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Kumar G, Kellogg M, Dey S, Oliver TAA, Bradforth SE. Unraveling the Photoionization Dynamics of Indole in Aqueous and Ethanol Solutions. J Phys Chem B 2024; 128:4158-4170. [PMID: 38655896 DOI: 10.1021/acs.jpcb.4c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole's complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two 1ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron-ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.
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Affiliation(s)
- Gaurav Kumar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Michael Kellogg
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shivalee Dey
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Thomas A A Oliver
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, U.K
| | - Stephen E Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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2
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Goryo S, Iwata K. Photoionization of 3-Methylindole Embedded in Sodium Dodecyl Sulfate and Dodecyltrimethylammonium Chloride Micelles: Migration of Electrons Generated in Micelle Cores and Their Solvation in Outside Water. J Phys Chem Lett 2023; 14:1479-1484. [PMID: 36744965 DOI: 10.1021/acs.jpclett.2c03799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Electrons were generated in the core of micelles formed by negatively charged sodium dodecyl sulfate (SDS) or positively charged dodecyltrimethylammonium chloride (DTAC) by photoionization of 3-methylindole embedded in the core. The electrons were hydrated after they moved out of the core to the outer aqueous phase. These processes were monitored with femtosecond time-resolved absorption spectroscopy. The migration of electrons from the micelle core to the outer aqueous phase was faster than the instrumental response time of 200 fs. Hot electrons in the aqueous phase were produced in ≤320 fs. There was no significant difference observed for the micellar solutions of negatively charged SDS and positively charged DTAC, or for water. The geminate recombination between the electrons and the radical cations was hindered to a large extent once the electrons hydrated at the outer aqueous phase were separated from the radical cations remaining in the micelle core.
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Affiliation(s)
- Shion Goryo
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo171-8588, Japan
| | - Koichi Iwata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo171-8588, Japan
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3
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Biswas S, Yamijala SSRKC, Wong BM. Degradation of Per- and Polyfluoroalkyl Substances with Hydrated Electrons: A New Mechanism from First-Principles Calculations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8167-8175. [PMID: 35481774 PMCID: PMC10365488 DOI: 10.1021/acs.est.2c01469] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are synthetic contaminants found in drinking groundwater sources and a wide variety of consumer products. Because of their adverse environmental and human health effects, remediation of these persistent compounds has attracted significant recent attention. To gain mechanistic insight into their remediation, we present the first ab initio study of PFAS degradation via hydrated electrons─a configuration that has not been correctly considered in previous computational studies up to this point. To capture these complex dynamical effects, we harness ab initio molecular dynamics (AIMD) simulations to probe the reactivities of perfluorooctanoic (PFOA) and perfluorooctane sulfonic acid (PFOS) with hydrated electrons in explicit water. We complement our AIMD calculations with advanced metadynamics sampling techniques to compute free energy profiles and detailed statistical analyses of PFOA/PFOS dynamics. Although our calculations show that the activation barrier for C-F bond dissociation in PFOS is three times larger than that in PFOA, all the computed free energy barriers are still relatively low, resulting in a diffusion-limited process. We discuss our results in the context of recent studies on PFAS degradation with hydrated electrons to give insight into the most efficient remediation strategies for these contaminants. Most importantly, we show that the degradation of PFASs with hydrated electrons is markedly different from that with excess electrons/charges, a common (but largely incomplete) approach used in several earlier computational studies.
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Affiliation(s)
- Sohag Biswas
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Physics & Astronomy, and Department of Chemistry, University of California-Riverside, Riverside, California 92521, United States
| | - Sharma S R K C Yamijala
- Department of Chemistry and Center for Atomistic Modelling and Materials Design, Indian Institute of Technology-Madras, Chennai 6000036, India
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Physics & Astronomy, and Department of Chemistry, University of California-Riverside, Riverside, California 92521, United States
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4
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Cui J, Gao P, Deng Y. Destruction of Per- and Polyfluoroalkyl Substances (PFAS) with Advanced Reduction Processes (ARPs): A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3752-3766. [PMID: 32162904 DOI: 10.1021/acs.est.9b05565] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Advanced reduction processes (ARPs) have emerged as a promising method for destruction of persistent per- and polyfluoroalkyl substances (PFAS) in water due to the generation of short-lived and highly reductive hydrated electrons (eaq-). This study provides a critical review on the mechanisms and performance of reductive destruction of PFAS with eaq-. Unique properties of eaq- and its generation in different ARP systems, particularly UV/sulfite and UV/iodide, are overviewed. Different degradation mechanisms of PFAS chemicals, such as perfluorooctanoic acid (PFOA), perfluorooctanesulfonate (PFOS), and others (e.g., short chain perfluorocarboxylic acids (PFCAs) and perfluorosulfonic acids (PFSAs), per- and polyfluoro dicarboxylic acids, and fluorotelomer carboxylic acids), are reviewed, discussed, and compared. The degradation pathways of these PFAS chemicals rely heavily upon their head groups. For specific PFAS types, fluoroalkyl chain lengths may also affect their reductive degradation patterns. Degradation and defluorination efficiencies of PFAS are considerably influenced by solution chemistry parameters and operating factors, such as pH, dose of chemical solute (i.e., sulfite or iodide) for eaq- photoproduction, dissolved oxygen, humic acid, nitrate, and temperature. Furthermore, implications of the state-of-the-art knowledge on practical PFAS control actions in water industries are discussed and the priority research needs are identified.
