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Ramamurthy V, Sen P, Elles CG. Ultrafast Excited State Dynamics of Spatially Confined Organic Molecules. J Phys Chem A 2022; 126:4681-4699. [PMID: 35786917 DOI: 10.1021/acs.jpca.2c03276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This Feature Article highlights the role of spatial confinement in controlling the fundamental behavior of molecules. Select examples illustrate the value of using space as a tool to control and understand excited-state dynamics through a combination of ultrafast spectroscopy and conventional steady-state methods. Molecules of interest were confined within a closed molecular capsule, derived from a cavitand known as octa acid (OA), whose internal void space is sufficient to accommodate molecules as long as tetracene and as wide as pyrene. The free space, i.e., the space that is left following the occupation of the guest within the host, is shown to play a significant role in altering the behavior of guest molecules in the excited state. The results reported here suggest that in addition to weak interactions that are commonly emphasized in supramolecular chemistry, the extent of empty space (i.e., the remaining void space within the capsule) is important in controlling the excited-state behavior of confined molecules on ultrafast time scales. For example, the role of free space in controlling the excited-state dynamics of guest molecules is highlighted by probing the cis-trans isomerization of stilbenes and azobenzenes within the OA capsule. Isomerization of both types of molecule are slowed when they are confined within a small space, with encapsulated azobenzenes taking a different reaction pathway compared to that in solution upon excitation to S2. In addition to steric constraints, confinement of reactive molecules in a small space helps to override the need for diffusion to bring the reactants together, thus enabling the measurement of processes that occur faster than the time scale for diffusion. The advantages of reducing free space and confining reactive molecules are illustrated by recording unprecedented excimer emission from anthracene and by measuring ultrafast electron transfer rates across the organic molecular wall. By monitoring the translational motion of anthracene pairs in a restricted space, it has been possible to document the pathway undertaken by excited anthracene from inception to the formation of the excimer on the excited-state surface. Similarly, ultrafast electron transfer experiments pursued here have established that the process is not hindered by a molecular wall. Apparently, the electron can cross the OA capsule wall provided the donor and acceptor are in close proximity. Measurements on the ultrafast time scale provide crucial insights for each of the examples presented here, emphasizing the value of both "space" and "time" in controlling and understanding the dynamics of excited molecules.
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Affiliation(s)
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP 208 016, India
| | - Christopher G Elles
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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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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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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Schroeder C, Werner K, Otten H, Krätzig S, Schwalbe H, Essen LO. Influence of a joining helix on the BLUF domain of the YcgF photoreceptor from Escherichia coli. Chembiochem 2008; 9:2463-73. [PMID: 18792053 DOI: 10.1002/cbic.200800280] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BLUF-domain-comprising photoreceptors sense blue light by utilizing FAD as a chromophore. The ycgF gene product of Escherichia coli is composed of a N-terminal BLUF domain and a C-terminal EAL domain, with the latter postulated to catalyze c-di-GMP hydrolysis. The linkage between these two domains involves a predominantly helical segment. Its role on the function of the YcgF photoreceptor domain was examined by characterizing BLUF domains with and without this segment and reconstituting them with either FAD, FMN or riboflavin. The stability of the light-adapted state of the YcgF BLUF domain depends on the presence of this joining, helical segment and the adenosine diphosphate moiety of FAD. In contrast to other BLUF domains, two-dimensional (1)H,(15)N and one-dimensional (1)H NMR spectra of isotope-labeled YcgF-(1-137) revealed large conformational changes during reversion from the light- to the dark-adapted state. Based on these results the function of the joining helix in YcgF during signal transfer and the role of the BLUF domain in regulating c-di-GMP levels is discussed.
