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Afsari S, Mukherjee S, Halloran N, Ghirlanda G, Ryan E, Wang X, Lindsay S. Heavy Water Reduces the Electronic Conductance of Protein Wires via Deuteron Interactions with Aromatic Residues. NANO LETTERS 2023; 23:8907-8913. [PMID: 37772726 PMCID: PMC11177565 DOI: 10.1021/acs.nanolett.3c02263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Proteins are versatile, self-assembling nanoelectronic components, but their hopping conductivity is expected to be influenced by solvent fluctuations. The role of the solvent was investigated by measuring the single molecule conductance of several proteins in both H2O and D2O. The conductance of a homologous series of protein wires decreases more rapidly with length in D2O, indicating a 6-fold decrease in carrier diffusion constant relative to the same protein in H2O. The effect was found to depend on the specific aromatic amino acid composition. A tryptophan zipper protein showed a decrease in conductance similar to that of the protein wires, whereas a phenylalanine zipper protein was insensitive to solvent changes. Tryptophan contains an indole amine, whereas the phenylalanine aromatic ring has no exchangeable protons, so the effect of heavy water on conductance is a consequence of specific D- or H-interactions with the aromatic residues.
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Affiliation(s)
- Sepideh Afsari
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Sohini Mukherjee
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Nicholas Halloran
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | | | - Eathen Ryan
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- Department of Physics, Arizona State University, Tempe, AZ 85287
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2
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Mostajabi Sarhangi S, Matyushov DV. Effect of Water Deuteration on Protein Electron Transfer. J Phys Chem Lett 2023; 14:723-729. [PMID: 36648391 DOI: 10.1021/acs.jpclett.2c03690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Traditional theories of long-range protein electron transfer describe the reaction rate in terms of the tunneling distance and the reaction free energy. They do not recognize two physical effects: (i) local wetting of the active site by hydration water and (ii) protein identity affecting the rate through dynamics and flexibility. We find, by molecular dynamics simulations, a significant, ∼25 times, slowing down of the rate of protein electron transfer upon deuteration. H/D substitution changes the rate constant pre-exponential factor in the regime of electron transfer controlled by medium dynamics. Switching from light to heavy water increases the effective medium relaxation time. The effect is caused by both a global change in the flexibility of the protein backbone and locally stronger hydrogen bonds to charged residues.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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3
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Rivera JJ, Trinh C, Kim JE. Photoinduced Electron Transfer from the Tryptophan Triplet State in Zn-Azurin. ACS PHYSICAL CHEMISTRY AU 2022; 3:63-73. [PMID: 36718260 PMCID: PMC9881450 DOI: 10.1021/acsphyschemau.2c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
Tryptophan is one of few residues that participates in biological electron transfer reactions. Upon substitution of the native Cu2+ center with Zn2+ in the blue-copper protein azurin, a long-lived tryptophan neutral radical can be photogenerated. We report the following quantum yield values for Zn-substituted azurin in the presence of the electron acceptor Cu(II)-azurin: formation of the tryptophan neutral radical (Φrad), electron transfer (ΦET), fluorescence (Φfluo), and phosphorescence (Φphos), as well as the efficiency of proton transfer of the cation radical (ΦPT). Increasing the concentration of the electron acceptor increased Φrad and ΦET values and decreased Φphos without affecting Φfluo. At all concentrations of the acceptor, the value of ΦPT was nearly unity. These observations indicate that the phosphorescent triplet state is the parent state of electron transfer and that nearly all electron transfer events lead to proton loss. Similar results regarding the parent state were obtained with a different electron acceptor, [Co(NH3)5Cl]2+; however, Stern-Volmer graphs revealed that [Co(NH3)5Cl]2+ was a more effective phosphorescence quencher (K SV = 230 000 M-1) compared to Cu(II)-azurin (K SV = 88 000 M-1). Competition experiments in the presence of both [Co(NH3)5Cl]2+ and Cu(II)-azurin suggested that [Co(NH3)5Cl]2+ is the preferred electron acceptor. Implications of these results in terms of quenching mechanisms are discussed.
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Mathis P, Sage E, Byrdin M. Pushing the limits of flash photolysis to unravel the secrets of biological electron and proton transfer. Photochem Photobiol Sci 2022; 21:1533-1544. [DOI: 10.1007/s43630-021-00134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2021] [Indexed: 11/25/2022]
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5
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Wong SY, Wei Y, Mouritsen H, Solov'yov IA, Hore PJ. Cryptochrome magnetoreception: four tryptophans could be better than three. J R Soc Interface 2021; 18:20210601. [PMID: 34753309 PMCID: PMC8580466 DOI: 10.1098/rsif.2021.0601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/14/2021] [Indexed: 12/28/2022] Open
Abstract
The biophysical mechanism of the magnetic compass sensor in migratory songbirds is thought to involve photo-induced radical pairs formed in cryptochrome (Cry) flavoproteins located in photoreceptor cells in the eyes. In Cry4a-the most likely of the six known avian Crys to have a magnetic sensing function-four radical pair states are formed sequentially by the stepwise transfer of an electron along a chain of four tryptophan residues to the photo-excited flavin. In purified Cry4a from the migratory European robin, the third of these flavin-tryptophan radical pairs is more magnetically sensitive than the fourth, consistent with the smaller separation of the radicals in the former. Here, we explore the idea that these two radical pair states of Cry4a could exist in rapid dynamic equilibrium such that the key magnetic and kinetic properties are weighted averages. Spin dynamics simulations suggest that the third radical pair is largely responsible for magnetic sensing while the fourth may be better placed to initiate magnetic signalling particularly if the terminal tryptophan radical can be reduced by a nearby tyrosine. Such an arrangement could have allowed independent optimization of the essential sensing and signalling functions of the protein. It might also rationalize why avian Cry4a has four tryptophans while Crys from plants have only three.
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Affiliation(s)
- Siu Ying Wong
- Institut für Physik, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - Yujing Wei
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Henrik Mouritsen
- Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
- Research Centre for Neurosensory Science, University of Oldenburg, Oldenburg 26111, Germany
| | - Ilia A. Solov'yov
- Institut für Physik, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - P. J. Hore
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
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Lee KS, Dumke R, Paterek T. Numerical tests of magnetoreception models assisted with behavioral experiments on American cockroaches. Sci Rep 2021; 11:12221. [PMID: 34108599 PMCID: PMC8190300 DOI: 10.1038/s41598-021-91815-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Many animals display sensitivity to external magnetic field, but it is only in the simplest organisms that the sensing mechanism is understood. Here we report on behavioural experiments where American cockroaches (Periplaneta americana) were subjected to periodically rotated external magnetic fields with a period of 10 min. The insects show increased activity when placed in a periodically rotated Earth-strength field, whereas this effect is diminished in a twelve times stronger periodically rotated field. We analyse established models of magnetoreception, the magnetite model and the radical pair model, in light of this adaptation result. A broad class of magnetite models, based on single-domain particles found in insects and assumption that better alignment of magnetic grains towards the external field yields better sensing and higher insect activity, is shown to be excluded by the measured data. The radical-pair model explains the data if we assume that contrast in the chemical yield on the order of one in a thousand is perceivable by the animal, and that there also exists a threshold value for detection, attained in an Earth-strength field but not in the stronger field.