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Affiliation(s)
- Junkui Cui
- Department of Earth and Environmental Studies, Montclair State University, Montclair, New Jersey 07043, United States
| | - Panpan Gao
- Department of Earth and Environmental Studies, Montclair State University, Montclair, New Jersey 07043, United States
- School of Environmental Studies, China University of Geosciences, Wuhan, Hubei Province 430074, P. R. China
| | - Yang Deng
- Department of Earth and Environmental Studies, Montclair State University, Montclair, New Jersey 07043, United States
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5
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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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6
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Maiti BK, Maia LB, Moro AJ, Lima JC, Cordas CM, Moura I, Moura JJG. Unusual Reduction Mechanism of Copper in Cysteine-Rich Environment. Inorg Chem 2018; 57:8078-8088. [PMID: 29956539 DOI: 10.1021/acs.inorgchem.8b00121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Copper-cysteine interactions play an important role in Biology and herein we used the copper-substituted rubredoxin (Cu-Rd) from Desulfovibrio gigas to gain further insights into the copper-cysteine redox chemistry. EPR spectroscopy results are consistent with Cu-Rd harboring a CuII center in a sulfur-rich coordination, in a distorted tetrahedral structure ( g∥,⊥ = 2.183 and 2.032 and A∥,⊥ = 76.4 × 10-4 and 12 × 10-4 cm-1). In Cu-Rd, two oxidation states at Cu-center (CuII and CuI) are associated with Cys oxidation-reduction, alternating in the redox cycle, as pointed by electrochemical studies that suggest internal geometry rearrangements associated with the electron transfer processes. The midpoint potential of [CuI(S-Cys)2(Cys-S-S-Cys)]/[CuII(S-Cys)4] redox couple was found to be -0.15 V vs NHE showing a large separation of cathodic and anodic peaks potential (Δ Ep = 0.575 V). Interestingly, sulfur-rich CuII-Rd is highly stable under argon in dark conditions, which is thermodynamically unfavorable to Cu-thiol autoreduction. The reduction of copper and concomitant oxidation of Cys can both undergo two possible pathways: oxidative as well as photochemical. Under O2, CuII plays the role of the electron carrier from one Cys to O2 followed by internal geometry rearrangement at the Cu site, which facilitates reduction at Cu-center to yield CuI(S-Cys)2(Cys-S-S-Cys). Photoinduced (irradiated at λex = 280 nm) reduction of the CuII center is observed by UV-visible photolysis (above 300 nm all bands disappeared) and tryptophan fluorescence (∼335 nm peak enhanced) experiments. In both pathways, geometry reorganization plays an important role in copper reduction yielding an energetically compatible donor-acceptor system. This model system provides unusual stability and redox chemistry rather than the universal Cu-thiol auto redox chemistry in cysteine-rich copper complexes.
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Affiliation(s)
- Biplab K Maiti
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Luisa B Maia
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Artur J Moro
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - João C Lima
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Isabel Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - José J G Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
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7
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Larson BC, Pomponio JR, Shafaat HS, Kim RH, Leigh BS, Tauber MJ, Kim JE. Photogeneration and Quenching of Tryptophan Radical in Azurin. J Phys Chem B 2015; 119:9438-49. [PMID: 25625660 PMCID: PMC5092234 DOI: 10.1021/jp511523z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan and tyrosine can form radical intermediates that enable long-range, multistep electron transfer (ET) reactions in proteins. This report describes the mechanisms of formation and quenching of a neutral tryptophan radical in azurin, a blue-copper protein that contains native tyrosine (Y108 and Y72) and tryptophan (W48) residues. A long-lived neutral tryptophan radical W48• is formed upon UV-photoexcitation of a zinc(II)-substituted azurin mutant in the presence of an external electron acceptor. The quantum yield of W48• formation (Φ) depends upon the tyrosine residues in the protein. A tyrosine-deficient mutant, Zn(II)Az48W, exhibited a value of Φ = 0.080 with a Co(III) electron acceptor. A nearly identical quantum yield was observed when the electron acceptor was the analogous tyrosine-free, copper(II) mutant; this result for the Zn(II)Az48W:Cu(II)Az48W mixture suggests there is an interprotein ET path. A single tyrosine residue at one of the native positions reduced the quantum yield to 0.062 (Y108) or 0.067 (Y72). Wild-type azurin with two tyrosine residues exhibited a quantum yield of Φ = 0.045. These data indicate that tyrosine is able to quench the tryptophan radical in azurin.
