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Król, Sylwia
Publications (7 of 7) Show all publications
Król, S. (2024). Respiration in Actinobacteria: Structure, function and inhibition of the III2IV2 supercomplex. (Doctoral dissertation). Stockholm: Department of Biochemistry and Biophysics, Stockholm Univeristy
Open this publication in new window or tab >>Respiration in Actinobacteria: Structure, function and inhibition of the III2IV2 supercomplex
2024 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The final step of aerobic respiration, oxidative phosphorylation, combines the activities of the electron transport chain and of ATP synthase. The electron transport chain is composed of membrane-bound energy transducers, which are organized in supramolecular assemblies known as respiratory supercomplexes. 

In this work we determined the cryo-EM structure of the obligate III2IV2 supercomplex from the Gram-positive bacterium Corynebacterium glutamicum. The structure shows that the individual complexes are intertwined and that the electron transfer between them occurs via a di-heme cc subunit instead of via soluble cytochrome c. The structure reveals additional features that distinguish the supercomplex from its canonical counterpart. These are a cytoplasmic QcrB loop that occludes the proton-entry point of the complex IV D-pathway, and an FeS cluster in a fixed position. These characteristics are conserved among actinobacteria. 

With the goal to elucidate the structure-function relationship for complexes III and IV in actinobacteria, we also investigated electron and proton transfer kinetics of an obligate respiratory supercomplex from Mycobacterium smegmatis, which is a model organism for Mycobacterium tuberculosis. The results show that the sequence of reactions involved in electron transfer in complex IV is similar to that observed in other A1-type oxidases, but the F to O transition of the catalytic cycle is slower than that reported for canonical complex IV. We also observed that reaction steps previously shown to display pH dependence in canonical complex IV were pH independent in Mycobacterium smegmatis. In addition, proton uptake kinetics through the D-pathway of complex IV were altered with no proton uptake during the F to O step. These findings can be attributed to the presence of the QcrB loop and point towards a possible unique regulatory mechanism for mycobacterial supercomplexes.

As the mycobacterial supercomplex is a promising drug target for tuberculosis treatment, we studied its interaction with the drug candidate Telacebec and the metabolite of an already approved drug, lansoprazole sulfide. We determined the cryo-EM structures of the III2IV2 supercomplex with Telacebec and with lansoprazole sulfide bound in the QP site of the QcrB subunit of complex III. In both structures the inhibitor replaces the natural substrate menaquinol in the inner position of the QP binding pocket and makes multiple interactions with the QcrA and QcrB subunits of complex III. Multiple turnover assays showed that this binding mode inhibits the supercomplex of Mycobacterium smegmatis. Results from our in silico studies show that lansoprazole sulfide is likely to bind to the supercomplex of Mycobacterium tuberculosis in a similar way as was observed for Mycobacterium smegmatis.

 

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm Univeristy, 2024. p. 78
Keywords
bioenergetics, structural biology, electron transport chain, respiratory supercomplex, electron transfer, proton transfer
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-227926 (URN)978-91-8014-747-7 (ISBN)978-91-8014-748-4 (ISBN)
Public defence
2024-05-17, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius Väg 16 B, Stockholm, 09:00 (English)
Opponent
Supervisors
Available from: 2024-04-24 Created: 2024-04-04 Last updated: 2024-04-12Bibliographically approved
Gallego-Villarejo, L., Wallin, C., Król, S., Enrich-Bengoa, J., Suades, A., Aguilella-Arzo, M., . . . Perálvarez-Marín, A. (2022). Big dynorphin is a neuroprotector scaffold against amyloid β-peptide aggregation and cell toxicity. Computational and Structural Biotechnology Journal, 20, 5672-5679
Open this publication in new window or tab >>Big dynorphin is a neuroprotector scaffold against amyloid β-peptide aggregation and cell toxicity
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2022 (English)In: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, p. 5672-5679Article in journal (Refereed) Published
Abstract [en]

Amyloid β-peptide (Aβ) misfolding into β-sheet structures triggers neurotoxicity inducing Alzheimer’s disease (AD). Molecules able to reduce or to impair Aβ aggregation are highly relevant as possible AD treatments since they should protect against Aβ neurotoxicity. We have studied the effects of the interaction of dynorphins, a family of opioid neuropeptides, with Aβ40 the most abundant species of Aβ. Biophysical measurements indicate that Aβ40 interacts with Big Dynorphin (BigDyn), lowering the amount of hydrophobic aggregates, and slowing down the aggregation kinetics. As expected, we found that BigDyn protects against Aβ40 aggregates when studied in human neuroblastoma cells by cell survival assays. The cross-interaction between BigDyn and Aβ40 provides insight into the mechanism of amyloid pathophysiology and may open up new therapy possibilities.

