| 1. |
- Axelsson, Martin, 1993-, et al.
(author)
-
A benzothiadiazole based molecule for CO2 capture and reduction in multiple reduced states
-
Other publication (other academic/artistic)abstract
- Using small organic molecular redox carriers to reversibly capture CO2 is a promising approach to mitigate the ongoing climate crisis. Some variants of this type of molecule can catalyse the reduction of CO2 into valuable chemicals. 2,1,3-benzothiadiazole (BT) is an interesting unit due to its proven interaction with CO2 upon reduction and the ease to tune its structure. In this work, the molecule 2,1,3-benzothiadiazole-4,7-dicarbonitrile (BTDN) is studied for CO2 and reduction at its different reduced states. The work is carried out with a combination of (spectro-)electrochemical and computational studies. In cyclic voltammetry, one can see a clear interaction between BTDN and CO2 upon BTDN’s second reduction and the appearance of a large current in its third reduction, in the presence of CO2. DFT calculations show a large variety of possible CO2-bound species that can potentially match the experimental data. The binding of CO2 on BTDN is shown to be irreversible upon the oxidation of the species, especially with low concentrations of CO2. From gas chromatography and NMR experiments, small amounts of CO and oxalate were detected after bulk electrolysis.
|
|
| 2. |
- Berggren, Gustav, et al.
(author)
-
15.02 - Hydrogenases and Model Complexes in Bioorganometallic Chemistry
- 2022
-
In: Comprehensive Organometallic Chemistry IV. - Oxford : Elsevier. - 9780323913508 ; , s. 3-40
-
Book chapter (other academic/artistic)abstract
- Hydrogenases are enzymes involved in H2 metabolism, and provide a blue-print for how efficient H2/H+ interconversion can be achieved utilizing base metals. The societal interest in H2 as a future energy carrier, and a desire for fundamental understanding of how their biologically unique cofactors operate, has promoted intense studies of these enzymes and their related biomimetic analogs. This book chapter provides an overview of both the biochemistry of these fascinating enzymes as well the extensive work related to preparing and characterizing organometallic complexes mimicking their catalytic cofactors.
|
|
| 3. |
- Bhowmick, Asmit, et al.
(author)
-
Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography
- 2023
-
In: IUCrJ. - : International Union Of Crystallography. - 2052-2525. ; 10:6, s. 642-655
-
Research review (peer-reviewed)abstract
- The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O-O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.
|
|
| 4. |
- Bhowmick, Asmit, et al.
(author)
-
Structural evidence for intermediates during O2 formation in photosystem II
- 2023
-
In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 617:7961, s. 629-636
-
Journal article (peer-reviewed)abstract
- In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.
|
|
| 5. |
- Boniolo, Manuel, et al.
(author)
-
Electronic and geometric structure effects on one-electron oxidation of first-row transition metals in the same ligand framework
- 2021
-
In: Dalton Transactions. - : Royal Society of Chemistry. - 1477-9226 .- 1477-9234. ; 50:2, s. 660-674
-
Journal article (peer-reviewed)abstract
- Developing new transition metal catalysts requires understanding of how both metal and ligand properties determine reactivity. Since metal complexes bearing ligands of the Py5 family (2,6-bis-[(2-pyridyl)methyl] pyridine) have been employed in many fields in the past 20 years, we set out here to understand their redox properties by studying a series of base metal ions (M = Mn, Fe, Co, and Ni) within the Py5OH (pyridine-2,6-diylbis[di-(pyridin-2-yl)methanol]) variant. Both reduced (M-II) and the one-electron oxidized (M-III) species were carefully characterized using a combination of X-ray crystallography, X-ray absorption spectroscopy, cyclic voltammetry, and density-functional theory calculations. The observed metal-ligand interactions and electrochemical properties do not always follow consistent trends along the periodic table. We demonstrate that this observation cannot be explained by only considering orbital and geometric relaxation, and that spin multiplicity changes needed to be included into the DFT calculations to reproduce and understand these trends. In addition, exchange reactions of the sixth ligand coordinated to the metal, were analysed. Finally, by including published data of the extensively characterised Py5OMe (pyridine-2,6-diylbis[di-(pyridin-2-yl)methoxymethane])complexes, the special characteristics of the less common Py5OH ligand were extracted. This comparison highlights the non-innocent effect of the distal OH functionalization on the geometry, and consequently on the electronic structure of the metal complexes. Together, this gives a complete analysis of metal and ligand degrees of freedom for these base metal complexes, while also providing general insights into how to control electrochemical processes of transition metal complexes.
|
|
| 6. |
|
|
| 7. |
- Boniolo, Manuel, et al.