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Affiliation(s)
- Bethany C. Larson
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jennifer R. Pomponio
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | - Rachel H. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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8
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Liu X, Sobolewski AL, Domcke W. Photoinduced Oxidation of Water in the Pyridine–Water Complex: Comparison of the Singlet and Triplet Photochemistries. J Phys Chem A 2014; 118:7788-95. [DOI: 10.1021/jp505188y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xiaojun Liu
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
- Key
Laboratory of Luminescence and Optical Information, Institute of Optoelectronic
Technology, Beijing Jiaotong University, Beijing 100044, People’s Republic of China
| | | | - Wolfgang Domcke
- Department
of Chemistry, Technische Universität München, D-85747 Garching, Germany
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9
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Ladner CL, Tran K, Le M, Turner RJ, Edwards RA. Excited State Photoreaction between the Indole Side Chain of Tryptophan and Halocompounds Generates New Fluorophores and Unique Modifications. Photochem Photobiol 2014; 90:1027-33. [DOI: 10.1111/php.12279] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Carol L. Ladner
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Khai Tran
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Mary Le
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Raymond J. Turner
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Robert A. Edwards
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
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10
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11
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Abel B, Buck U, Sobolewski AL, Domcke W. On the nature and signatures of the solvated electron in water. Phys Chem Chem Phys 2012; 14:22-34. [DOI: 10.1039/c1cp21803d] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Correia M, Neves-Petersen MT, Parracino A, di Gennaro AK, Petersen SB. Photophysics, photochemistry and energetics of UV light induced disulphide bridge disruption in apo-α-lactalbumin. J Fluoresc 2011; 22:323-37. [PMID: 21997288 DOI: 10.1007/s10895-011-0963-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/30/2011] [Indexed: 11/29/2022]
Abstract
Continuous 295 nm excitation of whey protein bovine apo-α-lactalbumin (apo-bLA) results in an increase of tryptophan fluorescence emission intensity, in a progressive red-shift of tryptophan fluorescence emission, and breakage of disulphide bridges (SS), yielding free thiol groups. The increase in fluorescence emission intensity upon continuous UV-excitation is correlated with the increase in concentration of free thiol groups in apo-bLA. UV-excitation and consequent SS breakage induce conformational changes on apo-bLA molecules, which after prolonged illumination display molten globule spectral features. The rate of tryptophan fluorescence emission intensity increase at 340 nm with excitation time increases with temperature in the interval 9.3-29.9°C. The temperature-dependent 340 nm emission kinetic traces were fitted by a 1st order reaction model. Native apo-bLA molecules with intact SS bonds and low tryptophan emission intensity are gradually converted upon excitation into apo-bLA molecules with disrupted SS, molten-globule-like conformation, high tryptophan emission intensity and red-shifted tryptophan emission. Experimental Ahrrenius activation energy was 21.8 ± 2.3 kJ x mol(-1). Data suggests that tryptophan photoionization from the S(1) state is the likely pathway leading to photolysis of SS in apo-bLA. Photoionization mechanism(s) of tryptophan in proteins and in solution and the activation energy of tryptophan photoionization from S(1) leading to SS disruption in proteins are discussed. The observations present in this paper raise concern regarding UV-light pasteurization of milk products. Though UV-light pasteurization is a faster and cheaper method than traditional thermal denaturation, it may also lead to loss of structure and functionality of milk proteins.
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Affiliation(s)
- Manuel Correia
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, DK-9220, Aalborg, Denmark.
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13
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Chen X, Larsen DS, Bradforth SE, van Stokkum IHM. Broadband Spectral Probing Revealing Ultrafast Photochemical Branching after Ultraviolet Excitation of the Aqueous Phenolate Anion. J Phys Chem A 2011; 115:3807-19. [DOI: 10.1021/jp107935f] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Stephen E. Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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14
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David O, Dedonder-Lardeux C, Jouvet C. Is there an Excited State Proton Transfer in phenol (or 1 -naphthol)-ammonia clusters? Hydrogen Detachment and Transfer to Solvent: A key for non-radiative processes in clusters. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350210164287] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Dobkowski J, Herbich J, Galievsky V, Thummel RP, Wu F, Waluk J. Diversity of excited state deactivation paths in heteroazaaromatics with multiple intermolecular hydrogen bonds. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19981020328] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Ultrafast excited-state dynamics of tryptophan in water observed by transient absorption spectroscopy. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.02.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Léonard J, Sharma D, Szafarowicz B, Torgasin K, Haacke S. Formation dynamics and nature of tryptophan's primary photoproduct in aqueous solution. Phys Chem Chem Phys 2010; 12:15744-50. [DOI: 10.1039/c0cp00615g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Dong CY, Yoon TW, Bates DG, Cho KH. Identification of feedback loops embedded in cellular circuits by investigating non-causal impulse response components. J Math Biol 2009; 60:285-312. [PMID: 19333603 DOI: 10.1007/s00285-009-0263-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 03/03/2009] [Indexed: 12/24/2022]
Abstract
Feedback circuits are crucial dynamic motifs which occur in many biomolecular regulatory networks. They play a pivotal role in the regulation and control of many important cellular processes such as gene transcription, signal transduction, and metabolism. In this study, we develop a novel computationally efficient method to identify feedback loops embedded in intracellular networks, which uses only time-series experimental data and requires no knowledge of the network structure. In the proposed approach, a non-parametric system identification technique, as well as a spectral factor analysis, is applied to derive a graphical criterion based on non-causal components of the system's impulse response. The appearance of non-causal components in the impulse response sequences arising from stochastic output perturbations is shown to imply the presence of underlying feedback connections within a linear network. In order to extend the approach to nonlinear networks, we linearize the intracellular networks about an equilibrium point, and then choose the magnitude of the output perturbations sufficiently small so that the resulting time-series responses remain close to the chosen equilibrium point. In this way, the impulse response sequences of the linearized system can be used to determine the presence or absence of feedback loops in the corresponding nonlinear network. The proposed method utilizes the time profile data from intracellular perturbation experiments and only requires the perturbability of output nodes. Most importantly, the method does not require any a priori knowledge of the system structure. For these reasons, the proposed approach is very well suited to identifying feedback loops in large-scale biomolecular networks. The effectiveness of the proposed method is illustrated via two examples: a synthetic network model with a negative feedback loop and a nonlinear caspase function model of apoptosis with a positive feedback loop.
