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Kim Y, Ganesan P, Jo J, Kim SO, Thamilselvan K, Ihee H. Chromophore-Removal-Induced Conformational Change in Photoactive Yellow Protein Determined through Spectroscopic and X-ray Solution Scattering Studies. J Phys Chem B 2018; 122:4513-4520. [PMID: 29648836 DOI: 10.1021/acs.jpcb.8b01768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoactive yellow protein (PYP) induces negative phototaxis in Halorhodospira halophila via photoactivation triggered by light-mediated chromophore isomerization. Chromophore isomerization proceeds via a volume-conserving isomerization mechanism due to the hydrogen-bond network and steric constraints inside the protein, and causes significant conformational changes accompanied by N-terminal protrusion. However, it is unclear how the structural change of the chromophore affects the remote N-terminal domain. To understand photocycle-related structural changes, we investigated the structural aspect of chromophore removal in PYP because it possesses a disrupted hydrogen-bond network similar to that in photocycle intermediates. A comparison of the structural aspects with those observed in the photocycle would give a clue related to the structural change mechanism in the photocycle. Chromophore removal effects were assessed via UV-vis spectroscopy, circular dichroism, and X-ray solution scattering. Molecular shape reconstruction and an experiment-restrained rigid-body molecular dynamics simulation based on the scattering data were performed to determine protein shape, size, and conformational changes upon PYP bleaching. Data show that chromophore removal disrupted the holo-PYP structure, resulting in a small N-terminal protrusion, but the extent of conformational changes was markedly less than those in the photocycle. This indicates that disruption of the hydrogen-bond network alone in bleached PYP does not induce the large conformational change observed in the photocycle, which thus must result from the organized structural transition around the chromophore triggered by chromophore photoisomerization along with disruption of the hydrogen-bond network between the chromophore and the PYP core.
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Affiliation(s)
- Youngmin Kim
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Prabhakar Ganesan
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea
| | - Junbeom Jo
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 34141 , Republic of Korea
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2
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Hori Y, Hirayama S, Kikuchi K. Development of cyanine probes with dinitrobenzene quencher for rapid fluorogenic protein labelling. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2017.0018. [PMID: 29038376 PMCID: PMC5647265 DOI: 10.1098/rsta.2017.0018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
A multicolour protein labelling technique using a protein tag and fluorogenic probes is a powerful approach for spatio-temporal analyses of proteins in living cells. Since cyanine fluorophores have attractive properties for multicolour imaging of proteins, there is a huge demand to develop fluorogenic cyanine probes for specific protein labelling in living cells. Herein, we develop fluorogenic cyanine probes for labelling a protein tag by using a dinitrobenzene fluorescence quencher. The probes enhanced fluorescence intensity upon labelling reactions and emitted orange or far-red fluorescence. Intramolecular interactions between the cyanine fluorophores and the dinitrobenzene quencher led not only to fluorescence quenching of the probes in the free state but also to promotion of labelling reactions. Furthermore, the probes successfully imaged cell-surface proteins without a washing process. These findings offer valuable information on the design of fluorogenic cyanine probes and indicate that the probes are useful as novel live-cell imaging tools.This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinya Hirayama
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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3
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Yu P, Song L, Qin J, Wang J. Capturing the photo-signaling state of a photoreceptor in a steady-state fashion by binding a transition metal complex. Protein Sci 2017; 26:2249-2256. [PMID: 28856755 DOI: 10.1002/pro.3284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/26/2017] [Indexed: 11/08/2022]
Abstract
Binding a small molecule to proteins causes conformational changes, but often to a limited extent. Here, we demonstrate that the interaction of a CO-releasing molecule (CORM3) with a photoreceptor photoactive yellow protein (PYP) drives large structural changes in the latter. The interaction of CORM3 and a mutant of PYP, Met100Ala, not only trigger the isomerization of its chromophore, p-coumaric acid, from its anionic trans configuration to a protonated cis configuration, but also increases the content of β-sheet at the cost of α-helix and random coil in the secondary structure of the protein. The CORM3 derived Met100Ala is found to highly resemble the signaling state, which is one of the key photo-intermediates of this photoactive protein, in both protein local conformation and chromophore configuration. The organometallic reagents hold promise as protein engineering tools. This work highlights a novel approach to structurally accessing short lived intermediates of proteins in a steady-state fashion.
