| 1. |
- Wu, Fei, 1993-
(författare)
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Exploring Membrane Proteins within the Inner Mitochondrial and Endoplasmic Reticulum Membranes : Mitochondrial respiratory complexes and ER-localized Shr3
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Membrane proteins play important roles in various life processes, for example, those in the inner mitochondrial membrane (IMM), endoplasmic reticulum (ER) membrane, and plasma membrane (PM). Oxidative phosphorylation complexes, densely packed in the IMM are crucial for energy transduction in eukaryotes. We determined three entire II2III2 IV2 supercomplex (SC) structures with 114 lipids at 2.1-2.4 Å resolution in Perkinsus marinus (P. marinus). The structures show a complete electron transfer pathway from complex II (CII) to complex IV (CIV). These architectures also reveal rotation states of the iron sulfur protein (ISP) in complex III (CIII), from one of which we observed two novel proteins that might impair the electron transfer. We also studied how the salt concentration and detergent affect the electron transfer. We determined the SC III2 IV-cytochrome c (cyt. c) cryo-EM structure at 20 mM salt concentration condition. Together with kinetic study, these data implicate that multiple cyt. c are involved in electron transfer between CIII and CIV. Our kinetic studies of CIV also indicate a native ligand bound near its K proton pathway which could be removed by detergent, leading to an increase in electron transfer rate and the activity of the enzyme. Most biogenesis of integral membrane proteins in eukaryotes is done in ER, such as the amino acid permeases (AAP), which function as amino acid transporters in the PM. Its synthesis and functional folding in Saccharomyces cerevisiae (S. cerevisiae) requires an ER membrane-localized chaperone, Shr3. We utilized a yeast growth-based genetic assay, in conjunction with a split-ubiquitin yeast two-hybrid assay, to demonstrate the selective interaction between Shr3 and nested C-terminal AAP truncations. This interaction exhibited a distinct pattern, wherein it gradually intensified and then weakened as more transmembrane helices folded. The work presented in this thesis contributions to an increased understanding of the organization and function of SCs, the effects of protein subunits, salt concentrations, and detergents on electron transfer, as well as the mechanism of Shr3 on AAP folding in the ER membrane. Together, these works have shed light on the understanding of the structure and function of several membrane proteins.
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| 2. |
- Lobez, Ana Paula, et al.
(författare)
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Electron transfer in the respiratory chain at low salinity
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Recent studies have established that cellular electrostatic interactions are more influential than assumed previously. Here, we used cryo-EM and performed steady-state kinetic studies to investigate electrostatic interactions between cytochrome (cyt.) c and the complex (C) III-IV supercomplex from Saccharomyces cerevisiae at low salinity. The kinetic studies show a sharp transition with a Hill coefficient ≥2, which together with the cryo-EM data at 2.4 Å resolution indicate multiple cyt. c molecules bound along the supercomplex surface. Previously unresolved negatively charged loops of CIII subunits Qcr6 and Qcr9 become structured to interact with cyt. c. In addition, the higher resolution allowed us to identify water molecules in proton pathways of CIV and previously unresolved cardiolipin molecules. In conclusion, the lowered electrostatic screening renders engagement of multiple cyt. c molecules that are directed by electrostatically structured CIII loops to conduct electron transfer between CIII and CIV.
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| 3. |
- Smirnova, Irina, et al.
(författare)
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Molecular basis for stimulation of cytochrome c oxidase activity by detergents
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Cytochrome c oxidase (CytcO) is an integral membrane protein, which catalyzes four-electron reduction of oxygen linked to proton uptake and pumping. Amphipathic molecules bind in sites near the so-called K proton pathway of CytcO to reversibly modulate its activity. However, purification of CytcO for mechanistic studies typically involves the use of detergents, which may interfere with binding of these regulatory molecules. Here, we investigated the CytcO enzymatic activity as well as intramolecular electron transfer linked to proton transfer upon addition of different detergents to bovine heart mitoplasts. The CytcO activity increased upon addition of alkyl glucosides (DDM and DM) and the steroid analog GDN. The maximum stimulating effect was observed for DDM and DM, and the half-stimulating effect correlated with their CMC values. With GDN the stimulation effect was smaller and occurred at a concentration higher than CMC. A kinetic analysis suggests that the stimulation of activity is due to removal of a ligand bound near the K proton pathway, which indicates that in the native membrane this site is occupied to yield a lower than maximal possible CytcO activity. Possible functional consequences are discussed.