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Affiliation(s)
- Chao-Yi Dong
- School of Electrical Engineering, Korea University, Seoul 136-713, Korea
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19
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Carrera A, Nielsen IB, Carçabal P, Dedonder C, Broquier M, Jouvet C, Domcke W, Sobolewski AL. Biradicalic excited states of zwitterionic phenol-ammonia clusters. J Chem Phys 2009; 130:024302. [PMID: 19154023 DOI: 10.1063/1.3054292] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phenol-ammonia clusters with more than five ammonia molecules are proton transferred species in the ground state. In the present work, the excited states of these zwitterionic clusters have been studied experimentally with two-color pump probe methods on the nanosecond time scale and by ab initio electronic-structure calculations. The experiments reveal the existence of a long-lived excited electronic state with a lifetime in the 50-100 ns range, much longer than the excited state lifetime of bare phenol and small clusters of phenol with ammonia. The ab initio calculations indicate that this long-lived excited state corresponds to a biradicalic system, consisting of a phenoxy radical that is hydrogen bonded to a hydrogenated ammonia cluster. The biradical is formed from the locally excited state of the phenolate anion via an electron transfer process, which neutralizes the charge separation of the ground state zwitterion.
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Affiliation(s)
- A Carrera
- University of Buenos Aires, Ciudad Universitaria, 3er piso, Pab. II, 1428 Buenos Aires, Argentina
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20
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Creed D. THE PHOTOPHYSICS AND PHOTOCHEMISTRY OF THE NEAR-UV ABSORBING AMINO ACIDS-I. TRYPTOPHAN AND ITS SIMPLE DERIVATIVES. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1984.tb03890.x] [Citation(s) in RCA: 429] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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22
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Crespo-Hernández CE, Arce R. Photoionization of DNA and RNA Bases, Nucleosides and Nucleotides Through a Combination of One- and Two-photon Pathways upon 266 nm Nanosecond Laser Excitation¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2002)0760259podarb2.0.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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23
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Ichino T, Fessenden RW. Reactions of Hydrated Electron with Various Radicals: Spin Factor in Diffusion-Controlled Reactions. J Phys Chem A 2007; 111:2527-41. [PMID: 17388346 DOI: 10.1021/jp0684527] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reactions of hydrated electron (eaq-) with various radicals have been studied in pulse radiolysis experiments. These radicals are hydroxyl radical (*OH), sulfite radical anion (*SO3-), carbonate radical anion (CO3*-), carbon dioxide radical anion (*CO2-), azidyl radical (*N3), dibromine radical anion (Br2*-), diiodine radical anion (I2*-), 2-hydroxy-2-propyl radical (*C(CH3)2OH), 2-hydroxy-2-methyl-1-propyl radical ((*CH2)(CH3)2COH), hydroxycyclohexadienyl radical (*C6H6OH), phenoxyl radical (C6H5O*), p-methylphenoxyl radical (p-(H3C)C6H4O*), p-benzosemiquinone radical anion (p-OC6H4O*-), and phenylthiyl radical (C6H5S*). The kinetics of eaq- was followed in the presence of the counter radicals in transient optical absorption measurements. The rate constants of the eaq- reactions with radicals have been determined over a temperature range of 5-75 degrees C from the kinetic analysis of systems of multiple second-order reactions. The observed high rate constants for all the eaq- + radical reactions have been analyzed with the Smoluchowski equation. This analysis suggests that many of the eaq- + radical reactions are diffusion-controlled with a spin factor of 1/4, while other reactions with *OH, *N3, Br2*-, I2*-, and C6H5S* have spin factors significantly larger than 1/4. Spin dynamics for the eaq-/radical pairs is discussed to explain the different spin factors. The reactions with *OH, *N3, Br2*-, and I2*- have also been found to have apparent activation energies less than that for diffusion control, and it is suggested that the spin factors for these reactions decrease with increasing temperature. Such a decrease in spin factor may reflect a changing competition between spin relaxation/conversion and diffusive escape from the radical pairs.
