1
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Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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2
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Tyson AL, Verlet JRR. On the Mechanism of Phenolate Photo-Oxidation in Aqueous Solution. J Phys Chem B 2019; 123:2373-2379. [PMID: 30768899 DOI: 10.1021/acs.jpcb.8b11766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photo-oxidation dynamics following ultraviolet (257 nm) excitation of the phenolate anion in aqueous solution is studied using broadband (550-950 nm) transient absorption spectroscopy. A clear signature from electron ejection is observed on a sub-picosecond timescale, followed by cooling dynamics and the decay of the signal to a constant offset that is assigned to the hydrated electron. The dynamics are compared to the charge-transfer-to-solvent dynamics from iodide at the same excitation wavelength and are shown to be very similar to these. This is in stark contrast to a previous study on the phenolate anion excited at 266 nm, in which electron emission was observed over longer timescales. We account for the differences using a simple Marcus picture for electron emission in which the electron tunneling rate depends sensitively on the initial excitation energy. After electron emission, a contact pair is formed which undergoes geminate recombination and dissociation to form the free hydrated electron at rates that are slightly faster than those for the iodide system. Our results show that, although the underlying chemical physics of electron emission differs between iodide and phenolate, the observed dynamics can appear very similar.
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Affiliation(s)
| | - Jan R R Verlet
- Department of Chemistry , Durham University , Durham DH1 3LE , U.K
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3
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Lee K, Kim Y, Jung J, Ihee H, Park Y. Measurements of complex refractive index change of photoactive yellow protein over a wide wavelength range using hyperspectral quantitative phase imaging. Sci Rep 2018; 8:3064. [PMID: 29449627 PMCID: PMC5814402 DOI: 10.1038/s41598-018-21403-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/31/2018] [Indexed: 12/25/2022] Open
Abstract
A novel optical holographic technique is presented to simultaneously measure both the real and imaginary components of the complex refractive index (CRI) of a protein solution over a wide visible wavelength range. Quantitative phase imaging was employed to precisely measure the optical field transmitted from a protein solution, from which the CRIs of the protein solution were retrieved using the Fourier light scattering technique. Using this method, we characterized the CRIs of the two dominant structural states of a photoactive yellow protein solution over a broad wavelength range (461-582 nm). The significant CRI deviation between the two structural states was quantified and analysed. The results of both states show the similar overall shape of the expected rRI obtained from the Kramers-Kronig relations.
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Affiliation(s)
- KyeoReh Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Youngmin Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - JaeHwang Jung
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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4
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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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5
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Ahamed G, Batuta S, Ghosh D, Begum NA, Mandal D. Photophysical studies on a photoactive yellow protein fluorophore analog with the 4-Hydroxy group replaced by 4-Dimethylamino group. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2016.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Parkes MA, Phillips C, Porter MJ, Fielding HH. Controlling electron emission from the photoactive yellow protein chromophore by substitution at the coumaric acid group. Phys Chem Chem Phys 2016; 18:10329-36. [PMID: 27025529 DOI: 10.1039/c6cp00565a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding how the interactions between a chromophore and its surrounding protein control the function of a photoactive protein remains a challenge. Here, we present the results of photoelectron spectroscopy measurements and quantum chemistry calculations aimed at investigating how substitution at the coumaryl tail of the photoactive yellow protein chromophore controls competing relaxation pathways following photoexcitation of isolated chromophores in the gas phase with ultraviolet light in the range 350-315 nm. The photoelectron spectra are dominated by electrons resulting from direct detachment and fast detachment from the 2(1)ππ* state but also have a low electron kinetic energy component arising from autodetachment from lower lying electronically excited states or thermionic emission from the electronic ground state. We find that substituting the hydrogen atom of the carboxylic acid group with a methyl group lowers the threshold for electron detachment but has very little effect on the competition between the different relaxation pathways, whereas substituting with a thioester group raises the threshold for electron detachment and appears to 'turn off' the competing electron emission processes from lower lying electronically excited states. This has potential implications in terms of tuning the light-induced electron donor properties of photoactive yellow protein.
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Affiliation(s)
- Michael A Parkes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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7
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García-Prieto FF, Muñoz-Losa A, Luz Sánchez M, Elena Martín M, Aguilar MA. Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore. Phys Chem Chem Phys 2016; 18:27476-27485. [DOI: 10.1039/c6cp03541h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.
