
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - David Ehrenberg
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Raphael Gasper
- Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Alexander Gorel
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Marco Kloos
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Jochen Reinstein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ramona Schlesinger
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Miriam Stricker
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, IPCMS, 23 Rue du Loess, 67034, Strasbourg, France
| | - Joachim Heberle
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Karsten Heyne
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
| | - Tatiana Domratcheva
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
| | - Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
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22
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Sjulstok E, Lüdemann G, Kubař T, Elstner M, Solov'yov IA. Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome. Biophys J 2019; 114:2563-2572. [PMID: 29874607 DOI: 10.1016/j.bpj.2018.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 01/23/2023] Open
Abstract
Cryptochrome proteins are activated by the absorption of blue light, leading to the formation of radical pairs through electron transfer in the active site. Recent experimental studies have shown that once some of the amino acid residues in the active site of Xenopus laevis cryptochrome DASH are mutated, radical-pair formation is still observed. In this study, we computationally investigate electron-transfer pathways in the X. laevis cryptochrome DASH by extensively equilibrating a previously established homology model using molecular dynamics simulations and then mutating key amino acids involved in the electron transfer. The electron-transfer pathways are then probed by using tight-binding density-functional theory. We report the alternative electron-transfer pathways resolved at the molecular level and, through comparison of amino acid sequences for cryptochromes from different species, we demonstrate that one of these alternative electron-transfer pathways could be general for all cryptochrome DASH proteins.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Gesa Lüdemann
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ilia A Solov'yov
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark.
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23
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Xu L, Wen B, Shao W, Yao P, Zheng W, Zhou Z, Zhang Y, Zhu G. Impacts of Cys392, Asp393, and ATP on the FAD Binding, Photoreduction, and the Stability of the Radical State of Chlamydomonas reinhardtii Cryptochrome. Chembiochem 2019; 20:940-948. [PMID: 30548754 DOI: 10.1002/cbic.201800660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Indexed: 12/16/2022]
Abstract
Plant cryptochromes (CRYs) are blue-light receptors that regulate light-dependent growth, development, and circadian rhythms. A flavin adenine dinucleotide (FAD) cofactor is bound to the photolyase homology region (PHR) of plant CRYs and can be photoreduced to a neutral radical state under blue light. This photoreaction can trigger subsequent signal transduction. Plant CRYs can also bind an ATP molecule adjacent to FAD in a pocket of the PHR. Chlamydomonas reinhardtii contains a single plant CRY, named Chlamydomonas photolyase homologue 1 (CPH1). In CPH1, Cys392 and Asp393 are located near the FAD cofactor. Here we have shown that replacing Cys392 with Ser has little effect on the properties of CPH1. The C392N mutant, however, showed a faster photoreduction rate than wild-type CPH1, together with a significantly lower oxidation rate of the neutral radical state. Substituting an Asn residue for Asp393 in CPH1 improved the binding affinity for FAD as well as the stability of the neutral radical, but photoreduction in the case of this mutant was severely inhibited. In the presence of ATP, CPH1 and its mutants exhibited significantly higher binding affinity for FAD and slower oxidation of the neutral radical. These results reveal that the residues at site 392 and the presence of ATP can tune the stability of the neutral radical, that the Asp residue at site 393 is crucial for photoreduction, and that the photoreduction rate is not determined merely by the stability of the neutral radical in CPH1.
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Affiliation(s)
- Lei Xu
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Bin Wen
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, P. R. China
| | - Wengui Shao
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Pengcheng Yao
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Wei Zheng
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Zhiqiang Zhou
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Yao Zhang
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, P. R. China
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24
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Ye S, Tan J, Tian K, Li C, Zhang J, Luo Y. Directly monitoring the active sites of charge transfer in heterocycles in situ and in real time. Chem Commun (Camb) 2019; 55:541-544. [PMID: 30556076 DOI: 10.1039/c8cc08452a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coherent degenerate infrared-infrared-visible sum frequency generation vibrational spectroscopy provides a powerful label-free sensitive probe for charge transfer active sites in heterocyclic molecules in situ and in real time.
