1
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He Y, Collado JT, Iuliano JN, Woroniecka HA, Hall CR, Gil AA, Laptenok SP, Greetham GM, Illarionov B, Bacher A, Fischer M, French JB, Lukacs A, Meech SR, Tonge PJ. Elucidating the Signal Transduction Mechanism of the Blue-Light-Regulated Photoreceptor YtvA: From Photoactivation to Downstream Regulation. ACS Chem Biol 2024; 19:696-706. [PMID: 38385342 PMCID: PMC10949197 DOI: 10.1021/acschembio.3c00722] [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: 11/27/2023] [Revised: 01/25/2024] [Accepted: 02/12/2024] [Indexed: 02/23/2024]
Abstract
The blue-light photoreceptor YtvA from Bacillus subtilis has an N-terminal flavin mononucleotide (FMN)-binding light-oxygen-voltage (LOV) domain that is fused to a C-terminal sulfate transporter and anti-σ factor antagonist (STAS) output domain. To interrogate the signal transduction pathway that leads to photoactivation, the STAS domain was replaced with a histidine kinase, so that photoexcitation of the flavin could be directly correlated with biological activity. N94, a conserved Asn that is hydrogen bonded to the FMN C2═O group, was replaced with Ala, Asp, and Ser residues to explore the role of this residue in triggering the structural dynamics that activate the output domain. Femtosecond to millisecond time-resolved multiple probe spectroscopy coupled with a fluorescence polarization assay revealed that the loss of the hydrogen bond between N94 and the C2═O group decoupled changes in the protein structure from photoexcitation. In addition, alterations in N94 also decreased the stability of the Cys-FMN adduct formed in the light-activated state by up to a factor of ∼25. Collectively, these studies shed light on the role of the hydrogen bonding network in the LOV β-scaffold in signal transduction.
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Affiliation(s)
- YongLe He
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | | | - James N. Iuliano
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Helena A. Woroniecka
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher R. Hall
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K.
| | - Agnieszka A. Gil
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | | | - Gregory M. Greetham
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K.
| | - Boris Illarionov
- Institut
für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Adelbert Bacher
- Institut
für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
- TUM School
of Natural Sciences, Technical University
of Munich, 85747 Garching, Germany
| | - Markus Fischer
- Institut
für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Jarrod B. French
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- The
Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Andras Lukacs
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K.
- Department
of Biophysics, Medical School, University
of Pecs, Szigeti ut 12, 7624 Pecs, Hungary
| | - Stephen R. Meech
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K.
| | - Peter J. Tonge
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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2
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Kang XW, Wang K, Zhang X, Zhong D, Ding B. Elementary Reactions in the Functional Triads of the Blue-Light Photoreceptor BLUF Domain. J Phys Chem B 2024; 128:2065-2075. [PMID: 38391132 DOI: 10.1021/acs.jpcb.3c07988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The blue light using the flavin (BLUF) domain is one of the smallest photoreceptors in nature, which consists of a unique bidirectional electron-coupled proton relay process in its photoactivation reaction cycle. This perspective summarizes our recent efforts in dissecting the photocycle into three elementary processes, including proton-coupled electron transfer (PCET), proton rocking, and proton relay. Using ultrafast spectroscopy, we have determined the temporal sequence, rates, kinetic isotope effects (KIEs), and concertedness of these elementary steps. Our findings provide important implications for illuminating the photoactivation mechanism of the BLUF domain and suggest an engineering platform to characterize intricate reactions involving proton motions that are ubiquitous in nonphotosensitive protein machines.