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Affiliation(s)
| | - Aurora Muñoz-Losa
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - M. Luz Sánchez
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
| | - M. Elena Martín
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
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8
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García-Prieto FF, Aguilar MA, Galván IF, Muñoz-Losa A, Olivares del Valle FJ, Sánchez ML, Martín ME. Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2015; 119:5504-14. [DOI: 10.1021/acs.jpca.5b01434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Fernández García-Prieto
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - M. A. Aguilar
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - I. Fdez. Galván
- Department
of Chemistry−Ångström, The Theoretical Chemistry
Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
| | - A. Muñoz-Losa
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - F. J. Olivares del Valle
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - M. L. Sánchez
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - M. E. Martín
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
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9
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Gromov EV. Unveiling the mechanism of photoinduced isomerization of the photoactive yellow protein (PYP) chromophore. J Chem Phys 2014; 141:224308. [DOI: 10.1063/1.4903174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Evgeniy V. Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany
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10
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Zhu J, Vreede J, Hospes M, Arents J, Kennis JTM, van Stokkum IHM, Hellingwerf KJ, Groot ML. Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield. J Phys Chem B 2014; 119:2372-83. [DOI: 10.1021/jp506785q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jingyi Zhu
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | | | | | - John T. M. Kennis
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | | | - Marie Louise Groot
- Department
of Physics and Astronomy, Faculty of Sciences, LaserLab, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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11
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Changenet-Barret P, Lacombat F, Plaza P. Reaction-coordinate tracking in the excited-state deactivation of the photoactive yellow protein chromophore in solution. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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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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13
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Gromov EV, Burghardt I, Köppel H, Cederbaum LS. Photoinduced Isomerization of the Photoactive Yellow Protein (PYP) Chromophore: Interplay of Two Torsions, a HOOP Mode and Hydrogen Bonding. J Phys Chem A 2011; 115:9237-48. [DOI: 10.1021/jp2011843] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Evgeniy V. Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
- Laboratory of Quantum Chemistry, Computer Center, Irkutsk State University, K. Marks 1, 664003 Irkutsk, Russian Federation
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D−60438 Frankfurt/Main, Germany
| | - Horst Köppel
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
| | - Lorenz S. Cederbaum
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
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14
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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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15
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Rajput J, Rahbek DB, Aravind G, Andersen LH. Spectral tuning of the photoactive yellow protein chromophore by H-bonding. Biophys J 2010; 98:488-92. [PMID: 20141763 DOI: 10.1016/j.bpj.2009.10.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 10/19/2009] [Accepted: 10/19/2009] [Indexed: 11/24/2022] Open
Abstract
Spectral tuning in the photoactive yellow protein (PYP) is investigated by performing gas-phase absorption measurements on a PYP-model chromophore with two water molecules hydrogen-bonded to it. The photoabsorption maximum shows an unusually large blue shift of 0.71 eV in going from the bare to the hydrogen-bonded chromophore. It is concluded that several interactions within the PYP protein are mutually cancelling each other, yielding an absorption maximum that is close to the absorption maximum of the bare chromophore. The system breaks apart upon photoexcitation in the gas phase by releasing the two water molecules, leaving the chromophore itself intact. The hydrogen-bonding interactions thus play an important role in stabilizing the gas phase chromophore against photofragmentation. The relaxation dynamics for the breakup process was also studied, and the timescale of relaxation via fragmentation was found to be < 25 ns.