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Affiliation(s)
- Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, and Synergetic Innovation Center for Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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25
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Kimø SM, Friis I, Solov'yov IA. Atomistic Insights into Cryptochrome Interprotein Interactions. Biophys J 2018; 115:616-628. [PMID: 30078611 DOI: 10.1016/j.bpj.2018.06.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/11/2018] [Accepted: 06/29/2018] [Indexed: 11/30/2022] Open
Abstract
It is striking that the mechanism by which birds sense geomagnetic fields during the biannual migration seasons is not entirely understood. A protein believed to be responsible for avian magnetoreception is the flavoprotein cryptochrome (CRY), which fulfills many of the criteria for a magnetic field sensor. Some experiments, however, indicate that magnetoreception in birds may be disturbed by extremely weak radio frequency fields, an effect that likely cannot be described by an isolated CRY protein. An explanation can possibly be delivered if CRY binds to another protein inside a cell that would possess certain biochemical properties, and it is, therefore, important to identify possible intracellular CRY interaction partners. The goal of this study is to investigate a possible interaction between CRY4 and the iron-sulfur-containing assembly protein (ISCA1) from Erithacus rubecula (European robin), which has recently been proposed to be relevant for magnetic field sensing. The interaction between the proteins is established through classical molecular dynamics simulations for several possible protein-docking modes. The analysis of these simulations concludes that the ISCA1 complex and CRY4 are capable of binding; however, the peculiarities of this binding argue strongly against ISCA1 as relevant for magnetoreception.
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Affiliation(s)
- Sarafina M Kimø
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.
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26
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Abstract
The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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27
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Magerl K, Stambolic I, Dick B. Switching from adduct formation to electron transfer in a light-oxygen-voltage domain containing the reactive cysteine. Phys Chem Chem Phys 2018; 19:10808-10819. [PMID: 28271102 DOI: 10.1039/c6cp08370f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
LOV (light-, oxygen- or voltage-sensitive) domains act as photosensory units of many prokaryotic and eukaryotic proteins. Upon blue light excitation they undergo a photocycle via the excited triplet state of their flavin chromophore yielding the flavin-cysteinyl adduct. Adduct formation is highly conserved among all LOV domains and constitutes the primary step of LOV domain signaling. But recently, it has been shown that signal propagation can also be triggered by flavin photoreduction to the neutral semiquinone offering new prospects for protein engineering. This, however, requires mutation of the photo-active Cys. Here, we report on LOV1 mutants of C. reinhardtii phototropin in which adduct formation is suppressed although the photo-active Cys is present. Introduction of a Tyr into the LOV core induces a proton coupled electron transfer towards the flavin chromophore. Flavin radical species are formed via either the excited flavin singlet or triplet state depending on the geometry of donor and acceptor. This photoreductive pathway resembles the photoreaction observed in other blue light photoreceptors, e.g. blue-light sensors using flavin adenine dinucleotide (BLUF) domains or cryptochromes. The ability to tune the photoreactivity of the flavin chromophore inside the LOV core has implications for the mechanism of adduct formation in the wild type and may be of use for protein engineering.
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Affiliation(s)
- Kathrin Magerl
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany.
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28
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Schroeder L, Oldemeyer S, Kottke T. Time-Resolved Infrared Spectroscopy on Plant Cryptochrome—Relevance of Proton Transfer and ATP Binding for Signaling. J Phys Chem A 2017; 122:140-147. [DOI: 10.1021/acs.jpca.7b10249] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lea Schroeder
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
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29
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Kopka B, Magerl K, Savitsky A, Davari MD, Röllen K, Bocola M, Dick B, Schwaneberg U, Jaeger KE, Krauss U. Electron transfer pathways in a light, oxygen, voltage (LOV) protein devoid of the photoactive cysteine. Sci Rep 2017; 7:13346. [PMID: 29042655 PMCID: PMC5645311 DOI: 10.1038/s41598-017-13420-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Blue-light absorption by the flavin chromophore in light, oxygen, voltage (LOV) photoreceptors triggers photochemical reactions that lead to the formation of a flavin-cysteine adduct. While it has long been assumed that adduct formation is essential for signaling, it was recently shown that LOV photoreceptor variants devoid of the photoactive cysteine can elicit a functional response and that flavin photoreduction to the neutral semiquinone radical is sufficient for signal transduction. Currently, the mechanistic basis of the underlying electron- (eT) and proton-transfer (pT) reactions is not well understood. We here reengineered pT into the naturally not photoreducible iLOV protein, a fluorescent reporter protein derived from the Arabidopsis thaliana phototropin-2 LOV2 domain. A single amino-acid substitution (Q489D) enabled efficient photoreduction, suggesting that an eT pathway is naturally present in the protein. By using a combination of site-directed mutagenesis, steady-state UV/Vis, transient absorption and electron paramagnetic resonance spectroscopy, we investigate the underlying eT and pT reactions. Our study provides strong evidence that several Tyr and Trp residues, highly conserved in all LOV proteins, constitute the eT pathway for flavin photoreduction, suggesting that the propensity for photoreduction is evolutionary imprinted in all LOV domains, while efficient pT is needed to stabilize the neutral semiquinone radical.
