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Fernández-Alarcón A, Guevara-Vela JM, Casals-Sainz JL, Costales A, Francisco E, Martín Pendás Á, Rocha Rinza T. Photochemistry in Real Space: Batho- and Hypsochromism in the Water Dimer. Chemistry 2020; 26:17035-17045. [PMID: 32822523 DOI: 10.1002/chem.202002854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 11/09/2022]
Abstract
The development of chemical intuition in photochemistry faces several difficulties that result from the inadequacy of the one-particle picture, the Born-Oppenheimer approximation, and other basic ideas used to build models. It is shown herein how real-space approaches can be efficiently used to gain valuable insights in photochemistry through a simple example of red and blue shift effects: the double hypso- and bathochromic shifts in the low-lying valence excited states of (H2 O)2 . It is demonstrated that 1) the use of these techniques allows the perturbative language used in the theory of intermolecular interactions, even in the strongly interacting short-range regime, to be maintained; 2) one and only one molecule is photoexcited in each of the addressed excited states and 3) the electrostatic interaction between the in-the-cluster molecular dipoles provides a fairly intuitive rationalisation of the observed batho- and hypsochromism. The methods exploited and illustrated herein are able to maintain the individuality and properties of the interacting entities in a molecular aggregate, and thereby they allow chemical intuition in general states, at any geometry and using a broad variety of electronic structure methods to be kept and built.
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Affiliation(s)
- Alberto Fernández-Alarcón
- Institute of Chemistry, National Autonomous University of Mexico, 04510, Mexico City, Mexico.,Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | | | - José Luis Casals-Sainz
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Aurora Costales
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Evelio Francisco
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, 33006, Oviedo, Spain
| | - Tomás Rocha Rinza
- Institute of Chemistry, National Autonomous University of Mexico, 04510, Mexico City, Mexico
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2
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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3
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Horbury MD, Baker LA, Rodrigues ND, Quan WD, Stavros VG. Photoisomerization of ethyl ferulate: A solution phase transient absorption study. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Lin CY, Both J, Do K, Boxer SG. Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs). Proc Natl Acad Sci U S A 2017; 114:E2146-E2155. [PMID: 28242710 PMCID: PMC5358378 DOI: 10.1073/pnas.1618087114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Split GFPs have been widely applied for monitoring protein-protein interactions by expressing GFPs as two or more constituent parts linked to separate proteins that only fluoresce on complementing with one another. Although this complementation is typically irreversible, it has been shown previously that light accelerates dissociation of a noncovalently attached β-strand from a circularly permuted split GFP, allowing the interaction to be reversible. Reversible complementation is desirable, but photodissociation has too low of an efficiency (quantum yield <1%) to be useful as an optogenetic tool. Understanding the physical origins of this low efficiency can provide strategies to improve it. We elucidated the mechanism of strand photodissociation by measuring the dependence of its rate on light intensity and point mutations. The results show that strand photodissociation is a two-step process involving light-activated cis-trans isomerization of the chromophore followed by light-independent strand dissociation. The dependence of the rate on temperature was then used to establish a potential energy surface (PES) diagram along the photodissociation reaction coordinate. The resulting energetics-function model reveals the rate-limiting process to be the transition from the electronic excited-state to the ground-state PES accompanying cis-trans isomerization. Comparisons between split GFPs and other photosensory proteins, like photoactive yellow protein and rhodopsin, provide potential strategies for improving the photodissociation quantum yield.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Johan Both
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Keunbong Do
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
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5
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García-Prieto FF, Muñoz-Losa A, Fdez Galván I, Sánchez ML, Aguilar MA, Martín ME. QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore. J Chem Theory Comput 2017; 13:737-748. [PMID: 28072537 DOI: 10.1021/acs.jctc.6b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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Affiliation(s)
- Francisco F García-Prieto
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Aurora Muñoz-Losa
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University , Box 518, 751 20 Uppsala, Sweden
| | - M Luz Sánchez
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
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6
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Hamada N, Tan Z, Kanematsu Y, Inazumi N, Nakamura R. Influence of a chromophore analogue in the protein cage of a photoactive yellow protein. Photochem Photobiol Sci 2015; 14:1722-8. [PMID: 26178816 DOI: 10.1039/c5pp00176e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved spectra of a photoactive yellow protein (PYP) containing cyano-p-coumaric acid (CHCA) were recorded. To understand the mechanism of photo-isomerization, an electron-withdrawing CN group was introduced into the PYP to alter the C[double bond, length as m-dash]C double bond character. Free CHCA chromophores in aqueous solution underwent photo-isomerization whereas PYP with a bound CHCA (PYP-CN) exhibited no photocycle at acidic or alkaline pH or in urea and other solutions. Furthermore, no photocycle was observed with PYP mutants after illumination. This phenomenon cannot be fully explained by the electron-withdrawing properties of the CN group. We conclude that the CHCA chromophore in PYP was locked in the protein cage and that the CN group interacted with the protein residues.