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Affiliation(s)
- Takatoshi Ichino
- Radiation Laboratory and Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5674, USA
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24
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Neves-Petersen MT, Klitgaard S, Carvalho ASL, Petersen SB, Aires de Barros MR, Pinho e Melo E. Photophysics and photochemistry of horseradish peroxidase A2 upon ultraviolet illumination. Biophys J 2006; 92:2016-27. [PMID: 17189303 PMCID: PMC1861803 DOI: 10.1529/biophysj.106.095455] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Detailed analysis of the effects of ultraviolet (UV) and blue light illumination of horseradish peroxidase A2, a heme-containing enzyme that reduces H(2)O(2) to oxidize organic and inorganic compounds, is presented. The effects of increasing illumination time on the protein's enzymatic activity, Reinheitzahl value, fluorescence emission, fluorescence lifetime distribution, fluorescence mean lifetime, and heme absorption are reported. UV illumination leads to an exponential decay of the enzyme activity followed by changes in heme group absorption. Longer UV illumination time leads to lower T(m) values as well as helical content loss. Prolonged UV illumination and heme irradiation at 403 nm has a pronounced effect on the fluorescence quantum yield correlated with changes in the prosthetic group pocket, leading to a pronounced decrease in the heme's Soret absorbance band. Analysis of the picosecond-resolved fluorescence emission of horseradish peroxidase A2 with streak camera shows that UV illumination induces an exponential change in the preexponential factors distribution associated to the protein's fluorescence lifetimes, leading to an exponential increase of the mean fluorescence lifetime. Illumination of aromatic residues and of the heme group leads to changes indicative of heme leaving the molecule and/or that photoinduced chemical changes occur in the heme moiety. Our studies bring new insight into light-induced reactions in proteins. We show how streak camera technology can be of outstanding value to follow such ultrafast processes and how streak camera data can be correlated with protein structural changes.
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Affiliation(s)
- Maria Teresa Neves-Petersen
- Department of Physics and Nanotechnology, NanoBiotechnology Section, UltrafastBioSpectroscopy Group, Aalborg University, Aalborg, Denmark.
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25
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Sherin PS, Snytnikova OA, Tsentalovich YP, Sagdeev RZ. Competition between ultrafast relaxation and photoionization in excited prefluorescent states of tryptophan and indole. J Chem Phys 2006; 125:144511. [PMID: 17042613 DOI: 10.1063/1.2348868] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quantum yield of photoionization of TrpH and IndH from the nonrelaxed prefluorescent state S* increases with the temperature decrease. This effect is attributed to the competition between temperature independent ionization and ultrafast thermal relaxation S* --> S1. The rate constant of the relaxation does not depend on the solvent and on the presence of the amino acid side chain: the temperature dependences of photoionization quantum yield, obtained for TrpH and IndH in different solvents, practically coincide. The activation energy for the relaxation rate constant Er approximately 4.5 kJ/mol probably corresponds to intramolecular process or to the formation of the vibronically excited transient complex between photoexcited molecule and solvent molecules.
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Affiliation(s)
- P S Sherin
- International Tomography Center, 630090 Novosibirsk, Russia and Novosibirsk State University, 630090 Novosibirsk, Russia
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26
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David O, Dedonder-Lardeux C, Jouvet C, Sobolewski AL. Role of the Intermolecular Vibrations in the Hydrogen Transfer Rate: The 3-Methylindole−NH3 Complex. J Phys Chem A 2006; 110:9383-7. [PMID: 16869687 DOI: 10.1021/jp062950y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The lifetimes of the 3-methylindole-NH3 complex have been measured on different vibronic levels involving intermolecular modes and decrease from 530 to 65 ps, in a mode specific manner. Geometry optimizations of the ground and excited states have been performed with ab initio methods, and as in the case of phenol and indole, a repulsive pi sigma* state lies close to the initially excited pi pi* state. From these calculations, it seems that both in-plane and out-of-plane vibrations induce a faster nonradiative decay.
