1
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Kim C, Yun SR, Lee SJ, Kim SO, Lee H, Choi J, Kim JG, Kim TW, You S, Kosheleva I, Noh T, Baek J, Ihee H. Structural dynamics of protein-protein association involved in the light-induced transition of Avena sativa LOV2 protein. Nat Commun 2024; 15:6991. [PMID: 39143073 PMCID: PMC11324726 DOI: 10.1038/s41467-024-51461-z] [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: 02/05/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore's electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A'α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A'α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs.
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Affiliation(s)
- Changin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jungkweon Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seyoung You
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, 60637, USA
| | - Taeyoon Noh
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jonghoon Baek
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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2
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Nishiyama Y, Nagatani H. Molecular diffusion and aggregate formation of photoproducts from ketoprofen in aqueous solutions. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions. J 2022. [DOI: 10.3390/j5010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thermodynamics and kinetics are two important scientific fields when studying chemical reactions. Thermodynamics characterize the nature of the material. Kinetics, mostly based on spectroscopy, have been used to determine reaction schemes and identify intermediate species. They are certainly important fields, but they are almost independent. In this review, our attempts to elucidate protein reaction kinetics and mechanisms by monitoring thermodynamic properties, including diffusion in the time domain, are described. The time resolved measurements are performed mostly using the time resolved transient grating (TG) method. The results demonstrate the usefulness and powerfulness of time resolved studies on protein reactions. The advantages and limitations of this TG method are also discussed.
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4
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Time-resolved detection of association/dissociation reactions and conformation changes in photosensor proteins for application in optogenetics. Biophys Rev 2021; 13:1053-1059. [DOI: 10.1007/s12551-021-00868-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 11/27/2022] Open
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5
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Affiliation(s)
- Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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6
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Takeda K, Terazima M. Dynamics of Conformational Changes in Full-Length Phytochrome from Cyanobacterium Synechocystis sp. PCC6803 (Cph1) Monitored by Time-Resolved Translational Diffusion Detection. Biochemistry 2019; 58:2720-2729. [DOI: 10.1021/acs.biochem.9b00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kimitoshi Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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7
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Kerruth S, Langner P, Raffelberg S, Gärtner W, Heberle J. Characterization of the Blue-Light-Activated Adenylyl Cyclase mPAC by Flash Photolysis and FTIR Spectroscopy. Photochem Photobiol 2018; 93:857-864. [PMID: 28500710 DOI: 10.1111/php.12746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/08/2017] [Indexed: 11/29/2022]
Abstract
The recently discovered photo-activated adenylyl cyclase (mPAC from Microcoleus chthonoplastes) is the first PAC that owes a light-, oxygen- and voltage-sensitive (LOV) domain for blue-light sensing. The photoreaction of the mPAC receptor was studied by time-resolved UV/vis and light-induced Fourier transform infrared (FTIR) absorption difference spectroscopy. The photocycle comprises of the typical triplet state LOV715 and the thio-adduct state LOV390 . While the adduct state decays with a time constant of 8 s, the lifetime of the triplet state is with 656 ns significantly shorter than in all other reported LOV domains. The light-induced FTIR difference spectrum shows the typical bands of the LOV390 and LOV450 intermediates. The negative S-H stretching vibration at 2573 cm-1 is asymmetric suggesting two rotamer configurations of the protonated side chain of C194. A positive band at 3632 cm-1 is observed, which is assigned to an internal water molecule. In contrast to other LOV domains, mPAC exhibits a second positive feature at 3674 cm-1 which is due to the O-H stretch of a second intrinsic water molecule and the side chain of Y476. We conclude that the latter might be involved in the dimerization of the cyclase domain which is crucial for ATP binding.
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Affiliation(s)
- Silke Kerruth
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Pit Langner
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Sarah Raffelberg
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Wolfgang Gärtner
- Max Planck Institute for Chemical Energy Conversion, Mülheim a. d. Ruhr, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
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8
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Takeda K, Terazima M. Photoinduced Orientation Change of the Dimer Structure of the Pr-I State of Cph1Δ2. Biochemistry 2018; 57:5058-5071. [DOI: 10.1021/acs.biochem.8b00605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kimitoshi Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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9
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Takakado A, Nakasone Y, Terazima M. Sequential DNA Binding and Dimerization Processes of the Photosensory Protein EL222. Biochemistry 2018; 57:1603-1610. [DOI: 10.1021/acs.biochem.7b01206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akira Takakado
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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10
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Nakasone Y, Ohshima M, Okajima K, Tokutomi S, Terazima M. Photoreaction Dynamics of LOV1 and LOV2 of Phototropin from Chlamydomonas reinhardtii. J Phys Chem B 2018; 122:1801-1815. [DOI: 10.1021/acs.jpcb.7b10266] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masumi Ohshima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Koji Okajima
- Graduate
School of Science and Technology, Keio University, Kanagawa 223-8522, Japan
| | - Satoru Tokutomi
- Department
of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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11
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Iwata T, Nozaki D, Yamamoto A, Koyama T, Nishina Y, Shiga K, Tokutomi S, Unno M, Kandori H. Hydrogen Bonding Environment of the N3-H Group of Flavin Mononucleotide in the Light Oxygen Voltage Domains of Phototropins. Biochemistry 2017; 56:3099-3108. [PMID: 28530801 DOI: 10.1021/acs.biochem.7b00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The light oxygen voltage (LOV) domain is a flavin-binding blue-light receptor domain, originally found in a plant photoreceptor phototropin (phot). Recently, LOV domains have been used in optogenetics as the photosensory domain of fusion proteins. Therefore, it is important to understand how LOV domains exhibit light-induced structural changes for the kinase domain regulation, which enables the design of LOV-containing optogenetics tools with higher photoactivation efficiency. In this study, the hydrogen bonding environment of the N3-H group of flavin mononucleotide (FMN) of the LOV2 domain from Adiantum neochrome (neo) 1 was investigated by low-temperature Fourier transform infrared spectroscopy. Using specifically 15N-labeled FMN, [1,3-15N2]FMN, the N3-H stretch was identified at 2831 cm-1 for the unphotolyzed state at 150 K, indicating that the N3-H group forms a fairly strong hydrogen bond. The N3-H stretch showed temperature dependence, with a shift to lower frequencies at ≤200 K and to higher frequencies at ≥250 K from the unphotolyzed to the intermediate states. Similar trends were observed in the LOV2 domains from Arabidopsis phot1 and phot2. By contrast, the N3-H stretch of the Q1029L mutant of neo1-LOV2 and neo1-LOV1 was not temperature dependent in the intermediate state. These results seemed correlated with our previous finding that the LOV2 domains show the structural changes in the β-sheet region and/or the adjacent Jα helix of LOV2 domain, but that such structural changes do not take place in the Q1029L mutant or neo1-LOV1 domain. The environment around the N3-H group was also investigated.