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Affiliation(s)
- Norio Hamada
- Science & Technology Entrepreneurship Laboratory (e-square), Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan.
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7
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Nakamura R, Hamada N. Vibrational Energy Flow in Photoactive Yellow Protein Revealed by Infrared Pump–Visible Probe Spectroscopy. J Phys Chem B 2015; 119:5957-61. [DOI: 10.1021/jp512994q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryosuke Nakamura
- Science
and Technology Entrepreneurship
Laboratory, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Norio Hamada
- Science
and Technology Entrepreneurship
Laboratory, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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8
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Chosrowjan H, Taniguchi S, Tanaka F. Ultrafast fluorescence upconversion technique and its applications to proteins. FEBS J 2015; 282:3003-15. [DOI: 10.1111/febs.13180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Haik Chosrowjan
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
| | - Seiji Taniguchi
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
| | - Fumio Tanaka
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
- Department of Chemistry; Faculty of Science; Chulalongkorn University; Bangkok Thailand
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9
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Tan EMM, Amirjalayer S, Mazzella P, Bakker BH, van Maarseveen JH, Bieraugel H, Buma WJ. Molecular Beam and ab Initio Studies of Photoactive Yellow Protein Chromophores: Influence of the Thioester Functionality and Single Bond Rotation. J Phys Chem B 2014; 118:12395-403. [DOI: 10.1021/jp5075169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric M. M. Tan
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Saeed Amirjalayer
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
- Physical
Institute and Center for Nanotechnology (CeNTech) Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
| | - Paul Mazzella
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Bert H. Bakker
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Jan H. van Maarseveen
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Hans Bieraugel
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Wybren J. Buma
- van
’t Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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10
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Creelman M, Kumauchi M, Hoff WD, Mathies RA. Chromophore Dynamics in the PYP Photocycle from Femtosecond Stimulated Raman Spectroscopy. J Phys Chem B 2014; 118:659-67. [DOI: 10.1021/jp408584v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Mark Creelman
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Masato Kumauchi
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Wouter D. Hoff
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard A. Mathies
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
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11
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Naseem S, Laurent AD, Carroll EC, Vengris M, Kumauchi M, Hoff WD, Krylov AI, Larsen DS. Photo-isomerization upshifts the pKa of the Photoactive Yellow Protein chromophore to contribute to photocycle propagation. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Mendonça L, Hache F, Changenet-Barret P, Plaza P, Chosrowjan H, Taniguchi S, Imamoto Y. Ultrafast Carbonyl Motion of the Photoactive Yellow Protein Chromophore Probed by Femtosecond Circular Dichroism. J Am Chem Soc 2013; 135:14637-43. [DOI: 10.1021/ja404503q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lucille Mendonça
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique/CNRS/INSERM, 91128 Palaiseau cedex, France
| | - François Hache
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique/CNRS/INSERM, 91128 Palaiseau cedex, France
| | | | - Pascal Plaza
- Ecole Normale Supérieure,
Département de Chimie, UMR 8640 CNRS-ENS-UPMC, 24 rue Lhomond,
75005 Paris, France
| | - Haik Chosrowjan
- Institute for Laser Technology, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Seiji Taniguchi
- Institute for Laser Technology, 2-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasushi Imamoto
- Department
of Biophysics, Graduate School of Sciences, Kyoto University, Kyoto 6068502, Japan