Keywords
Alzheimer’s disease, Amyloid b-peptide, Dynorphins, Peptide therapy, Biophysics
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:su:diva-212495 (URN)10.1016/j.csbj.2022.10.014 (DOI)000930753500004 ()2-s2.0-85140094234 (Scopus ID)
Available from: 2022-12-07 Created: 2022-12-07 Last updated: 2023-03-14Bibliographically approved
Król, S., Fedotovskaya, O., Högbom, M., Ädelroth, P. & Brzezinski, P. (2022). Electron and proton transfer in the M. smegmatis III2IV2 supercomplex. Biochimica et Biophysica Acta - Bioenergetics, 1863(7), Article ID 148585.
Open this publication in new window or tab >>Electron and proton transfer in the M. smegmatis III2IV2 supercomplex
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2022 (English)In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1863, no 7, article id 148585Article in journal (Refereed) Published
Abstract [en]

The M. smegmatis respiratory III2IV2 supercomplex consists of a complex III (CIII) dimer flanked on each side by a complex IV (CIV) monomer, electronically connected by a di-heme cyt. cc subunit of CIII. The supercomplex displays a quinol oxidation‑oxygen reduction activity of ~90 e/s. In the current work we have investigated the kinetics of electron and proton transfer upon reaction of the reduced supercomplex with molecular oxygen. The data show that, as with canonical CIV, oxidation of reduced CIV at pH 7 occurs in three resolved components with time constants ~30 μs, 100 μs and 4 ms, associated with the formation of the so-called peroxy (P), ferryl (F) and oxidized (O) intermediates, respectively. Electron transfer from cyt. cc to the primary electron acceptor of CIV, CuA, displays a time constant of ≤100 μs, while re-reduction of cyt. cc by heme b occurs with a time constant of ~4 ms. In contrast to canonical CIV, neither the P → F nor the F → O reactions are pH dependent, but the P → F reaction displays a H/D kinetic isotope effect of ~3. Proton uptake through the D pathway in CIV displays a single time constant of ~4 ms, i.e. a factor of ~40 slower than with canonical CIV. The slowed proton uptake kinetics and absence of pH dependence are attributed to binding of a loop from the QcrB subunit of CIII at the D proton pathway of CIV. Hence, the data suggest that function of CIV is modulated by way of supramolecular interactions with CIII.

Keywords
Cytochrome c oxidase, Cytochrome bc 1, Actinobacteria, Membrane protein, Bioenergetics and oxidative phosphorylation, Respiratory chain
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-207909 (URN)10.1016/j.bbabio.2022.148585 (DOI)000829443100003 ()35753381 (PubMedID)2-s2.0-85132963263 (Scopus ID)
Available from: 2022-08-23 Created: 2022-08-23 Last updated: 2024-04-04Bibliographically approved
Moe, A., Kovalova, T., Król, S., Yanofsky, D. J., Bott, M., Sjöstrand, D., . . . Brzezinski, P. (2022). The respiratory supercomplex from C. glutamicum. Structure, 30(3), 338-349
Open this publication in new window or tab >>The respiratory supercomplex from C. glutamicum
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2022 (English)In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 30, no 3, p. 338-349Article in journal (Refereed) Published
Abstract [en]

Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, respiratory complexes III and IV form a CIII2CIV2 supercomplex that catalyzes oxidation of menaquinol and reduction of dioxygen to water. We isolated the C. glutamicum supercomplex and used cryo-EM to determine its structure at 2.9 Å resolution. The structure shows a central CIII2 dimer flanked by a CIV on two sides. A menaquinone is bound in each of the QN and QP sites in each CIII and an additional menaquinone is positioned ∼14 Å from heme bL. A di-heme cyt. cc subunit electronically connects each CIII with an adjacent CIV, with the Rieske iron-sulfur protein positioned with the iron near heme bL. Multiple subunits interact to form a convoluted sub-structure at the cytoplasmic side of the supercomplex, which defines a path for proton transfer into CIV.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-203453 (URN)10.1016/j.str.2021.11.008 (DOI)000766494300005 ()34910901 (PubMedID)
Available from: 2022-04-07 Created: 2022-04-07 Last updated: 2024-04-04Bibliographically approved
Yanofsky, D. J., Di Trani, J. M., Król, S., Abdelaziz, R., Bueler, S. A., Imming, P., . . . Rubinstein, J. L. (2021). Structure of mycobacterial CIII2CIV2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203). eLIFE, 10, Article ID e71959.
Open this publication in new window or tab >>Structure of mycobacterial CIII2CIV2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203)
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2021 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 10, article id e71959Article in journal (Refereed) Published
Abstract [en]

The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified Mycobacterium smegmatis CIII2CIV2 at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and Mycobacterium tuberculosis growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIII2CIV2 both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIII2CIV2 activity.

