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- John, Juliane, et al.
(author)
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Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography
- 2022
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In: eLIFE. - 2050-084X. ; 11
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Journal article (peer-reviewed)abstract
- Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.
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| 4. |
- John, Juliane, et al.
(author)
-
Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography
- 2022
-
In: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 11
-
Journal article (peer-reviewed)abstract
- Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b–NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b–NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b–NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.
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- Lebrette, Hugo, 1986-, et al.
(author)
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Structure of a ribonucleotide reductase R2 protein radical
- 2023
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 382:6666, s. 109-113
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Journal article (peer-reviewed)abstract
- Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.
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- Ala-Kaila, K., et al.
(author)
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Apparent and actual delignification response in industrial oxygen-alkali delignification of birch kraft pulp
- 2003
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In: TAPPI Journal. - 0734-1415. ; 2:10, s. 23-27
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Journal article (peer-reviewed)abstract
- The time-dependent behavior of material that affects the kappa number of birch kraft pulp was experimentally tested in an industrial, two-stage, oxygen-alkali delignification process. The pulps were leached, and the leached material was divided into four different fractions: the wash loss fraction and the easily leachable, slowly leachable, and stagnant fractions. These fractions were further characterized according to their chemical natures, representing residual lignin, extractives, hexenuronic acids, and other chemical structures contributing to the kappa number of the pulps. The apparent and actual delignification responses in the two reactors and the effects of the leaching operation were thoroughly evaluated based on the behaviors to these different pulp components.
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- Ala-Kaila, K., et al.
(author)
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Chemical character of the response of softwood kraft pulp towards industrial two-stage oxygen-alkali delignification
- 2004
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In: Paperi ja puu. - 0031-1243. ; 86:5, s. 353-358
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Research review (peer-reviewed)abstract
- The transient behavior of residual material affecting the kappa number of softwood kraft pulp (termed residual lignin), was tested experimentally step-wise in an industrial two-stage oxygen-alkali delignification process. The behavior was characterized by leaching the pulps and dividing the residual lignin into four different fractions to represent the wash loss fraction, the easily leachable fraction, the slowly leachable fraction and the stagnant fraction of the lignin in pulp. Further characterization was made regarding the chemical character of these fractions, i.e. residual lignin, extractives, hexenuronic acid, and other chemical structures that contribute to the kappa number of the pulps. The componential delignification response in the two oxygen-alkali reactors and the effects of the leaching operation were comprehensively assessed regarding the behavior of these different pulp components. The results were compared with results obtained earlier for birch kraft pulp originating from the same industrial process and treated using identical experimental procedures. Application: This study gives a new perspective with which to evaluate apparent and actual responses in industrial oxygen-alkali delignification of kraft pulps.
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