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13
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Nakamura R, Hamada N, Abe K, Yoshizawa M. Ultrafast hydrogen-bonding dynamics in the electronic excited state of photoactive yellow protein revealed by femtosecond stimulated Raman spectroscopy. J Phys Chem B 2012; 116:14768-75. [PMID: 23210980 DOI: 10.1021/jp308433a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultrafast structural dynamics in the electronic excited state of photoactive yellow protein (PYP) is studied by femtosecond stimulated Raman spectroscopy. Stimulated Raman spectra in the electronic excited state, S(1), can be obtained by using a Raman pump pulse in resonance with the S(1)-S(0) transition. This is confirmed by comparing the experimental results with numerical calculations based on the density matrix treatment. We also investigate the hydrogen-bonding network surrounding the wild-type (WT)-PYP chromophore in the ground and excited states by comparing its stimulated Raman spectra with those of the E46Q-PYP mutant. We focus on the relative intensity of the Raman band at 1555 cm(-1), which includes both vinyl bond C═C stretching and ring vibrations and is sensitive to the hydrogen-bonding network around the phenolic oxygen of the chromophore. The relative intensity for the WT-PYP decreases after actinic excitation within the 150 fs time resolution and reaches a similar intensity to that for E46Q-PYP. These observations indicate that the WT-PYP hydrogen-bonding network is immediately rearranged in the electronic excited state to form a structure similar to that of E46Q-PYP.
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Affiliation(s)
- Ryosuke Nakamura
- Science and Technology Entrepreneurship Laboratory, Osaka University, Suita, Osaka, Japan.
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14
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Gromov EV, Burghardt I, Köppel H, Cederbaum LS. Native hydrogen bonding network of the photoactive yellow protein (PYP) chromophore: Impact on the electronic structure and photoinduced isomerization. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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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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16
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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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17
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Changenet-Barret P, Loukou C, Ley C, Lacombat F, Plaza P, Mallet JM, Martin MM. Primary photodynamics of a biomimetic model of photoactive yellow protein (PYP). Phys Chem Chem Phys 2010; 12:13715-23. [DOI: 10.1039/c0cp00618a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Nakamura R, Hamada N, Ichida H, Tokunaga F, Kanematsu Y. Transient Vibronic Structure in Ultrafast Fluorescence Spectra of Photoactive Yellow Protein. Photochem Photobiol 2008; 84:937-40. [DOI: 10.1111/j.1751-1097.2008.00329.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Nakamura R, Hamada N, Ichida H, Tokunaga F, Kanematsu Y. Coherent oscillations in ultrafast fluorescence of photoactive yellow protein. J Chem Phys 2008; 127:215102. [PMID: 18067379 DOI: 10.1063/1.2802297] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map of ultrafast fluorescence with 180 fs time resolution and 5 nm spectral resolution. The two-dimensional map revealed that four or more oscillatory components exist within the broad bandwidth of the fluorescence spectrum, each of which is restricted in the respective narrow spectral region. Typical frequencies of the oscillatory modes are 50 and 120 cm(-1). In the landscape on the map, the oscillatory components were recognized as the ridges which were winding and descending with time. The amplitude of the oscillatory and winding behaviors is a few hundred cm(-1), which is the same order as the frequencies of the oscillations. The mean spectral positions of the oscillatory components in the two-dimensional map are well explained by considering the vibrational energies of intramolecular modes in the electronic ground state of the chromophore. The entire view of the wave packet oscillations and broadening in the electronic excited state, accompanied by fluorescence transitions to the vibrational sublevels belonging to the electronic ground state, was obtained.