(author)
-
Spin transition in a ferrous chloride complex supported by a pentapyridine ligand
- 2020
-
In: Chemical Communications. - : Royal Society of Chemistry. - 1359-7345 .- 1364-548X. ; 56:18, s. 2703-2706
-
Journal article (peer-reviewed)abstract
- Ferrous chloride complexes [FeIILxCl] commonly attain a high-spin state independently of the supporting ligand(s) and temperature. Herein, we present the first report of a complete spin crossover with T1/2 = 80 K in [FeII(Py5OH)Cl]+ (Py5OH = pyridine-2,6-diylbis[di(pyridin-2-yl)methanol]). Both spin forms of the complex are analyzed by X-ray spectroscopy and DFT calculations.
|
|
| 8. |
- Boniolo, Manuel, et al.
(author)
-
Water Oxidation by Pentapyridyl Base Metal Complexes? : A Case Study
- 2022
-
In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 61:24, s. 9104-9118
-
Journal article (peer-reviewed)abstract
- The design of molecular water oxidation catalysts (WOCs) requires a rational approach that considers the intermediate steps of the catalytic cycle, including water binding, deprotonation, storage of oxidizing equivalents, O–O bond formation, and O2 release. We investigated several of these properties for a series of base metal complexes (M = Mn, Fe, Co, Ni) bearing two variants of a pentapyridyl ligand framework, of which some were reported previously to be active WOCs. We found that only [Fe(Py5OMe)Cl]+ (Py5OMe = pyridine-2,6-diylbis[di-(pyridin-2-yl)methoxymethane]) showed an appreciable catalytic activity with a turnover number (TON) = 130 in light-driven experiments using the [Ru(bpy)3]2+/S2O82– system at pH 8.0, but that activity is demonstrated to arise from the rapid degradation in the buffered solution leading to the formation of catalytically active amorphous iron oxide/hydroxide (FeOOH), which subsequently lost the catalytic activity by forming more extensive and structured FeOOH species. The detailed analysis of the redox and water-binding properties employing electrochemistry, X-ray absorption spectroscopy (XAS), UV–vis spectroscopy, and density-functional theory (DFT) showed that all complexes were able to undergo the MIII/MII oxidation, but none was able to yield a detectable amount of a MIV state in our potential window (up to +2 V vs SHE). This inability was traced to (i) the preference for binding Cl– or acetonitrile instead of water-derived species in the apical position, which excludes redox leveling via proton coupled electron transfer, and (ii) the lack of sigma donor ligands that would stabilize oxidation states beyond MIII. On that basis, design features for next-generation molecular WOCs are suggested.
|
|
| 9. |
- Chatterjee, Ruchira, et al.
(author)
-
Structural isomers of the S-2 state in photosystem II : do they exist at room temperature and are they important for function?
- 2019
-
In: Physiologia Plantarum. - : Wiley-Blackwell. - 0031-9317 .- 1399-3054. ; 166:1, s. 60-72
-
Journal article (peer-reviewed)abstract
- In nature, an oxo‐bridged Mn4CaO5 cluster embedded in photosystem II (PSII), a membrane‐bound multi‐subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light‐induced charge separations in the reaction center of PSII. The Mn4CaO5 cluster accumulates four oxidizing equivalents to enable the four‐electron four‐proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S‐states, S0 – S4 in the Kok cycle. One important question related to the catalytic mechanism of the oxygen‐evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S‐states and if such equilibria are essential for the mechanism of the O‐O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X‐ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S2state of PSII with structural data collected of the S1, S2 and S3 states by serial crystallography at neutral pH (∼6.5) using an X‐ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S2 state, the room temperature crystallography data can be well‐described by just one S2 structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.
|
|
| 10. |
- Chatterjee, Ruchira, et al.