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Affiliation(s)
- Kai Sheng Lee
- grid.59025.3b0000 0001 2224 0361School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371 Singapore
| | - Rainer Dumke
- grid.59025.3b0000 0001 2224 0361School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371 Singapore ,grid.4280.e0000 0001 2180 6431Centre for Quantum Technologies, National University of Singapore, Singapore, 117543 Singapore
| | - Tomasz Paterek
- grid.59025.3b0000 0001 2224 0361School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371 Singapore ,grid.8585.00000 0001 2370 4076Institute of Theoretical Physics and Astrophysics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, 80-308 Gdańsk, Poland
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Lacombat F, Espagne A, Dozova N, Plaza P, Müller P, Emmerich HJ, Saft M, Essen LO. Ultrafast photoreduction dynamics of a new class of CPD photolyases. Photochem Photobiol Sci 2021; 20:733-746. [PMID: 33977513 DOI: 10.1007/s43630-021-00048-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/22/2021] [Indexed: 01/09/2023]
Abstract
NewPHL is a recently discovered subgroup of ancestral DNA photolyases. Its domain architecture displays pronounced differences from that of canonical photolyases, in particular at the level of the characteristic electron transfer chain, which is limited to merely two tryptophans, instead of the "classical" three or four. Using transient absorption spectroscopy, we show that the dynamics of photoreduction of the oxidized FAD cofactor in the NewPHL begins similarly as that in canonical photolyases, i.e., with a sub-ps primary reduction of the excited FAD cofactor by an adjacent tryptophan, followed by migration of the electron hole towards the second tryptophan in the tens of ps regime. However, the resulting tryptophanyl radical then undergoes an unprecedentedly fast deprotonation in less than 100 ps in the NewPHL. In spite of the stabilization effect of this deprotonation, almost complete charge recombination follows in two phases of ~ 950 ps and ~ 50 ns. Such a rapid recombination of the radical pair implies that the first FAD photoreduction step, i.e., conversion of the fully oxidized to the semi-quinone state, should be rather difficult in vivo. We hence suggest that the flavin chromophore likely switches only between its semi-reduced and fully reduced form in NewPHL under physiological conditions.
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Affiliation(s)
- Fabien Lacombat
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France
| | - Agathe Espagne
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France
| | - Nadia Dozova
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France
| | - Pascal Plaza
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France.
| | - Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| | - Hans-Joachim Emmerich
- Department of Chemistry, Center for Synthetic Microbiology, Philipps University, 35032, Marburg, Germany
| | - Martin Saft
- Department of Chemistry, Center for Synthetic Microbiology, Philipps University, 35032, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Center for Synthetic Microbiology, Philipps University, 35032, Marburg, Germany.
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8
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Emmerich HJ, Saft M, Schneider L, Kock D, Batschauer A, Essen LO. A topologically distinct class of photolyases specific for UV lesions within single-stranded DNA. Nucleic Acids Res 2021; 48:12845-12857. [PMID: 33270891 PMCID: PMC7736829 DOI: 10.1093/nar/gkaa1147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022] Open
Abstract
Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.
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Affiliation(s)
- Hans-Joachim Emmerich
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Martin Saft
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Leonie Schneider
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Dennis Kock
- Department of Biology, Philipps University Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Alfred Batschauer
- Department of Biology, Philipps University Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany.,Center of Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
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9
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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10
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Hosokawa Y, Sato R, Iwai S, Yamamoto J. Implications of a Water Molecule for Photoactivation of Plant (6-4) Photolyase. J Phys Chem B 2019; 123:5059-5068. [PMID: 31117614 DOI: 10.1021/acs.jpcb.9b03030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photolyases (PLs) are flavoproteins able to repair cross-links formed between adjacent pyrimidine bases in DNA in a light-dependent manner via an electron transfer. The catalytically active redox state of the flavin chromophore for the DNA repair is a fully reduced form of flavin adenine dinucleotide (FADH-). PLs and their relative, cryptochromes (CRYs), share a physicochemical process attributable to the light-dependent reduction of the chromophore via an ultrafast successive electron transfer through exclusively conserved three tryptophan side chains. In some (6-4) PLs and animal CRYs, an additional tryptophan participates in this photoactivation process. In a search for the intrinsic difference between the Trp triad and tetrad, a water molecule proximal to the second and third Trp was found in the reported crystal structure of Arabidopsis thaliana (6-4) PL. Here, we investigated the involvement of the water molecule in photoactivation. Molecular dynamics simulations indicated that the water molecule is stably captured in the binding site, while mutation of S412 increased water displacement from the binding site. Photochemical analysis of recombinant proteins revealed that the S412A mutation significantly decelerated the FAD photoreduction as compared to the wild type. The hydrogen-bonding network including the water molecule would play a key role in the stabilization of the FAD-Trp radical pair.
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Affiliation(s)
- Yuhei Hosokawa
- Division of Chemistry, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Ryuma Sato
- Center for Biosystems Dynamics Research , RIKEN , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
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11
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Lacombat F, Espagne A, Dozova N, Plaza P, Ignatz E, Kiontke S, Essen LO. Delocalized hole transport coupled to sub-ns tryptophanyl deprotonation promotes photoreduction of class II photolyases. Phys Chem Chem Phys 2018; 20:25446-25457. [PMID: 30272080 DOI: 10.1039/c8cp04548h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Class II photolyases utilize for the photoreduction of their flavin cofactor (FAD) a completely different tryptophan triad than most other photolyases and cryptochromes. To counter sped-up back electron transfer, they evolved an unusually fast deprotonation of the distal tryptophanyl radical cation (WH˙+) that is produced after excitation of the flavin. We studied the primary aspects of oxidized FAD photoreduction by ultrafast transient absorption spectroscopy, using the class II photolyase from Methanosarcina mazei. With a time constant of 9.2 ps, the initial reduction step of the excited flavin by the proximal W381 tryptophan proceeds almost twentyfold slower than in other photolyases carrying oxidized FAD, most likely because of the larger distance between the flavin and the proximal tryptophan. The thus formed W381H˙+ radical is tracked by transient anisotropy measurements to migrate in 29 ps with delocalization over several members of the tryptophan triad. This 29 ps phase also includes the decay of a small fraction of excited flavin, reacting on a slower timescale, and partial recombination of the FAD˙-/WH˙+ radical pair. A final kinetic phase in 230 ps is assigned to the deprotonation of W388H˙+ that occurs in competition with partial charge recombination. Interestingly, we show by comparison with the Y345F mutant that this last phase additionally involves oxidation of the Y345 phenolic group by W388H˙+, producing a small amount of neutral tyrosyl radical (YO˙). The rate of this electron transfer step is about six orders of magnitude faster than the corresponding oxidation of Y345 by the deprotonated W388˙ radical. Unlike conventional photolyases, where the electron hole accumulates on the distal tryptophan before the much slower tryptophanyl deprotonation, our data show that delocalized hole transport is concomitantly concluded by ultrafast deprotonation of W388H˙+.
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Affiliation(s)
- Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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12
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Antill LM, Takizawa SY, Murata S, Woodward JR. Photoinduced flavin-tryptophan electron transfer across vesicle membranes generates magnetic field sensitive radical pairs. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1524525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Lewis M. Antill
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin-ya Takizawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeru Murata
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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13
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Mao Z, Liou SH, Khadka N, Jenney FE, Goodin DB, Seefeldt LC, Adams MWW, Cramer SP, Larsen DS. Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins. Biochemistry 2018; 57:978-990. [PMID: 29303562 DOI: 10.1021/acs.biochem.7b01159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.