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Affiliation(s)
- Ryosuke Nakamura
- JST-CREST, Venture Business Laboratory, Center for Advanced Science and Innovation, Osaka University, Suita, Osaka 565-0871, Japan.
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20
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Leenders EJM, VandeVondele J, Bolhuis PG, Meijer EJ. Solvation of p-Coumaric Acid in Water. J Phys Chem B 2007; 111:13591-9. [DOI: 10.1021/jp075341e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elske J. M. Leenders
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Joost VandeVondele
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter G. Bolhuis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Evert Jan Meijer
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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21
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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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Kühn O, Wöste L. Biological systems: Applications and perspectives. ANALYSIS AND CONTROL OF ULTRAFAST PHOTOINDUCED REACTIONS 2007. [PMCID: PMC7122019 DOI: 10.1007/978-3-540-68038-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Oliver Kühn
- Institut f. Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Ludger Wöste
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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24
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Changenet-Barret P, Plaza P, Martin MM, Chosrowjan H, Taniguchi S, Mataga N, Imamoto Y, Kataoka M. Role of arginine 52 on the primary photoinduced events in the PYP photocycle. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.12.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Brouwer AM, Fazio SM, Haraszkiewicz N, Leigh DA, Lennon CM. Coumaric amide rotaxanes: effects of hydrogen bonding and mechanical interlocking on the photochemistry and photophysics. Photochem Photobiol Sci 2007; 6:480-6. [PMID: 17404644 DOI: 10.1039/b618795a] [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: 01/17/2023]
Abstract
Secondary amide derivatives of coumaric and ferulic acid are shown to undergo photoisomerization, forming a photostationary mixture of E- and Z-isomers. When the same chromophores are incorporated in rotaxanes, the extent of conversion to the Z-isomers is much smaller. Low temperature fluorescence experiments show that the energy barrier for non-radiative decay of the excited state is higher in the rotaxanes than in the corresponding threads, but the barriers are low in all cases.
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Affiliation(s)
- Albert M Brouwer
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018, WS Amsterdam, The Netherlands.
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26
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Espagne A, Paik DH, Changenet-Barret P, Plaza P, Martin MM, Zewail AH. Ultrafast light-induced response of photoactive yellow protein chromophore analogues. Photochem Photobiol Sci 2007; 6:780-7. [PMID: 17609772 DOI: 10.1039/b700927e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The fluorescence decays of several analogues of the photoactive yellow protein (PYP) chromophore in aqueous solution have been measured by femtosecond fluorescence up-conversion and the corresponding time-resolved fluorescence spectra have been reconstructed. The native chromophore of PYP is a thioester derivative of p-coumaric acid in its trans deprotonated form. Fluorescence kinetics are reported for a thioester phenyl analogue and for two analogues where the thioester group has been changed to amide and carboxylate groups. The kinetics are compared to those we previously reported for the analogues bearing ketone and ester groups. The fluorescence decays of the full series are found to lie in the 1-10 ps range depending on the electron-acceptor character of the substituent, in good agreement with the excited-state relaxation kinetics extracted from transient absorption measurements. Steady-state photolysis is also examined and found to depend strongly on the nature of the substituent. While it has been shown that the ultrafast light-induced response of the chromophore in PYP is controlled by the properties of the protein nanospace, the present results demonstrate that, in solution, the relaxation dynamics and pathway of the chromophore is controlled by its electron donor-acceptor structure: structures of stronger electron donor-acceptor character lead to faster decays and less photoisomerisation.