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Affiliation(s)
- Benita Kopka
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Kathrin Magerl
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053, Regensburg, Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion, 45470, Mülheim an der Ruhr, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Katrin Röllen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Bernhard Dick
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053, Regensburg, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.,DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.,IBG-1: Biotechnologie, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
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30
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Kottke T, Oldemeyer S, Wenzel S, Zou Y, Mittag M. Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:4-14. [PMID: 28619534 DOI: 10.1016/j.jplph.2017.05.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Green algae have a highly complex and diverse set of cryptochrome photoreceptor candidates including members of the following subfamilies: plant, plant-like, animal-like, DASH and cryptochrome photolyase family 1 (CPF1). While some green algae encode most or all of them, others lack certain members. Here we present an overview about functional analyses of so far investigated cryptochrome photoreceptors from the green algae Chlamydomonas reinhardtii (plant and animal-like cryptochromes) and Ostreococcus tauri (CPF1) with regard to their biological significance and spectroscopic properties. Cryptochromes of both algae have been demonstrated recently to be involved to various extents in circadian clock regulation and in Chlamydomonas additionally in life cycle control. Moreover, CPF1 even performs light-driven DNA repair. The plant cryptochrome and CPF1 are UVA/blue light receptors, whereas the animal-like cryptochrome responds to almost the whole visible spectrum including red light. Accordingly, plant cryptochrome, animal-like cryptochrome and CPF1 differ fundamentally in their structural response to light as revealed by their visible and infrared spectroscopic signatures, and in the role of the flavin neutral radical acting as dark form or signaling state.
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Affiliation(s)
- Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Yong Zou
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
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31
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Nohr D, Franz S, Rodriguez R, Paulus B, Essen LO, Weber S, Schleicher E. Extended Electron-Transfer in Animal Cryptochromes Mediated by a Tetrad of Aromatic Amino Acids. Biophys J 2017; 111:301-311. [PMID: 27463133 DOI: 10.1016/j.bpj.2016.06.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/24/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023] Open
Abstract
The cryptochrome/photolyase protein family possesses a conserved triad of tryptophans that may act as a molecular wire to transport electrons from the protein surface to the FAD cofactor for activation and/or signaling-state formation. Members from the animal (and animal-like) cryptochrome subclade use this process in a light-induced fashion in a number of exciting responses, such as the (re-)setting of circadian rhythms or magnetoreception; however, electron-transfer pathways have not been explored in detail yet. Therefore, we present an in-depth time-resolved optical and electron-paramagnetic resonance spectroscopic study of two cryptochromes from Chlamydomonas reinhardtii and Drosophila melanogaster. The results do not only reveal the existence of a fourth, more distant aromatic amino acid that serves as a terminal electron donor in both proteins, but also show that a tyrosine is able to fulfill this very role in Chlamydomonas reinhardtii cryptochrome. Additionally, exchange of the respective fourth aromatic amino acid to redox-inactive phenylalanines still leads to light-induced radical pair formation; however, the lifetimes of these species are drastically reduced from the ms- to the μs-range. The results presented in this study open up a new chapter, to our knowledge, in the diversity of electron-transfer pathways in cryptochromes. Moreover, they could explain unique functions of animal cryptochromes, in particular their potential roles in magnetoreception because magnetic-field effects of light-induced radical pairs strongly depend on distance and orientation parameters.
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Affiliation(s)
- Daniel Nohr
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | | | - Ryan Rodriguez
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Bernd Paulus
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | | | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Erik Schleicher
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.