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Affiliation(s)
- Claudia Schroeder
- Department of Chemistry and Biochemistry, Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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Weigel A, Dobryakov AL, Veiga M, Pérez Lustres JL. Photoinduced Processes in Riboflavin: Superposition of ππ*−nπ* States by Vibronic Coupling, Transfer of Vibrational Coherence, and Population Dynamics under Solvent Control. J Phys Chem A 2008; 112:12054-65. [DOI: 10.1021/jp805962u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Weigel
- Institut für Chemie, Humboldt Universität zu Berlin, Brook Taylor Str. 2, 12489 Berlin, Germany
| | - Alexander L. Dobryakov
- Institut für Chemie, Humboldt Universität zu Berlin, Brook Taylor Str. 2, 12489 Berlin, Germany
| | - Manoel Veiga
- Institut für Chemie, Humboldt Universität zu Berlin, Brook Taylor Str. 2, 12489 Berlin, Germany
| | - J. Luis Pérez Lustres
- Institut für Chemie, Humboldt Universität zu Berlin, Brook Taylor Str. 2, 12489 Berlin, Germany
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6
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Imamoto Y, Kataoka M, Liu RSH. Mechanistic Pathways for the Photoisomerization Reaction of the Anchored, Tethered Chromophore of the Photoactive Yellow Protein and its Mutants¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2002)0760584mpftpr2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Kort R, Ravelli RB, Schotte F, Bourgeois D, Crielaard W, Hellingwerf KJ, Wulff M. Characterization of Photocycle Intermediates in Crystalline Photoactive Yellow Protein†¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780131copiic2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Laan W, Horst MA, Van Stokkum IH, Hellingwerf KJ. Initial Characterization of the Primary Photochemistry of AppA, a Blue-light-using Flavin Adenine Dinucleotide-domain Containing Transcriptional Antirepressor Protein from Rhodobacter sphaeroides: A Key Role for Reversible Intramolecular Proton Transfer f. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780290icotpp2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Montagnoli G, Podestà A, Bonaretti S. Photomodulated Azoaldolase: A Model for Light Intervention in Biological Systems? Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720727paamfl2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Steglich C, Futschik M, Rector T, Steen R, Chisholm SW. Genome-wide analysis of light sensing in Prochlorococcus. J Bacteriol 2006; 188:7796-806. [PMID: 16980454 PMCID: PMC1636322 DOI: 10.1128/jb.01097-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prochlorococcus MED4 has, with a total of only 1,716 annotated protein-coding genes, the most compact genome of a free-living photoautotroph. Although light quality and quantity play an important role in regulating the growth rate of this organism in its natural habitat, the majority of known light-sensing proteins are absent from its genome. To explore the potential for light sensing in this phototroph, we measured its global gene expression pattern in response to different light qualities and quantities by using high-density Affymetrix microarrays. Though seven different conditions were tested, only blue light elicited a strong response. In addition, hierarchical clustering revealed that the responses to high white light and blue light were very similar and different from that of the lower-intensity white light, suggesting that the actual sensing of high light is mediated via a blue-light receptor. Bacterial cryptochromes seem to be good candidates for the blue-light sensors. The existence of a signaling pathway for the redox state of the photosynthetic electron transport chain was suggested by the presence of genes that responded similarly to red and blue light as well as genes that responded to the addition of DCMU [3-(3,4-dichlorophenyl)-1,1-N-N'-dimethylurea], a specific inhibitor of photosystem II-mediated electron transport.
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Affiliation(s)
- Claudia Steglich
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Larsen DS, van Stokkum IHM, Vengris M, van Der Horst MA, de Weerd FL, Hellingwerf KJ, van Grondelle R. Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy. Biophys J 2005; 87:1858-72. [PMID: 15345564 PMCID: PMC1304590 DOI: 10.1529/biophysj.104.043794] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photoactive yellow protein is the protein responsible for initiating the "blue-light vision" of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This "incoherent" manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I(0) and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates.
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Affiliation(s)
- Delmar S Larsen
- Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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12
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Laan W, van der Horst MA, van Stokkum IH, Hellingwerf KJ. Initial characterization of the primary photochemistry of AppA, a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from Rhodobacter sphaeroides: a key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine? Photochem Photobiol 2003; 78:290-7. [PMID: 14556317 DOI: 10.1562/0031-8655(2003)078<0290:icotpp>2.0.co;2] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The flavin adenine dinucleotide (FAD)-containing photoreceptor protein AppA (in which the FAD is bound to a novel so-called BLUF domain) from the purple nonsulfur bacterium Rhodobacter sphaeroides was previously shown to be photoactive by the formation of a slightly redshifted long-lived intermediate that is thought to be the signaling state. In this study, we provide further characterization of the primary photochemistry of this photoreceptor protein using UV-Vis and Fourier-transform infrared spectroscopy, pH measurements and site-directed mutagenesis. Available evidence indicates that the FAD chromophore of AppA may be protonated in the receptor state, and that it becomes exposed to solvent in the signaling state. Furthermore, experimental data lead to the suggestion that intramolecular proton transfer (that may involve [anionic] Tyr-17) forms the basis for the stabilization of the signaling state.