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Affiliation(s)
- Pengyun Yu
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory; CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, People's Republic of China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, People's Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory; CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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4
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Oktaviani NA, Pool TJ, Yoshimura Y, Kamikubo H, Scheek RM, Kataoka M, Mulder FAA. Active-Site pKa Determination for Photoactive Yellow Protein Rationalizes Slow Ground-State Recovery. Biophys J 2017; 112:2109-2116. [PMID: 28538148 DOI: 10.1016/j.bpj.2017.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 11/16/2022] Open
Abstract
The ability to avoid blue-light radiation is crucial for bacteria to survive. In Halorhodospira halophila, the putative receptor for this response is known as photoactive yellow protein (PYP). Its response to blue light is mediated by changes in the optical properties of the chromophore para-coumaric acid (pCA) in the protein active site. PYP displays photocycle kinetics with a strong pH dependence for ground-state recovery, which has remained enigmatic. To resolve this problem, a comprehensive pKa determination of the active-site residues of PYP is required. Herein, we show that Glu-46 stays protonated from pH 3.4 to pH 11.4 in the ground (pG) state. This conclusion is supported by the observed hydrogen-bonded protons between Glu-46 and pCA and Tyr-42 and pCA, which are persistent over the entire pH range. Our experimental results show that none of the active-site residues of PYP undergo pH-induced changes in the pG state. Ineluctably, the pH dependence of pG recovery is linked to conformational change that is dependent upon the population of the relevant protonation state of Glu-46 and the pCA chromophore in the excited state, collaterally explaining why pG recovery is slow.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Trijntje J Pool
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Ruud M Scheek
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Frans A A Mulder
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands; Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark.
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5
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Tamura K, Hayashi S. Role of Bulk Water Environment in Regulation of Functional Hydrogen-Bond Network in Photoactive Yellow Protein. J Phys Chem B 2015; 119:15537-49. [DOI: 10.1021/acs.jpcb.5b07555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Tamura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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6
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Hori Y, Norinobu T, Sato M, Arita K, Shirakawa M, Kikuchi K. Development of Fluorogenic Probes for Quick No-Wash Live-Cell Imaging of Intracellular Proteins. J Am Chem Soc 2013; 135:12360-5. [DOI: 10.1021/ja405745v] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Kyohei Arita
- Graduate School of Medical Life
Science, Yokohama City University, Yokohama,
Kanagawa 230-0045, Japan
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You I, Kang SM, Lee S, Cho YO, Kim JB, Lee SB, Nam YS, Lee H. Polydopamine Microfluidic System toward a Two-Dimensional, Gravity-Driven Mixing Device. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200329] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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You I, Kang SM, Lee S, Cho YO, Kim JB, Lee SB, Nam YS, Lee H. Polydopamine Microfluidic System toward a Two-Dimensional, Gravity-Driven Mixing Device. Angew Chem Int Ed Engl 2012; 51:6126-30. [DOI: 10.1002/anie.201200329] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/22/2012] [Indexed: 11/09/2022]
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9
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Hori Y, Nakaki K, Sato M, Mizukami S, Kikuchi K. Development of Protein-Labeling Probes with a Redesigned Fluorogenic Switch Based on Intramolecular Association for No-Wash Live-Cell Imaging. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200867] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Hori Y, Nakaki K, Sato M, Mizukami S, Kikuchi K. Development of Protein-Labeling Probes with a Redesigned Fluorogenic Switch Based on Intramolecular Association for No-Wash Live-Cell Imaging. Angew Chem Int Ed Engl 2012; 51:5611-4. [DOI: 10.1002/anie.201200867] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/19/2012] [Indexed: 01/28/2023]
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11
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Oktaviani NA, Pool TJ, Kamikubo H, Slager J, Scheek RM, Kataoka M, Mulder FAA. Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy. Biophys J 2012; 102:579-86. [PMID: 22325281 DOI: 10.1016/j.bpj.2011.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/23/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022] Open
Abstract
Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activity of its flagellar motor and thereby evade potentially harmful UV radiation. The 14 kDa soluble cytosolic photoactive yellow protein (PYP) is believed to be the primary mediator of this photophobic response, and yields a UV/Vis absorption spectrum that closely matches the bacterium's motility spectrum. In the electronic ground state, the para-coumaric acid (pCA) chromophore of PYP is negatively charged and forms two short hydrogen bonds to the side chains of Glu-46 and Tyr-42. The resulting acid triad is central to the marked pH dependence of the optical-absorption relaxation kinetics of PYP. Here, we describe an NMR approach to sequence-specifically follow all tyrosine side-chain protonation states in PYP from pH 3.41 to 11.24. The indirect observation of the nonprotonated (13)C(γ) resonances in sensitive and well-resolved two-dimensional (13)C-(1)H spectra proved to be pivotal in this effort, as observation of other ring-system resonances was hampered by spectral congestion and line-broadening due to ring flips. We observe three classes of tyrosine residues in PYP that exhibit very different pK(a) values depending on whether the phenolic side chain is solvent-exposed, buried, or hydrogen-bonded. In particular, our data show that Tyr-42 remains fully protonated in the pH range of 3.41-11.24, and that pH-induced changes observed in the photocycle kinetics of PYP cannot be caused by changes in the charge state of Tyr-42. It is therefore very unlikely that the pCA chromophore undergoes changes in its electrostatic interactions in the electronic ground state.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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12
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Determination of Peptide and Protein Disulfide Linkages by MALDI Mass Spectrometry. Top Curr Chem (Cham) 2012; 331:79-116. [DOI: 10.1007/128_2012_384] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Rupenyan AB, Vreede J, van Stokkum IHM, Hospes M, Kennis JTM, Hellingwerf KJ, Groot ML. Proline 68 enhances photoisomerization yield in photoactive yellow protein. J Phys Chem B 2011; 115:6668-77. [PMID: 21542640 DOI: 10.1021/jp112113s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In proteins and enzymes, the local environment of an active cofactor plays an important role in controlling the outcome of a functional reaction. In photoactive yellow protein (PYP), it ensures photoisomerization of the chromophore, a prerequisite for formation of a signaling state. PYP is the prototype of a PAS domain, and the preferred model system for the studies of molecular mechanisms of biological light sensing. We investigated the effect of replacing proline-68, positioned near but not in direct contact with the chromophore, with other neutral amino acids (alanine, glycine, and valine), using ultrafast spectroscopy probing the visible and the mid-IR spectral regions, and molecular simulation to understand the interactions tuning the efficiency of light signaling. Transient absorption measurements indicate that the quantum yield of isomerization in the mutants is lower than the yield observed for the wild type. Subpicosecond mid-IR spectra and molecular dynamics simulations of the four proteins reveal that the hydrogen bond interactions around the chromophore and the access of water molecules in the active site of the protein determine the efficiency of photoisomerization. The mutants provide additional hydrogen bonds to the chromophore, directly and by allowing more water molecules access to its binding pocket. We conclude that proline-68 in the wild type protein optimizes the yield of photochemistry by maintaining a weak hydrogen bond with the chromophore, at the same time restraining the entrance of water molecules close to the alkylic part of pCa. This study provides a molecular basis for the structural optimization of biological light sensing.
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Affiliation(s)
- Alisa B Rupenyan
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
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Loukou C, Changenet-Barret P, Rager MN, Plaza P, Martin MM, Mallet JM. The design, synthesis and photochemical study of a biomimetic cyclodextrin model of photoactive yellow protein (PYP). Org Biomol Chem 2011; 9:2209-18. [PMID: 21301710 DOI: 10.1039/c0ob00646g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The design, synthesis and study of the photophysical and photochemical properties of the first biomimetic cyclodextrin (CD) model of photoactive yellow protein (PYP) are described. This model bears a deprotonated trans-p-coumaric acid chromophore, covalently linked via a cysteine moiety to a permethylated 6-monoamino β-CD. NMR and UV/Visible spectroscopy studies showed the formation of strong self-inclusion complexes in water at basic pH. Steady-state photolysis demonstrated that, unlike the free chromophore in solution, excitation of the model molecule leads to the formation of a photoproduct identified as the cis isomer by NMR spectroscopy. These observations provide evidence that the restricted CD cavity offers a promising framework for the design of biomimetic models of the PYP hydrophobic pocket.
