1
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Fujisawa T, Shingae T, Ren J, Haraguchi S, Hanamoto T, Hoff WD, Unno M. Spectroscopic Validation of Crystallographic Structures of a Protein Active Site by Chiroptical Spectroscopy. J Phys Chem Lett 2023; 14:9304-9309. [PMID: 37816034 DOI: 10.1021/acs.jpclett.3c01954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Out-of-plane distortions of a cofactor molecule in a protein active site are functionally important, and in photoreceptors, it has been proposed that they are crucial for spectral tuning and energy storage in photocycle intermediates. However, these subtle structural features are often beyond the grasp of structural biology. This issue is strikingly exemplified by photoactive yellow protein: its 14 independently determined crystal structures exhibit considerable differences in the dihedral angles defining the chromophore geometry, even though most of these are at excellent resolution. Here we developed a strategy to verify cofactor distortions in crystal structures by using quantum chemical calculations and chiroptical spectroscopy, particularly Raman optical activity and electronic circular dichroism spectroscopies. Based on this approach, we identify seven crystal structures with the chromophore geometries inconsistent with the experimentally observed data. The strategy implemented here promises to be widely applicable to uncovering cofactor distortions at active sites and to studies of reaction intermediates.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takahito Shingae
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Jie Ren
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Shojiro Haraguchi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takeshi Hanamoto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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2
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Pociecha D, Walker R, Cruickshank E, Szydlowska J, Rybak P, Makal A, Matraszek J, Wolska JM, Storey JM, Imrie CT, Gorecka E. Intrinsically chiral ferronematic liquid crystals: An inversion of the helical twist sense at the chiral nematic – Chiral ferronematic phase transition. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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3
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Effect of Hydrated Ionic Liquid on Photocycle and Dynamics of Photoactive Yellow Protein. Molecules 2021; 26:molecules26154554. [PMID: 34361707 PMCID: PMC8348629 DOI: 10.3390/molecules26154554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
The mechanism by which proteins are solvated in hydrated ionic liquids remains an open question. Herein, the photoexcitation dynamics of photoactive yellow protein dissolved in hydrated choline dihydrogen phosphate (Hy[ch][dhp]) were studied by transient absorption and transient grating spectroscopy. The photocyclic reaction of the protein in Hy[ch][dhp] was similar to that observed in the buffer solution, as confirmed by transient absorption spectroscopy. However, the structural change of the protein during the photocycle in Hy[ch][dhp] was found to be different from that observed in the buffer solution. The known change in the diffusion coefficient of the protein was apparently suppressed in high concentrations of [ch][dhp], plausibly due to stabilization of the secondary structure.
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4
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Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Influence of Electronic Polarization on the Spectral Density. J Phys Chem B 2019; 124:531-543. [DOI: 10.1021/acs.jpcb.9b10250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Hanbo Hong
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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5
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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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6
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Seibert J, Bannwarth C, Grimme S. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation. J Am Chem Soc 2017; 139:11682-11685. [DOI: 10.1021/jacs.7b05833] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jakob Seibert
- Mulliken Center for Theoretical
Chemistry, University of Bonn, D-53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, University of Bonn, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, University of Bonn, D-53115 Bonn, Germany
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7
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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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8
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Haraguchi S, Hara M, Shingae T, Kumauchi M, Hoff WD, Unno M. Experimental Detection of the Intrinsic Difference in Raman Optical Activity of a Photoreceptor Protein under Preresonance and Resonance Conditions. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201505466] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shojiro Haraguchi
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840‐8502 (Japan)
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 (USA)
| | - Takahito Shingae
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840‐8502 (Japan)
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 (USA)
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 (USA)
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840‐8502 (Japan)
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9
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Haraguchi S, Hara M, Shingae T, Kumauchi M, Hoff WD, Unno M. Experimental Detection of the Intrinsic Difference in Raman Optical Activity of a Photoreceptor Protein under Preresonance and Resonance Conditions. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505466] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Abstract
Plant phytochromes are photoswitchable red/far-red photoreceptors that allow competition with neighboring plants for photosynthetically active red light. In aquatic environments, red and far-red light are rapidly attenuated with depth; therefore, photosynthetic species must use shorter wavelengths of light. Nevertheless, phytochrome-related proteins are found in recently sequenced genomes of many eukaryotic algae from aquatic environments. We examined the photosensory properties of seven phytochromes from diverse algae: four prasinophyte (green algal) species, the heterokont (brown algal) Ectocarpus siliculosus, and two glaucophyte species. We demonstrate that algal phytochromes are not limited to red and far-red responses. Instead, different algal phytochromes can sense orange, green, and even blue light. Characterization of these previously undescribed photosensors using CD spectroscopy supports a structurally heterogeneous chromophore in the far-red-absorbing photostate. Our study thus demonstrates that extensive spectral tuning of phytochromes has evolved in phylogenetically distinct lineages of aquatic photosynthetic eukaryotes.