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Affiliation(s)
- Wouter Laan
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, The Netherlands
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13
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Kort R, Ravelli RB, Schotte F, Bourgeois D, Crielaard W, Hellingwerf KJ, Wulff M. Characterization of photocycle intermediates in crystalline photoactive yellow protein. Photochem Photobiol 2003; 78:131-7. [PMID: 12945580 DOI: 10.1562/0031-8655(2003)078<0131:copiic>2.0.co;2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The photocycle in photoactive yellow protein (PYP) crystals was studied by single-crystal absorption spectroscopy with experimental setups for low-temperature and time-resolved measurements. Thin and flat PYP crystals, suitable for light absorption studies, were obtained using special crystallization conditions. Illumination of PYP crystals at 100 K led to the formation of a photostationary state, which includes at least one hypsochromic and one bathochromic photoproduct that resemble PYP(H) and PYP(B), respectively. The effect of temperature, light color and light pulse duration on the occupancy of these low-temperature photoproducts was determined and appeared similar to that observed in solution. At room temperature a blueshifted photocycle intermediate was identified that corresponds to the blueshifted state of PYP (pB). Kinetic studies show that the decay of this blueshifted intermediate is biphasic at -12 degrees C and 15-fold faster than that observed in solution at room temperature. These altered pB decay kinetics confirm a model that holds that the photocycle in crystals takes place in a shortcut version. In this version the key structural events of the photocycle, such as photoisomerization and reversible protonation of the chromophore, take place, but large conformational changes in the surrounding protein are limited by constraints imposed by the crystal lattice.
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Affiliation(s)
- Remco Kort
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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Crosson S, Rajagopal S, Moffat K. The LOV domain family: photoresponsive signaling modules coupled to diverse output domains. Biochemistry 2003; 42:2-10. [PMID: 12515534 DOI: 10.1021/bi026978l] [Citation(s) in RCA: 326] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For single-cell and multicellular systems to survive, they must accurately sense and respond to their cellular and extracellular environment. Light is a nearly ubiquitous environmental factor, and many species have evolved the capability to respond to this extracellular stimulus. Numerous photoreceptors underlie the activation of light-sensitive signal transduction cascades controlling these responses. Here, we review the properties of the light, oxygen, or voltage (LOV) family of blue-light photoreceptor domains, a subset of the Per-ARNT-Sim (PAS) superfamily. These flavin-binding domains, first identified in the higher-plant phototropins, are now shown to be present in plants, fungi, and bacteria. Notably, LOV domains are coupled to a wide array of other domains, including kinases, phosphodiesterases, F-box domains, STAS domains, and zinc fingers, which suggests that the absorption of blue light by LOV domains regulates the activity of these structurally and functionally diverse domains. LOV domains contain a conserved molecular volume extending from the flavin cofactor, which is the locus for light-driven structural change, to the molecular surface. We discuss the role of this conserved volume of structure in LOV-regulated processes.
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Affiliation(s)
- Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
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Laan W, van der Horst MA, van Stokkum IH, Hellingwerf KJ. Initial Characterization of the Primary Photochemistry of AppA, a Blue-light–using Flavin Adenine Dinucleotide–domain Containing Transcriptional Antirepressor Protein from Rhodobacter sphaeroides: A Key Role for Reversible Intramolecular Proton Transfer from the Flavin Adenine Dinucleotide Chromophore to a Conserved Tyrosine?¶. Photochem Photobiol 2003. [DOI: 10.1562/0031-8655(2003)078%3c0290:icotpp%3e2.0.co%3b2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Losi A, Braslavsky SE. The time-resolved thermodynamics of the chromophore–protein interactions in biological photosensors as derived from photothermal measurements. Phys Chem Chem Phys 2003. [DOI: 10.1039/b303848c] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Imamoto Y, Kataoka M, Liu RSH. Mechanistic pathways for the photoisomerization reaction of the anchored, tethered chromophore of the photoactive yellow protein and its mutants. Photochem Photobiol 2002; 76:584-9. [PMID: 12511037 DOI: 10.1562/0031-8655(2002)076<0584:mpftpr>2.0.co;2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We show by way of physical organic reasoning that the currently known photochemical results of the chromophore of photoactive yellow protein (PYP) are consistent with that expected of a least volume-demanding process for an anchored, tethered chromophore. The primary photoreaction, interestingly, does not appear to involve a hula-twist process. However, the latter might be involved during subsequent transition of dark intermediates. Absorption data of intermediates obtained from a microsecond time-resolved spectroscopic study of three PYP mutants (E46Q, T50V and R52Q) are consistent with the above analyses.