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Affiliation(s)
- Christina Loukou
- Département de Chimie, UMR-CNRS 7203, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, Cedex 05, France
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Yasaki K, Suzuki T, Yazawa K, Kaneko D, Kaneko T. Effects of double photoreactions on polycoumarate photomechanics. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/pola.24525] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Katsuaki Yasaki
- Department of Materials Science, Japan Advanced Institute of Science and Technology, 1‐1 Asahidai, Nomi, Ishikawa 923‐1292, Japan
| | - Takuya Suzuki
- Department of Materials Science, Japan Advanced Institute of Science and Technology, 1‐1 Asahidai, Nomi, Ishikawa 923‐1292, Japan
| | - Koji Yazawa
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259‐B‐55 Nagatsuta‐cho, Midori‐ku, Yokohama 226‐8501, Japan
| | - Daisaku Kaneko
- Department of Materials Science, Japan Advanced Institute of Science and Technology, 1‐1 Asahidai, Nomi, Ishikawa 923‐1292, Japan
| | - Tatsuo Kaneko
- Department of Materials Science, Japan Advanced Institute of Science and Technology, 1‐1 Asahidai, Nomi, Ishikawa 923‐1292, Japan
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Fagerquist CK, Garbus BR, Williams KE, Bates AH, Harden LA. Covalent attachment and dissociative loss of sinapinic acid to/from cysteine-containing proteins from bacterial cell lysates analyzed by MALDI-TOF-TOF mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:819-832. [PMID: 20188588 DOI: 10.1016/j.jasms.2010.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 01/12/2010] [Accepted: 01/14/2010] [Indexed: 05/28/2023]
Abstract
We report covalent attachment via a thiol ester linkage of 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid or SA) to cysteine-containing protein biomarkers from bacterial cell lysates of E. coli analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry when using SA as the matrix. Evidence to support this conclusion is the appearance of additional peaks in the MS spectra when using SA, which are absent when using alpha-cyano-4-hydroxycinnamic acid (HCCA). The additional peaks appear at a mass-to-charge (m/z) approximately 208 greater to the m/z of a more abundant protein ion peak. Protein biomarkers were identified by tandem mass spectrometry (MS/MS) using a MALDI time-of-flight/time-of-flight (TOF-TOF) mass spectrometer and top-down proteomics. Three protein biomarkers, HdeA, HdeB, and homeobox or YbgS (each containing two cysteine residues) were identified as having reactivity to SA. Non-cysteine-containing protein biomarkers showed no evidence of reactivity to SA. MS ions and MS/MS fragment ions were consistent with covalent attachment of SA via a thiol ester linkage to the side-chain of cysteine residues. MS/MS of a protein biomarker ion with a covalently attached SA revealed fragment ion peaks suggesting dissociative loss SA. We propose dissociative loss of SA is facilitated by a pentacyclic transition-state followed by proton abstraction of the beta-hydrogen of the bound SA by a sulfur lone pair followed by dissociative loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal. The apparent reactivity of SA to cysteine/disulfide-containing proteins may complicate identification of such proteins, however the apparent differential reactivity of SA and HCCA toward cysteine/disulfide-containing proteins may be exploited for identification of unknown cysteine-containing proteins.
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Affiliation(s)
- Clifton K Fagerquist
- Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, California 94710, USA.
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17
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den Heeten R, Muñoz BK, Popa G, Laan W, Kamer PCJ. Synthesis of hybrid transition-metalloproteins via thiol-selective covalent anchoring of Rh-phosphine and Ru-phenanthroline complexes. Dalton Trans 2010; 39:8477-83. [DOI: 10.1039/c0dt00239a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hendriks J, Hellingwerf KJ. pH Dependence of the Photoactive Yellow Protein Photocycle Recovery Reaction Reveals a New Late Photocycle Intermediate with a Deprotonated Chromophore. J Biol Chem 2009; 284:5277-88. [DOI: 10.1074/jbc.m805904200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Abdulghader K, Nojavan M, Naghshbandi N. Chemical stress induced by heliotrope (Heliotropium europaeum L.) allelochemicals and increased activity of antioxidant enzymes. Pak J Biol Sci 2008; 11:915-919. [PMID: 18814656 DOI: 10.3923/pjbs.2008.915.919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The aims of this study were to evaluate the allelopathic potential of heliotrope on some biochemical processes of dodder. The preliminary experiments revealed that the effect of aqueous extract of leaves of heliotrope is higher than its seeds and roots. So, the aqueous extract of leaves was used in remaining experiments. Leaf extracts of 5 g powder per 100 mL H2O inhibited the germination of dodder seeds up to 95% and that