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11
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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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12
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Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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13
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Boggio-Pasqua M, Groenhof G. Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. J Phys Chem B 2011; 115:7021-8. [PMID: 21561119 PMCID: PMC3102441 DOI: 10.1021/jp108977x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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We have performed ab initio CASSCF, CASPT2, and EOM-CCSD calculations on doubly deprotonated p-coumaric acid (pCA2−), the chromophore precursor of the photoactive yellow protein. The results of the calculations demonstrate that pCA2− can undergo only photoisomerization of the double bond. In contrast, the chromophore derivative with the acid replaced by a ketone (p-hydroxybenzylidene acetone, pCK−) undergoes both single- and double-bond photoisomerization, with the single-bond relaxation channel more favorable than the double-bond channel. The substitution alters the nature of the first excited states and the associated potential energy landscape. The calculations show that the electronic nature of the first two (π,π*) excited states are interchanged in vacuo due to the substitution. In pCK−, the first excited state is a charge-transfer (CT π,π*) state, in which the negative charge has migrated from the phenolate ring onto the alkene tail of the chromophore, whereas the locally excited (LE π,π*) state, in which the excitation involves the orbitals on the phenol ring, lies higher in energy and is the fourth excited state. In pCA2−, the CT state is higher in energy due the presence of a negative charge on the tail of the chromophore, and the first excited state is the LE state. In isolated pCA2−, there is a 68 kJ/mol barrier for double-bond photoisomerization on the potential energy surface of this LE state. In water, however, hydrogen bonding with water molecules reduces this barrier to 9 kJ/mol. The barrier separates the local trans minimum near the Franck−Condon region from the global minimum on the excited-state potential energy surface. The lowest energy conical intersection was located near this minimum. In contrast to pCK−, single-bond isomerization is highly unfavorable both in the LE and CT states of pCA2−. These results demonstrate that pCA2− can only decay efficiently in water and exclusively by double-bond photoisomerization. These findings provide a rationale for the experimental observations that pCA2− has both a longer excited-state lifetime and a higher isomerization quantum yield than pCK−.