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Affiliation(s)
- Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Dai Nozaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Atsushi Yamamoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Takayuki Koyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Yasuzo Nishina
- Department of Molecular Physiology, Graduate School of Medical Sciences, Kumamoto University , Honjo, Kumamoto 860-8556, Japan
| | - Kiyoshi Shiga
- Department of Physiology, School of Health Sciences, Kumamoto University , Kuhonji, Kumamoto 862-0976, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University , Sakai, Osaka 599-8531, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University , Saga 840-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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12
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Kuroi K, Sato F, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Time-resolved fluctuation during the photochemical reaction of a photoreceptor protein: phototropin1LOV2-linker. Phys Chem Chem Phys 2017; 18:6228-38. [PMID: 26854261 DOI: 10.1039/c5cp07472j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although the relationship between structural fluctuations and reactions is important for elucidating reaction mechanisms, experimental data describing such fluctuations of reaction intermediates are sparse. In order to investigate structural fluctuations during a protein reaction, the compressibilities of intermediate species after photoexcitation of a phot1LOV2-linker, which is a typical LOV domain protein with the C-terminal linker including the J-α helix and used recently for optogenetics, were measured in the time-domain by the transient grating and transient lens methods with a high pressure optical cell. The yield of covalent bond formation between the chromophore and a Cys residue (S state formation) relative to that at 0.1 MPa decreased very slightly with increasing pressure. The fraction of the reactive species that yields the T state (linker-unfolded state) decreased almost proportionally with pressure (0.1-200 MPa) to about 65%. Interestingly, the volume change associated with the reaction was much more pressure sensitive. By combining these data, the compressibility changes for the short lived intermediate (S state) and the final product (T state) formation were determined. The compressibility of the S state was found to increase compared with the dark (D) state, and the compressibility decreased during the transition from the S state to the T state. The compressibility change is discussed in terms of cavities inside the protein. By comparing the crystal structures of the phot1LOV2-linker at dark and light states, we concluded that the cavity volumes between the LOV domain and the linker domain increase in the S state, which explains the enhanced compressibility.
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Affiliation(s)
- Kunisato Kuroi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Francielle Sato
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Kazunori Zikihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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13
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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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14
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Takakado A, Nakasone Y, Terazima M. Photoinduced dimerization of a photosensory DNA-binding protein EL222 and its LOV domain. Phys Chem Chem Phys 2017; 19:24855-24865. [DOI: 10.1039/c7cp03686h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Blue light sensor protein EL222, which regulates DNA-binding affinity, exhibits photoinduced dimerization in the absence of target DNA.
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Affiliation(s)
- Akira Takakado
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Yusuke Nakasone
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Masahide Terazima
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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15
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Akiyama Y, Nakasone Y, Nakatani Y, Hisatomi O, Terazima M. Time-Resolved Detection of Light-Induced Dimerization of Monomeric Aureochrome-1 and Change in Affinity for DNA. J Phys Chem B 2016; 120:7360-70. [PMID: 27404115 DOI: 10.1021/acs.jpcb.6b05760] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aureochrome (Aureo) is a recently discovered blue light sensor protein initially from Vaucheria frigida, in which it controls blue light-dependent branch formation and/or development of a sex organ by a light-dependent change in the affinity for DNA. Although photochemical reactions of Aureo-LOV (LOV is a C-terminal light-oxygen-voltage domain) and the N-terminal truncated construct containing a bZIP (N-terminal basic leucine zipper domain) and a LOV domain have previously been reported, the reaction kinetics of the change in affinity for DNA have never been elucidated. The reactions of Aureo where the cysteines are replaced by serines (AureoCS) as well as the kinetics of the change in affinity for a target DNA are investigated in the time-domain. The dimerization rate constant is obtained as 2.8 × 10(4) M(-1) s(-1), which suggests that the photoinduced dimerization occurs in the LOV domain and the bZIP domain dimerizes using the interaction with DNA. Surprisingly, binding with the target DNA is completed very quickly, 7.7 × 10(4) M(-1) s(-1), which is faster than the protein dimerization rate. It is proposed that the nonspecific electrostatic interaction, which is observed as a weak binding with DNA, may play a role in the efficient searching for the target sequence within the DNA.
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Affiliation(s)
- Yuki Akiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University , Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University , Osaka 560-0043, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
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16
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Nakasone Y, Ooi H, Kamiya Y, Asanuma H, Terazima M. Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA. J Am Chem Soc 2016; 138:9001-4. [DOI: 10.1021/jacs.6b02525] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | | | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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17
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Choi S, Nakasone Y, Hellingwerf KJ, Terazima M. Photochemical Reactions of the LOV and LOV-Linker Domains of the Blue Light Sensor Protein YtvA. Biochemistry 2016; 55:3107-15. [PMID: 27203230 DOI: 10.1021/acs.biochem.6b00263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
YtvA is a blue light sensor protein composed of an N-terminal LOV (light-oxygen-voltage) domain, a linker helix, and the C-terminal sulfate transporter and anti-σ factor antagonist domain. YtvA is believed to act as a positive regulator for light and salt stress responses by regulating the σB transcription factor. Although its biological function has been studied, the reaction dynamics and molecular mechanism underlying the function are not well understood. To improve our understanding of the signaling mechanism, we studied the reaction of the LOV domain (YLOV, amino acids 26-127), the LOV domain with its N-terminal extension (N-YLOV, amino acids 1-127), the LOV domain with its C-terminal linker helix (YLOV-linker, amino acids 26-147), and the YLOV domain with the N-terminal extension and the C-terminal linker helix (N-YLOV-linker, amino acids 1-147) using the transient grating method. The signals of all constructs showed adduct formation, thermal diffusion, and molecular diffusion. YLOV showed no change in the diffusion coefficient (D), while the other three constructs showed a significant decrease in D within ∼70 μs of photoexcitation. This indicates that conformational changes in both the N- and C-terminal helices of the YLOV domain indeed do occur. The time constant in the YtvA derivatives was much faster than the corresponding dynamics of phototropins. Interestingly, an additional reaction was observed as a volume expansion as well as a slight increase in D only when both helices were included. These findings suggest that although the rearrangement of the N- and C-terminal helices occurs independently on the fast time scale, this change induces an additional conformational change only when both helices are present.
