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Koroidov, Sergey
Publications (10 of 15) Show all publications
Fuller, F. D., Gul, S., Chatterjee, R., Burgie, E. S., Young, I. D., Lebrette, H., . . . Yano, J. (2017). Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature Methods, 14, 443-449
Open this publication in new window or tab >>Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers
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2017 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 14, p. 443-449Article in journal (Refereed) Published
Abstract [en]

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

Place, publisher, year, edition, pages
Macmillan Publishers Ltd., 2017
Keywords
BiocatalyBiophysical methods; Enzymes; Molecular biophysics; Nanocrystallography
National Category
Chemical Sciences Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:umu:diva-132074 (URN)10.1038/nmeth.4195 (DOI)000397900500029 ()
Note

Article

Available from: 2017-03-02 Created: 2017-03-02 Last updated: 2018-06-09Bibliographically approved
Kubin, M., Kern, J., Gul, S., Kroll, T., Chatterjee, R., Löchel, H., . . . Wernet, P. (2017). Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers. Structural dynamics, 4(5), Article ID 054307.
Open this publication in new window or tab >>Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers
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2017 (English)In: Structural dynamics, ISSN 2329-7778, Vol. 4, no 5, article id 054307Article in journal (Refereed) Published
Abstract [en]

X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn similar to 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2017
National Category
Physical Chemistry
Identifiers
urn:nbn:se:umu:diva-142003 (URN)10.1063/1.4986627 (DOI)000414175400011 ()28944255 (PubMedID)
Available from: 2017-11-21 Created: 2017-11-21 Last updated: 2018-06-09Bibliographically approved
Shevela, D., Arnold, J., Reisinger, V., Berends, H.-M., Kmiec, K., Koroidov, S., . . . Eichacker, L. A. (2016). Biogenesis of water splitting by photosystem II during de-etiolation of barley (Hordeum vulgare L.). Plant, Cell and Environment, 39(7), 1524-1536
Open this publication in new window or tab >>Biogenesis of water splitting by photosystem II during de-etiolation of barley (Hordeum vulgare L.)
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2016 (English)In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 39, no 7, p. 1524-1536Article in journal (Refereed) Published
Abstract [en]

Etioplasts lack thylakoid membranes and photosystem complexes. Light triggers differentiation of etioplasts into mature chloroplasts, and photosystem complexes assemble in parallel with thylakoid membrane development. Plastids isolated at various time points of de-etiolation are ideal to study the kinetic biogenesis of photosystem complexes during chloroplast development. Here, we investigated the chronology of photosystem II (PSII) biogenesis by monitoring assembly status of chlorophyll-binding protein complexes and development of water splitting via O2 production in plastids (etiochloroplasts) isolated during de-etiolation of barley (Hordeum vulgare L.). Assembly of PSII monomers, dimers and complexes binding outer light-harvesting antenna [PSII-light-harvesting complex II (LHCII) supercomplexes] was identified after 1, 2 and 4 h of de-etiolation, respectively. Water splitting was detected in parallel with assembly of PSII monomers, and its development correlated with an increase of bound Mn in the samples. After 4 h of de-etiolation, etiochloroplasts revealed the same water-splitting efficiency as mature chloroplasts. We conclude that the capability of PSII to split water during de-etiolation precedes assembly of the PSII-LHCII supercomplexes. Taken together, data show a rapid establishment of water-splitting activity during etioplast-to-chloroplast transition and emphasize that assembly of the functional water-splitting site of PSII is not the rate-limiting step in the formation of photoactive thylakoid membranes.

Place, publisher, year, edition, pages
John Wiley & Sons, 2016
Keywords
chloroplast biogenesis, oxygen evolution, oxygen-evolving complex, photosystem II assembly
National Category
Chemical Sciences Botany
Identifiers
urn:nbn:se:umu:diva-123557 (URN)10.1111/pce.12719 (DOI)000381496900012 ()26836813 (PubMedID)
External cooperation:
Available from: 2016-07-06 Created: 2016-07-06 Last updated: 2018-06-07Bibliographically approved
Sauter, N. K., Echols, N., Adams, P. D., Zwart, P. H., Kern, J., Brewster, A. S., . . . Yachandra, V. K. (2016). No observable conformational changes in PSII [Letter to the editor]. Nature, 533(7603), E1-E2
Open this publication in new window or tab >>No observable conformational changes in PSII
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2016 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 533, no 7603, p. E1-E2Article in journal, Letter (Refereed) Published
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-121440 (URN)10.1038/nature17983 (DOI)000376004300001 ()
Available from: 2016-06-23 Created: 2016-06-02 Last updated: 2018-06-07Bibliographically approved
Young, I. D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F. D., Koroidov, S., . . . Yano, J. (2016). Structure of photosystem II and substrate binding at room temperature. Nature, 540(7633), 453-457
Open this publication in new window or tab >>Structure of photosystem II and substrate binding at room temperature
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2016 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 540, no 7633, p. 453-457Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Macmillan Publishers Ltd., 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-128748 (URN)10.1038/nature20161 (DOI)000389716800046 ()27871088 (PubMedID)
Available from: 2016-12-14 Created: 2016-12-14 Last updated: 2018-06-09Bibliographically approved
Koroidov, S., Anderlund, M. F., Styring, S., Thapper, A. & Messinger, J. (2015). First turnover analysis of water-oxidation catalyzed by Co-oxide nanoparticles. Energy & Environmental Science, 8(8), 2492-2503
Open this publication in new window or tab >>First turnover analysis of water-oxidation catalyzed by Co-oxide nanoparticles
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2015 (English)In: Energy & Environmental Science, ISSN 1754-5692, E-ISSN 1754-5706, Vol. 8, no 8, p. 2492-2503Article in journal (Refereed) Published
Abstract [en]