Keywords
Mycobacterium smegmatis, telacebec (Q203), cryoEM, respiration, tuberculosis, structure
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-198837 (URN)10.7554/eLife.71959 (DOI)000709344600001 ()34590581 (PubMedID)2-s2.0-85116880110 (Scopus ID)
Available from: 2021-11-25 Created: 2021-11-25 Last updated: 2024-04-04Bibliographically approved
Król, S., Österlund, N., Vosough, F., Jarvet, J., Wärmländer, S., Barth, A., . . . Mörman, C. (2021). The amyloid-inhibiting NCAM-PrP peptide targets Aβ peptide aggregation in membrane-mimetic environments. iScience, 24(8), Article ID 102852.
Open this publication in new window or tab >>The amyloid-inhibiting NCAM-PrP peptide targets Aβ peptide aggregation in membrane-mimetic environments
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2021 (English)In: iScience, E-ISSN 2589-0042 , Vol. 24, no 8, article id 102852Article in journal (Refereed) Published
Abstract [en]

Substantial research efforts have gone into elucidating the role of protein misfolding and self-assembly in the onset and progression of Alzheimer’s disease (AD). Aggregation of the Amyloid-β (Aβ) peptide into insoluble fibrils is closely associated with AD. Here, we use biophysical techniques to study a peptide-based approach to target Aβ amyloid aggregation. A peptide construct, NCAM-PrP, consists of a largely hydrophobic signal sequence linked to a positively charged hexapeptide. The NCAM-PrP peptide inhibits Aβ amyloid formation by forming aggregates which are unavailable for further amyloid aggregation. In a membrane-mimetic environment, Aβ and NCAM-PrP form specific heterooligomeric complexes, which are of lower aggregation states compared to Aβ homooligomers. The Aβ:NCAM-PrP interaction appears to take place on different aggregation states depending on the absence or presence of a membrane-mimicking environment. These insights can be useful for the development of potential future therapeutic strategies targeting Aβ at several aggregation states.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-198433 (URN)10.1016/j.isci.2021.102852 (DOI)000686897200039 ()34381976 (PubMedID)
Available from: 2021-11-09 Created: 2021-11-09 Last updated: 2023-09-04Bibliographically approved
Henning-Knechtel, A., Kumar, S., Wallin, C., Król, S., Wärmländer, S. K. T., Jarvet, J., . . . Magzoub, M. (2020). Designed Cell-Penetrating Peptide Inhibitors of Amyloid-beta Aggregation and Cytotoxicity. Cell Reports Physical Science, 1(2), Article ID 100014.
Open this publication in new window or tab >>Designed Cell-Penetrating Peptide Inhibitors of Amyloid-beta Aggregation and Cytotoxicity
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2020 (English)In: Cell Reports Physical Science, E-ISSN 2666-3864, Vol. 1, no 2, article id 100014Article in journal (Refereed) Published
Abstract [en]

Amyloid proteins and peptides are a major contributing factor to the development of various neurodegenerative disorders, including Alzheimer’s and prion diseases. Previously, a designed cell-penetrating peptide (CPP) comprising a hydrophobic signal sequence followed by a prion protein (PrP)-derived polycationic sequence (PrP23–28: KKRPKP) was shown to have potent anti-prion properties. Here, we extend this approach toward the amyloid-beta (Aβ) peptide amyloid formation, which is associated with Alzheimer’s disease. We characterized the interactions of the CPP with Aβ using complementary in vitro and in silico experiments. We report that the CPP stabilizes Aβ in a non-amyloid state and inhibits Aβ-induced neurotoxicity. Moreover, replacing PrP23–28 with a corresponding segment from Aβ results in a construct with similar CPP functionality and antagonism of Aβ aggregation and neurotoxicity. Our findings reveal a general underlying principle for inhibition of pathogenic protein aggregation that may facilitate the design of CPP-based therapeutics for amyloid diseases.

Keywords
aggregation, Alzheimer’s disease, amyloid-beta peptide, cell-penetrating peptides, drug design, neurodegeneration, oligomers, prion protein, protein engineering, signal sequence
National Category
Chemical Sciences
Research subject
Biophysics
Identifiers
urn:nbn:se:su:diva-181494 (URN)10.1016/j.xcrp.2020.100014 (DOI)
Available from: 2020-05-06 Created: 2020-05-06 Last updated: 2022-07-27Bibliographically approved
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