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Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine , Suwanee, Georgia 30024, United States
| | - David B Goodin
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Michael W W Adams
- Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
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14
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Schelvis JPM, Gindt YM. A Review of Spectroscopic and Biophysical-Chemical Studies of the Complex of Cyclobutane Pyrimidine Dimer Photolyase and Cryptochrome DASH with Substrate DNA. Photochem Photobiol 2017; 93:26-36. [PMID: 27891613 DOI: 10.1111/php.12678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/02/2016] [Indexed: 01/02/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair CPD on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, although some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical-chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH. This will be performed in the backdrop of the available X-ray crystal structures of these enzymes bound to a CPD-like lesion. These structures helped to confirm conclusions that were drawn earlier from spectroscopic and biophysical-chemical experiments, and they have a critical function as a framework to design new experiments and to interpret new experimental data. This review will show the important synergy between X-ray crystallography and spectroscopic/biophysical-chemical investigations that is essential to obtain a sufficiently detailed picture of the overall mechanism of CPD photolyases and CRY DASH proteins.
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Affiliation(s)
| | - Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ
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15
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von Zadow A, Ignatz E, Pokorny R, Essen LO, Klug G. Rhodobacter sphaeroides CryB is a bacterial cryptochrome with (6-4) photolyase activity. FEBS J 2016; 283:4291-4309. [PMID: 27739235 DOI: 10.1111/febs.13924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022]
Abstract
Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions; instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Here we present evidence for a repair activity of (6-4) photoproducts by CryB and suggest a dual character combining the functions of cryptochromes and photolyases. We investigated the effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation). Remarkably, impairment of one of the two light absorbing cofactors, FAD or 6,7-dimethyl-8-ribityllumazine, only marginally affected the final survival rate but strongly decelerated photoreactivation kinetics. The impairment of both of them together through mutagenesis decreased CryB-dependent photoreactivation to the level of the ∆cryB knockout strain. The third cofactor, a [4Fe4S] iron-sulfur cluster, is indispensable for the structural integrity of the protein. The reduction of FAD via the conserved tryptophan W338, which is crucial for in vitro reduction and consequently DNA repair, is not required for in vivo photoreactivation, suggesting that this reduction pathway to FAD is dispensable in the cellular environment. This demonstrates that in vitro experiments give only limited information on in vivo photolyase activity.
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Affiliation(s)
- Andrea von Zadow
- Institute of Microbiology and Molecular Biology, Giessen University, Germany
| | - Elisabeth Ignatz
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Germany
| | - Richard Pokorny
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps University Marburg, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Giessen University, Germany
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16
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Miller DC, Tarantino KT, Knowles RR. Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities. Top Curr Chem (Cham) 2016; 374:30. [PMID: 27573270 PMCID: PMC5107260 DOI: 10.1007/s41061-016-0030-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
Abstract
Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups.
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Affiliation(s)
- David C Miller
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Kyle T Tarantino
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Robert R Knowles
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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17
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Chia A, Górecka A, Kurzyński P, Paterek T, Kaszlikowski D. Coherent chemical kinetics as quantum walks. II. Radical-pair reactions in Arabidopsis thaliana. Phys Rev E 2016; 93:032408. [PMID: 27078391 DOI: 10.1103/physreve.93.032408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Indexed: 11/07/2022]
Abstract
We apply the quantum-walk approach proposed in the preceding paper [A. Chia et al., preceding paper, Phys. Rev. E 93, 032407 (2016)] to a radical-pair reaction where realistic estimates for the intermediate transition rates are available. The well-known average hitting time from quantum walks can be adopted as a measure of how quickly the reaction occurs and we calculate this for varying degrees of dephasing in the radical pair. The time for the radical pair to react to a product is found to be independent of the amount of dephasing introduced, even in the limit of no dephasing where the transient population dynamics exhibits strong coherent oscillations. This can be seen to arise from the existence of a rate-limiting step in the reaction and we argue that in such examples, a purely classical model based on rate equations can be used for estimating the time scale of the reaction but not necessarily its population dynamics.
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Affiliation(s)
- A Chia
- Centre for Quantum Technologies, National University of Singapore, Singapore
| | - A Górecka
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - P Kurzyński
- Centre for Quantum Technologies, National University of Singapore, Singapore.,Faculty of Physics, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - T Paterek
- Centre for Quantum Technologies, National University of Singapore, Singapore.,Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - D Kaszlikowski
- Centre for Quantum Technologies, National University of Singapore, Singapore
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18
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Müller P, Brettel K, Grama L, Nyitrai M, Lukacs A. Photochemistry of Wild-Type and N378D Mutant E. coli DNA Photolyase with Oxidized FAD Cofactor Studied by Transient Absorption Spectroscopy. Chemphyschem 2016; 17:1329-40. [PMID: 26852903 DOI: 10.1002/cphc.201501077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/02/2023]
Abstract
DNA photolyases (PLs) and evolutionarily related cryptochrome (CRY) blue-light receptors form a widespread superfamily of flavoproteins involved in DNA photorepair and signaling functions. They share a flavin adenine dinucleotide (FAD) cofactor and an electron-transfer (ET) chain composed typically of three tryptophan residues that connect the flavin to the protein surface. Four redox states of FAD are relevant for the various functions of PLs and CRYs: fully reduced FADH(-) (required for DNA photorepair), fully oxidized FADox (blue-light-absorbing dark state of CRYs), and the two semireduced radical states FAD(.-) and FADH(.) formed in ET reactions. The PL of Escherichia coli (EcPL) has been studied for a long time and is often used as a reference system; however, EcPL containing FADox has so far not been investigated on all relevant timescales. Herein, a detailed transient absorption study of EcPL on timescales from nanoseconds to seconds after excitation of FADox is presented. Wild-type EcPL and its N378D mutant, in which the asparagine facing the N5 of the FAD isoalloxazine is replaced by aspartic acid, known to protonate FAD(.-) (formed by ET from the tryptophan chain) in plant CRYs in about 1.5 μs, are characterized. Surprisingly, the mutant protein does not show this protonation. Instead, FAD(.-) is converted in 3.3 μs into a state with spectral features that are different from both FADH(.) and FAD(.-) . Such a conversion does not occur in wild-type EcPL. The chemical nature and formation mechanism of the atypical FAD radical in N378D mutant EcPL are discussed.
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Affiliation(s)
- Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Laszlo Grama
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary
| | - Miklos Nyitrai
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary.
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19
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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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20
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Abstract
It was recently demonstrated that in ferric myoglobins (Mb) the fluorescence quenching of the photoexcited tryptophan 14 (*Trp(14)) residue is in part due to an electron transfer to the heme porphyrin (porph), turning it to the ferrous state. However, the invariance of *Trp decay times in ferric and ferrous Mbs raises the question as to whether electron transfer may also be operative in the latter. Using UV pump/visible probe transient absorption, we show that this is indeed the case for deoxy-Mb. We observe that the reduction generates (with a yield of about 30%) a low-valence Fe-porphyrin π [Fe(II)(porph(●-))] -anion radical, which we observe for the first time to our knowledge under physiological conditions. We suggest that the pathway for the electron transfer proceeds via the leucine 69 (Leu(69)) and valine 68 (Val(68)) residues. The results on ferric Mbs and the present ones highlight the generality of Trp-porphyrin electron transfer in heme proteins.