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Affiliation(s)
- Seokwoo Choi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto, Japan
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam , 1090 GE Amsterdam, The Netherlands
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto, Japan
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18
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Yoshitake T, Toyooka T, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Macromolecular crowding effect for photoreactions of LOV2 domains of Arabidopsis thaliana phototropin 1. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Nakasone Y, Kawaguchi Y, Kong SG, Wada M, Terazima M. Photoinduced Oligomerization of Arabidopsis thaliana Phototropin 2 LOV1. J Phys Chem B 2014; 118:14314-25. [DOI: 10.1021/jp509448b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Kawaguchi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Sam-Geun Kong
- Department
of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Masamitsu Wada
- Department
of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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20
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Kerruth S, Ataka K, Frey D, Schlichting I, Heberle J. Aureochrome 1 illuminated: structural changes of a transcription factor probed by molecular spectroscopy. PLoS One 2014; 9:e103307. [PMID: 25058114 PMCID: PMC4110000 DOI: 10.1371/journal.pone.0103307] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/29/2014] [Indexed: 11/19/2022] Open
Abstract
Aureochrome 1 from Vaucheria frigida is a recently identified blue-light receptor that acts as a transcription factor. The protein comprises a photosensitive light-, oxygen- and voltage-sensitive (LOV) domain and a basic zipper (bZIP) domain that binds DNA rendering aureochrome 1 a prospective optogenetic tool. Here, we studied the photoreaction of full-length aureochrome 1 by molecular spectroscopy. The kinetics of the decay of the red-shifted triplet state and the blue-shifted signaling state were determined by time-resolved UV/Vis spectroscopy. It is shown that the presence of the bZIP domain further prolongs the lifetime of the LOV390 signaling state in comparison to the isolated LOV domain whereas bound DNA does not influence the photocycle kinetics. The light-dark Fourier transform infrared (FTIR) difference spectrum shows the characteristic features of the flavin mononucleotide chromophore except that the S-H stretching vibration of cysteine 254, which is involved in the formation of the thio-adduct state, is significantly shifted to lower frequencies compared to other LOV domains. The presence of the target DNA influences the light-induced FTIR difference spectrum of aureochrome 1. Vibrational bands that can be assigned to arginine and lysine side chains as well to the phosphate backbone, indicate crucial changes in interactions between transcription factor and DNA.
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Affiliation(s)
- Silke Kerruth
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Kenichi Ataka
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Daniel Frey
- Biomolecular Mechanisms, Max Planck Institut for Medical Research, Heidelberg, Germany
| | - Ilme Schlichting
- Biomolecular Mechanisms, Max Planck Institut for Medical Research, Heidelberg, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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21
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Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Photochemistry of Arabidopsis phototropin 1 LOV1: transient tetramerization. Photochem Photobiol Sci 2014; 12:1171-9. [PMID: 23743549 DOI: 10.1039/c3pp50047k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photochemical reaction of the LOV1 (light-oxygen-voltage 1) domain of phototropin 1 from Arabidopsis thaliana was investigated by the time-resolved transient grating method. As with other LOV domains, an absorption spectral change associated with an adduct formation between its chromophore (flavin mononucleotide) and a cysteine residue was observed with a time constant of 1.1 μs. After this reaction, a significant diffusion coefficient (D) change (D of the reactant = 8.2 × 10(-11) m(2) s(-1), and D of the photoproduct = 6.4 × 10(-11) m(2) s(-1)) was observed with a time constant of 14 ms at a protein concentration of 270 μM. From the D value of the ground state and the peak position in size exclusion chromatography, we have confirmed that the phot1LOV1 domain exists as a dimer in the dark. The D-value and the concentration dependence of the rate indicated that the phot1LOV1 domain associates to form a tetramer (dimerization of the dimer) upon photoexcitation. We also found that the chromophore is released from the binding pocket of the LOV domain when it absorbs two photons within a pulse duration, which occurs in addition to the normal photocycle reaction. On the basis of these results, we discuss the molecular mechanism of the light dependent role of the phot1LOV1 domain.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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22
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Halavaty AS, Moffat K. Coiled-coil dimerization of the LOV2 domain of the blue-light photoreceptor phototropin 1 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1316-21. [PMID: 24316821 PMCID: PMC3855711 DOI: 10.1107/s1744309113029199] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/23/2013] [Indexed: 01/05/2023]
Abstract
A key role in signal transduction and dimerization mediated by Per-Arnt-Sim (PAS) domains is played by α-helical linkers that flank the structurally similar α/β cores of these domains. However, crystal-packing forces and the different construct lengths and sequences of the PAS domains influence the final length and orientation of the linkers relative to the core and create uncertainty in the exact mechanism of the linker function. Thus, structural characterization and comparison of the linkers within isolated PAS-domain constructs and/or full-length PAS-containing proteins is important for clarification of the mechanism. The plant blue-light photoreceptors phototropins possess two N-terminal flavin mononucleotide-based light, oxygen or voltage (LOV) domains (LOV1 and LOV2) that comprise a subclass of the PAS family and one C-terminal serine/threonine kinase domain whose enzymatic activity is regulated by blue light. The dark-adapted state crystal structures of the Arabidopsis thaliana phototropin 1 and phototropin 2 LOV1-domain constructs flanked by an N-terminal A'α helix and the structure of the phototropin 2 core LOV2 domain are known. Here, the crystal structure of the A. thaliana phototropin 1 LOV2 domain has been determined in its dark-adapted state. The core is flanked by an N-terminal A'α helix and a C-terminal Jα helix similar to those in the previously reported structure of Avena sativa phototropin 1 LOV2. In contrast to the monomeric A. sativa LOV2, A. thaliana LOV2 is a dimer in which two A'α helices adopt a scissor-like orientation at the dimer interface and form a short α-helical coiled coil. The Jα helix predominantly interacts with the β-sheet and plays a role in coiled-coil formation and dimerization.
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Affiliation(s)
- Andrei S. Halavaty
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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23
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Takeda K, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Dynamics of the amino-terminal and carboxyl-terminal helices of Arabidopsis phototropin 1 LOV2 studied by the transient grating. J Phys Chem B 2013; 117:15606-13. [PMID: 23931584 DOI: 10.1021/jp406109j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, conformational changes of the amino-terminal helix (A'α helix), in addition to the reported conformational changes of the carboxyl-terminal helix (Jα helix), have been proposed to be important for the regulatory function of the light-oxygen-voltage 2 domain (LOV2) of phototropin 1 from Arabidopsis. However, the reaction dynamics of the A'α helix have not been examined. Here, the unfolding reactions of the A'α and Jα helices of the LOV2 domain of phototropin 1 from Arabidopsis thaliana were investigated by the time-resolved transient grating (TG) method. A mutant (T469I mutant) that renders the A'α helix unfolded in the dark state showed unfolding of the Jα helix with a time constant of 1 ms, which is very similar to the time constant reported for the wild-type LOV2-linker sample. Furthermore, a mutant (I608E mutant) that renders the Jα helix unfolded in the dark state exhibited an unfolding process of the A'α helix with a time constant of 12 ms. On the basis of these experimental results, it is suggested that the unfolding reactions of these helices occurs independently.