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Affiliation(s)
- J Rajput
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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16
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Usman A, Asahi T, Sugiyama T, Masuhara H, Tohnai N, Miyata M. Photochemical Reaction of p-hydroxycinnamic-thiophenyl Ester in the Microcrystalline State. J Phys Chem B 2010; 114:14233-40. [DOI: 10.1021/jp909850r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anwar Usman
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Tsuyoshi Asahi
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Teruki Sugiyama
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Hiroshi Masuhara
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Norimitsu Tohnai
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
| | - Mikiji Miyata
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan, Department of Applied Physics, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan, Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan, and Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka
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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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Carroll EC, Song SH, Kumauchi M, van Stokkum IHM, Jailaubekov A, Hoff WD, Larsen DS. Subpicosecond Excited-State Proton Transfer Preceding Isomerization During the Photorecovery of Photoactive Yellow Protein. J Phys Chem Lett 2010; 1:2793-2799. [PMID: 20953237 PMCID: PMC2955422 DOI: 10.1021/jz101049v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The ultrafast excited-state dynamics underlying the receptor state photorecovery is resolved in the M100A mutant of the photoactive yellow protein (PYP) from Halorhodospira halophila. The M100A PYP mutant, with its distinctly slower photocycle than wt PYP, allows isolation of the pB signaling state for study of the photodynamics of the protonated chromophore cis-p-coumaric acid. Transient absorption signals indicate a subpicosecond excited-state proton-transfer reaction in the pB state that results in chromophore deprotonation prior to the cis-trans isomerization required in the photorecovery dynamics of the pG state. Two terminal photoproducts are observed, a blue-absorbing species presumed to be deprotonated trans-p-coumaric acid and an ultraviolet-absorbing protonated photoproduct. These two photoproducts are hypothesized to originate from an equilibrium of open and closed folded forms of the signaling state, I(2) and I(2)'.
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Affiliation(s)
- Elizabeth C. Carroll
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Sang-Hun Song
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Ivo H. M. van Stokkum
- Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Askat Jailaubekov
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
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19
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Abstract
Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.
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Affiliation(s)
- Villy Sundström
- Department of Chemical Physics, Lund University, S-221 00 Lund, Sweden.
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20
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Putschögl M, Zirak P, Penzkofer A. Absorption and emission behaviour of trans-p-coumaric acid in aqueous solutions and some organic solvents. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.10.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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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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22
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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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23
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Gromov EV, Burghardt I, Köppel H, Cederbaum LS. Electronic Structure of the PYP Chromophore in Its Native Protein Environment. J Am Chem Soc 2007; 129:6798-806. [PMID: 17474743 DOI: 10.1021/ja069185l] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report on supermolecular ab initio calculations which clarify the role of the local amino acid environment in determining the unique electronic structure properties of the photoactive yellow protein (PYP) chromophore. The extensive ab initio calculations, at the level of the CC2 and EOM-CCSD methods, allow us to explicitly address how the interactions between the deprotonated p-coumaric thio-methyl ester (pCTM-) chromophore and the surrounding amino acids act together to create a specifically stabilized pCTM- species. Particularly noteworthy is the role of the Arg52 amino acid in stabilizing the chromophore against autoionization, and the role of the Tyr42 and Glu46 amino acids in determining the hydrogen-bonding properties that carry the dominant energetic effects.
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Affiliation(s)
- Evgeniy V Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany.
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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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Plaza P, Mahet M, Martin MM, Checcucci G, Lenci F. Target Analysis of Primary Photoprocesses Involved in the Oxyblepharismin-Binding Protein. J Phys Chem B 2007; 111:690-6. [PMID: 17249812 DOI: 10.1021/jp0642591] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Target analysis is performed on previously published transient absorption spectra of the 200-kDa oxyblepharismin-binding protein (OBIP) thought to trigger the photophobic response of the ciliate Blepharisma japonicum. The OBIP sample is considered as heterogeneous and made of two distinct classes of chromophore-protein complexes. A so-called nonreactive class is seen to be comparable to free oxyblepharismin in organic solution. Another, reactive, class is shown to undergo a fast picosecond photocycle involving the formation in 4 ps of an intermediate state noted Y1. The spectrum associated to Y1 bears striking similarities with that of the oxyblepharismin radical cation. This element favors the hypothesis that an excited-state intermolecular electron-transfer could be the primary step of the sensory transduction chain of B. japonicum. Proton release is also considered as a possible secondary step. These possibilities support the idea that reactive OBIP functions like an electron or proton pump. We alternatively propose a new hypothesis stating that the fast photocycle of reactive OBIP actually does not generate any photoproduct or protein change of conformation but is involved in another biological function. It would act as a kind of solar screen, providing additional protection to the light-adapted form of B. japonicum in case of excessive illumination.
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Affiliation(s)
- Pascal Plaza
- Département de Chimie, UMR 8640 CNRS-ENS, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France.