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21
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Wang J, Du X, Pan W, Wang X, Wu W. Photoactivation of the cryptochrome/photolyase superfamily. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2015. [DOI: 10.1016/j.jphotochemrev.2014.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Wang H, Chen X, Fang W. Excited-state proton coupled electron transfer between photolyase and the damaged DNA through water wire: a photo-repair mechanism. Phys Chem Chem Phys 2014; 16:25432-41. [PMID: 25341360 DOI: 10.1039/c4cp04130e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photolyase enzyme absorbs blue light to repair damaged DNA through a cyclic electron transfer reaction. A description of the underlying mechanism has proven to be a challenging issue for both experimental and theoretical studies. In the present work, combined CASPT2//CASSCF/AMBER (QM/MM) calculations have been performed for damaged DNA in photolyase. A proton-coupled electron transfer (PCET) mechanism has been determined for restoring cyclobutane pyrimidine dimer (CPD) to two normal thymine bases by irradiation of photolyase. A well-defined water wire between FADH(-) and CPD was determined as a bridge to assist the PCET process within FADH(-) and thereby trigger the forward electron transfer to CPD. The subsequent CPD splitting and the alternation of the H-bond pattern proceed in a concerted way, which makes the productive backward electron transfer occur on an ultrafast timescale. A local minimum of SCT((1)ππ*)-LMin was identified on the pathway of the futile backward electron transfer (BET), which is stabilized by the strong H-bond interaction between the water wire and CPD. As a result, the futile BET process is endothermic by ∼18.0 kcal mol(-1), which is responsible for a 2.4 ns timescale inferred experimentally for the futile BET process. Besides the unbiased interpretation for the majority of the experimental findings, the present study provides a new excited-state PCET mechanism, which leads to a significant step toward a deeper understanding of the photo-repair process of damaged-DNA by the photolyase enzyme.
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Affiliation(s)
- Hongjuan Wang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, China.
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23
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Abstract
Flavoproteins often employ radical mechanisms in their enzymatic reactions. This involves paramagnetic species, which can ideally be investigated with electron paramagnetic resonance (EPR) spectroscopy. In this chapter we focus on the example of flavin-based photoreceptors and discuss, how different EPR methods have been used to extract information about the flavin radical's electronic state, its binding pocket, electron-transfer pathways, and about the protein's tertiary and quaternary structure.
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Affiliation(s)
- Richard Brosi
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany,
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24
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Evans EW, Dodson CA, Maeda K, Biskup T, Wedge CJ, Timmel CR. Magnetic field effects in flavoproteins and related systems. Interface Focus 2013; 3:20130037. [PMID: 24511388 PMCID: PMC3915827 DOI: 10.1098/rsfs.2013.0037] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Within the framework of the radical pair mechanism, magnetic fields may alter the rate and yields of chemical reactions involving spin-correlated radical pairs as intermediates. Such effects have been studied in detail in a variety of chemical systems both experimentally and theoretically. In recent years, there has been growing interest in whether such magnetic field effects (MFEs) also occur in biological systems, a question driven most notably by the increasing body of evidence for the involvement of such effects in the magnetic compass sense of animals. The blue-light photoreceptor cryptochrome is placed at the centre of this debate and photoexcitation of its bound flavin cofactor has indeed been shown to result in the formation of radical pairs. Here, we review studies of MFEs on free flavins in model systems as well as in blue-light photoreceptor proteins and discuss the properties that are crucial in determining the magnetosensitivity of these systems.
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Affiliation(s)
- Emrys W. Evans
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Charlotte A. Dodson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Kiminori Maeda
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Till Biskup
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - C. J. Wedge
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
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25
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Lüdemann G, Woiczikowski PB, Kubař T, Elstner M, Steinbrecher TB. Charge transfer in E. coli DNA photolyase: understanding polarization and stabilization effects via QM/MM simulations. J Phys Chem B 2013; 117:10769-78. [PMID: 23964783 DOI: 10.1021/jp406319b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We study fast hole transfer events in E. coli DNA photolyase, a key step in the photoactivation process, using a multiscale computational method that combines nonadiabatic propagation schemes and linear-scaling quantum chemical methods with molecular mechanics force fields. This scheme allows us to follow the time-dependent evolution of the electron hole in an unbiased fashion; that is, no assumptions about hole wave function localization, time scale separation, or adiabaticity of the process have to be made beforehand. DNA photolyase facilitates an efficient long-range charge transport between its flavin adenine dinucleotide (FAD) cofactor and the protein surface via a chain of evolutionary conserved Trp residues on the sub-nanosecond time scale despite the existence of multiple potential trap states. By including a large number of aromatic residues along the charge transfer pathway into the quantum description, we are able to identify the main pathway among alternative possible routes. The simulations show that charge transfer, which is extremely fast in this protein, occurs on the same time scale as the protein response to the electrostatic changes; that is, time-scale separation as often presupposed in charge transfer studies seems to be inappropriate for this system. Therefore, coupled equations of motion, which propagate electrons and nuclei simultaneously, appear to be necessary. The applied computational model is shown to capture the essentials of the reaction kinetics and thermodynamics while allowing direct simulations of charge transfer events on their natural time scale.
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Affiliation(s)
- Gesa Lüdemann
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology , Kaiserstr. 12, 76131 Karlsruhe, Germany
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26
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Dodson CA, Hore PJ, Wallace MI. A radical sense of direction: signalling and mechanism in cryptochrome magnetoreception. Trends Biochem Sci 2013; 38:435-46. [PMID: 23938034 DOI: 10.1016/j.tibs.2013.07.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 10/26/2022]
Abstract
The remarkable phenomenon of magnetoreception in migratory birds and other organisms has fascinated biologists for decades. Much evidence has accumulated to suggest that birds sense the magnetic field of the Earth using photochemical transformations in cryptochrome flavoproteins. In the last 5 years this highly interdisciplinary field has seen advances in structural biology, biophysics, spin chemistry, and genetic studies in model organisms. We review these developments and consider how this chemical signal can be integrated into the cellular response.
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Affiliation(s)
- Charlotte A Dodson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK.
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27
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Benjdia A. DNA photolyases and SP lyase: structure and mechanism of light-dependent and independent DNA lyases. Curr Opin Struct Biol 2012; 22:711-20. [PMID: 23164663 DOI: 10.1016/j.sbi.2012.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/30/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
Abstract
Light is essential for many critical biological processes including vision, circadian rhythms, photosynthesis and DNA repair. DNA photolyases use light energy and a fully reduced flavin cofactor to repair the major UV-induced DNA damages, the cis-syn cyclobutane pyrimidine dimers (CPDs) and the pyrimidine-pyrimidone (6-4) photoproducts. Catalysis involves two photoreactions, the photoactivation which leads to the conversion of the flavin cofactor to its catalytic active form and the photorepair whose efficiency depends on a light-harvesting antenna chromophore. Very interestingly, an alternative and light-independent direct reversal mechanism to repair a distinct photolesion is found in bacterial spores, catalyzed by spore photoproduct lyase. This radical SAM enzyme uses an iron-sulfur cluster and S-adenosyl-l-methionine (SAM) to split a specific photoproduct, the so-called spore photoproduct (SP), back to two thymidine residues. The recently solved crystal structure of SP lyase provides new insights into this unique DNA repair mechanism and allows a detailed comparison with DNA photolyases. Similarities as well as divergences between DNA photolyases and SP lyase are highlighted in this review.