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Affiliation(s)
- Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, CNRS et Université de Toulouse, Toulouse, France
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14
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Kyndt JA, Fitch JC, Seibeck S, Borucki B, Heyn MP, Meyer TE, Cusanovich MA. Regulation of the Ppr Histidine Kinase by Light-Induced Interactions between Its Photoactive Yellow Protein and Bacteriophytochrome Domains. Biochemistry 2010; 49:1744-54. [DOI: 10.1021/bi901591m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John A. Kyndt
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - John C. Fitch
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Sven Seibeck
- Biophysics group, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Berthold Borucki
- Biophysics group, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Maarten P. Heyn
- Biophysics group, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Terry E. Meyer
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Michael A. Cusanovich
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
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15
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Borucki B, Seibeck S, Heyn MP, Lamparter T. Characterization of the covalent and noncovalent adducts of Agp1 phytochrome assembled with biliverdin and phycocyanobilin by circular dichroism and flash photolysis. Biochemistry 2009; 48:6305-17. [PMID: 19496558 DOI: 10.1021/bi900436v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The functional role of the covalent attachment of the bilin chromophores biliverdin (BV) and phycocyanobilin (PCB) was investigated for phytochrome Agp1 from Agrobacterium tumefaciens using circular dichroism (CD) and transient absorption spectroscopy. Covalent and noncovalent adducts with these chromophores were prepared by using wild-type (WT) Agp1 (covalent BV and noncovalent PCB binding), mutant C20A in which the covalent BV binding site is eliminated, and mutant V249C in which the covalent PCB binding site is introduced. While the CD spectra of the P(r) forms of all these photochromic adducts are qualitatively the same, the CD spectrum of the P(fr) form of the covalent PCB adduct is unique in having a positive rotational strength in the Q-band which we assign to the Z-E isomerization of the C-D methine bridge. In the three other adducts, the Q-band CD in the P(fr) state is almost zero, suggesting that upon photoconversion a negative contribution from an out-of-plane rotation of the A ring of the chromophore compensates for the positive contribution from ring D. The contribution from ring A is absent or strongly reduced in the shorter pi-conjugation system of the covalent PCB adduct. The results from CD spectroscopy are consistent with a uniform geometry of the bilin chromophore in the covalent and noncovalent adducts. Transient absorption spectroscopy showed that the spectral changes and the kinetics of the P(r) to P(fr) photoconversion are not substantially affected by the covalent attachment of BV and PCB. The kinetics in the BV and PCB adducts mainly differ in the formation of P(fr) that is accelerated by 2 orders of magnitude in the PCB adducts, whereas the sequence of spectral transitions and the associated proton transfer processes are quite similar. We conclude that the P(r) to P(fr) photoconversion in the BV and PCB adducts of Agp1 involves the same relaxation processes and is thus governed by specific protein-cofactor interactions rather than by the chemical structure of the chromophore or the mode of attachment. The strongly reduced photostability of the noncovalent BV adduct suggests that covalent attachment in native Agp1 phytochrome prevents irreversible photobleaching and stabilizes the chromophore. The N-terminal peptide segment including amino acids 2-19 is essential for covalent attachment of the chromophore but dispensable for the spectral and kinetic properties of Agp1.
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Affiliation(s)
- Berthold Borucki
- Biophysics Group, Department of Physics, Freie Universitat Berlin, Arnimallee 14, 14195 Berlin, Germany.
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16
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Borucki B, Lamparter T. A polarity probe for monitoring light-induced structural changes at the entrance of the chromophore pocket in a bacterial phytochrome. J Biol Chem 2009; 284:26005-16. [PMID: 19640848 DOI: 10.1074/jbc.m109.049056] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Light-induced structural changes at the entrance of the chromophore pocket of Agp1 phytochrome were investigated by using a thiol-reactive fluorescein derivative that is covalently attached to the genuine chromophore binding site (Cys-20) and serves as a polarity probe. In the apoprotein, the absorption spectrum of bound fluorescein is red-shifted with respect to that of the free label suggesting that the probe enters the hydrophobic chromophore pocket. Assembly of this construct with the chromophores phycocyanobilin or biliverdin is associated with a blue-shift of the fluorescein absorption band indicating the displacement of the probe out of the pocket. The probe does not affect the photochromic and kinetic properties of the noncovalent bilin adducts. Upon photoconversion to Pfr, the probe spectrum undergoes again a bathochromic shift and a strong rise in CD indicating a more hydrophobic and asymmetric environment. We propose that the environmental changes of the probe reflect conformational changes at the entrance of the chromophore pocket and are indicative for rearrangements of the chromophore ring A. Flash photolysis measurements showed that the absorption changes of the probe are kinetically coupled to the formation of Meta-R(C) and Pfr. In the biliverdin adduct, an additional component occurs that probably reflects a transition between two Meta-RC substates. Analogous results to that of the noncovalent phycocyanobilin adduct were obtained with the mutant V249C in which probe and chromophore are covalently attached. The conformational changes of the chromophore are correlated to proton transfer to the protein surface.