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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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Sgarbossa A, Checcucci G, Lenci F. Photoreception and photomovements of microorganisms. Photochem Photobiol Sci 2002; 1:459-67. [PMID: 12659155 DOI: 10.1039/b110629e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many freely motile microorganisms can perceive and transduce external photic stimuli to the motor apparatus, eventually moving, by means of various behavioural strategies, into environments in which the illumination conditions are the most favourable for their life. In different microorganisms, a wide range of chromophores operate as light detectors, each of them set in a special molecular pocket that, in its turn, can be linked to another component of the transduction chain. The diverse photosensors are organized in special (and in many cases dedicated) photoreceptor units or subcellular organelles. The main molecular mechanisms connecting the early event of photon absorption to the formation of the signalling state down to the dark steps of the transduction chain are discussed in a selected number of case examples. The possible importance of an intensive multidisciplinary approach to these problems in an evolutionary perspective is finally briefly outlined.
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Schenkl S, Portuondo E, Zgrablić G, Chergui M, Haacke S, Friedman N, Sheves M. Ultrafast energy relaxation in bacteriorhodopsin studied by time-integrated fluorescence. Phys Chem Chem Phys 2002. [DOI: 10.1039/b205453a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
ALiu and Hammond recently reasoned that the hula-twist (HT), a volume-conserving cis-trans isomerization mechanism, is involved in reactions of confined systems. We now show that HT can be applied to various reported photochemical isomerization of chromophores (small organic systems as well as photoactive bio-pigments). The results, when taken as a whole, argue powerfully that HT is a common supramolecular photoisomerization reaction mechanism.
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Affiliation(s)
- R S Liu
- Department of Chemistry, University of Hawaii, Honolulu 96822, USA.
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21
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Losi A, Wegener AA, Engelhard M, Braslavsky SE. Enthalpy--entropy compensation in a photocycle: the K-to-L transition in sensory rhodopsin II from Natronobacterium pharaonis. J Am Chem Soc 2001; 123:1766-7. [PMID: 11456781 DOI: 10.1021/ja002677s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A Losi
- Max-Planck-Institut für Strahlenchemie, Postfach 10 13 65, D-45413 Mülheim an der Ruhr, Germany
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Montagnoli G, Podestà A, Bonaretti S. Photomodulated azoaldolase: a model for light intervention in biological systems? Photochem Photobiol 2000; 72:727-30. [PMID: 11140259 DOI: 10.1562/0031-8655(2000)072<0727:paamfl>2.0.co;2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Azoaldolase is obtained from rabbit muscle aldolase by adding an azo chromophore to a cysteine side chain in each of the four enzyme subunits. The enzyme becomes photosensitive whereas both its catalytic activity and the michaelian kinetics are retained. Chromophore excitation causes E to Z isomerization of the azo bond, and mutually influences the protein-substrate equilibria. The various isomerization and substrate binding equilibria have been investigated under the hypothesis of a cyclic process described by four linked equilibrium constants. The mechanism of the light effect is a continuous adaptation of the specific parameters of the active protein, that is substrate recognition and rate of the catalyzed process. Absorbed light allows the rapid modification of the concentrations of various related molecules, depending on the used frequencies. At present such a mechanism has not been described in photobiology; so azoaldolase can be taken as a model for a possible new mechanism of light regulation of a biological system, based on changes in the molecular recognition by an active protein against its substrate.
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Affiliation(s)
- G Montagnoli
- Department of Veterinary Anatomy, Biochemistry and Physiology, University of Pisa, Pisa, Italy.
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Liu RS, Hammond GS. The case of medium-dependent dual mechanisms for photoisomerization: one-bond-flip and hula-twist. Proc Natl Acad Sci U S A 2000; 97:11153-8. [PMID: 11016972 PMCID: PMC17169 DOI: 10.1073/pnas.210323197] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper critically reviews examples in the literature of photochemical cis-trans isomerization paying particular attention to the medium effect and accompanied conformational changes. A case is made that the Hula-Twist mechanism, postulated in 1985 as a photochemical reaction pathway for a polyene chromophore imbedded in a protein binding cavity such as those of rhodopsin and bacteriorhodopsin, is also a dominant reaction pathway for a diene, or a longer polyene confined in a rigid (relative to isomerization rate) medium. The conventional one-bond-flip process is the preferred reaction pathway in a fluid medium. While defining experiments are proposed, this dual mechanistic approach successfully accounts for all examples in the literature on photoisomerization reactions whether involving conformational changes or not.
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Affiliation(s)
- R S Liu
- Department of Chemistry, University of Hawaii, 2545 The Mall, Honolulu, HI 96822, USA.
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