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Affiliation(s)
- Olivier David
- Laboratoire de Photophysique Moléculaire du CNRS, Bât. 210, Université Paris-Sud, 91405 Orsay, France
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27
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Courvoisier F, Boutou V, Guyon L, Roth M, Rabitz H, Wolf JP. Discriminating bacteria from other atmospheric particles using femtosecond molecular dynamics. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2006.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Sherin PS, Snytnikova OA, Tsentalovich YP. Tryptophan photoionization from prefluorescent and fluorescent states. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.04.068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Tsentalovich YP, Snytnikova OA, Sagdeev RZ. Properties of excited states of aqueous tryptophan. J Photochem Photobiol A Chem 2004. [DOI: 10.1016/s1010-6030(03)00376-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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30
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Fischer CJ, Gafni A, Steel DG, Schauerte JA. The triplet-state lifetime of indole in aqueous and viscous environments: significance to the interpretation of room temperature phosphorescence in proteins. J Am Chem Soc 2002; 124:10359-66. [PMID: 12197738 DOI: 10.1021/ja016609x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interpretation of room temperature phosphorescence studies of proteins requires an understanding of the mechanisms governing the tryptophan triplet-state lifetimes of residues fully exposed to solvent and those deeply buried in the hydrophobic core of proteins. Since solvents exposed tryptophans are expected to behave similarly to indole free in solution, it is important to have an accurate measure of the triplet state lifetime of indole in aqueous solution. Using photon counting techniques and low optical fluence (J/cm(2)), we observed the triplet-state lifetime of aqueous, deoxygenated indole and several indole derivatives to be approximately 40 micros, closely matching the previous reports by Bent and Hayon based on flash photolysis (12 micros; Bent, D. V.; Hayon, E. J. Am. Chem. Soc. 1975, 97, 2612-2619) but much shorter than the 1.2 ms lifetime observed more recently (Strambini, G. B.; Gonnelli, M. J. Am. Chem. Soc. 1995, 117, 7646-7651). However, we have now been able to reproduce the long lifetime reported by the latter workers for aqueous indole solutions and show that it likely arises from geminate recombination of the indole radical cation and solvated electron, a conclusion based on studies of the indole radical cation in water (Bent and Hayon, 1975). The evidence for this comes from a fast rise in the phosphorescence emission and measurements of a corresponding enhanced quantum yield in unbuffered solutions. This species can be readily quenched, and the corresponding fast rise disappears, leaving a monoexponential 40 micros decay, which we argue is the true indole triplet lifetime. The work is put in the context of room temperature phosphorescence studies of proteins.
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Affiliation(s)
- Christopher J Fischer
- Biophysics Research Program, Applied Physics Program, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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31
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Crespo-Hernández CE, Arce R. Photoionization of DNA and RNA bases, nucleosides and nucleotides through a combination of one- and two-photon pathways upon 266 nm nanosecond laser excitation. Photochem Photobiol 2002; 76:259-67. [PMID: 12403446 DOI: 10.1562/0031-8655(2002)076<0259:podarb>2.0.co;2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The 266 nm nanosecond laser photolysis of various purine and pyrimidine derivatives results in their photoionization (PI) as one of the primary photochemical pathways. Electron photoejection occurs through a combination of one- and two-photon mechanisms. The PI values depend on the substituents attached to the chromophore of the base. The net PI of the purine bases at 266 nm are of the same order of magnitude (10(-2)) as those of the pyrimidine bases under similar experimental conditions. The monophotonic component is approximately one-third of the net PI yield of the bases. A nonrelaxed singlet excited state intermediate is tentatively proposed for this pathway. It is proposed that this state is significantly stabilized by water solvation, transforming it into a charge transfer to solvent state from which the hydrated electron evolves.
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32
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Abstract
The light-dependent reaction between N-acetyl-L-tryptophanamide (NATA) and chloroform has been examined using fluorescence, NMR and reverse phase chromatography. The emission of NATA in the presence of CHCl3 decreases at 360 nm and increases at longer wavelengths (approximately 480 nm) upon illumination with 280 nm light. The action spectrum for the formation of the 480 nm emitting product(s) has the same shape as the excitation spectra of the indole fluorophore in NATA. The pH of the solution decreases as the reaction proceeds. The reaction rate depends on the intensity of the illumination and is of the first order with respect to both [NATA] and [CHCl3]. NMR and reverse phase chromatography results demonstrate that multiple products are formed. The reaction products give new peaks between 8.9 and 10.5 ppm in the 1H-NMR that are assigned to -CHO groups, which are added to the indole ring. Some of the products react with 2,4-dinitrophenylhydrazine and thus confirm this assignment. A scheme is proposed in which the excited indole gives off a solvated electron to initiate a series of steps that yield indole derivatives in which a -CHO group has replaced a -H in the indole ring. Similar reactions are observed when 5-hydroxytryptophan, 5-fluorotryptophan or N-methylindolacetate is used instead of tryptophan or when the chloroform is replaced with other trichlorinated compounds, such as trichloroacetic acid, trichloroethanol and trichloroethane, as well as the tribrominated compound, bromoform, and the monoiodinated compound, iodoactetate.