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Affiliation(s)
- Alhosna Benjdia
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany.
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28
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Magnetically sensitive light-induced reactions in cryptochrome are consistent with its proposed role as a magnetoreceptor. Proc Natl Acad Sci U S A 2012; 109:4774-9. [PMID: 22421133 DOI: 10.1073/pnas.1118959109] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among the biological phenomena that fall within the emerging field of "quantum biology" is the suggestion that magnetically sensitive chemical reactions are responsible for the magnetic compass of migratory birds. It has been proposed that transient radical pairs are formed by photo-induced electron transfer reactions in cryptochrome proteins and that their coherent spin dynamics are influenced by the geomagnetic field leading to changes in the quantum yield of the signaling state of the protein. Despite a variety of supporting evidence, it is still not clear whether cryptochromes have the properties required to respond to magnetic interactions orders of magnitude weaker than the thermal energy, k(B)T. Here we demonstrate that the kinetics and quantum yields of photo-induced flavin-tryptophan radical pairs in cryptochrome are indeed magnetically sensitive. The mechanistic origin of the magnetic field effect is clarified, its dependence on the strength of the magnetic field measured, and the rates of relevant spin-dependent, spin-independent, and spin-decoherence processes determined. We argue that cryptochrome is fit for purpose as a chemical magnetoreceptor.
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29
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Solov'yov IA, Schulten K. Reaction kinetics and mechanism of magnetic field effects in cryptochrome. J Phys Chem B 2012; 116:1089-99. [PMID: 22171949 PMCID: PMC3266978 DOI: 10.1021/jp209508y] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Creatures as varied as mammals, fish, insects, reptiles, and birds have an intriguing sixth sense that allows them to orient themselves in the Earth's magnetic field. Despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically sensitive radical pair reactions occurring in the retina, the light-sensitive part of animal eyes. A photoreceptor, cryptochrome, has been suggested to endow birds with magnetoreceptive abilities as the protein has been shown to exhibit the biophysical properties required for an animal magnetoreceptor to operate properly. Here, we propose a theoretical analysis method for identifying cryptochrome's signaling reactions involving comparison of measured and calculated reaction kinetics in cryptochrome. Application of the method yields an exemplary light-driven reaction cycle, supported through transient absorption and electron-spin-resonance observations together with known facts on avian magnetoreception. The reaction cycle permits one to predict magnetic field effects on cryptochrome activation and deactivation. The suggested analysis method gives insight into structural and dynamic design features required for optimal detection of the geomagnetic field by cryptochrome and suggests further experimental and theoretical studies.
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30
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Oberpichler I, Pierik AJ, Wesslowski J, Pokorny R, Rosen R, Vugman M, Zhang F, Neubauer O, Ron EZ, Batschauer A, Lamparter T. A photolyase-like protein from Agrobacterium tumefaciens with an iron-sulfur cluster. PLoS One 2011; 6:e26775. [PMID: 22066008 PMCID: PMC3204975 DOI: 10.1371/journal.pone.0026775] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/03/2011] [Indexed: 01/08/2023] Open
Abstract
Photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. While photolyases can repair UV-induced DNA lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. Here we report about two photolyase-related proteins, named PhrA and PhrB, found in the phytopathogen Agrobacterium tumefaciens. PhrA belongs to the class III cyclobutane pyrimidine dimer (CPD) photolyases, the sister class of plant cryptochromes, while PhrB belongs to a new class represented in at least 350 bacterial organisms. Both proteins contain flavin adenine dinucleotide (FAD) as a primary catalytic cofactor, which is photoreduceable by blue light. Spectral analysis of PhrA confirmed the presence of 5,10-methenyltetrahydrofolate (MTHF) as antenna cofactor. PhrB comprises also an additional chromophore, absorbing in the short wavelength region but its spectrum is distinct from known antenna cofactors in other photolyases. Homology modeling suggests that PhrB contains an Fe-S cluster as cofactor which was confirmed by elemental analysis and EPR spectroscopy. According to protein sequence alignments the classical tryptophan photoreduction pathway is present in PhrA but absent in PhrB. Although PhrB is clearly distinguished from other photolyases including PhrA it is, like PhrA, required for in vivo photoreactivation. Moreover, PhrA can repair UV-induced DNA lesions in vitro. Thus, A. tumefaciens contains two photolyase homologs of which PhrB represents the first member of the cryptochrome/photolyase family (CPF) that contains an iron-sulfur cluster.
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Affiliation(s)
- Inga Oberpichler
- Karlsruhe Institute of Technology, Botany I, Karlsruhe, Germany.
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31
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Woiczikowski PB, Steinbrecher T, Kubař T, Elstner M. Nonadiabatic QM/MM Simulations of Fast Charge Transfer in Escherichia coli DNA Photolyase. J Phys Chem B 2011; 115:9846-63. [DOI: 10.1021/jp204696t] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Benjamin Woiczikowski
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
| | - Thomas Steinbrecher
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
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32
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Zieba AA, Richardson C, Lucero C, Dieng SD, Gindt YM, Schelvis JPM. Evidence for concerted electron proton transfer in charge recombination between FADH- and 306Trp• in Escherichia coli photolyase. J Am Chem Soc 2011; 133:7824-36. [PMID: 21534528 DOI: 10.1021/ja2001488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proton-coupled electron-transfer (PCET) is a mechanism of great importance in protein electron transfer and enzyme catalysis, and the involvement of aromatic amino acids in this process is of much interest. The DNA repair enzyme photolyase provides a natural system that allows for the study of PCET using a neutral radical tryptophan (Trp(•)). In Escherichia coli photolyase, photoreduction of the flavin adenine dinucleotide (FAD) cofactor in its neutral radical semiquinone form (FADH(•)) results in the formation of FADH(-) and (306)Trp(•). Charge recombination between these two intermediates requires the uptake of a proton by (306)Trp(•). The rate constant of charge recombination has been measured as a function of temperature in the pH range from 5.5 to 10.0, and the data are analyzed with both classical Marcus and semi-classical Hopfield electron transfer theory. The reorganization energy associated with the charge recombination process shows a pH dependence ranging from 2.3 eV at pH ≤ 7 and 1.2 eV at pH(D) 10.0. These findings indicate that at least two mechanisms are involved in the charge recombination reaction. Global analysis of the data supports the hypothesis that PCET during charge recombination can follow two different mechanisms with an apparent switch around pH 6.5. At lower pH, concerted electron proton transfer (CEPT) is the favorable mechanism with a reorganization energy of 2.1-2.3 eV. At higher pH, a sequential mechanism becomes dominant with rate-limiting electron-transfer followed by proton uptake which has a reorganization energy of 1.0-1.3 eV. The observed 'inverse' deuterium isotope effect at pH < 8 can be explained by a solvent isotope effect that affects the free energy change of the reaction and masks the normal, mass-related kinetic isotope effect that is expected for a CEPT mechanism. To the best of our knowledge, this is the first time that a switch in PCET mechanism has been observed in a protein.