(author)
-
XANES and EXAFS of dilute solutions of transition metals at XFELs
- 2019
-
In: Journal of Synchrotron Radiation. - : INT UNION CRYSTALLOGRAPHY. - 0909-0495 .- 1600-5775. ; 26, s. 1716-1724
-
Journal article (peer-reviewed)abstract
- This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.
|
|
| 11. |
- Cheah, Mun Hon, et al.
(author)
-
Assessment of the manganese cluster’s oxidation state via photoactivation of photosystem II microcrystals
- 2020
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:1, s. 141-145
-
Journal article (peer-reviewed)abstract
- Knowledge of the manganese oxidation states of the oxygen-evolving Mn4CaO5 cluster in photosystem II (PSII) is crucial toward understanding the mechanism of biological water oxidation. There is a 4 decade long debate on this topic that historically originates from the observation of a multiline electron paramagnetic resonance (EPR) signal with effective total spin of S = 1/2 in the singly oxidized S2 state of this cluster. This signal implies an overall oxidation state of either Mn(III)3Mn(IV) or Mn(III)Mn(IV)3 for the S2 state. These 2 competing assignments are commonly known as “low oxidation (LO)” and “high oxidation (HO)” models of the Mn4CaO5 cluster. Recent advanced EPR and Mn K-edge X-ray spectroscopy studies converge upon the HO model. However, doubts about these assignments have been voiced, fueled especially by studies counting the number of flash-driven electron removals required for the assembly of an active Mn4CaO5 cluster starting from Mn(II) and Mn-free PSII. This process, known as photoactivation, appeared to support the LO model since the first oxygen is reported to evolve already after 7 flashes. In this study, we improved the quantum yield and sensitivity of the photoactivation experiment by employing PSII microcrystals that retained all protein subunits after complete manganese removal and by oxygen detection via a custom built thin-layer cell connected to a membrane inlet mass spectrometer. We demonstrate that 9 flashes by a nanosecond laser are required for the production of the first oxygen, which proves that the HO model provides the correct description of the Mn4CaO5 cluster’s oxidation states.
|
|
| 12. |
|
|
| 13. |
- Cheah, Mun Hon, et al.
(author)
-
Electrochemical oxidation of ferricyanide
- 2021
-
In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11
-
Journal article (peer-reviewed)abstract
- We report the electrochemical oxidation of ferricyanide, [Fe-III(CN)(6)](3-) and characterised the oxidation product by in-situ FTIR and XAS spectroelectrochemistry methods. Oxidation of [Fe-III(CN)(6)](3-) is proposed to proceed via a tentative Fe(IV) intermediate that undergoes reduction elimination to give cis-[Fe-III(CN)(4)(CH3CN)(2)](1-) as stable product in acetonitrile. Speciation of the oxidation product by DFT calculations is underpinned by good agreement to experimental data.
|
|
| 14. |
- Fransson, Thomas, et al.
(author)
-
Effects of x-ray free-electron laser pulse intensity on the Mn K beta(1,3) x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions
- 2021
-
In: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 8:6
-
Journal article (peer-reviewed)abstract
- In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and K beta x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the K beta XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn K beta(1,3) XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from & SIM;5 x 10(15) to 5 x 10(17) W/cm(2) at a pulse length of & SIM;35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.& nbsp;
|
|
| 15. |
- Fransson, Thomas, et al.
(author)
-
Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3x-ray emission spectrum in photosystem II - A case study for metalloprotein crystals and solutions
- 2021
-
In: Structural Dynamics. - : American Institute of Physics (AIP). - 2329-7778. ; 8:6
-
Journal article (peer-reviewed)abstract
- In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
|
|
| 16. |
|
|
| 17. |
- Hussein, Rana, et al.
(author)
-
Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition
- 2021
-
In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 12:1
-
Journal article (peer-reviewed)abstract
- Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.
|
|
| 18. |
- Ibrahim, Mohamed, et al.