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Affiliation(s)
- Robert A Edwards
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Alberta, Canada
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33
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Hudgins RR, Huang F, Gramlich G, Nau WM. A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides. J Am Chem Soc 2002; 124:556-64. [PMID: 11804484 DOI: 10.1021/ja010493n] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fluorescent amino acid derivative (Fmoc-DBO) has been synthesized, which contains 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a small, hydrophilic fluorophore with an extremely long fluorescence lifetime (325 ns in H2O and 505 ns in D2O under air). Polypeptides containing both the DBO residue and an efficient fluorescence quencher allow the measurement of rate constants for intramolecular end-to-end contact formation. Bimolecular quenching experiments indicated that Trp, Cys, Met, and Tyr are efficient quenchers of DBO (k(q) = 20, 5.1, 4.5, and 3.6 x 10(8) M(-1) x s(-1) in D2O), while the other amino acids are inefficient. The quenching by Trp, which was selected as an intrinsic quencher, is presumed to involve exciplex-induced deactivation. Flexible, structureless polypeptides, Trp-(Gly-Ser)n-DBO-NH2, were prepared by standard solid-phase synthesis, and the rates of contact formation were measured through the intramolecular fluorescence quenching of DBO by Trp with time-correlated single-photon counting, laser flash photolysis, and steady-state fluorometry. Rate constants of 4.1, 6.8, 4.9, 3.1, 2.0, and 1.1 x 10(7) s(-1) for n = 0, 1, 2, 4, 6, and 10 were obtained. Noteworthy was the relatively slow quenching for the shortest peptide (n = 0). The kinetic data are in agreement with recent transient absorption studies of triplet probes for related peptides, but the rate constants are significantly larger. In contrast to the flexible structureless Gly-Ser polypeptides, the polyproline Trp-Pro4-DBO-NH2 showed insignificant fluorescence quenching, suggesting that a high polypeptide flexibility and the possibility of probe-quencher contact is essential to induce quenching. Advantages of the new fluorescence-based method for measuring contact formation rates in biopolymers include high accuracy, fast time range (100 ps-1 micros), and the possibility to perform measurements in water under air.
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Affiliation(s)
- Robert R Hudgins
- Departement Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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34
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Ababou A, Bombarda E. On the involvement of electron transfer reactions in the fluorescence decay kinetics heterogeneity of proteins. Protein Sci 2001; 10:2102-13. [PMID: 11567101 PMCID: PMC2374218 DOI: 10.1110/ps.05501] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Time-resolved fluorescence study of single tryptophan-containing proteins, nuclease, ribonuclease T1, protein G, glucagon, and mastoparan, has been carried out. Three different methods were used for the analysis of fluorescence decays: the iterative reconvolution method, as reviewed and developed in our laboratory, the maximum entropy method, and the recent method that we called "energy transfer" method. All the proteins show heterogeneous fluorescence kinetics (multiexponential decay). The origin of this heterogeneity is interpreted in terms of current theories of electron transfer process, which treat the electron transfer process as a radiationless transition. The theoretical electron transfer rate was calculated assuming the peptide bond carbonyl as the acceptor site. The good agreement between experimental and theoretical electron-transfer rates leads us to suggest that the electron-transfer process is the principal quenching mechanism of Trp fluorescence in proteins, resulting in heterogeneous fluorescence kinetics. Furthermore, the origin of apparent homogeneous fluorescence kinetics (monoexponential decay) in some proteins also can be explained on the basis of electron-transfer mechanism.
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Affiliation(s)
- A Ababou
- Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7034 CNRS, Université Louis Pasteur, Strasbourg 1, Illkirch, France.
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35
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Tajima S, Tobita S, Shizuka H. Acid−Base Equilibrium and Electron-Ejection Processes in the Excited States of N,N-Dimethyl-1-aminonaphthalene in Aqueous Solution. J Phys Chem A 2000. [DOI: 10.1021/jp000489i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- So Tajima
- Department of Chemistry, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Seiji Tobita
- Department of Chemistry, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Haruo Shizuka
- Department of Chemistry, Gunma University, Kiryu, Gunma 376-8515, Japan
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36
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Nanosecond UV laser photoionization of aqueous tryptophan: temperature dependence of quantum yield, mechanism, and kinetics of hydrated electron decay. J Photochem Photobiol A Chem 2000. [DOI: 10.1016/s1010-6030(00)00235-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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37
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Peon J, Hess GC, Pecourt JML, Yuzawa T, Kohler B. Ultrafast Photoionization Dynamics of Indole in Water. J Phys Chem A 1999. [DOI: 10.1021/jp9840782] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jorge Peon
- The Ohio State University, Department of Chemistry, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Gina C. Hess
- The Ohio State University, Department of Chemistry, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Jean-Marc L. Pecourt
- The Ohio State University, Department of Chemistry, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Tetsuro Yuzawa
- The Ohio State University, Department of Chemistry, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Bern Kohler
- The Ohio State University, Department of Chemistry, 100 West 18th Avenue, Columbus, Ohio 43210
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38
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Saito F, Tobita S, Shizuka H. Photoionization mechanism of aniline derivatives in aqueous solution studied by laser flash photolysis. J Photochem Photobiol A Chem 1997. [DOI: 10.1016/s1010-6030(97)00048-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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39