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Affiliation(s)
- Berthold Borucki
- Department of Physics, Biophysics Group, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany
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17
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Coto PB, Martí S, Oliva M, Olivucci M, Merchán M, Andrés J. Origin of the Absorption Maxima of the Photoactive Yellow Protein Resolved via Ab Initio Multiconfigurational Methods. J Phys Chem B 2008; 112:7153-6. [DOI: 10.1021/jp711396b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pedro B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Sergio Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Mónica Oliva
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Massimo Olivucci
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Manuela Merchán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Juan Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
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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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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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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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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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Otto H, Hoersch D, Meyer TE, Cusanovich MA, Heyn MP. Time-Resolved Single Tryptophan Fluorescence in Photoactive Yellow Protein Monitors Changes in the Chromophore Structure during the Photocycle via Energy Transfer. Biochemistry 2005; 44:16804-16. [PMID: 16363794 DOI: 10.1021/bi051448l] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show from time-resolved fluorescence intensity and depolarization experiments that the fluorescence of the unique tryptophan W119 of PYP is quenched by energy transfer to the 4-hydroxycinnamoyl chromophore. Whereas the intensity decay has a time constant of 0.18 ns in P, the decay in the absence of the cofactor (apo-PYP) has a single exponential lifetime of 4.8 ns. This difference in lifetime with and without acceptor can be explained quantitatively on the basis of energy transfer and the high-resolution X-ray structure of P, which allows an accurate calculation of the kappa2 factor. Fluorescence depolarization experiments with donor and acceptor indicate that both are immobilized so that kappa2 is constant on the fluorescence time scale. Using background illumination from an LED emitting at 470 nm, we measured the time-resolved fluorescence in a photostationary mixture of P and the intermediates I2 and I2'. The composition of the photostationary mixture depends on pH and changes from mainly I2 at low pH to predominantly I2' at high pH. The I2/I2' equilibrium is pH-dependent with a pKa of approximately 6.3. In I2 the lifetime increases to approximately 0.82 ns. This is not due to a change in distance or to the increase in spectral overlap but is primarily a consequence of a large decrease in kappa2. Kappa2 was calculated from the available X-ray structures and decreases from approximately 2.7 in P to 0.27 in I2. This change in kappa2 is caused by the isomerization of the acceptor, which leads to a reorientation of its transition dipole moment. We have here a rare case of the kappa2 factor dominating the change in energy transfer. The fluorescence decay in the light is pH-dependent. From an SVD analysis of the light/dark difference intensity decay at a number of pH values, we identify three species with associated lifetimes: P (0.18 ns), I2 (0.82 ns), and X (0.04 ns). On the basis of the pH dependence of the amplitudes associated with I2 and X, with a pKa of approximately 6.3, we assign the third species to the signaling state I2'. The absorption spectra of the 0.82 and 0.04 ns species were calculated from the pH dependence of their fluorescence amplitudes and of the photostationary light/dark difference absorption spectra. The lambda(max) values of these spectra (372 and 352 nm) identify the 0.82 and 0.04 ns components with I2 and I2', respectively, and validate the fluorescence data analysis. The mutant E46Q allows a further test of the energy transfer explanation, since lowering the pH in the dark leads to a bleached state with an increased spectral overlap but without the isomerization-induced decrease in kappa2. The measured lifetime of 0.04 ns is in excellent agreement with predictions based on energy transfer and the X-ray structure.
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Affiliation(s)
- Harald Otto
- Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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