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Affiliation(s)
- Kimitoshi Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa, Kyoto 606-8502, Japan
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24
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Herman E, Sachse M, Kroth PG, Kottke T. Blue-Light-Induced Unfolding of the Jα Helix Allows for the Dimerization of Aureochrome-LOV from the Diatom Phaeodactylum tricornutum. Biochemistry 2013; 52:3094-101. [DOI: 10.1021/bi400197u] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena Herman
- Department of Chemistry, Physical
and Biophysical Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Matthias Sachse
- Fachbereich Biologie, Universität Konstanz, Universitätsstraße
10, 78457 Konstanz, Germany
| | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, Universitätsstraße
10, 78457 Konstanz, Germany
| | - Tilman Kottke
- Department of Chemistry, Physical
and Biophysical Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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25
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Ito S, Song YH, Imaizumi T. LOV domain-containing F-box proteins: light-dependent protein degradation modules in Arabidopsis. MOLECULAR PLANT 2012; 5:573-82. [PMID: 22402262 PMCID: PMC3355347 DOI: 10.1093/mp/sss013] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants constantly survey the surrounding environment using several sets of photoreceptors. They can sense changes in the quantity (=intensity) and quality (=wavelength) of light and use this information to adjust their physiological responses, growth, and developmental patterns. In addition to the classical photoreceptors, such as phytochromes, cryptochromes, and phototropins, ZEITLUPE (ZTL), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), and LOV KELCH PROTEIN 2 (LKP2) proteins have been recently identified as blue-light photoreceptors that are important for regulation of the circadian clock and photoperiodic flowering. The ZTL/FKF1/LKP2 protein family possesses a unique combination of domains: a blue-light-absorbing LOV (Light, Oxygen, or Voltage) domain along with domains involved in protein degradation. Here, we summarize recent advances in our understanding of the function of the Arabidopsis ZTL/FKF1/LKP2 proteins. We summarize the distinct photochemical properties of their LOV domains and discuss the molecular mechanisms by which the ZTL/FKF1/LKP2 proteins regulate the circadian clock and photoperiodic flowering by controlling blue-light-dependent protein degradation.
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Iwata T, Tokutomi S, Kandori H. Light-induced structural changes of the LOV2 domains in various phototropins revealed by FTIR spectroscopy. Biophysics (Nagoya-shi) 2011; 7:89-98. [PMID: 27857596 PMCID: PMC5036776 DOI: 10.2142/biophysics.7.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/08/2011] [Indexed: 12/01/2022] Open
Abstract
Phototropin (Phot), a blue-light photoreceptor in plants, consists of two FMN-binding domains (named LOV1 and LOV2) and a serine/threonine (Ser/Thr) kinase domain. We have investigated light-induced structural changes of LOV domains, which lead to the activation of the kinase domain, by means of light-induced difference FTIR spectroscopy. FTIR spectroscopy revealed that the reactive cysteine is protonated in both unphotolyzed and triplet-excited states, which is difficult to detect by other methods such as X-ray crystallography. In this review, we describe the light-induced structural changes of hydrogen-bonding environment of FMN chromophore and protein backbone in Adiantum neo1-LOV2 in the C=O stretching region by use of 13C-labeled samples. We also describe the comprehensive FTIR analysis of LOV2 domains among Arabidopsis phot1, phot2, and Adiantum neo1 with and without Jα helix domain.
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Affiliation(s)
- Tatsuya Iwata
- Center for Fostering Young and Innovative Researchers, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Satoru Tokutomi
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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27
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Toyooka T, Hisatomi O, Takahashi F, Kataoka H, Terazima M. Photoreactions of aureochrome-1. Biophys J 2011; 100:2801-9. [PMID: 21641326 DOI: 10.1016/j.bpj.2011.02.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/22/2011] [Accepted: 02/24/2011] [Indexed: 10/18/2022] Open
Abstract
Aureochrome is a recently discovered blue light photosensor that controls a light-dependent morphology change. As a photosensor, it has a unique DNA binding domain (bZIP). Although the biological functions of aureochrome have been revealed, the fundamental photochemistry of this protein has not been elucidated. The photochemical reaction dynamics of the LOV (light, oxygen, or voltage) domain of aureochrome-1 (AUREO1-LOV) and the LOV domain with the bZIP domain (AUREO1-ZL) were studied by employing the transient-grating (TG) technique, using size-exclusion chromatography to verify results. For both samples, adduct formation takes place with a time constant of 2.8 μs. Although significant diffusion changes were observed for both AUREO1-LOV and AUREO1-ZL after adduct formation, the origins of these changes were significantly different. The TG signal of AUREO1-LOV was strongly concentration-dependent. From analysis of the signal, it was concluded that AUREO1-LOV exists in equilibrium between the monomer and dimer, and dimerization of the monomer is the main reaction, i.e., irradiation with blue light enhances the strength of the interdomain interaction. On the other hand, the reaction of AUREO1-ZL is independent of concentration, suggesting that an intraprotein conformational change occurs in the bZIP domain with a time constant of 160 ms. These results revealed the different reactions and roles of the two domains; the LOV domain acts as a photosensor, leading to a subsequent conformational change in the bZIP domain, which should change its ability to bind to DNA. A model is proposed that demonstrates how aureochrome uses blue light to control its affinity for DNA.
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Affiliation(s)
- Tsuguyoshi Toyooka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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28
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Kondoh M, Shiraishi C, Müller P, Ahmad M, Hitomi K, Getzoff ED, Terazima M. Light-induced conformational changes in full-length Arabidopsis thaliana cryptochrome. J Mol Biol 2011; 413:128-37. [PMID: 21875594 DOI: 10.1016/j.jmb.2011.08.031] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 08/11/2011] [Accepted: 08/15/2011] [Indexed: 11/17/2022]
Abstract
Cryptochromes (CRYs) are widespread flavoproteins with homology to photolyases (PHRs), a class of blue-light-activated DNA repair enzymes. Unlike PHRs, both plant and animal CRYs have a C-terminal domain. This cryptochrome C-terminal (CCT) domain mediates interactions with other proteins, while the PHR-like domain converts light energy into a signal via reduction and radical formation of the flavin adenine dinucleotide cofactor. However, the mechanism by which the PHR-like domain regulates the CCT domain is not known. Here, we applied the pulsed-laser-induced transient grating method to detect conformational changes induced by blue-light excitation of full-length Arabidopsis thaliana cryptochrome 1 (AtCRY1). A significant reduction in the diffusion coefficient of AtCRY1 was observed upon photoexcitation, indicating that a large conformational change occurs in this monomeric protein. AtCRY1 containing a single mutation (W324F) that abolishes an intra-protein electron transfer cascade did not exhibit this conformational change. Moreover, the conformational change was much reduced in protein lacking the CCT domain. Thus, we conclude that the observed large conformational changes triggered by light excitation of the PHR-like domain result from C-terminal domain rearrangement. This inter-domain modulation would be critical for CRYs' ability to transduce a blue-light signal into altered protein-protein interactions for biological activity. Lastly, we demonstrate that the transient grating technique provides a powerful method for the direct observation and understanding of photoreceptor dynamics.