of radish up to 100%. While, the aqueous extract of vine leaves which is a non-allelopathic plant did not have any inhibitory effect on these seeds. Vine leaf was used as a control to show that the inhibitory effect of heliotrope is due to an inhibitory compound but not due to the concentration. The leaf extract of heliotrope at 0.0, 0.1, 1.0, 2, 3, 4 and 5 g powder per 100 mL H2O reduced the radish seedling growth from 14 cm to about 0.5 cm and that of dodder from 7.5 cm to about 0.25 cm. The effects of heliotrope allelochemicals on some physiological and biochemical processes of radish was also Investigated. The activity of auxin oxidase increased in leaves and roots of radish. Suggesting that the reduced radish growth is due to the decreased active auxin levels in its leaves and roots. The activity of alpha-amylase was reduced, so reduction of starch degradation and lack of respiratory energy is the prime reason of germination inhibition in dodder and radish seeds. The level of soluble sugars increased. This is an indication of reduction of the activity of some respiratory enzymes and reduced consumption of these sugars. Proline levels were also increased, indicating that, the chemical stress is induced by leaf extract. Finally, the activities of GPX and CAT which are antioxidant enzymes were increased, along with increased extract concentration. These finding shows that the chemical stress induced by leaf extract produces super oxide (O2*) and H2O2, which is neutralized to H2O and O2 by these enzymes.
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Affiliation(s)
- Kalantar Abdulghader
- Department of Biology, Oshnaviyeh Payam Noor University, Islamic Republic of Iran
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Abstract
The role of glycine residues was studied by alanine-scanning mutagenesis using photoactive yellow protein, a structural prototype of PER ARNT SIM domain proteins, as a template. Mutation of glycine located close to the end of beta-strands with dihedral angles disallowed for alanine (Gly-37, Gly-59, Gly-86, and Gly-115) induces destabilization of the protein structure. On the other hand, substitution for Gly-77 and Gly-82, incorporated into the fifth alpha-helix, slows the photocycle by 15-20 times, suggesting that these residues regulate the light-induced structural switch between dark-state structure and signaling-state structure. Most importantly, a significant amount of G29A is in the bleached state and showed a 1000-fold slower photocycle. As O(epsilon2) of the carboxylic acid of Glu-46 is close enough for contact with C(alpha) of Gly-29, alanine mutation perturbs this packing. Fourier transform infrared spectroscopy demonstrated that the C=O(epsilon2) stretching mode of Glu-46 is 6 cm(-1) upshifted in G29A, suggesting that C(alpha) of Gly-29 acts as a proton donor for the C(alpha)-H...O(epsilon2) hydrogen bond with Glu-46, which stabilizes the dark-state structure. During the photocycle, Glu-46 becomes negatively charged by donating a proton to the chromophore, resulting in breakage of this hydrophobic packing and consequent conformational change of the protein.
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Gromov EV, Burghardt I, Hynes JT, Köppel H, Cederbaum LS. Electronic structure of the photoactive yellow protein chromophore: Ab initio study of the low-lying excited singlet states. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2007.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Imamoto Y, Kataoka M. Structure and photoreaction of photoactive yellow protein, a structural prototype of the PAS domain superfamily. Photochem Photobiol 2007; 83:40-9. [PMID: 16939366 DOI: 10.1562/2006-02-28-ir-827] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Photoactive yellow protein (PYP) is a water-soluble photosensor protein found in purple photosynthetic bacteria. Unlike bacterial rhodopsins, photosensor proteins composed of seven transmembrane helices and a retinal chromophore in halophilic archaebacteria, PYP is a highly soluble globular protein. The alpha/beta fold structure of PYP is a structural prototype of the PAS domain superfamily, many members of which function as sensors for various kinds of stimuli. To absorb a photon in the visible region, PYP has a p-coumaric acid chromophore binding to the cysteine residue via a thioester bond. It exists in a deprotonated trans form in the dark. The primary photochemical event is photo-isomerization of the chromophore from trans to cis form. The twisted cis chromophore in early intermediates is relaxed and finally protonated. Consequently, the chromophore becomes electrostatically neutral and rearrangement of the hydrogen-bonding network triggers overall structural change of the protein moiety, in which local conformational change around the chromophore is propagated to the N-terminal region. Thus, it is an ideal model for protein conformational changes that result in functional change, responding to stimuli and expressing physiological activity. In this paper, recent progress in investigation of the photoresponse of PYP is reviewed.