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32
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Sommer C, Dietz MS, Patschkowski T, Mathes T, Kottke T. Light-Induced Conformational Changes in the Plant Cryptochrome Photolyase Homology Region Resolved by Selective Isotope Labeling and Infrared Spectroscopy. Photochem Photobiol 2017; 93:881-887. [DOI: 10.1111/php.12750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/10/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Constanze Sommer
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld Germany
| | - Marina S. Dietz
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld Germany
| | - Thomas Patschkowski
- Proteome and Metabolome Research (Bio 27); Department of Biology; Bielefeld University; Bielefeld Germany
| | - Tilo Mathes
- Department of Biology; Experimental Biophysics; Humboldt-Universität zu Berlin; Berlin Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld Germany
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33
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Sheppard DMW, Li J, Henbest KB, Neil SRT, Maeda K, Storey J, Schleicher E, Biskup T, Rodriguez R, Weber S, Hore PJ, Timmel CR, Mackenzie SR. Millitesla magnetic field effects on the photocycle of an animal cryptochrome. Sci Rep 2017; 7:42228. [PMID: 28176875 PMCID: PMC5296725 DOI: 10.1038/srep42228] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/06/2017] [Indexed: 11/09/2022] Open
Abstract
Drosophila have been used as model organisms to explore both the biophysical mechanisms of animal magnetoreception and the possibility that weak, low-frequency anthropogenic electromagnetic fields may have biological consequences. In both cases, the presumed receptor is cryptochrome, a protein thought to be responsible for magnetic compass sensing in migratory birds and a variety of magnetic behavioural responses in insects. Here, we demonstrate that photo-induced electron transfer reactions in Drosophila melanogaster cryptochrome are indeed influenced by magnetic fields of a few millitesla. The form of the protein containing flavin and tryptophan radicals shows kinetics that differ markedly from those of closely related members of the cryptochrome-photolyase family. These differences and the magnetic sensitivity of Drosophila cryptochrome are interpreted in terms of the radical pair mechanism and a photocycle involving the recently discovered fourth tryptophan electron donor.
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Affiliation(s)
- Dean M. W. Sheppard
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Jing Li
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Kevin B. Henbest
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Simon R. T. Neil
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Kiminori Maeda
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Jonathan Storey
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Erik Schleicher
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Till Biskup
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Ryan Rodriguez
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - P. J. Hore
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Christiane R. Timmel
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Stuart R. Mackenzie
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
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34
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Kondoh M, Terazima M. Conformational and Intermolecular Interaction Dynamics of Photolyase/Cryptochrome Proteins Monitored by the Time-Resolved Diffusion Technique. Photochem Photobiol 2017; 93:15-25. [DOI: 10.1111/php.12681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Masato Kondoh
- Department of Chemistry; Graduate School of Pure and Applied Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - Masahide Terazima
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku, Kyoto Japan
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35
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Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
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36
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Multiscale description of avian migration: from chemical compass to behaviour modeling. Sci Rep 2016; 6:36709. [PMID: 27830725 PMCID: PMC5103213 DOI: 10.1038/srep36709] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/19/2016] [Indexed: 11/08/2022] Open
Abstract
Despite decades of research the puzzle of the magnetic sense of migratory songbirds has still not been unveiled. Although the problem really needs a multiscale description, most of the individual research efforts were focused on single scale investigations. Here we seek to establish a multiscale link between some of the scales involved, and in particular construct a bridge between electron spin dynamics and migratory bird behaviour. In order to do that, we first consider a model cyclic reaction scheme that could form the basis of the avian magnetic compass. This reaction features a fast spin-dependent process which leads to an unusually precise compass. We then propose how the reaction could be realized in a realistic molecular environment, and argue that it is consistent with the known facts about avian magnetoreception. Finally we show how the microscopic dynamics of spins could possibly be interpreted by a migrating bird and used for the navigational purpose.
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37
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Oldemeyer S, Franz S, Wenzel S, Essen LO, Mittag M, Kottke T. Essential Role of an Unusually Long-lived Tyrosyl Radical in the Response to Red Light of the Animal-like Cryptochrome aCRY. J Biol Chem 2016; 291:14062-14071. [PMID: 27189948 DOI: 10.1074/jbc.m116.726976] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Cryptochromes constitute a group of flavin-binding blue light receptors in bacteria, fungi, plants, and insects. Recently, the response of cryptochromes to light was extended to nearly the entire visible spectral region on the basis of the activity of the animal-like cryptochrome aCRY in the green alga Chlamydomonas reinhardtii This finding was explained by the absorption of red light by the flavin neutral radical as the dark state of the receptor, which then forms the anionic fully reduced state. In this study, time-resolved UV-visible spectroscopy on the full-length aCRY revealed an unusually long-lived tyrosyl radical with a lifetime of 2.6 s, which is present already 1 μs after red light illumination of the flavin radical. Mutational studies disclosed the tyrosine 373 close to the surface to form the long-lived radical and to be essential for photoreduction. This residue is conserved exclusively in the sequences of other putative aCRY proteins distinguishing them from conventional (6-4) photolyases. Size exclusion chromatography showed the full-length aCRY to be a dimer in the dark at 0.5 mm injected concentration with the C-terminal extension as the dimerization site. Upon illumination, partial oligomerization was observed via disulfide bridge formation at cysteine 482 in close proximity to tyrosine 373. The lack of any light response in the C-terminal extension as evidenced by FTIR spectroscopy differentiates aCRY from plant and Drosophila cryptochromes. These findings imply that aCRY might have evolved a different signaling mechanism via a light-triggered redox cascade culminating in photooxidation of a yet unknown substrate or binding partner.