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Affiliation(s)
- Masato Kondoh
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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29
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Abstract
LOV (light, oxygen or voltage) domains are protein photosensors that are conserved in bacteria, archaea, plants and fungi, and detect blue light via a flavin cofactor. LOV domains are present in both chemotrophic and phototrophic bacterial species, in which they are found amino-terminally of signalling and regulatory domains such as sensor histidine kinases, diguanylate cyclases-phosphodiesterases, DNA-binding domains and regulators of RNA polymerase σ-factors. In this Review, we describe the current state of knowledge about the function of bacterial LOV proteins, the structural basis of LOV domain-mediated signal transduction, and the use of LOV domains as genetically encoded photoswitches in synthetic biology.
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Kondoh M, Inoue K, Sasaki J, Spudich JL, Terazima M. Transient dissociation of the transducer protein from anabaena sensory rhodopsin concomitant with formation of the M state produced upon photoactivation. J Am Chem Soc 2011; 133:13406-12. [PMID: 21774544 DOI: 10.1021/ja202329u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anabaena sensory rhodopsin (ASR), a microbial rhodopsin in the cyanobacterium sp. PCC7120, has been suggested to regulate cell processes in a light-quality-dependent manner (color-discrimination) through interaction with a water-soluble transducer protein (Tr). However, light-dependent ASR-Tr interaction changes have yet to be demonstrated. We applied the transient grating (TG) method to investigate protein-protein interaction between ASR with Tr. The molecular diffusion component of the TG signal upon photostimulation of ASR(AT) (ASR with an all-trans retinylidene chromophore) revealed that Tr dissociates from ASR upon formation of the M-intermediate and rebinds to ASR during the decay of M; that is, light induces transient dissociation of ASR and Tr during the photocycle. Further correlating the dissociation of the ASR-Tr pair with the M-intermediate, no transient dissociation was observed after the photoexcitation of the blue-shifted ASR(13C) (ASR with 13-cis, 15-syn chromophore), which does not produce M. This distinction between ASR(AT) and ASR(13C), the two isomeric forms in a color-sensitive equilibrium in ASR, provides a potential mechanism for color-sensitive signaling by ASR.
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Affiliation(s)
- Masato Kondoh
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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31
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Veetil SK, Mittal C, Ranjan P, Kateriya S. A conserved isoleucine in the LOV1 domain of a novel phototropin from the marine alga Ostreococcus tauri modulates the dark state recovery of the domain. Biochim Biophys Acta Gen Subj 2011; 1810:675-82. [PMID: 21554927 DOI: 10.1016/j.bbagen.2011.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 04/15/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022]
Abstract
BACKGROUND Phototropins are UV-A/blue light receptor proteins with two LOV (Light-Oxygen-Voltage) sensor domains at their N terminus and a kinase domain at the C-terminus in photoautotrophic organisms. This is the first research report of a canonical phototropin from marine algae Ostreococcus tauri. METHODS We synthesized core LOV1 (OtLOV1) domain-encoding portion of the phototropin gene of O. tauri, the domain was heterologously expressed, purified and assessed for its spectral properties and dark recovery kinetics by UV-Visible, fluorescence spectroscopy and mutational studies. Quaternary structure characteristics were studied by SEC and glutaraldehyde crosslinking. RESULTS The absorption spectrum of OtLOV1 lacks the characteristic 361nm peak shown by other LOV1 domains. It undergoes a photocycle with a dark state recovery time of approximately 30min (τ=300.35s). Native OtLOV1 stayed as dimer in aqueous solution and the dimer formation was light and concentration independent. Mutating isoleucine at 43rd position to valine accelerated the dark recovery time by more than 10-fold. Mutating it to serine reduced sensitivity to blue light, but the dark recovery time remained unaltered. I43S mutation also destabilized the FMN binding to a great extent. CONCLUSION The OtLOV1 domain of the newly identified OtPhot is functional and the isoleucine at position 43 of OtLOV1 is the key residue responsible for fine-tuning the domain properties. GENERAL SIGNIFICANCE This is the first characterized LOV1 domain of a canonical phototropin from a marine alga and spectral properties of the domain are similar to that of the LOV1 domain of higher plants.
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Affiliation(s)
- Sindhu Kandoth Veetil
- Department of Biochemistry, University of Delhi South Campus, Benito Juares Road, New Delhi-110021, India
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32
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Losi A, Gärtner W. Old Chromophores, New Photoactivation Paradigms, Trendy Applications: Flavins in Blue Light-Sensing Photoreceptors†. Photochem Photobiol 2011; 87:491-510. [DOI: 10.1111/j.1751-1097.2011.00913.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Kinetics of conformational changes of the FKF1-LOV domain upon photoexcitation. Biophys J 2011; 99:3831-9. [PMID: 21112308 DOI: 10.1016/j.bpj.2010.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 10/01/2010] [Accepted: 10/06/2010] [Indexed: 01/16/2023] Open
Abstract
The photochemical reaction dynamics of a light-oxygen-voltage (LOV) domain from the blue light sensor protein, FKF1 (flavin-binding Kelch repeat F-box) was studied by means of the pulsed laser-induced transient grating method. The observed absorption spectral changes upon photoexcitation were similar to the spectral changes observed for typical LOV domain proteins (e.g., phototropins). The adduct formation took place with a time constant of 6 μs. After this reaction, a significant conformational change with a time constant of 6 ms was observed as a change in the diffusion coefficient. An FKF1-LOV mutant without the conserved loop connecting helices E and F, which is present only in the FKF1/LOV Kelch protein 2/ZEITLUPE family, did not show these slow phase dynamics. This result indicates that the conformational change in the loop region represents a major change in the FKF1-LOV photoreaction.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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34
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Kondoh M, Hitomi K, Yamamoto J, Todo T, Iwai S, Getzoff ED, Terazima M. Light-induced conformational change and product release in DNA repair by (6-4) photolyase. J Am Chem Soc 2011; 133:2183-91. [PMID: 21271694 DOI: 10.1021/ja107691w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Proteins of the cryptochrome/photolyase family share high sequence similarities, common folds, and the flavin adenine dinucleotide (FAD) cofactor, but exhibit diverse physiological functions. Mammalian cryptochromes are essential regulatory components of the 24 h circadian clock, whereas (6-4) photolyases recognize and repair UV-induced DNA damage by using light energy absorbed by FAD. Despite increasing knowledge about physiological functions from genetic analyses, the molecular mechanisms and conformational dynamics involved in clock signaling and DNA repair remain poorly understood. The (6-4) photolyase, which has strikingly high similarity to human clock cryptochromes, is a prototypic biological system to study conformational dynamics of cryptochrome/photolyase family proteins. The entire light-dependent DNA repair process for (6-4) photolyase can be reproduced in a simple in vitro system. To decipher pivotal reactions of the common FAD cofactor, we accomplished time-resolved measurements of radical formation, diffusion, and protein conformational changes during light-dependent repair by full-length (6-4) photolyase on DNA carrying a single UV-induced damage. The (6-4) photolyase by itself showed significant volume changes after blue-light activation, indicating protein conformational changes distant from the flavin cofactor. A drastic diffusion change was observed only in the presence of both (6-4) photolyase and damaged DNA, and not for (6-4) photolyase alone or with undamaged DNA. Thus, we propose that this diffusion change reflects the rapid (50 μs time constant) dissociation of the protein from the repaired DNA product. Conformational changes with such fast turnover would likely enable DNA repair photolyases to access the entire genome in cells.