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Affiliation(s)
- Yasushi Imamoto
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
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23
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Yamada H, Kumauchi M, Hamada N, Zheng XG, Park IIH, Masuda K, Yoshihara K, Tokunaga F. Analogue Chromophore Study of the Influence of Electronic Perturbation on Color Regulation of Photoactive Yellow Protein. Photochem Photobiol 2006. [DOI: 10.1111/j.1751-1097.2006.tb09794.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Nibbering NMM. Four decades of joy in mass spectrometry. MASS SPECTROMETRY REVIEWS 2006; 25:962-1017. [PMID: 16736509 DOI: 10.1002/mas.20099] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Tremendous developments in mass spectrometry have taken place in the last 40 years. This holds for both the science and the instrumental revolutions in this field. In chemistry the research was heavily focused on organic molecules that upon electron ionization fragmented via complex mechanistic pathways as shown by isotopic labeling experiments. These studies, including ion structure determinations, were performed with use of double focusing mass spectrometers of both conventional and reversed geometry, and equipped with various types of metastable ion scanning and collision-induced dissociation techniques developed by physical and analytical chemists. Time-resolved mass spectrometry by use of the field ionization kinetics method, developed by physical chemists, was another powerful way to unravel details of unimolecular gas phase ion dissociations. Then the development of new ionization methods, such as desorption chemical ionization, field desorption, and fast atom bombardment permitted not only to analyze unvolatile, thermally labile and higher molecular weight compounds, but also to study their chemical behavior in the gas phase, initially with use of double focusing instruments and later on with multisector and hybrid mass spectrometers. These ionization methods also enabled to study organometallic compounds and increasingly the field of medium-sized to large biomolecules, the latter being exploded in the last decade by the development of electrospray- and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. Another area of research concerned the bimolecular chemistry of organic ions with organic molecules in the gas phase. Initially this was performed with use of among others drift-cell ion cyclotron resonance spectroscopy, that later on was replaced by the developed method of ion trapping and Fourier transform ion cyclotron resonance. Combination of the latter with the afore-mentioned ionization methods has shifted also in this case the research on organic molecules to organometallic/inorganic systems, and predominantly to biomolecules in the last decade. This invited review will describe the research efforts made by the author's group over the last 40 years together with some personal experiences during his career.
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Affiliation(s)
- Nico M M Nibbering
- Physical Chemistry, Laser Center, Division Chemistry, Faculty of Exact Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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25
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Yamada H, Kumauchi M, Hamada N, Zheng XG, Park IH, Masuda K, Yoshihara K, Tokunaga F. Analogue chromophore study of the influence of electronic perturbation on color regulation of photoactive yellow protein. Photochem Photobiol 2006; 82:1422-5. [PMID: 16709144 DOI: 10.1562/2006-01-17-ra-781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We report a unique lambdamax shift of the absorption maximum of a photoactive yellow protein (PYP) analogue reconstituted with a fluorinated chromophore (F-PYP). The difference in lambdamax between the free chromophore and the protein was significantly larger than that with the native chromophore. We concluded that the unusual lambdamax shift is caused by the electronegative character of the fluorine atom and not by steric hindrance. This result suggests that formation of a hydrogen bond between the fluorine atom and one or more amino acid residues could neutralize its electron-withdrawing character. The properties of analogues of PYP with brominated and methylated chromophore could be explained as an effect of steric hindrance.