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Affiliation(s)
- Agathe Espagne
- UMR CNRS-ENS 8640 PASTEUR, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005, Paris, France
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27
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van der Horst MA, Arents JC, Kort R, Hellingwerf KJ. Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein. Photochem Photobiol Sci 2007; 6:571-9. [PMID: 17487311 DOI: 10.1039/b701072a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bacterial photoreceptor protein photoactive yellow protein (PYP) covalently binds the chromophore 4-hydroxy coumaric acid, tuning (spectral) characteristics of this cofactor. Here, we study this binding and tuning using a combination of pointmutations and chromophore analogs. In all photosensor proteins studied to date the covalent linkage of the chromophore to the apoprotein is dispensable for light-induced catalytic activation. We analyzed the functional importance of the covalent linkage using an isosteric chromophore-protein variant in which the cysteine is replaced by a glycine residue and the chromophore by thiomethyl-p-coumaric acid (TMpCA). The model compound TMpCA is shown to weakly complex with the C69G protein. This non-covalent binding results in considerable tuning of both the pKa and the color of the chromophore. The photoactivity of this system, however, was strongly impaired, making PYP the first known photosensor protein in which the covalent linkage of the chromophore is of paramount importance for the functional activity of the protein in vitro. We also studied the influence of chromophore analogs on the color and photocycle of PYP, not only in WT, but especially in the E46Q mutant, to test if effects from both chromophore and protein modifications are additive. When the E46Q protein binds the sinapinic acid chromophore, the color of the protein is effectively changed from yellow to orange. The altered charge distribution in this protein also results in a changed pKa value for chromophore protonation, and a strongly impaired photocycle. Both findings extend our knowledge of the photochemistry of PYP for signal generation.
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Affiliation(s)
- Michael A van der Horst
- Laboratory for Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV, Amsterdam, The Netherlands
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28
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van Wilderen LJGW, van der Horst MA, van Stokkum IHM, Hellingwerf KJ, van Grondelle R, Groot ML. Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein. Proc Natl Acad Sci U S A 2006; 103:15050-5. [PMID: 17015839 PMCID: PMC1940041 DOI: 10.1073/pnas.0603476103] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactive proteins such as PYP (photoactive yellow protein) are generally accepted as model systems for studying protein signal state formation. PYP is a blue-light sensor from the bacterium Halorhodospira halophila. The formation of PYP's signaling state is initiated by trans-cis isomerization of the p-coumaric acid chromophore upon the absorption of light. The quantum yield of signaling state formation is approximately 0.3. Using femtosecond visible pump/mid-IR probe spectroscopy, we investigated the structure of the very short-lived ground state intermediate (GSI) that results from an unsuccessful attempt to enter the photocycle. This intermediate and the first stable GSI on pathway into the photocycle, I0, both have a mid-IR difference spectrum that is characteristic of a cis isomer, but only the I0 intermediate has a chromophore with a broken hydrogen bond with the backbone N atom of Cys-69. We suggest, therefore, that breaking this hydrogen bond is decisive for a successful entry into the photocycle. The chromophore also engages in a hydrogen-bonding network by means of its phenolate group with residues Tyr-42 and Glu-46. We have investigated the role of this hydrogen bond by exchanging the H bond-donating residue Glu-46 with the weaker H bond-donating glutamine (i.e., Gln-46). We have observed that this mutant exhibits virtually identical kinetics and product yields as WT PYP, even though during the I0-to-I1 transition, on the 800-ps time scale, the hydrogen bond of the chromophore with Gln-46 is broken, whereas this hydrogen bond remains intact with Glu-46.
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Affiliation(s)
- L J G W van Wilderen
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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29
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Usman A, Masuhara H, Asahi T. trans−cis Photoisomerization of a Photoactive Yellow Protein Model Chromophore in Crystalline Phase. J Phys Chem B 2006; 110:20085-8. [PMID: 17034177 DOI: 10.1021/jp064984b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the photoinduced trans/cis isomerization of the protonated form of p-hydroxycinnamic thiophenyl ester, a model chromophore of the photoactive yellow protein (PYP), in crystalline phase, by both fluorescence and infrared spectroscopies. The conversion from trans to cis configuration is revealed by a shift of the fluorescence peak and by inspection of the infrared maker bands. The crystal packing apparently stabilizes the cis photoproduct, suggesting different environmental effects from the solvent molecules for this model chromophore in liquid solutions or from the amino acid residues for the PYP chromophore.