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Affiliation(s)
- Masato Kondoh
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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35
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Zoltowski BD, Gardner KH. Tripping the light fantastic: blue-light photoreceptors as examples of environmentally modulated protein-protein interactions. Biochemistry 2011; 50:4-16. [PMID: 21141905 PMCID: PMC3137735 DOI: 10.1021/bi101665s] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Blue-light photoreceptors play a pivotal role in detecting the quality and quantity of light in the environment, controlling a wide range of biological responses. Several families of blue-light photoreceptors have been characterized in detail using biophysics and biochemistry, beginning with photon absorption, through intervening signal transduction, to regulation of biological activities. Here we review the light oxygen voltage, cryptochrome, and sensors of blue light using FAD families, three different groups of proteins that offer distinctly different modes of photochemical activation and signal transduction yet play similar roles in a vast array of biological responses. We cover mechanisms of light activation and propagation of conformational responses that modulate protein-protein interactions involved in biological signaling. Discovery and characterization of these processes in natural proteins are now allowing the design of photoregulatable engineered proteins, facilitating the generation of novel reagents for biochemical and cell biological research.
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Affiliation(s)
- Brian D. Zoltowski
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816 USA
| | - Kevin H. Gardner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816 USA
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36
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Terazima M. Studies of photo-induced protein reactions by spectrally silent reaction dynamics detection methods: applications to the photoreaction of the LOV2 domain of phototropin from Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1093-105. [PMID: 21211575 DOI: 10.1016/j.bbapap.2010.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 12/06/2010] [Accepted: 12/22/2010] [Indexed: 01/28/2023]
Abstract
Biological function involves a series of chemical reactions of biological molecules, and during these reactions, there are numerous spectrally silent dynamic events that cannot be monitored by absorption or emission spectroscopic techniques. Such spectrally silent dynamics include changes in conformation, intermolecular interactions (hydrogen bonding, hydrophobic interactions), inter-protein interactions (oligomer formation, dissociation reactions) and conformational fluctuations. These events might be associated with biological function. To understand the molecular mechanisms of reactions, time-resolved detection of such dynamics is essential. Recently, it has been shown that time-resolved detection of the refractive index is a powerful tool for measuring dynamic events. This technique is complementary to optical absorption detection methods and the signal contains many unique properties, which are difficult to obtain by other methods. The advantages and methods for signal analyses are described in detail in this review. A typical example of an application of time-resolved refractive index change detection is given in the second part: The photoreaction of the LOV2 domain of a blue light photoreceptor from Arabidopsis Thaliana (phototropin). This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Terazima M. Time-dependent intermolecular interaction during protein reactions. Phys Chem Chem Phys 2011; 13:16928-40. [DOI: 10.1039/c1cp21868a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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38
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Wilson A, Kinney JN, Zwart PH, Punginelli C, D'Haene S, Perreau F, Klein MG, Kirilovsky D, Kerfeld CA. Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria. J Biol Chem 2010; 285:18364-75. [PMID: 20368334 PMCID: PMC2881762 DOI: 10.1074/jbc.m110.115709] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 03/21/2010] [Indexed: 01/14/2023] Open
Abstract
The photoprotective processes of photosynthetic organisms involve the dissipation of excess absorbed light energy as heat. Photoprotection in cyanobacteria is mechanistically distinct from that in plants; it involves the orange carotenoid protein (OCP), a water-soluble protein containing a single carotenoid. The OCP is a new member of the family of blue light-photoactive proteins; blue-green light triggers the OCP-mediated photoprotective response. Here we report structural and functional characterization of the wild type and two mutant forms of the OCP, from the model organism Synechocystis PCC6803. The structural analysis provides high resolution detail of the carotenoid-protein interactions that underlie the optical properties of the OCP, unique among carotenoid-proteins in binding a single pigment per polypeptide chain. Collectively, these data implicate several key amino acids in the function of the OCP and reveal that the photoconversion and photoprotective responses of the OCP to blue-green light can be decoupled.