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Affiliation(s)
- Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld
| | - Sophie Franz
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straβe 4, 35039 Marburg
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straβe 4, 35039 Marburg
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld,.
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38
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Kattnig DR, Solov'yov IA, Hore PJ. Electron spin relaxation in cryptochrome-based magnetoreception. Phys Chem Chem Phys 2016; 18:12443-56. [PMID: 27020113 DOI: 10.1039/c5cp06731f] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The magnetic compass sense of migratory birds is thought to rely on magnetically sensitive radical pairs formed photochemically in cryptochrome proteins in the retina. An important requirement of this hypothesis is that electron spin relaxation is slow enough for the Earth's magnetic field to have a significant effect on the coherent spin dynamics of the radicals. It is generally assumed that evolutionary pressure has led to protection of the electron spins from irreversible loss of coherence in order that the underlying quantum dynamics can survive in a noisy biological environment. Here, we address this question for a structurally characterized model cryptochrome expected to share many properties with the putative avian receptor protein. To this end we combine all-atom molecular dynamics simulations, Bloch-Redfield relaxation theory and spin dynamics calculations to assess the effects of spin relaxation on the performance of the protein as a compass sensor. Both flavin-tryptophan and flavin-Z˙ radical pairs are studied (Z˙ is a radical with no hyperfine interactions). Relaxation is considered to arise from modulation of hyperfine interactions by librational motions of the radicals and fluctuations in certain dihedral angles. For Arabidopsis thaliana cryptochrome 1 (AtCry1) we find that spin relaxation implies optimal radical pair lifetimes of the order of microseconds, and that flavin-Z˙ pairs are less affected by relaxation than flavin-tryptophan pairs. Our results also demonstrate that spin relaxation in isolated AtCry1 is incompatible with the long coherence times that have been postulated to explain the disruption of the avian magnetic compass sense by weak radiofrequency magnetic fields. We conclude that a cryptochrome sensor in vivo would have to differ dynamically, if not structurally, from isolated AtCry1. Our results clearly mark the limits of the current hypothesis and lead to a better understanding of the operation of radical pair magnetic sensors in noisy biological environments.
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Affiliation(s)
- Daniel R Kattnig
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, OX1 3QZ, UK.
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Müller P, Brettel K, Grama L, Nyitrai M, Lukacs A. Photochemistry of Wild-Type and N378D Mutant E. coli DNA Photolyase with Oxidized FAD Cofactor Studied by Transient Absorption Spectroscopy. Chemphyschem 2016; 17:1329-40. [PMID: 26852903 DOI: 10.1002/cphc.201501077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/02/2023]
Abstract
DNA photolyases (PLs) and evolutionarily related cryptochrome (CRY) blue-light receptors form a widespread superfamily of flavoproteins involved in DNA photorepair and signaling functions. They share a flavin adenine dinucleotide (FAD) cofactor and an electron-transfer (ET) chain composed typically of three tryptophan residues that connect the flavin to the protein surface. Four redox states of FAD are relevant for the various functions of PLs and CRYs: fully reduced FADH(-) (required for DNA photorepair), fully oxidized FADox (blue-light-absorbing dark state of CRYs), and the two semireduced radical states FAD(.-) and FADH(.) formed in ET reactions. The PL of Escherichia coli (EcPL) has been studied for a long time and is often used as a reference system; however, EcPL containing FADox has so far not been investigated on all relevant timescales. Herein, a detailed transient absorption study of EcPL on timescales from nanoseconds to seconds after excitation of FADox is presented. Wild-type EcPL and its N378D mutant, in which the asparagine facing the N5 of the FAD isoalloxazine is replaced by aspartic acid, known to protonate FAD(.-) (formed by ET from the tryptophan chain) in plant CRYs in about 1.5 μs, are characterized. Surprisingly, the mutant protein does not show this protonation. Instead, FAD(.-) is converted in 3.3 μs into a state with spectral features that are different from both FADH(.) and FAD(.-) . Such a conversion does not occur in wild-type EcPL. The chemical nature and formation mechanism of the atypical FAD radical in N378D mutant EcPL are discussed.