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McLaughlin ML, Barkley MD. Time-resolved fluorescence of constrained tryptophan derivatives: implications for protein fluorescence. Methods Enzymol 1997; 278:190-202. [PMID: 9170314 DOI: 10.1016/s0076-6879(97)78011-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- M L McLaughlin
- Department of Chemistry, Louisiana State University, Baton Rouge 70803, USA
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40
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McGimpsey WG, Görner H. Photoionization of Indole, N-Methylindole and Tryptophan In Aqueous Solution upon Excitation at 193 nm. Photochem Photobiol 1996. [DOI: 10.1111/j.1751-1097.1996.tb03097.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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42
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Photolysis (193 nm) of aliphatic amino acids in aqueous solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1995. [DOI: 10.1016/1011-1344(95)07187-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Görner H, Schulte-Frohlinde D. Ion-forming processes on 248 NM laser excitation of uracil and methyl-monosubstituted uracils: A time-resolved transient conductivity study in aqueous solution. Radiat Phys Chem Oxf Engl 1993 1995. [DOI: 10.1016/0969-806x(94)00110-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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44
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Abstract
The fluorescence decay of tryptophan residues in the bovine lens protein gamma-II crystallin has been measured in aqueous buffer solutions. Results were obtained as a function of emission wavelength, temperature, dissolved oxygen, and denaturing solvent. The protein displayed complex fluorescence decay which fit a biexponential model with a long component (ns) and a short component (few hundred ps). Measured fluorescence quantum yields data for gamma-II crystallin allowed calculation of radiative and non-radiative rate constants. The radiative rate constant was consistent with that observed in other indole derivatives, while the non-radiative rate constant was quite large and accounted for the short lifetime in gamma-II. The temperature dependence of the non-radiative decay in gamma-II crystallin yielded a small activation energy of only 1-2 kcal/mol, compared to 4 kcal/mol for the reference compound NATA whose barrier is known to derive from the rotamer model.
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Affiliation(s)
- R F Borkman
- Institute for Molecular Science Myodaiji, Okazaki, Japan
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45
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Medina F, Poyato J, Rodriguez J. Photophysical study of some indole derivatives. J Photochem Photobiol A Chem 1992. [DOI: 10.1016/1010-6030(92)87004-s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Nikogosyan DN, Görner H. Photolysis of aromatic amino acids in aqueous solution by nanosecond 248 and 193 nm laser light. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1992. [DOI: 10.1016/1011-1344(92)85062-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Greenaway FT, Redmond RW, Ledbetter JW. Hydrated electron formation on laser excitation of P-pyridoxyl amino acids and proteins. Photochem Photobiol 1991; 54:667-72. [PMID: 1798742 DOI: 10.1111/j.1751-1097.1991.tb02073.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Evidence from a characteristic transient spectrum, its lifetime and quenching by N2O demonstrates that XeCl excimer laser excitation of the reduced form of pyridoxal 5'-phosphate bound to lysine residues will produce the hydrated electron. The phenoxyl-type radical coproduct was also observed. The results identify a useful label of protein structures for site-specific electron generation which can occur outside the region of light absorption by aromatic residues of protein. The results also represent the first observation of hydrated electron formation from flash excitation of a vitamin B6 cofactor.
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Affiliation(s)
- F T Greenaway
- Department of Chemistry, Clark University, Worcester, MA 01610
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48
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Mahmoud GS. An electron paramagnetic resonance study of the influence of spermine on the photophysical reactions of tryptophan in aqueous solution at 77–200 K. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1991. [DOI: 10.1016/1011-1344(91)80021-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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49
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Mahmoud GS, Melø TB. The effect of the antioxidant spermine on the photophysical reactions of tryptophan in aqueous solution at 77 K. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1990; 5:467-80. [PMID: 2165525 DOI: 10.1016/1011-1344(90)85059-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fluorescence, phosphorescence and electron paramagnetic resonance techniques were used to investigate the effect of the antioxidant spermine on the initial photophysical reactions of tryptophan (Trp) in aqueous salt solutions at 77 K. At low concentrations of Trp (3.5 X 10(-5) M) a ground state complex was formed between one Trp and two spermine molecules (a 1:2 complex). Complexed Trp was photodegraded at a rate 65% lower than the free molecule due to a change in the charge-transfer character of the excited 1La state. At high concentrations of Trp (3.5 X 10(-3) M) the phosphorescence was almost completely quenched due to hydrogen-bond formation between two neighbouring Trp molecules. A strong complex was formed between this Trp dimer and one spermine molecule on addition of spermine (a 2:1 complex). Spermine enhanced intersystem crossing in one of the two Trp molecules in the 2:1 complex and phosphorescence was observed. From this triplet state the tryptophyl radical was formed with high efficiency by hydrogen-atom transfer. The yield of radical formation from the triplet state in the 2:1 complex was much larger than from the excited singlet state in the 1:2 complex.
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Affiliation(s)
- G S Mahmoud
- Institute of Physics, AVH University of Trondheim, Norway
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50
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Young T, Kim ST, Van Camp JR, Hartman RF, Rose SD. Transient intermediates in intramolecularly photosensitized pyrimidine dimer splitting by indole derivatives. Photochem Photobiol 1988; 48:635-41. [PMID: 3241836 DOI: 10.1111/j.1751-1097.1988.tb02874.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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