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Affiliation(s)
- Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kailin Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofan Zhang
- 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, Programs of Chemical Physics, and Programs of Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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4
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Tolentino Collado J, Bodis E, Pasitka J, Szucs M, Fekete Z, Kis-Bicskei N, Telek E, Pozsonyi K, Kapetanaki SM, Greetham G, Tonge PJ, Meech SR, Lukacs A. Single Amino Acid Mutation Decouples Photochemistry of the BLUF Domain from the Enzymatic Function of OaPAC and Drives the Enzyme to a Switched-on State. J Mol Biol 2024; 436:168312. [PMID: 37827329 DOI: 10.1016/j.jmb.2023.168312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Photoactivated adenylate cyclases (PACs) are light-activated enzymes that combine a BLUF (blue-light using flavin) domain and an adenylate cyclase domain that are able to increase the levels of the important second messenger cAMP (cyclic adenosine monophosphate) upon blue-light excitation. The light-induced changes in the BLUF domain are transduced to the adenylate cyclase domain via a mechanism that has not yet been established. One critical residue in the photoactivation mechanism of BLUF domains, present in the vicinity of the flavin is the glutamine amino acid close to the N5 of the flavin. The role of this residue has been investigated extensively both experimentally and theoretically. However, its role in the activity of the photoactivated adenylate cyclase, OaPAC has never been addressed. In this work, we applied ultrafast transient visible and infrared spectroscopies to study the photochemistry of the Q48E OaPAC mutant. This mutation altered the primary electron transfer process and switched the enzyme into a permanent 'on' state, able to increase the cAMP levels under dark conditions compared to the cAMP levels of the dark-adapted state of the wild-type OaPAC. Differential scanning calorimetry measurements point to a less compact structure for the Q48E OaPAC mutant. The ensemble of these findings provide insight into the important elements in PACs and how their fine tuning may help in the design of optogenetic devices.
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Affiliation(s)
| | - Emoke Bodis
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Jonatan Pasitka
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Mihaly Szucs
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Nikolett Kis-Bicskei
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Elek Telek
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Kinga Pozsonyi
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Sofia M Kapetanaki
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Greg Greetham
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, New York 11794, United States.
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti str. 12, 7624 Pecs, Hungary.
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5
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Ujfalusi-Pozsonyi K, Bódis E, Nyitrai M, Kengyel A, Telek E, Pécsi I, Fekete Z, Varnyuné Kis-Bicskei N, Mas C, Moussaoui D, Pernot P, Tully MD, Weik M, Schirò G, Kapetanaki SM, Lukács A. ATP-dependent conformational dynamics in a photoactivated adenylate cyclase revealed by fluorescence spectroscopy and small-angle X-ray scattering. Commun Biol 2024; 7:147. [PMID: 38307988 PMCID: PMC10837130 DOI: 10.1038/s42003-024-05842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Structural insights into the photoactivated adenylate cyclases can be used to develop new ways of controlling cellular cyclic adenosine monophosphate (cAMP) levels for optogenetic and other applications. In this work, we use an integrative approach that combines biophysical and structural biology methods to provide insight on the interaction of adenosine triphosphate (ATP) with the dark-adapted state of the photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata (OaPAC). A moderate affinity of the nucleotide for the enzyme was calculated and the thermodynamic parameters of the interaction have been obtained. Stopped-flow fluorescence spectroscopy and small-angle solution scattering have revealed significant conformational changes in the enzyme, presumably in the adenylate cyclase (AC) domain during the allosteric mechanism of ATP binding to OaPAC with small and large-scale movements observed to the best of our knowledge for the first time in the enzyme in solution upon ATP binding. These results are in line with previously reported drastic conformational changes taking place in several class III AC domains upon nucleotide binding.