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Affiliation(s)
- Adjele Wilson
- From the Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, and
- CNRS, URA 2906, 91191 Gif sur Yvette, France
| | - James N. Kinney
- the Joint Genome Institute, United States Department of Energy, Walnut Creek, California 94598
| | - Petrus H. Zwart
- the Joint Genome Institute, United States Department of Energy, Walnut Creek, California 94598
| | - Claire Punginelli
- From the Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, and
- CNRS, URA 2906, 91191 Gif sur Yvette, France
| | - Sandrine D'Haene
- From the Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, and
- CNRS, URA 2906, 91191 Gif sur Yvette, France
| | - François Perreau
- the Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, INRA Versailles-Grignon, Route de Saint Cyr, F-78026 Versailles, France, and
| | - Michael G. Klein
- the Joint Genome Institute, United States Department of Energy, Walnut Creek, California 94598
| | - Diana Kirilovsky
- From the Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, and
- CNRS, URA 2906, 91191 Gif sur Yvette, France
| | - Cheryl A. Kerfeld
- the Joint Genome Institute, United States Department of Energy, Walnut Creek, California 94598
- the Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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39
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Nakasone Y, Ono TA, Ishii A, Masuda S, Terazima M. Temperature-sensitive reaction of a photosensor protein YcgF: possibility of a role of temperature sensor. Biochemistry 2010; 49:2288-96. [PMID: 20141167 DOI: 10.1021/bi902121z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The spectrally silent photoreaction of a blue light sensor protein YcgF, composed of the N-terminal BLUF domain and the C-terminal EAL domain, was investigated by the time-resolved transient grating method. Comparing photoinduced reactions of full-length YcgF with that of the BLUF-linker construct, it was found that a major conformation change after photoinduced dimerization is predominantly localized on the EAL domain. Furthermore, the photoinduced conformational change displayed significant temperature dependence. This result is explained by an equilibrium of reactive and nonreactive YcgF species, with the population of photoreactive species decreasing as the temperature is lowered in the dark state. We consider that the dimer form is the nonreactive species and it is the dominant species at lower temperatures. The temperature sensitivity of the photoreaction of YcgF suggests that this protein could have a biological function as a temperature sensor as well as behaving as a light sensor.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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40
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Grünberg R, Ferrar TS, van der Sloot AM, Constante M, Serrano L. Building blocks for protein interaction devices. Nucleic Acids Res 2010; 38:2645-62. [PMID: 20215443 PMCID: PMC2860130 DOI: 10.1093/nar/gkq152] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Here, we propose a framework for the design of synthetic protein networks from modular protein–protein or protein–peptide interactions and provide a starter toolkit of protein building blocks. Our proof of concept experiments outline a general work flow for part–based protein systems engineering. We streamlined the iterative BioBrick cloning protocol and assembled 25 synthetic multidomain proteins each from seven standardized DNA fragments. A systematic screen revealed two main factors controlling protein expression in Escherichia coli: obstruction of translation initiation by mRNA secondary structure or toxicity of individual domains. Eventually, 13 proteins were purified for further characterization. Starting from well-established biotechnological tools, two general–purpose interaction input and two readout devices were built and characterized in vitro. Constitutive interaction input was achieved with a pair of synthetic leucine zippers. The second interaction was drug-controlled utilizing the rapamycin-induced binding of FRB(T2098L) to FKBP12. The interaction kinetics of both devices were analyzed by surface plasmon resonance. Readout was based on Förster resonance energy transfer between fluorescent proteins and was quantified for various combinations of input and output devices. Our results demonstrate the feasibility of parts-based protein synthetic biology. Additionally, we identify future challenges and limitations of modular design along with approaches to address them.
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Affiliation(s)
- Raik Grünberg
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), UPF, Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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41
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Möglich A, Yang X, Ayers RA, Moffat K. Structure and function of plant photoreceptors. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:21-47. [PMID: 20192744 DOI: 10.1146/annurev-arplant-042809-112259] [Citation(s) in RCA: 335] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Signaling photoreceptors use the information contained in the absorption of a photon to modulate biological activity in plants and a wide range of organisms. The fundamental-and as yet imperfectly answered-question is, how is this achieved at the molecular level? We adopt the perspective of biophysicists interested in light-dependent signal transduction in nature and the three-dimensional structures that underpin signaling. Six classes of photoreceptors are known: light-oxygen-voltage (LOV) sensors, xanthopsins, phytochromes, blue-light sensors using flavin adenine dinucleotide (BLUF), cryptochromes, and rhodopsins. All are water-soluble proteins except rhodopsins, which are integral membrane proteins; all are based on a modular architecture except cryptochromes and rhodopsins; and each displays a distinct, light-dependent chemical process based on the photochemistry of their nonprotein chromophore, such as isomerization about a double bond (xanthopsins, phytochromes, and rhodopsins), formation or rupture of a covalent bond (LOV sensors), or electron transfer (BLUF sensors and cryptochromes).
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Affiliation(s)
- Andreas Möglich
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.
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Lamb JS, Zoltowski BD, Pabit SA, Li L, Crane BR, Pollack L. Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering. J Mol Biol 2009; 393:909-19. [PMID: 19712683 PMCID: PMC2858630 DOI: 10.1016/j.jmb.2009.08.045] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 08/14/2009] [Accepted: 08/18/2009] [Indexed: 02/04/2023]
Abstract
The PAS-LOV domain is a signal-transducing component found in a large variety of proteins that is responsible for sensing different stimuli such as light, oxygen, and voltage. The LOV protein VVD regulates blue light responses in the filamentous fungi Neurospora crassa. Using photocoupled, time-resolved small-angle X-ray scattering, we extract the solution protein structure in both dark-adapted and light-activated states. Two distinct dark-adapted conformations are detected in the wild-type protein: a compact structure that corresponds to the crystal structure of the dark-state monomer as well as an extended structure that is well modeled by introducing conformational disorder at the N-terminus of the protein. These conformations are accentuated in carefully selected variants, in which a key residue for propagating structural transitions, Cys71, has been mutated or oxidized. Despite different dark-state conformations, all proteins form a common dimer in response to illumination. Taken together, these data support a reaction scheme that describes the mechanism for light-induced dimerization of VVD. Envelope reconstructions of the transient light-state dimer reveal structures that are best described by a parallel arrangement of subunits that have significantly changed conformation compared to the crystal structure.
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Affiliation(s)
- Jessica S Lamb
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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43
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Tanaka K, Nakasone Y, Okajima K, Ikeuchi M, Tokutomi S, Terazima M. Oligomeric-state-dependent conformational change of the BLUF protein TePixD (Tll0078). J Mol Biol 2009; 386:1290-300. [PMID: 19452599 DOI: 10.1016/j.jmb.2009.01.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The photochemical reaction dynamics of a BLUF (sensors of blue light using FAD) protein, PixD, from a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) were studied by pulsed laser-induced transient grating method. After the formation of an intermediate species with a red-shifted absorption spectrum, two new reaction phases reflecting protein conformational changes were discovered; one reaction phase manifested itself as expansion of partial molar volume with a time constant of 40 micros, whereas the other reaction phase represented a change in the diffusion coefficient D [i.e., the diffusion-sensitive conformational change (DSCC)]. D decreased from 4.9 x 10(-11) to 4.4 x 10(-11) m2 s(-1) upon the formation of the first intermediate, and subsequently showed a more pronounced decrease to 3.2 x 10(-11) m2 s(-1) upon formation of the second intermediate. From a global analysis of signals at various grating wavenumbers, the time constant of D-change was determined to be 4 ms. Although the magnitude and rate constant of the faster volume change were independent of protein concentration, the amplitude of the signal that reflects the later DSCC significantly decreased as the protein concentration decreased. This concentration dependence suggests that two species exist in solution: a reactive species exhibiting the DSCC, and a second species that is nonreactive. The fraction of these species was found to be dependent on the concentration. The difference in reactivity was attributed to the different oligomeric states of TePixD (i.e., pentamer and decamer). The equilibrium of these states in the dark was confirmed by size-exclusion chromatography at various concentrations. These results demonstrated that only the decamer state is responsible for the conformational change. The results may suggest that the oligomeric state is functionally important in the signal transduction of this photosensory protein.