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Affiliation(s)
- Agnieszka A Zieba
- Department of Chemistry and Biochemistry, Montclair State University, 1 Normal Avenue, Montclair, New Jersey 07043, USA
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Bonin J, Costentin C, Louault C, Robert M, Savéant JM. Water (in water) as an intrinsically efficient proton acceptor in concerted proton electron transfers. J Am Chem Soc 2011; 133:6668-74. [PMID: 21476550 DOI: 10.1021/ja110935c] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxidation of PhOH in water by photochemically generated Ru(III)(bpy)(3) is taken as prototypal example disclosing the special character of water, in the solvent water, as proton acceptor in concerted proton-electron transfer reactions. The variation of the rate constant with temperature and driving force, as well as the variation of the H/D kinetic isotope effect with temperature, allowed the determination of the reaction mechanism characterized by three intrinsic parameters, the reorganization energy, a pre-exponential factor measuring the vibronic coupling of electronic states at equilibrium distance, and a distance-sensitivity parameter. Analysis of these characteristics and comparison with a standard base, hydrogen phosphate, revealed that electron transfer is concerted with a Grotthus-type proton translocation, leading to a charge delocalized over a cluster involving several water molecules. A mechanism is thus uncovered that may help in understanding how protons could be transported along water chains over large distances in concert with electron transfer in biological systems.
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Affiliation(s)
- Julien Bonin
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université - CNRS No 7591, Université Paris Diderot, Bâtiment Lavoisier, 15 rue Jean de Baïf, 75205 Paris Cedex 13, France
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Heijde M, Zabulon G, Corellou F, Ishikawa T, Brazard J, Usman A, Sanchez F, Plaza P, Martin M, Falciatore A, Todo T, Bouget FY, Bowler C. Characterization of two members of the cryptochrome/photolyase family from Ostreococcus tauri provides insights into the origin and evolution of cryptochromes. PLANT, CELL & ENVIRONMENT 2010; 33:1614-1626. [PMID: 20444223 DOI: 10.1111/j.1365-3040.2010.02168.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cryptochromes (Crys) are blue light receptors believed to have evolved from the DNA photolyase protein family, implying that light control and light protection share a common ancient origin. In this paper, we report the identification of five genes of the Cry/photolyase family (CPF) in two green algae of the Ostreococcus genus. Phylogenetic analyses were used to confidently assign three of these sequences to cyclobutane pyrimidine dimer (CPD) photolyases, one of them to a DASH-type Cry, and a third CPF gene has high homology with the recently described diatom CPF1 that displays a bifunctional activity. Both purified OtCPF1 and OtCPF2 proteins show non-covalent binding to flavin adenine dinucleotide (FAD), and additionally to 5,10-methenyl-tetrahydrofolate (MTHF) for OtCPF2. Expression analyses revealed that all five CPF members of Ostreococcus tauri are regulated by light. Furthermore, we show that OtCPF1 and OtCPF2 display photolyase activity and that OtCPF1 is able to interact with the CLOCK:BMAL heterodimer, transcription factors regulating circadian clock function in other organisms. Finally, we provide evidence for the involvement of OtCPF1 in the maintenance of the Ostreococcus circadian clock. This work improves our understanding of the evolutionary transition between photolyases and Crys.
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Affiliation(s)
- Marc Heijde
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, CNRS UMR 8197, Paris, F-75005 France
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Brettel K, Byrdin M. Reaction mechanisms of DNA photolyase. Curr Opin Struct Biol 2010; 20:693-701. [PMID: 20705454 DOI: 10.1016/j.sbi.2010.07.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH° occur in overall 1ns. Whereas the kinetics of FADH° was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH° to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.
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Affiliation(s)
- Klaus Brettel
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, 91191 Gif-sur-Yvette, France.
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Weber S, Biskup T, Okafuji A, Marino AR, Berthold T, Link G, Hitomi K, Getzoff ED, Schleicher E, Norris JR. Origin of light-induced spin-correlated radical pairs in cryptochrome. J Phys Chem B 2010; 114:14745-54. [PMID: 20684534 DOI: 10.1021/jp103401u] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Blue-light excitation of cryptochromes and homologues uniformly triggers electron transfer (ET) from the protein surface to the flavin adenine dinucleotide (FAD) cofactor. A cascade of three conserved tryptophan residues has been considered to be critically involved in this photoreaction. If the FAD is initially in its fully oxidized (diamagnetic) redox state, light-induced ET via the tryptophan triad generates a series of short-lived spin-correlated radical pairs comprising an FAD radical and a tryptophan radical. Coupled doublet-pair species of this type have been proposed as the basis, for example, of a biological magnetic compass in migratory birds, and were found critical for some cryptochrome functions in vivo. In this contribution, a cryptochrome-like protein (CRYD) derived from Xenopus laevis has been examined as a representative system. The terminal radical-pair state FAD(•)···W324(•) of X. laevis CRYD has been characterized in detail by time-resolved electron-paramagnetic resonance (TREPR) at X-band microwave frequency (9.68 GHz) and magnetic fields around 345 mT, and at Q-band (34.08 GHz) at around 1215 mT. Different precursor states, singlet versus triplet, of radical-pair formation have been considered in spectral simulations of the experimental electron-spin polarized TREPR signals. Conclusively, we present evidence for a singlet-state precursor of FAD(•)···W324(•) radical-pair generation because at both magnetic fields, where radical pairs were studied by TREPR, net-zero electron-spin polarization has been detected. Neither a spin-polarized triplet precursor nor a triplet at thermal equilibrium can explain such an electron-spin polarization. It turns out that a two-microwave-frequency TREPR approach is essential to draw conclusions on the nature of the precursor electronic states in light-induced spin-correlated radical pair formations.
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Affiliation(s)
- Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.
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Light-induced activation of class II cyclobutane pyrimidine dimer photolyases. DNA Repair (Amst) 2010; 9:495-505. [PMID: 20227927 DOI: 10.1016/j.dnarep.2010.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/16/2010] [Accepted: 01/19/2010] [Indexed: 11/23/2022]
Abstract
Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution.
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Brazard J, Usman A, Lacombat F, Ley C, Martin MM, Plaza P, Mony L, Heijde M, Zabulon G, Bowler C. Spectro−Temporal Characterization of the Photoactivation Mechanism of Two New Oxidized Cryptochrome/Photolyase Photoreceptors. J Am Chem Soc 2010; 132:4935-45. [DOI: 10.1021/ja1002372] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johanna Brazard
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Anwar Usman
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Fabien Lacombat
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Christian Ley
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Monique M. Martin
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Pascal Plaza
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Laetitia Mony
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Marc Heijde
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Gérald Zabulon
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
| | - Chris Bowler
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France, UMR 8601 CNRS, Laboratoire de Chimie et Biochimie Pharmacologies et Toxicologiques, Université Paris Descartes, 12 rue de l’Ecole de médecine, 75006 Paris, France, and UMR 8186 CNRS-ENS, Département de Biologie, Ecole Normale Supérieure, 46 rue d’Ulm, 75005 Paris, France
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Maeda K, Robinson AJ, Henbest KB, Dell EJ, Timmel CR. Protein surface interactions probed by magnetic field effects on chemical reactions. J Am Chem Soc 2010; 132:1466-7. [PMID: 20085319 DOI: 10.1021/ja908988u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we have employed the effects of weak static magnetic fields (not exceeding 46 mT) on radical recombination reactions to investigate protein-substrate interactions. Pulsed laser excitation of an aqueous solution of anthraquinone-2,6-disulfonate (AQDS(2-)) and either hen egg white lysozyme (HEWL) or bovine serum albumin (BSA) produces the triplet state of the radical pair (T)[AQDS(3-*) Trp(*)] by a photoinduced electron transfer reaction from tryptophan residues. Time-resolved absorption techniques were employed to study the recombination characteristics of these radical pairs at different static magnetic fields and ionic strengths. The experimental data in connection with the simulated curves unequivocally show that the radical pair has a lifetime of the order of microseconds in both systems (HEWL and BSA). However, the radical pair is embedded within a binding pocket of the BSA protein, while the (otherwise identical) radical pair, being subject to attractive Coulomb forces, resides on the protein surface in the HEWL system.