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30
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Abstract
The photoactive yellow protein (PYP) is the photoreceptor protein responsible for initiating the blue-light repellent response of the Halorhodospira halophila bacterium. Optical excitation of the intrinsic chromophore in PYP, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. The dynamical processes responsible for the initiation of the PYP photocycle have been explored with several time-resolved techniques, which include ultrafast electronic and vibrational spectroscopies. Ultrafast electronic spectroscopies, such as pump-visible probe, pump-dump-visible probe, and fluorescence upconversion, are useful in identifying the timescales and connectivity of the transient intermediates, while ultrafast vibrational spectroscopies link these intermediates to dynamic structures. Herein, we present the use of these techniques for exploring the initial dynamics of PYP, and show how these techniques provide the basis for understanding the complex relationship between protein and chromophore, which ultimately results in biological function.
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Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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31
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Vengris M, Larsen DS, van der Horst MA, Larsen OFA, Hellingwerf KJ, van Grondelle R. Ultrafast Dynamics of Isolated Model Photoactive Yellow Protein Chromophores: “Chemical Perturbation Theory” in the Laboratory. J Phys Chem B 2005; 109:4197-208. [PMID: 16851482 DOI: 10.1021/jp045763d] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pump-probe and pump-dump probe experiments have been performed on several isolated model chromophores of the photoactive yellow protein (PYP). The observed transient absorption spectra are discussed in terms of the spectral signatures ascribed to solvation, excited-state twisting, and vibrational relaxation. It is observed that the protonation state has a profound effect on the excited-state lifetime of p-coumaric acid. Pigments with ester groups on the coumaryl tail end and charged phenolic moieties show dynamics that are significantly different from those of other pigments. Here, an unrelaxed ground-state intermediate could be observed in pump-probe signals. A similar intermediate could be identified in the sinapinic acid and in isomerization-locked chromophores by means of pump-dump probe spectroscopy; however, in these compounds it is less pronounced and could be due to ground-state solvation and/or vibrational relaxation. Because of strong protonation-state dependencies and the effect of electron donor groups, it is argued that charge redistribution upon excitation determines the twisting reaction pathway, possibly through interaction with the environment. It is suggested that the same pathway may be responsible for the initiation of the photocycle in native PYP.
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Affiliation(s)
- Mikas Vengris
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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32
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Excited state dynamics of a PYP chromophore model system explored with ultrafast infrared spectroscopy. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Changenet-Barret P, Espagne A, Plaza P, Hellingwerf KJ, Martin MM. Investigations of the primary events in a bacterial photoreceptor for photomotility: photoactive yellow protein (PYP). NEW J CHEM 2005. [DOI: 10.1039/b418134d] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Larsen DS, Vengris M, van Stokkum IHM, van der Horst MA, de Weerd FL, Hellingwerf KJ, van Grondelle R. Photoisomerization and photoionization of the photoactive yellow protein chromophore in solution. Biophys J 2004; 86:2538-50. [PMID: 15041690 PMCID: PMC1304101 DOI: 10.1016/s0006-3495(04)74309-x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Dispersed pump-dump-probe spectroscopy has the ability to characterize and identify the underlying ultrafast dynamical processes in complicated chemical and biological systems. This technique builds on traditional pump-probe techniques by exploring both ground- and excited-state dynamics and characterizing the connectivity between constituent transient states. We have used the dispersed pump-dump-probe technique to investigate the ground-state dynamics and competing excited-state processes in the excitation-induced ultrafast dynamics of thiomethyl p-coumaric acid, a model chromophore for the photoreceptor photoactive yellow protein. Our results demonstrate the parallel formation of two relaxation pathways (with multiple transient states) that jointly lead to two different types of photochemistry: cis-trans isomerization and detachment of a hydrated electron. The relative transition rates and quantum yields of both pathways have been determined. We find that the relaxation of the photoexcited chromophores involves multiple, transient ground-state intermediates and the chromophore in solution does not generate persistent photoisomerized products, but instead undergoes photoionization resulting in the generation of detached electrons and radicals. These results are of great value in interpreting the more complex dynamical changes in the optical properties of the photoactive yellow protein.