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Affiliation(s)
- Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Laszlo Grama
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary
| | - Miklos Nyitrai
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary.
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Sjulstok E, Olsen JMH, Solov'yov IA. Quantifying electron transfer reactions in biological systems: what interactions play the major role? Sci Rep 2015; 5:18446. [PMID: 26689792 PMCID: PMC4686879 DOI: 10.1038/srep18446] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022] Open
Abstract
Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.,Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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Signal transduction in light-oxygen-voltage receptors lacking the adduct-forming cysteine residue. Nat Commun 2015; 6:10079. [PMID: 26648256 PMCID: PMC4682037 DOI: 10.1038/ncomms10079] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/30/2015] [Indexed: 01/19/2023] Open
Abstract
Light–oxygen–voltage (LOV) receptors sense blue light through the photochemical generation of a covalent adduct between a flavin-nucleotide chromophore and a strictly conserved cysteine residue. Here we show that, after cysteine removal, the circadian-clock LOV-protein Vivid still undergoes light-induced dimerization and signalling because of flavin photoreduction to the neutral semiquinone (NSQ). Similarly, photoreduction of the engineered LOV histidine kinase YF1 to the NSQ modulates activity and downstream effects on gene expression. Signal transduction in both proteins hence hinges on flavin protonation, which is common to both the cysteinyl adduct and the NSQ. This general mechanism is also conserved by natural cysteine-less, LOV-like regulators that respond to chemical or photoreduction of their flavin cofactors. As LOV proteins can react to light even when devoid of the adduct-forming cysteine, modern LOV photoreceptors may have arisen from ancestral redox-active flavoproteins. The ability to tune LOV reactivity through photoreduction may have important implications for LOV mechanism and optogenetic applications. Light-oxygen-voltage receptors sense blue light through the photochemical generation of a covalent adduct between a flavin-nucleotide chromophore and a strictly conserved cysteine residue. Here, the authors show that these proteins can react to light even when devoid of the adduct-forming cysteine.
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Kutta RJ, Magerl K, Kensy U, Dick B. A search for radical intermediates in the photocycle of LOV domains. Photochem Photobiol Sci 2015; 14:288-99. [PMID: 25380177 DOI: 10.1039/c4pp00155a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LOV domains are the light sensitive parts of phototropins and many other light-activated enzymes that regulate the response to blue light in plants and algae as well as some fungi and bacteria. Unlike all other biological photoreceptors known so far, the photocycle of LOV domains involves the excited triplet state of the chromophore. This chromophore is flavin mononucleotide (FMN) which forms a covalent adduct with a cysteine residue in the signaling state. Since the formation of this adduct from the triplet state involves breaking and forming of two bonds as well as a change from the triplet to the singlet spin state, various intermediates have been proposed, e.g. a protonated triplet state (3)FMNH(+), the radical anion (2)FMN˙(-), or the neutral semiquinone radical (2)FMNH˙. We performed an extensive search for these intermediates by two-dimensional transient absorption (2D-TA) with a streak camera. However, no transient with a rate constant between the decay of fluorescence and the decay of the triplet state could be detected. Analysis of the decay associated difference spectra results in quantum yields for the formation of the adduct from the triplet of ΦA(LOV1) ≈ 0.75 and ΦA(LOV2) ≈ 0.80. This is lower than the values ΦA(LOV1) ≈ 0.95 and ΦA(LOV2) ≈ 0.99 calculated from the rate constants, giving indirect evidence of an intermediate that reacts either to form the adduct or to decay back to the ground state. Since there is no measurable delay between the decay of the triplet and the formation of the adduct, we conclude that this intermediate reacts much faster than it is formed. The LOV1-C57S mutant shows a weak and slowly decaying (τ > 100 μs) transient whose decay associated spectrum has bands at 375 and 500 nm, with a shoulder at 400 nm. This transient is insensitive to the pH change in the range 6.5-10.0 but increases on addition of β-mercaptoethanol as the reducing agent. We assign this intermediate to the radical anion which is protected from protonation by the protein. We propose that the adduct is formed via the same intermediate by combination of the radical ion pair.
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Affiliation(s)
- Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053 Regensburg, Germany.