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Affiliation(s)
- Hiroshi Yamada
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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26
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Chandrakuntal K, Thomas NM, Kumar PG, Laloraya M, Laloraya MM. Fluorescence Resonance Energy Transfer Between Polyphenolic Compounds and Riboflavin Indicates a Possible Accessory Photoreceptor Function for Some Polyphenolic Compounds. Photochem Photobiol 2006; 82:1358-64. [PMID: 16842022 DOI: 10.1562/2005-08-09-ra-644] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The photoreceptive extreme tip of the wheat coleoptile exhibits intense green-yellow fluorescence under UV light, suggesting the presence of UV-absorbing materials. Fluorescence spectra of the intact coleoptile tip and tip homogenate showed the presence of the known photoreceptor pigments flavin and carotene, and a preponderance of phenolic compounds. Absorption spectra and fluorescence spectra of various phenolic compounds showed close overlap with the absorption and fluorescence spectra of the wheat coleoptile tip homogenate. Fluorescence spectra of several phenolic compounds showed close overlap with the absorption bands of flavin, carotene and pterine, suggesting possible energy transduction from phenols to these photoreceptors. Excitation of gentisic acid and ferulic acid with 340 nm light in the presence of flavin showed enhancement of flavin fluorescence in a concentration- and viscosity-dependent fashion, indicating fluorescence resonance energy transfer between them and riboflavin. Furthermore, several phenolic compounds tested generated superoxide anion on excitation at 340 nm, suggesting that superoxide-dependent signal cascades could operate in a polyphenol-mediated pathway. Phenolic compounds thus may act as accessory photoreceptors bringing about excitation energy transfer to the reactive photoreceptor molecules, or they may take over the function of the normal photoreceptor in genetic mutations lacking the system, or both processes may occur. The responses of plants to UV-B and UV-A light in mutants may be explained in terms of various phenolics acting as energy transducers in photoreceptor functioning.
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Affiliation(s)
- Kumar Chandrakuntal
- Rajiv Gandhi Centre for Biotechnology, Thycaud, Poojappura, Thiruvananthapuram 695 014, Kerala, India
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27
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Glasbeek M, Zhang H. Femtosecond Studies of Solvation and Intramolecular Configurational Dynamics of Fluorophores in Liquid Solution. Chem Rev 2004; 104:1929-54. [PMID: 15080717 DOI: 10.1021/cr0206723] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Max Glasbeek
- Laboratory for Physical Chemistry, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands.
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28
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Dugave C, Demange L. Cis-trans isomerization of organic molecules and biomolecules: implications and applications. Chem Rev 2003; 103:2475-532. [PMID: 12848578 DOI: 10.1021/cr0104375] [Citation(s) in RCA: 744] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christophe Dugave
- CEA/Saclay, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Bâtiment 152, 91191 Gif-sur-Yvette, France.
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29
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Toniolo A, Granucci G, Martínez TJ. Conical Intersections in Solution: A QM/MM Study Using Floating Occupation Semiempirical Configuration Interaction Wave Functions. J Phys Chem A 2003. [DOI: 10.1021/jp022468p] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- A. Toniolo
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, v. Risorgimento, Pisa, Italy
| | - G. Granucci
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, v. Risorgimento, Pisa, Italy
| | - Todd J. Martínez
- Department of Chemistry and The Beckman Institute, University of Illinois, Urbana, Illinois 61801, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, v. Risorgimento, Pisa, Italy
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30
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Changenet-Barret P, Espagne A, Katsonis N, Charier S, Baudin JB, Jullien L, Plaza P, Martin MM. Excited-state relaxation dynamics of a PYP chromophore model in solution: influence of the thioester group. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)01480-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Changenet-Barret P, Plaza P, Martin MM. Primary events in the photoactive yellow protein chromophore in solution. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00137-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Metzler DE, Metzler CM, Sauke DJ. Light and Life. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Haker A, Hendriks J, Gensch T, Hellingwerf K, Crielaard W. Isolation, reconstitution and functional characterisation of the Rhodobacter sphaeroides photoactive yellow protein. FEBS Lett 2000; 486:52-6. [PMID: 11108842 DOI: 10.1016/s0014-5793(00)02242-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report the isolation, functional reconstitution and photophysical characterisation of Rhodobacter sphaeroides photoactive yellow protein (PYP), of which the gene was recently cloned. Reconstitution of the his-tagged purified apo-protein with 4-hydroxy-cinnamic acid yields the characteristic blue absorbance at 446 nm, but surprisingly also an absorbance peak at 360 nm. This additional peak is not caused by binding of a second chromophore, as confirmed with mass spectroscopy. Moreover, reconstitution with the 'locked' analogue 7-hydroxy-coumarin-3-carboxylic acid yields only a single absorbance peak at 441 nm. The 446 nm and 360 nm species are part of a temperature- and pH-dependent equilibrium. Photoactivation of the protein leads to formation of a blue-shifted intermediate as in other PYPs, with a 100-fold increased groundstate recovery rate (k(pB-->pG)=500 s(-1)) compared to E-PYP.