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Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
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35
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Vengris M, van Stokkum IHM, He X, Bell AF, Tonge PJ, van Grondelle R, Larsen DS. Ultrafast Excited and Ground-State Dynamics of the Green Fluorescent Protein Chromophore in Solution. J Phys Chem A 2004. [DOI: 10.1021/jp037902h] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mikas Vengris
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
| | - Ivo H. M. van Stokkum
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
| | - Xiang He
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
| | - Alasdair F. Bell
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
| | - Peter J. Tonge
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
| | - Rienk van Grondelle
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
| | - Delmar S. Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400
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36
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Yamada A, Ishikura T, Yamato T. Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: Application to photoisomerization reaction. Proteins 2004; 55:1070-7. [PMID: 15146504 DOI: 10.1002/prot.20063] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photoreceptor proteins serve as efficient nano-machines for the photoenergy conversion and the photosignal transduction of living organisms. For instance, the photoactive yellow protein derived from a halophilic bacterium has the p-coumaric acid chromophore, which undergoes an ultrafast photoisomerization reaction after light illumination. To understand the structure-function relationship at the atomic level, we used a computational method to find functionally important atoms for the photoisomerization reaction of the photoactive yellow protein. In the present study, a "direct" measure of the functional significance was quantitatively evaluated for each atom by calculating the partial atomic driving force for the photoisomerization reaction. As a result, we revealed the reaction mechanism in which the specific role of each functionally important atom has been well characterized in a systematic manner. In addition, we observed that this mechanism is strongly conserved during the thermal fluctuation of the photoactive yellow protein. We compared the experimental data of fluorescence decay constant of several different mutants and the present analysis. As a result, we found that the reaction rate constant is decreased when a large positive driving force is missing.
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Affiliation(s)
- Atsushi Yamada
- Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
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37
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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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38
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Chosrowjan H, Taniguchi S, Mataga N, Unno M, Yamauchi S, Hamada N, Kumauchi M, Tokunaga F. Low-Frequency Vibrations and Their Role in Ultrafast Photoisomerization Reaction Dynamics of Photoactive Yellow Protein. J Phys Chem B 2004. [DOI: 10.1021/jp031126w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haik Chosrowjan
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Seiji Taniguchi
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Noboru Mataga
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Masashi Unno
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Seigo Yamauchi
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Norio Hamada
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Masato Kumauchi
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
| | - Fumio Tokunaga
- Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004, Japan, Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan, and Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 550-0043, Japan
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39
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Hellingwerf KJ, Hendriks J, Gensch T. Photoactive Yellow Protein, A New Type of Photoreceptor Protein: Will This “Yellow Lab” Bring Us Where We Want to Go? J Phys Chem A 2003. [DOI: 10.1021/jp027005y] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Klaas J. Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| | - Johnny Hendriks
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| | - Thomas Gensch
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
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40
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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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41
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Kandori H, Tomioka H, Sasabe H. Excited-State Dynamics of pharaonis Phoborhodopsin Probed by Femtosecond Fluorescence Spectroscopy. J Phys Chem A 2002. [DOI: 10.1021/jp012447f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hideki Kandori