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Thöing C, Oldemeyer S, Kottke T. Microsecond Deprotonation of Aspartic Acid and Response of the α/β Subdomain Precede C-Terminal Signaling in the Blue Light Sensor Plant Cryptochrome. J Am Chem Soc 2015; 137:5990-9. [PMID: 25909499 DOI: 10.1021/jacs.5b01404] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plant cryptochromes are photosensory receptors that regulate various central aspects of plant growth and development. These receptors consist of a photolyase homology region (PHR) carrying the oxidized flavin adenine dinucleotide (FAD) cofactor, and a cryptochrome C-terminal extension (CCT), which is essential for signaling. Absorption of blue/UVA light leads to formation of the FAD neutral radical as the likely signaling state, and ultimately activates the CCT. Little is known about the signal transfer from the flavin to the CCT. Here, we investigated the photoreaction of the PHR by time-resolved step-scan FT-IR spectroscopy complemented by UV-vis spectroscopy. The first spectrum at 500 ns shows major contributions from the FAD anion radical, which is demonstrated to then be protonated by aspartic acid 396 to the neutral radical within 3.5 μs. The analysis revealed the existence of three intermediates characterized by changes in secondary structure. A marked loss of β-sheet structure is observed in the second intermediate evolving with a time constant of 500 μs. This change is accompanied by a conversion of a tyrosine residue, which is identified as the formation of a tyrosine radical in the UV-vis. The only β-sheet in the PHR is located within the α/β subdomain, ∼25 Å away from the flavin. This subdomain has been previously attributed a role as a putative antenna binding site, but is now suggested to have evolved to a component in the signaling of plant cryptochromes by mediating the interaction with the CCT.
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Affiliation(s)
- Christian Thöing
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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Paulus B, Bajzath C, Melin F, Heidinger L, Kromm V, Herkersdorf C, Benz U, Mann L, Stehle P, Hellwig P, Weber S, Schleicher E. Spectroscopic characterization of radicals and radical pairs in fruit fly cryptochrome - protonated and nonprotonated flavin radical-states. FEBS J 2015; 282:3175-89. [PMID: 25879256 DOI: 10.1111/febs.13299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/21/2015] [Accepted: 04/14/2015] [Indexed: 01/05/2023]
Abstract
Drosophila melanogaster cryptochrome is one of the model proteins for animal blue-light photoreceptors. Using time-resolved and steady-state optical spectroscopy, we studied the mechanism of light-induced radical-pair formation and decay, and the photoreduction of the FAD cofactor. Exact kinetics on a microsecond to minutes timescale could be extracted for the wild-type protein using global analysis. The wild-type exhibits a fast photoreduction reaction from the oxidized FAD to the FAD(•-) state with a very positive midpoint potential of ~ +125 mV, although no further reduction could be observed. We could also demonstrate that the terminal tryptophan of the conserved triad, W342, is directly involved in electron transfer; however, photoreduction could not be completely inhibited in a W342F mutant. The investigation of another mutation close to the FAD cofactor, C416N, rather unexpectedly reveals accumulation of a protonated flavin radical on a timescale of several seconds. The obtained data are critically discussed with the ones obtained from another protein, Escherichia coli photolyase, and we conclude that the amino acid opposite N(5) of the isoalloxazine moiety of FAD is able to (de)stabilize the protonated FAD radical but not to significantly modulate the kinetics of any light-inducted reactions.
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Affiliation(s)
- Bernd Paulus
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Csaba Bajzath
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Viktoria Kromm
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | | | - Ulrike Benz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Lisa Mann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Patricia Stehle
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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45
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QM/MM calculations with deMon2k. Molecules 2015; 20:4780-812. [PMID: 25786164 PMCID: PMC6272552 DOI: 10.3390/molecules20034780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 02/25/2015] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.
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46
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Hong G, Pachter R. Photoactivation of cryptochromes from Drosophila melanogaster and Sylvia borin: insight into the chemical compass mechanism by computational investigation. J Phys Chem B 2015; 119:3883-92. [PMID: 25710635 DOI: 10.1021/jp508871h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although behavioral studies demonstrated light-induced magnetoreception in the insect Drosophila melanogaster, gaining insight into the possibility that a radical-pair mechanism accounts for the magnetic response of the cryptochrome (DmCry1) is complicated by a number of factors. In addition, the mechanism of magnetoreception for the cryptochrome from the garden warbler bird Sylvia borin (gwCry1a), which demonstrated a long-lived radical pair by transient optical absorption measurements, has also not been rationalized. To assess potential feasibility of a radical-pair mechanism in DmCry1 and gwCry1a, formed by excitation and electron transfer between a Trp-triad and flavin adenine dinucleotide (FAD), further separated by electron transfer within the triad, we applied a combination of theoretical methods, including homology modeling and molecular dynamics (MD) for structure refinement, high-level ab initio theory, and MD simulations using a polarizable force-field for prediction of pKa and the electron transfer rate. Calculated excitation energies, followed by electron transfer in model compounds of DmCry1 that assume proton transfer in conjunction with electron transfer from Trp (W420) to FAD and the predicted pKa for the proximate residue to FAD (Cys416), support a radical-pair mechanism. Furthermore, free-energy and reorganization energies for the Trp-triad in DmCry1 demonstrate facile electron transfer, explained by the local protein environment and exposure to solvent, which in turn enables a large enough distance separation for the radical-pair partners. Results for gwCry1a demonstrated the importance of accounting for relaxed excited-state geometries in validating the first stage of a radical-pair mechanism. This work provides insight into the so-called chemical compass mechanism to explain magnetic-field sensing in DmCry1 and gwCry1a, expanding on previous work on the cyrptochrome from the plant Arabidopsis thaliana (Solov'yov et al. J. Am. Chem. Soc. 2012, 134, 18046-18052. Solov'yov et al., Sci. Rep. 2014, 4, 1-8.).