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Affiliation(s)
- Kiminori Maeda
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
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41
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Intrinsic reactivity and driving force dependence in concerted proton-electron transfers to water illustrated by phenol oxidation. Proc Natl Acad Sci U S A 2010; 107:3367-72. [PMID: 20139306 DOI: 10.1073/pnas.0914693107] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three experimental techniques, laser flash photolysis, redox catalysis, and stopped-flow, were used to investigate the variation of the oxidation rate constant of phenol in neat water with the driving force offered by a series of electron acceptors. Taking into account a result previously obtained with a low-driving force electron acceptor thus allowed scanning more than half an electron-volt driving force range. Variation of the rate constant with pH showed the transition between a direct phenol oxidation reaction at low pH, where the rate constant does not vary with pH, and a stepwise reaction involving the prior deprotonation of phenol by OH(-), characterized by a unity-slope variation. Analyses of the direct oxidation kinetics, based on its variation with the driving force and on the determination of H/D isotope effects, ruled out a stepwise mechanism in which electron transfer is followed by the deprotonation of the initial cation radical at the benefit of a pathway in which proton and electron are transferred concertedly. Derivation of the characteristics of counterdiffusion in termolecular reactions allowed showing that the concerted process is under activation control. It is characterized by a remarkably small reorganization energy, in line with the electrochemical counterpart of the reaction, underpinning the very peculiar behavior of water as proton acceptor when it is used as the solvent.
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42
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Thiagarajan V, Villette S, Espagne A, Eker APM, Brettel K, Byrdin M. DNA Repair by Photolyase: A Novel Substrate with Low Background Absorption around 265 nm for Transient Absorption Studies in the UV. Biochemistry 2009; 49:297-303. [DOI: 10.1021/bi901562a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Viruthachalam Thiagarajan
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Sandrine Villette
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Agathe Espagne
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Andre P. M. Eker
- Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Klaus Brettel
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Martin Byrdin
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
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Byrdin M, Lukacs A, Thiagarajan V, Eker APM, Brettel K, Vos MH. Quantum Yield Measurements of Short-Lived Photoactivation Intermediates in DNA Photolyase: Toward a Detailed Understanding of the Triple Tryptophan Electron Transfer Chain. J Phys Chem A 2009; 114:3207-14. [DOI: 10.1021/jp9093589] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Byrdin
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, Gif sur Yvette, F-91191, France, CNRS, URA2096, Gif sur Yvette, F-91191, France, Laboratoire d’Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France, INSERM U696, F-91128 Palaiseau, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Andras Lukacs
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, Gif sur Yvette, F-91191, France, CNRS, URA2096, Gif sur Yvette, F-91191, France, Laboratoire d’Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France, INSERM U696, F-91128 Palaiseau, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Viruthachalam Thiagarajan
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, Gif sur Yvette, F-91191, France, CNRS, URA2096, Gif sur Yvette, F-91191, France, Laboratoire d’Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France, INSERM U696, F-91128 Palaiseau, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - André P. M. Eker
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, Gif sur Yvette, F-91191, France, CNRS, URA2096, Gif sur Yvette, F-91191, France, Laboratoire d’Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France, INSERM U696, F-91128 Palaiseau, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Klaus Brettel
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, Gif sur Yvette, F-91191, France, CNRS, URA2096, Gif sur Yvette, F-91191, France, Laboratoire d’Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France, INSERM U696, F-91128 Palaiseau, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Marten H. Vos
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, Gif sur Yvette, F-91191, France, CNRS, URA2096, Gif sur Yvette, F-91191, France, Laboratoire d’Optique et Biosciences, CNRS, Ecole Polytechnique, F-91128 Palaiseau, France, INSERM U696, F-91128 Palaiseau, France, and Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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The electrochemical approach to concerted proton--electron transfers in the oxidation of phenols in water. Proc Natl Acad Sci U S A 2009; 106:18143-8. [PMID: 19822746 DOI: 10.1073/pnas.0910065106] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Establishing mechanisms and intrinsic reactivity in the oxidation of phenol with water as the proton acceptor is a fundamental task relevant to many reactions occurring in natural systems. Thanks to the easy measure of the reaction kinetics by the current and the setting of the driving force by the electrode potential, the electrochemical approach is particularly suited to this endeavor. Despite challenging difficulties related to self-inhibition blocking the electrode surface, experimental conditions were established that allowed a reliable analysis of the thermodynamics and mechanisms of the proton-coupled electron-transfer oxidation of phenol to be carried out by means of cyclic voltammetry. The thermodynamic characterization was conducted in buffer media whereas the mechanisms were revealed in unbuffered water. Unambiguous evidence of a concerted proton-electron transfer mechanism, with water as proton acceptor, was thus gathered by simulation of the experimental data with appropriately derived theoretical relationships, leading to the determination of a remarkably large intrinsic rate constant. The same strategy also allowed the quantitative analysis of the competition between the concerted proton-electron transfer pathway and an OH(-)-triggered stepwise pathway (proton transfer followed by electron transfer) at high pHs. Investigation of the passage between unbuffered and buffered media with the example of the PO(4)H(2)(-)/PO(4)H(2-) couple revealed the prevalence of a mechanism involving a proton transfer preceding an electron transfer over a PO(4)H(2-)-triggered concerted process.
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Schleicher E, Bittl R, Weber S. New roles of flavoproteins in molecular cell biology: Blue-light active flavoproteins studied by electron paramagnetic resonance. FEBS J 2009; 276:4290-303. [DOI: 10.1111/j.1742-4658.2009.07141.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Concerted proton-coupled electron transfers in aquo/hydroxo/oxo metal complexes: electrochemistry of [OsII(bpy)2py(OH2)]2+ in water. Proc Natl Acad Sci U S A 2009; 106:11829-36. [PMID: 19584254 DOI: 10.1073/pnas.0905020106] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinetic analysis of the successive oxidative cyclic voltammetric responses of [Os(II)(bpy)(2)py(OH(2))](2+) in buffered water, together with determination of H/D isotope effects, has allowed the determination of the mechanisms of the successive proton-coupled electron transfers that convert the Os(II)-aquo complex into the Os(III)-hydroxo complex and the later into the Os(IV)-oxo complex. The stepwise pathways prevail over the concerted pathway in the first case. However, very large concentrations of a base, such as acetate, trigger the beginning of a concerted reaction. The same trend appears, but to a much larger extent, when high local concentration of carboxylates are attached close to the Os complex. The Os(III)-hydroxo/Os(IV)-oxo couple is globally much slower and concerted pathways predominate over the stepwise pathways. Water is, however, not an appropriate proton acceptor in this respect. Other bases, such as citrate or phosphate, are instead quite effective for triggering concerted pathways. Here, we suggest factors causing these contrasting behaviors, providing a practical illustration of the prediction that concerted processes are an efficient way of avoiding high-energy intermediates. Observation of a strong decelerating effect of inactive ions together with the positive role of high local concentrations of carboxylates to initiate a concerted route underscores the variety of structural and medium factors that may operate to modulate and control the occurrence of concerted pathways. These demonstrations and analyses of the occurrence of concerted pathways in an aquo-hydroxo-oxo series are expected to serve as guidelines for studies in term of methodology and factor analysis.