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Affiliation(s)
- A Haker
- Laboratory for Microbiology, E.C. Slater Institute, BioCentrum, University of Amsterdam, Nieuwe Achtergracht 127, 1018 WS, Amsterdam, The Netherlands
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Hendriks J, Hoff WD, Crielaard W, Hellingwerf KJ. Protonation/deprotonation reactions triggered by photoactivation of photoactive yellow protein from Ectothiorhodospira halophila. J Biol Chem 1999; 274:17655-60. [PMID: 10364204 DOI: 10.1074/jbc.274.25.17655] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Light-dependent pH changes were measured in unbuffered solutions of wild type photoactive yellow protein (PYP) and its H108F and E46Q variants, using two independent techniques: transient absorption changes of added pH indicator dyes and direct readings with a combination pH electrode. Depending on the absolute pH of the sample, a reversible protonation as well as a deprotonation can be observed upon formation of the transient, blue-shifted photocycle intermediate (pB) of this photoreceptor protein. The latter is observed at very alkaline pH, the former at acidic pH values. At neutral pH, however, the formation of the pB state is not paralleled by significant protonation/deprotonation of PYP, as expected for concomitant protonation of the chromophore and deprotonation of Glu-46 during pB formation. We interpret these results as further evidence that a proton is transferred from Glu-46 to the coumaric acid chromophore of PYP, during pB formation. One cannot exclude the possibility, however, that this transfer proceeds through the bulk aqueous phase. Simultaneously, an amino acid side chain(s) (e.g. His-108) changes from a buried to an exposed position. These results, therefore, further support the idea that PYP significantly unfolds in the pB state and resolve the controversy regarding proton transfer during the PYP photocycle.
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Affiliation(s)
- J Hendriks
- Laboratory for Microbiology, E. C. Slater Institute, BioCentrum, University of Amsterdam, 1018 WS Amsterdam, The Netherlands
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35
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Changenet P, Zhang H, van der Meer M, Hellingwerf K, Glasbeek M. Subpicosecond fluorescence upconversion measurements of primary events in yellow proteins. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(97)01334-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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36
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Hoff WD, Van Stokkum IH, Gural J, Hellingwerf KJ. Comparison of acid denaturation and light activation in the eubacterial blue-light receptor photoactive yellow protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1997. [DOI: 10.1016/s0005-2728(97)00082-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Kroon AR, Hoff WD, Fennema HP, Gijzen J, Koomen GJ, Verhoeven JW, Crielaard W, Hellingwerf KJ. Spectral tuning, fluorescence, and photoactivity in hybrids of photoactive yellow protein, reconstituted with native or modified chromophores. J Biol Chem 1996; 271:31949-56. [PMID: 8943241 DOI: 10.1074/jbc.271.50.31949] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Photoactive yellow proteins (PYPs) constitute a new class of eubacterial photoreceptors, containing a deprotonated thiol ester-linked 4-hydroxycinnamic acid chromophore. Interactions with the protein dramatically change the (photo)chemical properties of this cofactor. Here we describe the reconstitution of apoPYP with anhydrides of various chromophore analogues. The resulting hybrid PYPs, their acid-denatured states, and corresponding model compounds were characterized with respect to their absorption spectrum, pK for chromophore deprotonation, fluorescence quantum yield, and Stokes shift. Three factors contributing to the tuning of the absorption of the hybrid PYPs were quantified: (i) thiol ester bond formation, (ii) chromophore deprotonation, and (iii) specific chromophore-protein interactions. Analogues lacking the 4-hydroxy substituent lack both contributions (chromophore deprotonation and specific chromophore-protein interactions), confirming the importance of this substituent in optical tuning of PYP. Hydroxy and methoxy substituents in the 3- and/or 5-position do not disrupt strong interactions with the protein but increase their pK for protonation and the fluorescence quantum yield. Both deprotonation and binding to apoPYP strongly decrease the Stokes shift of chromophore fluorescence. Therefore, coupling of the chromophore to the apoprotein not only reduces the energy gap between its ground and excited state but also the extent of reorganization between these two states. Two of the PYP hybrids show photoactivity comparable with native PYP, although with retarded recovery of the initial state.
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Affiliation(s)
- A R Kroon
- Laboratory for Microbiology, E. C. Slater Institute, BioCentrum Amsterdam, Nieuwe Achtergracht 127, 1018 WS, Amsterdam, The Netherlands.
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