(author)
-
Untangling the sequence of events during the S-2 -> S-3 transition in photosystem II and implications for the water oxidation mechanism
- 2020
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 117:23, s. 12624-12635
-
Journal article (peer-reviewed)abstract
- In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S-1, S-2, S-3, and S-0, showing that a water molecule is inserted during the S-2 -> S-3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O-2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S-2 -> S-3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 mu s after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (t of similar to 350 mu s) during the S-2 -> S-3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
|
|
| 19. |
- Ibrahim, Mohamed, et al.
(author)
-
Untangling the sequence of events during the S2 -> S3 transition in photosystem II and implications for the water oxidation mechanism
- 2020
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:23, s. 12624-12635
-
Journal article (peer-reviewed)abstract
- In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 -> S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 -> S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 μs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 μs) during the S2 -> S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
|
|
| 20. |
- 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. - 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.
|
|
| 21. |
- 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.
|
|
| 22. |
- Keable, Stephen M., et al.
(author)
-
Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I
- 2021
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
-
Journal article (peer-reviewed)abstract
- Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.
|
|
| 23. |
- Kern, Jan, et al.
(author)
-
Structures of the intermediates of Kok’s photosynthetic water oxidation clock
- 2018
-
In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 563, s. 421-425
-
Journal article (peer-reviewed)abstract
- Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok’s S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3–7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok’s cycle as high-resolution structures (2.04–2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional ‘water’, Ox, during the S2→S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O–O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.
|
|
| 24. |
- Rabe, Patrick, et al.
(author)
-
X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis
- 2021
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:34
-
Journal article (peer-reviewed)abstract
- Isopenicillin N synthase (IPNS) catalyzes the unique reaction of L-delta-(alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
|
|
| 25. |
- Redman, Holly J., et al.
(author)
-
Lewis acid protection turns cyanide containing [FeFe]-hydrogenase mimics into proton reduction catalysts
- 2022
-
In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 51:12, s. 4634-4643
-
Journal article (peer-reviewed)abstract
- Sustainable sources of hydrogen are a vital component of the envisioned energy transition. Understanding and mimicking the [FeFe]-hydrogenase provides a route to achieving this goal. In this study we re-visit a molecular mimic of the hydrogenase, the propyl dithiolate bridged complex [Fe2(μ-pdt)(CO)4(CN)2]2−, in which the cyanide ligands are tuned via Lewis acid interactions. This system provides a rare example of a cyanide containing [FeFe]-hydrogenase mimic capable of catalytic proton reduction, as demonstrated by cyclic voltammetry. EPR, FTIR, UV-vis and X-ray absorption spectroscopy are employed to characterize the species produced by protonation, and reduction or oxidation of the complex. The results reveal that biologically relevant iron-oxidation states can be generated, potentially including short-lived mixed valent Fe(I)Fe(II) species. We propose that catalysis is initiated by protonation of the diiron complex and the resulting di-ferrous bridging hydride species can subsequently follow two different pathways to promote H2 gas formation depending on the applied reduction potential.
|
|
| 26. |
- Selan, Odi Th E, et al.
(author)
-
Impact of the 2Fe2P core geometry on the reduction chemistry of phosphido-bridged diiron hexacarbonyl compounds
- 2022
-
In: Australian journal of chemistry (Print). - : CSIRO Publishing. - 0004-9425 .- 1445-0038. ; 75:9, s. 649-659
-
Journal article (peer-reviewed)abstract
- The effect of core geometry constraints of hydrogenase H-cluster analogues on reduction chemistry have been explored by a combination of structural, electrochemical and IR spectro-electrochemical (IR-SEC) studies. A series of phosphido-bridged diiron hexacarbonyl complexes, Fe-2(mu(2)-PPh2(CH2)(x)PPh2)(CO)(6), x = 2 (2P) and 4 (4P) and previously reported with x = 3 (3P) and the unlinked bis-diphenylphosphido (DP) analogues were investigated. The X-ray structures of the neutral complexes demonstrate the effect of the linking group on the Fe2P2 core geometry with P-Fe-Fe-P torsion angles of 95 (2P), 101 (3P), 108 (4P) and 109 degrees (DP) and a twisting of the Fe(CO)(3) fragments from an eclipsed geometry (2P, 3P and DP) for 4P. For all four compounds the primary reduction process involves two close-spaced one-electron reactions (E-1 and E-2) with a systematic trend to more negative reduction potentials with a shorter link between the bridging phosphorus atoms. This reflects the greater constraint that the bridging group places on the adoption of a planar 2Fe2P geometry. The sensitivity of the core geometry is greater for E-2 than E-1 and this impacts the stability of the monoanion with respect to disproportion (K-disp(298 K) = 0.02 (2P), 2.4 (3P) and 3540 (4P and DP)). 4P has a stable dianion and gives reversible cyclic voltammetry at 298 K and is quasi-reversible at 253 K, whereas the response of 2P is irreversible at 298 K, with two distinct daughter products, but becomes quasi-reversible at 253 K. IR-SEC measurements enabled elucidation of the spectra and time evolution of the reduction products. These results are consistent with a bimolecular reaction giving a distinct reduced product modelled as a dimeric, 4Fe species. The sensitivity of the reduction chemistry of the bridged diiron compounds underpins their utility as catalytic proton reduction catalysts and the systematic trends delineated in this investigation provide the framework for charting the path of their redox-coupled chemical reactions.