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Affiliation(s)
- Gongyi Hong
- Air Force Research Laboratory, Wright-Patterson Air Force Base , AFRL/RX, 3005 Hobson Way, Dayton, Ohio 45433, United States
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47
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Christie JM, Blackwood L, Petersen J, Sullivan S. Plant flavoprotein photoreceptors. PLANT & CELL PHYSIOLOGY 2015; 56:401-13. [PMID: 25516569 PMCID: PMC4357641 DOI: 10.1093/pcp/pcu196] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 12/02/2014] [Indexed: 05/18/2023]
Abstract
Plants depend on the surrounding light environment to direct their growth. Blue light (300-500 nm) in particular acts to promote a wide variety of photomorphogenic responses including seedling establishment, phototropism and circadian clock regulation. Several different classes of flavin-based photoreceptors have been identified that mediate the effects of blue light in the dicotyledonous genetic model Arabidopsis thaliana. These include the cryptochromes, the phototropins and members of the Zeitlupe family. In this review, we discuss recent advances, which contribute to our understanding of how these photosensory systems are activated by blue light and how they initiate signaling to regulate diverse aspects of plant development.
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Affiliation(s)
- John M Christie
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Lisa Blackwood
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jan Petersen
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Stuart Sullivan
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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Lüdemann G, Solov’yov IA, Kubař T, Elstner M. Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome. J Am Chem Soc 2015; 137:1147-56. [DOI: 10.1021/ja510550g] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gesa Lüdemann
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Tomáš Kubař
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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Hense A, Herman E, Oldemeyer S, Kottke T. Proton transfer to flavin stabilizes the signaling state of the blue light receptor plant cryptochrome. J Biol Chem 2014; 290:1743-51. [PMID: 25471375 DOI: 10.1074/jbc.m114.606327] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant cryptochromes regulate the circadian rhythm, flowering time, and photomorphogenesis in higher plants as responses to blue light. In the dark, these photoreceptors bind oxidized FAD in the photolyase homology region (PHR). Upon blue light absorption, FAD is converted to the neutral radical state, the likely signaling state, by electron transfer via a conserved tryptophan triad and proton transfer from a nearby aspartic acid. Here we demonstrate, by infrared and time-resolved UV-visible spectroscopy on the PHR domain, that replacement of the aspartic acid Asp-396 with cysteine prevents proton transfer. The lifetime of the radical is decreased by 6 orders of magnitude. This short lifetime does not permit to drive conformational changes in the C-terminal extension that have been associated with signal transduction. Only in the presence of ATP do both the wild type and mutant form a long-lived radical state. However, in the mutant, an anion radical is formed instead of the neutral radical, as found previously in animal type I cryptochromes. Infrared spectroscopic experiments demonstrate that the light-induced conformational changes of the PHR domain are conserved in the mutant despite the lack of proton transfer. These changes are not detected in the photoreduction of the non-photosensory d-amino acid oxidase to the anion radical. In conclusion, formation of the anion radical is sufficient to generate a protein response in plant cryptochromes. Moreover, the intrinsic proton transfer is required for stabilization of the signaling state in the absence of ATP.
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Affiliation(s)
- Anika Hense
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Elena Herman
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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50
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Cailliez F, Müller P, Gallois M, de la Lande A. ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome. J Am Chem Soc 2014; 136:12974-86. [PMID: 25157750 DOI: 10.1021/ja506084f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°(-)). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud and CNRS , Orsay F-91405, France
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