- Department of Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hiroaki Tomioka
- Department of Chemistry, Faculty of Education, Saitama University, 255 Shimo-Ohokubo, Saitama 338-8570, Japan
| | - Hiroyuki Sasabe
- Department of Photonics Materials Science, Chitose Institute of Science & Technology, 758-65 Bibi, Chitose, Hokkaido 066-8655, Japan
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42
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Mataga N, Chosrowjan H, Shibata Y, Imamoto Y, Kataoka M, Tokunaga F. Ultrafast photoinduced reaction dynamics of photoactive yellow protein (PYP): observation of coherent oscillations in the femtosecond fluorescence decay dynamics. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(01)01448-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Mataga N, Chosrowjan H, Shibata Y, Tanaka F, Nishina Y, Shiga K. Dynamics and Mechanisms of Ultrafast Fluorescence Quenching Reactions of Flavin Chromophores in Protein Nanospace. J Phys Chem B 2000. [DOI: 10.1021/jp002145y] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Fumio Tanaka
- Mie Prefectural College of Nursing, Yumegaoka, 1-1-1, Tsu 514-0116, Japan
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Devanathan S, Lin S, Cusanovich MA, Woodbury N, Tollin G. Early intermediates in the photocycle of the Glu46Gln mutant of photoactive yellow protein: femtosecond spectroscopy. Biophys J 2000; 79:2132-7. [PMID: 11023916 PMCID: PMC1301102 DOI: 10.1016/s0006-3495(00)76460-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Transient absorption spectroscopy in the time range from -1 ps to 4 ns, and over the wavelength range from 420 to 550 nm, was applied to the Glu46Gln mutant of the photoactive yellow protein (PYP) from Ectothiorhodospira halophila. This has allowed us to elucidate the kinetic constants of excited state formation and decay and photochemical product formation, and the spectral characteristics of stimulated emission and the early photocycle intermediates. Both the quantum efficiency ( approximately 0.5) and the rate constants for excited state decay and the formation of the initial photochemical intermediate (I(0)) were found to be quite similar to those obtained for wild-type PYP. In contrast, the rate constants for the formation of the subsequent photocycle intermediates (I(0)(double dagger) and I(1)), as well as for I(2) and for ground state regeneration as determined in earlier studies, were found to be from 3- to 30-fold larger. The structural implications of these results are discussed.
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Affiliation(s)
- S Devanathan
- Department of Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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Mataga N, Chosrowjan H, Shibata Y, Imamoto Y, Tokunaga F. Effects of Modification of Protein Nanospace Structure and Change of Temperature on the Femtosecond to Picosecond Fluorescence Dynamics of Photoactive Yellow Protein. J Phys Chem B 2000. [DOI: 10.1021/jp994205+] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Radding W, Romo T, Phillips GN. Protein-assisted pericyclic reactions: an alternate hypothesis for the action of quantal receptors. Biophys J 1999; 77:2920-9. [PMID: 10585916 PMCID: PMC1300565 DOI: 10.1016/s0006-3495(99)77125-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The rules for allowable pericyclic reactions indicate that the photoisomerizations of retinals in rhodopsins can be formally analogous to thermally promoted Diels-Alder condensations of monoenes with retinols. With little change in the seven-transmembrane helical environment these latter reactions could mimic the retinal isomerization while providing highly sensitive chemical reception. In this way archaic progenitors of G-protein-coupled chemical quantal receptors such as those for pheromones might have been evolutionarily plagiarized from the photon quantal receptor, rhodopsin, or vice versa. We investigated whether the known structure of bacteriorhodopsin exhibited any similarity in its active site with those of the two known antibody catalysts of Diels-Alder reactions and that of the photoactive yellow protein. A remarkable three-dimensional motif of aromatic side chains emerged in all four proteins despite the drastic differences in backbone structure. Molecular orbital calculations supported the possibility of transient pericyclic reactions as part of the isomerization-signal transduction mechanisms in both bacteriorhodopsin and the photoactive yellow protein. It appears that reactions in all four of the proteins investigated may be biological analogs of the organic chemists' chiral auxiliary-aided Diels-Alder reactions. Thus the light receptor and the chemical receptor subfamilies of the heptahelical receptor family may have been unified at one time by underlying pericyclic chemistry.
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Affiliation(s)
- W Radding
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.
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