Co-oxides are promising water oxidation catalysts for artificial photosynthesis devices. Presently, several different proposals exist for how they catalyze O-2 formation from water. Knowledge about this process at molecular detail will be required for their further improvement. Here we present time-resolved O-18-labelling isotope-ratio membrane-inlet mass spectrometry (MIMS) experiments to study the mechanism of water oxidation in Co/methylenediphosphonate (Co/M2P) oxide nanoparticles using [Ru(bpy)(3)](3+) (bpy = 2,2'-bipyridine) as chemical oxidant. We show that O-16-Co/M2P-oxide nanoparticles produce O-16(2) during their first turnover after simultaneous addition of (H2O)-O-18 and [Ru(bpy)(3)](3+), while sequential addition with a delay of 3 s yields oxygen reflecting bulk water O-18-enrichment. This result is interpreted to show that the O-O bond formation in Co/M2P-oxide nanoparticles occurs via intramolecular oxygen coupling between two terminal Co-OHn ligands that are readily exchangeable with bulk water in the resting state of the catalyst. Importantly, our data allow the determination of the number of catalytic sites within this amorphous nanoparticular material, to calculate the TOF per catalytic site and to derive the number of holes needed for the production of the first O-2 molecule per catalytic site. We propose that the mechanism of O-O bond formation during bulk catalysis in amorphous Co-oxides may differ from that taking place at the surface of crystalline materials.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2015
National Category
Inorganic Chemistry Chemical Process Engineering
Identifiers
urn:nbn:se:umu:diva-107316 (URN)10.1039/c5ee00700c (DOI)000358730600027 ()
Available from: 2015-08-21 Created: 2015-08-21 Last updated: 2018-06-07Bibliographically approved
Koroidov, S., Shevela, D., Shutova, T., Samuelsson, G. & Messinger, J. (2014). Mobile hydrogen carbonate acts as proton acceptor in photosynthetic water oxidation. Proceedings of the National Academy of Sciences of the United States of America, 11(17), 6299-6304
Open this publication in new window or tab >>Mobile hydrogen carbonate acts as proton acceptor in photosynthetic water oxidation
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2014 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 11, no 17, p. 6299-6304Article in journal (Refereed) Published
Abstract [en]

Cyanobacteria, algae and plants oxidize water to the O2 we breathe, and consume CO2 during the synthesis of biomass. Although these vital processes are functionally and structurally well separated in photosynthetic organisms, there is a long-debated role for CO2/HCO3 in water oxidation. Using membrane-inlet mass spectrometry we demonstrate that HCO3 acts as a mobile proton acceptor that helps to transport the protons produced inside of photosystem II by water-oxidation out into the chloroplast's lumen, resulting in a light-driven production of O2 and CO2. Depletion of HCO3 from the media leads, in the absence of added buffers, to a reversible down-regulation of O2 production by about 20%. These findings add a previously unidentified component to the regulatory network of oxygenic photosynthesis, and conclude the more than 50-y-long quest for the function of CO2/ HCO3 in photosynthetic water oxidation.

Place, publisher, year, edition, pages
National Academy of Sciences, 2014
Keywords
carbon dioxide, bicarbonate, proton release, oxygen evolution, water splitting
National Category
Biophysics Physical Chemistry
Identifiers
urn:nbn:se:umu:diva-86300 (URN)10.1073/pnas.1323277111 (DOI)000335199000053 ()
Note

Included in thesis in manuscript form.