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47
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Cryptochrome mediates light-dependent magnetosensitivity of Drosophila's circadian clock. PLoS Biol 2009; 7:e1000086. [PMID: 19355790 PMCID: PMC2667543 DOI: 10.1371/journal.pbio.1000086] [Citation(s) in RCA: 397] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 03/03/2009] [Indexed: 11/20/2022] Open
Abstract
Since 1960, magnetic fields have been discussed as Zeitgebers for circadian clocks, but the mechanism by which clocks perceive and process magnetic information has remained unknown. Recently, the radical-pair model involving light-activated photoreceptors as magnetic field sensors has gained considerable support, and the blue-light photoreceptor cryptochrome (CRY) has been proposed as a suitable molecule to mediate such magnetosensitivity. Since CRY is expressed in the circadian clock neurons and acts as a critical photoreceptor of Drosophila's clock, we aimed to test the role of CRY in magnetosensitivity of the circadian clock. In response to light, CRY causes slowing of the clock, ultimately leading to arrhythmic behavior. We expected that in the presence of applied magnetic fields, the impact of CRY on clock rhythmicity should be altered. Furthermore, according to the radical-pair hypothesis this response should be dependent on wavelength and on the field strength applied. We tested the effect of applied static magnetic fields on the circadian clock and found that flies exposed to these fields indeed showed enhanced slowing of clock rhythms. This effect was maximal at 300 μT, and reduced at both higher and lower field strengths. Clock response to magnetic fields was present in blue light, but absent under red-light illumination, which does not activate CRY. Furthermore, cryb and cryOUT mutants did not show any response, and flies overexpressing CRY in the clock neurons exhibited an enhanced response to the field. We conclude that Drosophila's circadian clock is sensitive to magnetic fields and that this sensitivity depends on light activation of CRY and on the applied field strength, consistent with the radical pair mechanism. CRY is widespread throughout biological systems and has been suggested as receptor for magnetic compass orientation in migratory birds. The present data establish the circadian clock of Drosophila as a model system for CRY-dependent magnetic sensitivity. Furthermore, given that CRY occurs in multiple tissues of Drosophila, including those potentially implicated in fly orientation, future studies may yield insights that could be applicable to the magnetic compass of migratory birds and even to potential magnetic field effects in humans. Magnetic fields influence endogenous clocks controlling the sleep–wake cycle of animals, but the underyling mechanisms are unclear. Birds that can do magnetic compass orientation also depend on light, and the blue-light photopigment cryptochrome was proposed to act as a navigational magnetosensor. Here we tested the role of cryptochrome as a light-dependent magnetosensor of the clock in the fruit fly Drosophila melanogaster. In wild-type flies we found that constant magnetic fields slowed down the speed of the clock in a dose-dependent manner—but only in the presence of blue light. In mutants lacking functional cryptochrome, the magnetic fields had no significant effects on the endogenous clock, whereas the effects were enhanced after overexpression of cryptochrome. Our data suggest that cryptochrome works as a magnetosensor in the endogenous clock when it is excited by blue light. Our work supports previous data showing that fruit flies need functional cryptochrome to perceive a magnetic field, demonstrating that the interaction of cryptochome and magnetic fields are not just for the birds. The molecular clock of the fruit fly is sensitive to magnetic fields in a manner dependent on blue light and the photopigment cryptochrome.
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Usman A, Brazard J, Martin MM, Plaza P, Heijde M, Zabulon G, Bowler C. Spectroscopic characterization of a (6-4) photolyase from the green alga Ostreococcus tauri. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:38-48. [PMID: 19427226 DOI: 10.1016/j.jphotobiol.2009.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 03/10/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022]
Abstract
The cofactor content of OtCPF1, a (6-4) photolyase isolated from the green marine alga Ostreococcus tauri, was characterized by steady-state absorption and fluorescence spectroscopy. The heterologously expressed, GST-fused, purified protein (MW: 89kDa) is non-covalently bound to flavin adenine dinucleotide (FAD), with a flavin to apoprotein molecular ratio of 64%. No light-harvesting chromophore was found in this protein. In freshly purified OtCPF1, FAD is present in three different redox states: the fully oxidized form (FAD(ox), 82%), the neutral semiquinone (FADH*, 14%) and the fully reduced anion (FADH-, 4%). Keeping the sample in the dark, at 5 degrees C, yields oxidation of FADH* and FADH-, partial release of FAD to the solution and slow degradation of the protein. Upon steady-state blue-light irradiation of OtCPF1 at 450nm, photoreduction processes leading to an accumulation of stable FADH* and FADH- species are observed. We demonstrate that this accumulation is due to the presence of an external electron donor agent in the purification buffer. Composition changes observed under steady-state photoexcitation are interpreted in terms of photoinduced reductions of FAD(ox) and FADH* states and competitive back reactions. Specific irradiation by red light at 620 nm shows both photoreduction of FADH* to FADH- and irreversible oxidation of FADH* to FAD(ox). The photoinduced oxidation reaction is believed to be indirectly caused by the external donor agent present in the buffer. Photoexcitation is also shown to stabilize the binding of FAD to the protein. We suggest this effect to be due to slight changes in the protein conformation, possibly strengthening the hydrogen-bonding network surrounding FAD.
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Affiliation(s)
- Anwar Usman
- UMR 8640 CNRS-ENS-UPMC, Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, Paris, France
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Ultrafast catalytic processes and conformational changes in the light-driven enzyme protochlorophyllide oxidoreductase (POR). Biochem Soc Trans 2009; 37:387-91. [DOI: 10.1042/bst0370387] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The enzyme POR (protochlorophyllide oxidoreductase), from the family of alcohol dehydrogenases, reduces protochlorophyllide into chlorophyllide on the absorption of light. The reduction involves the transfer of two protons and two electrons and is an important regulatory step in the biosynthesis of chlorophyll. In recent years, due to the availability of large quantities of the pure enzyme, much of the catalytic reaction has been unravelled by using a variety of spectroscopic methods, including ultrafast initial events in catalysis. In addition, it has been demonstrated that a light-activated conformational change of the protein is necessary to activate catalysis. This makes POR a very important model system to study the relationship between structural changes of enzymes and functionality.
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Murphy AK, Tammaro M, Cortazar F, Gindt YM, Schelvis JPM. Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase. J Phys Chem B 2009; 112:15217-26. [PMID: 18973361 DOI: 10.1021/jp806526y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T< >T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C< >C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C< >C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C< >C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T< >T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C< >C is stronger (12.1 D) and oriented differently than that of T< >T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.
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Affiliation(s)
- Anar K Murphy
- Department of Chemistry, New York University, New York, New York 10003, USA
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