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Affiliation(s)
- Keisuke Tanaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Koyama T, Iwata T, Yamamoto A, Sato Y, Matsuoka D, Tokutomi S, Kandori H. Different Role of the Jα Helix in the Light-Induced Activation of the LOV2 Domains in Various Phototropins. Biochemistry 2009; 48:7621-8. [DOI: 10.1021/bi9009192] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Takayuki Koyama
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Atsushi Yamamoto
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yoshiaki Sato
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Daisuke Matsuoka
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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45
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Inoue K, Kubo M, Demura M, Kamo N, Terazima M. Reaction dynamics of halorhodopsin studied by time-resolved diffusion. Biophys J 2009; 96:3724-34. [PMID: 19413978 DOI: 10.1016/j.bpj.2008.12.3932] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 12/24/2008] [Accepted: 12/31/2008] [Indexed: 11/26/2022] Open
Abstract
Reaction dynamics of a chloride ion pump protein, halorhodopsin (HR), from Natronomonas pharaonis (N. pharaonis) (NpHR) was studied by the pulsed-laser-induced transient grating (TG) method. A detailed investigation of the TG signal revealed that there is a spectrally silent diffusion process besides the absorption-observable reaction dynamics. We interpreted these dynamics in terms of release, diffusion, and uptake of the Cl(-) ion. From a quantitative global analysis of the signals at various grating wavenumbers, it was concluded that the release of the Cl(-) ion is associated with the L2 --> (L2 (or N) <==> O) process, and uptake of Cl(-) occurs with the (L2 (or N) <==> O) -->NpHR' process. The diffusion coefficient of NpHR solubilized in a detergent did not change during the cyclic reaction. This result contrasts the behavior of many photosensor proteins and implies that the change in the H-bond network from intra- to intermolecular is not significant for the activity of this protein pump.
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Affiliation(s)
- Keiichi Inoue
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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46
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Light signal transduction pathway from flavin chromophore to the J alpha helix of Arabidopsis phototropin1. Biophys J 2009; 96:2771-8. [PMID: 19348760 DOI: 10.1016/j.bpj.2008.12.3924] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 12/09/2008] [Accepted: 12/16/2008] [Indexed: 11/23/2022] Open
Abstract
In the plant blue-light sensor phototropin, illumination of the chromophoric LOV domains causes activation of the serine/threonine kinase domain. Flavin mononucleotide (FMN) is a chromophore molecule in the two LOV domains (LOV1 and LOV2), but only LOV2 is responsible for kinase activation. Previous studies reported an important role of an additional helix connected to the C-terminal of LOV2 (Jalpha helix) for the function of phototropin; however, it remains unclear how the Jalpha helix affects light-induced structural changes in LOV2. In this study we compared light-induced protein structural changes of the LOV2 domain of Arabidopsis phot1 in the absence (LOV2-core) and presence (LOV2-Jalpha) of the Jalpha helix by Fourier-transform infrared spectroscopy. Prominent peaks were observed only in the amide-I region (1650 (-)/1625 (+) cm(-1)) of LOV2-Jalpha at physiological temperatures (>/=260 K), corresponding to structural perturbation of the alpha-helix. The peaks were diminished by point mutation of functionally important amino acids such as Phe-556 between FMN and the beta-sheet, Gln-575 being hydrogen-bonded with FMN, and Ile-608 on the Jalpha helix. We thus conclude that a light signal is relayed from FMN through these amino acids and eventually changes the interaction between LOV2-core and the Jalpha helix in Arabidopsis phot1.
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47
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Nishiyama Y, Terazima M, Kimura Y. Charge effect on the diffusion coefficient and the bimolecular reaction rate of diiodide anion radical in room temperature ionic liquids. J Phys Chem B 2009; 113:5188-93. [PMID: 19301892 DOI: 10.1021/jp811306b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The diffusion coefficients of diiodide anion radical, I(2)(-), in room temperature ionic liquids (RTILs) were determined by the transient grating (TG) method using the photochemical reaction of iodide. The diffusion coefficients we obtained were larger in RTILs than the theoretical predictions by the Stokes-Einstein relation, whereas both values are similar in conventional solvents. By comparison with the diffusion coefficients of neutral molecules, it was suggested that the Coulomb interaction between I(2)(-) and constituent ions of RTILs strongly affects the diffusion coefficients. The bimolecular reaction rates between I(2)(-) were calculated by the Debye-Smoluchowski equation using the experimentally determined diffusion coefficients. These calculated reaction rate were much smaller than the experimentally determined rates (Takahashi, K.; et al. J. Phys. Chem. B 2007, 111, 4807), indicating the charge screening effect of RTILs.
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Affiliation(s)
- Yoshio Nishiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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48
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Katsura H, Zikihara K, Okajima K, Yoshihara S, Tokutomi S. Oligomeric structure of LOV domains in Arabidopsis phototropin. FEBS Lett 2009; 583:526-30. [PMID: 19166850 DOI: 10.1016/j.febslet.2009.01.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 12/25/2008] [Accepted: 01/07/2009] [Indexed: 11/30/2022]
Abstract
Oligomeric structures of the four LOV domains in Arabidopsis phototropin1 (phot1) and 2 (phot2) were studied using crosslinking. Both LOV1 domains of phot1 and phot2 form a dimer independently on the light conditions, suggesting that the LOV1 domain can be a stable dimerization site of phot in vivo. In contrast, phot1-LOV2 is in a monomer-dimer equilibrium and phot2-LOV2 exists as a monomer in the dark. Blue light-induced a slight increase in the monomer population in phot1-LOV2, suggesting a possible blue light-inducible dissociation of dimers. Furthermore, blue light caused a band shift of the phot2-LOV2 monomer. CD spectra revealed the unfolding of helices and the formation of strand structures. Both light-induced changes were reversible in the dark.
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Affiliation(s)
- Hitomi Katsura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Naka-ku, Sakai, Osaka, Japan
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49
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Nakasone Y, Eitoku T, Zikihara K, Matsuoka D, Tokutomi S, Terazima M. Stability of Dimer and Domain–Domain Interaction of Arabidopsis Phototropin 1 LOV2. J Mol Biol 2008; 383:904-13. [DOI: 10.1016/j.jmb.2008.08.074] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 08/25/2008] [Accepted: 08/30/2008] [Indexed: 10/21/2022]
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50
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Nakasako M, Zikihara K, Matsuoka D, Katsura H, Tokutomi S. Structural Basis of the LOV1 Dimerization of Arabidopsis Phototropins 1 and 2. J Mol Biol 2008; 381:718-33. [DOI: 10.1016/j.jmb.2008.06.033] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 06/09/2008] [Accepted: 06/11/2008] [Indexed: 01/18/2023]
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