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Affiliation(s)
- K Ujfalusi-Pozsonyi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Bódis
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - M Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - A Kengyel
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Telek
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - I Pécsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Z Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | | | - C Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | - D Moussaoui
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - P Pernot
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M D Tully
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M Weik
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - G Schirò
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - S M Kapetanaki
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
| | - A Lukács
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
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6
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Zhou Y, Tang S, Chen Z, Zhou Z, Huang J, Kang XW, Zou S, Wang B, Zhang T, Ding B, Zhong D. Origin of the multi-phasic quenching dynamics in the BLUF domains across the species. Nat Commun 2024; 15:623. [PMID: 38245518 PMCID: PMC10799861 DOI: 10.1038/s41467-023-44565-5] [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: 07/27/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
Blue light using flavin (BLUF) photoreceptors respond to light via one of nature's smallest photo-switching domains. Upon photo-activation, the flavin cofactor in the BLUF domain exhibits multi-phasic dynamics, quenched by a proton-coupled electron transfer reaction involving the conserved Tyr and Gln. The dynamic behavior varies drastically across different species, the origin of which remains controversial. Here, we incorporate site-specific fluorinated Trp into three BLUF proteins, i.e., AppA, OaPAC and SyPixD, and characterize the percentages for the Wout, WinNHin and WinNHout conformations using 19F nuclear magnetic resonance spectroscopy. Using femtosecond spectroscopy, we identify that one key WinNHin conformation can introduce a branching one-step proton transfer in AppA and a two-step proton transfer in OaPAC and SyPixD. Correlating the flavin quenching dynamics with the active-site structural heterogeneity, we conclude that the quenching rate is determined by the percentage of WinNHin, which encodes a Tyr-Gln configuration that is not conducive to proton transfer.
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Affiliation(s)
- 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
| | - 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
| | - Jiulong Huang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuhua Zou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bingyao Wang
- 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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7
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Nakasone Y, Murakami H, Tokonami S, Oda T, Terazima M. Time-resolved study on signaling pathway of photoactivated adenylate cyclase and its nonlinear optical response. J Biol Chem 2023; 299:105285. [PMID: 37742920 PMCID: PMC10634658 DOI: 10.1016/j.jbc.2023.105285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Photoactivated adenylate cyclases (PACs) are multidomain BLUF proteins that regulate the cellular levels of cAMP in a light-dependent manner. The signaling route and dynamics of PAC from Oscillatoria acuminata (OaPAC), which consists of a light sensor BLUF domain, an adenylate cyclase domain, and a connector helix (α3-helix), were studied by detecting conformational changes in the protein moiety. Although circular dichroism and small-angle X-ray scattering measurements did not show significant changes upon light illumination, the transient grating method successfully detected light-induced changes in the diffusion coefficient (diffusion-sensitive conformational change (DSCC)) of full-length OaPAC and the BLUF domain with the α3-helix. DSCC of full-length OaPAC was observed only when both protomers in a dimer were photoconverted. This light intensity dependence suggests that OaPAC is a cyclase with a nonlinear light intensity response. The enzymatic activity indeed nonlinearly depends on light intensity, that is, OaPAC is activated under strong light conditions. It was also found that both DSCC and enzymatic activity were suppressed by a mutation in the W90 residue, indicating the importance of the highly conserved Trp in many BLUF domains for the function. Based on these findings, a reaction scheme was proposed together with the reaction dynamics.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroto Murakami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shunrou Tokonami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takashi Oda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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8
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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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9
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Chen Z, Kang XW, Zhou Y, Zhou Z, Tang S, Zou S, Wang K, Huang J, Ding B, Zhong D. Dissecting the Ultrafast Stepwise Bidirectional Proton Relay in a Blue-Light Photoreceptor. J Am Chem Soc 2023; 145:3394-3400. [PMID: 36722850 DOI: 10.1021/jacs.2c10206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proton relays through H-bond networks are essential in realizing the functionality of protein machines such as in photosynthesis and photoreceptors. It has been challenging to dissect the rates and energetics of individual proton-transfer steps during the proton relay. Here, we have designed a proton rocking blue light using a flavin (BLUF) domain with the flavin mononucleotide (FMN)-glutamic acid (E)-tryptophan (W) triad and have resolved the four individual proton-transfer steps kinetically using ultrafast spectroscopy. We have found that after the photo-induced charge separation forming FMN·-/E-COOH/WH·+, the proton first rapidly jumps from the bridging E-COOH to FMN- (τfPT2 = 3.8 ps; KIE = 1.0), followed by a second proton transfer from WH·+ to E-COO- (τfPT1 = 336 ps; KIE = 2.6) which immediately rocks back to W· (τrPT1 = 85 ps; KIE = 6.7), followed by a proton return from FMNH· to E-COO- (τrPT2 = 34 ps; KIE = 3.3) with the final charge recombination between FMN·- and WH·+ to close the reaction cycle. Our results revisited the Grotthuss mechanism on the ultrafast timescale using the BLUF domain as a paradigm protein.