|
|
| 27. |
- Simon, Philipp S., et al.
(author)
-
Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs
- 2023
-
In: FEBS Letters. - : John Wiley & Sons. - 0014-5793 .- 1873-3468. ; 597:1, s. 30-37
-
Journal article (peer-reviewed)abstract
- Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4CaO5 complex, in the intermediate Si (i = 0–4)-states of the Kok cycle, obtained using XFELs.
|
|
| 28. |
- Spallacci, Claudia, et al.
(author)
-
Fabricating high-purity graphite disk electrodes as a cost-effective alternative in fundamental electrochemistry research
- 2024
-
In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14
-
Journal article (peer-reviewed)abstract
- Graphite electrodes offer remarkable electrochemical properties, emerging as a viable alternative to glassy carbon (GCE) and other carbon-based electrodes for fundamental electrochemistry research. We report the fabrication and characterization of high-purity graphite disk electrodes (GDEs), made from cost-effective materials and a solvent-free methodology employing readily available laboratory equipment. Analysis of their physical properties via SEM, EDX and XPS reveals no metallic interferences and a notably high porosity, emphasizing their potential. The electrochemical performances of GDEs were found to be comparable to those of GCE. Immobilization of peptides and enzymes, both via covalent coupling and surface adsorption, was used to explore potential applications of GDEs in bioelectrochemistry. Enzyme activity could be addressed both via direct electron transfer and mediated electron transfer mechanism. These results highlight the interesting properties of our GDEs and make them a low-cost alternative to other carbon-based electrodes, with potential for future real-world applications.
|
|
| 29. |
- Young, Iris D., et al.
(author)
-
Structure of photosystem II and substrate binding at room temperature
- 2016
-
In: Nature. - : Macmillan Publishers Ltd.. - 0028-0836 .- 1476-4687. ; 540:7633, s. 453-457
-
Journal article (peer-reviewed)abstract
- Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2,3. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site4–6. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8,9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10–13. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.
|
|
| 30. |
- Zavafer, Alonso, et al.
(author)
-
Two Quenchers Formed During Photodamage of Phostosystem II and The Role of One Quencher in Preemptive Photoprotection
- 2019
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 9
-
Journal article (peer-reviewed)abstract
- The quenching of chlorophyll fluorescence caused by photodamage of Photosystem II (qI) is a well recognized phenomenon, where the nature and physiological role of which are still debatable. Paradoxically, photodamage to the reaction centre of Photosystem II is supposed to be alleviated by excitation quenching mechanisms which manifest as fluorescence quenchers. Here we investigated the time course of PSII photodamage in vivo and in vitro and that of picosecond time-resolved chlorophyll fluorescence (quencher formation). Two long-lived fluorescence quenching processes during photodamage were observed and were formed at different speeds. The slow-developing quenching process exhibited a time course similar to that of the accumulation of photodamaged PSII, while the fast-developing process took place faster than the light-induced PSII damage. We attribute the slow process to the accumulation of photodamaged PSII and the fast process to an independent quenching mechanism that precedes PSII photodamage and that alleviates the inactivation of the PSII reaction centre.
|
|