Available from: 2014-02-21 Created: 2014-02-21 Last updated: 2018-06-08Bibliographically approved
Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., . . . Yachandra, V. K. (2014). Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications, 5, 4371
Open this publication in new window or tab >>Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy
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2014 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4371-Article in journal (Refereed) Published
Abstract [en]

The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O-2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 mu s after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 mu s after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 angstrom. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

National Category
Organic Chemistry
Identifiers
urn:nbn:se:umu:diva-93240 (URN)10.1038/ncomms5371 (DOI)000340615500062 ()
Available from: 2014-12-22 Created: 2014-09-15 Last updated: 2018-06-07Bibliographically approved
Tran, R., Kern, J., Hattne, J., Koroidov, S., Hellmich, J., Alonso-Mori, R., . . . Yachandra, V. K. (2014). The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. Philosophical Transactions of the Royal Society of London. Biological Sciences, 369(1647), 20130324
Open this publication in new window or tab >>The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser
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2014 (English)In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1647, p. 20130324-Article, review/survey (Refereed) Published
Abstract [en]

The structure of photosystem II and the catalytic intermediate states of the Mn4CaO5 cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.

Keywords
manganese, oxygen-evolving complex, photosystem II, X-ray crystallography, X-ray emission spectroscopy, X-ray free-electron laser
National Category
Organic Chemistry
Identifiers
urn:nbn:se:umu:diva-91183 (URN)10.1098/rstb.2013.0324 (DOI)000337367600009 ()
Available from: 2014-07-23 Created: 2014-07-21 Last updated: 2018-06-07Bibliographically approved
Koroidov, S. (2014). Water splitting in natural and artificial photosynthetic systems. (Doctoral dissertation). Umeå: Umeå University
Open this publication in new window or tab >>Water splitting in natural and artificial photosynthetic systems
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Photosynthesis is the unique biological process that converts carbon dioxide into organic compounds, for example sugars, using the energy of sunlight. Thereby solar energy is converted into chemical energy. Nearly all life depends on this reaction, either directly, or indirectly as the ultimate source of their food. Oxygenic photosynthesis occurs in plants, algae and cyanobacteria. This process created the present level of oxygen in the atmosphere, which allowed the formation of higher life, since respiration allows extracting up to 15-times more energy from organic matter than anaerobic fermentation. Oxygenic photosynthesis uses as substrate for the ubiquitous water. The light-induced oxidation of water to molecular oxygen (O2), catalyzed by the Mn4CaO5 cluster associated with the photosystem II (PS II) complex, is thus one of the most important and wide spread chemical processes occurring in the biosphere. Understanding the mechanism of water-oxidation by the Mn4CaO5 cluster is one of today’s great challenges in science. It is believed that one can extract basic principles of catalyst design from the natural system that than can be applied to artificial systems. Such systems can be used in the future for the generation of fuel from sunlight.

In this thesis the light-induced production of molecular oxygen and carbon dioxide (CO2) by PSII was observed by membrane-inlet mass spectrometry. By analyzing this observation is shown that CO2 not only is the substrate in photosynthesis for the production of sugars, but that it also regulates the efficiency of the initial steps of the electron transport chain of oxygenic photosynthesis by acting, in form of HCO3-, as acceptor for protons produced during water-splitting. This finding concludes the 50-years old search for the function of CO2/HCO3 in photosynthetic water oxidation.

For understanding the mechanism of water oxidation it is crucial to resolve the structures of all oxidation states, including transient once, of the Mn4CaO5 cluster. With this application in mind a new illumination setup was developed and characterized that allowed to bring the Mn4CaO5 cluster of PSII microcrystals into known oxidation states while they flow through a narrow capillary. The optimized illumination conditions were employed at the X-ray free electron laser at the Linac Coherent Light Source (LCLS) to obtain simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) at room temperature. This two methods probe the overall protein structure and the electronic structure of the Mn4CaO5 cluster, respectively. Data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. This approach opens new directions for studying structural changes during the catalytic cycle of the Mn4CaO5 cluster, and for resolving the mechanism of O-O bond formation.

In two other projects the mechanism of molecular oxygen formation by artificial water oxidation catalysts containing inexpensive and abundant elements were studied. Oxygen evolution catalyzed by calcium manganese and manganese only oxides was studied in 18O-enriched water. It was concluded that molecular oxygen is formed by entirely different pathways depending on what chemical oxidant was used.  Only strong non-oxygen donating oxidants were found to support ‘true’ water-oxidation. For cobalt oxides a study was designed to understand the mechanistic details of how the O-O bond forms. The data demonstrate that O-O bond formation occurs by direct coupling between two terminal water-derived ligands. Moreover, by detailed theoretical modelling of the data the number of cobalt atoms per catalytic site was derived.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2014. p. 96
Keywords
Water splitting, photosystem II, artificial catalyst, MIMS, inorganic carbon
National Category
Chemical Sciences Biophysics
Identifiers
urn:nbn:se:umu:diva-86363 (URN)978-91-7459-800-1 (ISBN)
Public defence
2014-03-21, KB3B3, stora hörsalen, KBC-huset, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2014-02-28 Created: 2014-02-24 Last updated: 2018-06-08Bibliographically approved
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