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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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Espagne A, Changenet-Barret P, Baudin JB, Plaza P, Martin MM. Photoinduced charge shift as the driving force for the excited-state relaxation of analogues of the Photoactive Yellow Protein chromophore in solution. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.06.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Espagne A, Paik DH, Changenet-Barret P, Martin MM, Zewail AH. Ultrafast Photoisomerization of Photoactive Yellow Protein Chromophore Analogues in Solution: Influence of the Protonation State. Chemphyschem 2006; 7:1717-26. [PMID: 16847839 DOI: 10.1002/cphc.200600137] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans-p-hydroxybenzylidene acetone and trans-p-hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S(1). A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas "concerted" intramolecular motions are proposed for the neutral forms.
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Affiliation(s)
- Agathe Espagne
- UMR CNRS-ENS 8640 Pasteur, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
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29
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Espagne A, Changenet-Barret P, Plaza P, Martin MM. Solvent Effect on the Excited-State Dynamics of Analogues of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2006; 110:3393-404. [PMID: 16526618 DOI: 10.1021/jp0563843] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously reported that two analogues of the Photoactive Yellow Protein chromophore, trans-p-hydroxycinnamic acid (pCA(2-)) and its amide derivative (pCM-) in their deprotonated forms, undergo a trans-cis photoisomerization whereas the thioester derivative, trans-p-hydroxythiophenyl cinnamate (pCT-), does not. pCT- is also the only one to exhibit a short-lived intermediate on its excited-state deactivation pathway. We here further stress the existence of two different relaxation mechanisms for these molecules and examine the reaction coordinates involved. We looked at the effect of the solvent properties (viscosity, polarity, solvation dynamics) on their excited-state relaxation dynamics, probed by ultrafast transient absorption spectroscopy. Sensitivity to the solvent properties is found to be larger for pCT- than for pCA(2-) and pCM-. This difference is considered to reveal that either the relaxation pathway or the reaction coordinate is different for these two classes of analogues. It is also found to be correlated to the electron donor-acceptor character of the molecule. We attribute the excited-state deactivation of analogues bearing a weaker acceptor group, pCA(2-) and pCM-, to a stilbene-like photoisomerization mechanism with the concerted rotation of the ethylenic bond and one adjacent single bond. For pCT-, which contains a stronger acceptor group, we consider a photoisomerization mechanism mainly involving the single torsion of the ethylenic bond. The excited-state deactivation of pCT- would lead to the formation of a ground-state intermediate at the "perp" geometry, which would return to the initial trans conformation without net isomerization.
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Affiliation(s)
- Agathe Espagne
- Département de Chimie, Ecole Normale Supérieure (UMR CNRS 8640 PASTEUR), 24 rue Lhomond, 75231 Paris Cedex 05, France
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Lee IR, Lee W, Zewail AH. Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function. Proc Natl Acad Sci U S A 2006; 103:258-62. [PMID: 16407155 PMCID: PMC1326191 DOI: 10.1073/pnas.0510015103] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the protein.
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Affiliation(s)
- I-Ren Lee
- Arthur Amos Noyes Laboratory of Chemical Physics, Laboratory for Molecular Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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31
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El-Gezawy H, Rettig W, Danel A, Jonusauskas G. Probing the Photochemical Mechanism in Photoactive Yellow Protein. J Phys Chem B 2005; 109:18699-705. [PMID: 16853405 DOI: 10.1021/jp0513972] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Selectively bridged model compounds related to the chromophore in photoactive yellow protein have been synthesized where the single bond adjacent to the benzene ring (bond 1) and where both bond 1 and the adjacent double bond (bond 2) are bridged. They were compared to the nonbridged reference compound regarding their photophysical properties using steady-state and time-resolved fluorescence at various temperatures. Quantum chemical calculations were additionally performed and showed that several conformers are populated in the ground state. The neutral model compounds show that the nonradiative deactivation channel is linked to both single- and double-bond twisting. The relative importance of single-bond twisting is increased for the corresponding deprotonated hydroxy compounds with an enhanced donor character. The simultaneous photochemical activity of both single and double bonds explains the ease of photochemical isomerization in the confined environment of the natural PYP protein and also of the primary step in the vision process in rhodopsin.
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Affiliation(s)
- Hani El-Gezawy
- Institut für Chemie, Humboldt-Universtät zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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