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Affiliation(s)
- Zijing Chen
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Siwei Tang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Shuhua Zou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Kailin Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jiulong Huang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China.,Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai200240, China
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10
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Chaudhari AS, Chatterjee A, Domingos CAO, Andrikopoulos PC, Liu Y, Andersson I, Schneider B, Lórenz-Fonfría VA, Fuertes G. Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222. Protein Sci 2023; 32:e4590. [PMID: 36764820 PMCID: PMC10019195 DOI: 10.1002/pro.4590] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Aditya S Chaudhari
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Aditi Chatterjee
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Catarina A O Domingos
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Lavradio, Portugal
| | | | - Yingliang Liu
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Inger Andersson
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | | | - Gustavo Fuertes
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
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11
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Hontani Y, Mehlhorn J, Domratcheva T, Beck S, Kloz M, Hegemann P, Mathes T, Kennis JTM. Spectroscopic and Computational Observation of Glutamine Tautomerization in the Blue Light Sensing Using Flavin Domain Photoreaction. J Am Chem Soc 2023; 145:1040-1052. [PMID: 36607126 PMCID: PMC9853863 DOI: 10.1021/jacs.2c10621] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Blue light sensing using flavin (BLUF) domains constitute a family of flavin-binding photoreceptors of bacteria and eukaryotic algae. BLUF photoactivation proceeds via a light-driven hydrogen-bond switch among flavin adenine dinucleotide (FAD) and glutamine and tyrosine side chains, whereby FAD undergoes electron and proton transfer with tyrosine and is subsequently re-oxidized by a hydrogen back-shuttle in picoseconds, constituting an important model system to understand proton-coupled electron transfer in biology. The specific structure of the hydrogen-bond patterns and the prevalence of glutamine tautomeric states in dark-adapted (DA) and light-activated (LA) states have remained controversial. Here, we present a combined femtosecond stimulated Raman spectroscopy (FSRS), computational chemistry, and site-selective isotope labeling Fourier-transform infrared spectroscopy (FTIR) study of the Slr1694 BLUF domain. FSRS showed distinct vibrational bands from the FADS1 singlet excited state. We observed small but significant shifts in the excited-state vibrational frequency patterns of the DA and LA states, indicating that these frequencies constitute a sensitive probe for the hydrogen-bond arrangement around FAD. Excited-state model calculations utilizing four different realizations of hydrogen bond patterns and glutamine tautomeric states were consistent with a BLUF reaction model that involved glutamine tautomerization to imidic acid, accompanied by a rotation of its side chain. A combined FTIR and double-isotope labeling study, with 13C labeling of FAD and 15N labeling of glutamine, identified the glutamine imidic acid C═N stretch vibration in the LA state and the Gln C═O in the DA state. Hence, our study provides support for glutamine tautomerization and side-chain rotation in the BLUF photoreaction.
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Affiliation(s)
- Yusaku Hontani
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands
| | - Jennifer Mehlhorn
- Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tatiana Domratcheva
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany,Department
of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sebastian Beck
- Department
of Chemistry, Humboldt-Universität
zu Berlin, Brook-Taylor-Str.
2, 12489 Berlin, Germany
| | - Miroslav Kloz
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,Institute
of Physics, ELI-Beamlines, Na Slovance 2, 182
21 Praha 8, Czech Republic
| | - Peter Hegemann
- Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tilo Mathes
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - John T. M. Kennis
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,
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