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| 4. |
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| 5. |
- Collins, Ruairi, et al.
(författare)
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Biochemical discrimination between selenium and sulfur 1 : a single residue provides selenium specificity to human selenocysteine lyase
- 2012
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Ingår i: PLoS One. - Stockholm : Karolinska Institutet, Dept of Medical Biochemistry and Biophysics. - 1932-6203.
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Tidskriftsartikel (refereegranskat)abstract
- Selenium and sulfur are two closely related basic elements utilized in nature for a vast array of biochemical reactions. While toxic at higher concentrations, selenium is an essential trace element incorporated into selenoproteins as selenocysteine (Sec), the selenium analogue of cysteine (Cys). Sec lyases (SCLs) and Cys desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys and generally act on both substrates. In contrast, human SCL (hSCL) is specific for Sec although the only difference between Sec and Cys is the identity of a single atom. The chemical basis of this selenium-over-sulfur discrimination is not understood. Here we describe the X-ray crystal structure of hSCL and identify Asp146 as the key residue that provides the Sec specificity. A D146K variant resulted in loss of Sec specificity and appearance of CD activity. A dynamic active site segment also provides the structural prerequisites for direct product delivery of selenide produced by Sec cleavage, thus avoiding release of reactive selenide species into the cell. We thus here define a molecular determinant for enzymatic specificity discrimination between a single selenium versus sulfur atom, elements with very similar chemical properties. Our findings thus provide molecular insights into a key level of control in human selenium and selenoprotein turnover and metabolism.
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| 6. |
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| 7. |
- Moe, Agnes, 1990-
(författare)
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Role of respiratory supercomplexes : Electronic connection between complexes III and IV
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the final step of cellular respiration, electrons are transferred through the respiratory chain to reduce molecular oxygen to water. The energy released in this chain is used to maintain a proton electrochemical gradient across the cell membrane, which is used, for example, by the ATP synthase to produce ATP. The enzyme complexes of the respiratory chain are known to organize in supramolecular assemblies, so-called respiratory supercomplexes.In this work we investigated the functional significance of respiratory supercomplexes consisting of complexes III and IV in mitochondria. By combining structural and kinetic studies we showed that at the commonly assumed "physiological" ionic strength of 150 mM monovalent salt, the water-soluble cyt. c associates with the negatively charged surface of III2-IV1-2 supercomplexes in the yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. The data showed that one cyt. c diffuses in 2D, between complexes III and IV, indicating a kinetic advantage of forming supercomplexes. These studies also showed different relative orientation of the individual complexes in the supercomplexes from the two yeast species, indicating that 2D diffusion is a general mechanism, not limited to a specific relative orientation of complexes III and IV. More recent data in the literature indicate that a more realistic mimic of intracellular conditions is a monovalent salt concentration of 20 mM. We showed that under these conditions two cyt. c molecules bind simultaneously to the supercomplex. This result further supports a kinetic advantage of forming supercomplexes.We also determined the cryo-EM structure of the obligate III2-IV2 supercomplex from the Gram-positive bacterium Corynebacterium glutamicum. The structure revealed an electronic connection between complexes III and IV by a di-heme cyt. cc subunit. The structure also showed that complexes III and IV are structurally intertwined and strongly connected with unique features conserved in the phylum actinobacteria.
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| 8. |
- Näsvik Öjemyr, Linda, et al.
(författare)
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Reaction of wild-type and Glu243Asp variant yeast cytochrome c oxidase with O-2
- 2014
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1837:7, s. 1012-1018
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Tidskriftsartikel (refereegranskat)abstract
- We have studied internal electron transfer during the reaction of Saccharomyces cerevisiae mitochondrial cytochrome c oxidase with dioxygen. Similar absorbance changes were observed with this yeast oxidase as with the previously studied Rhodobacter sphaeroides and bovine mitochondrial oxidases, which suggests that the reaction proceeds along the same trajectory. However, notable differences were observed in rates and electron-transfer equilibrium constants of specific reaction steps, for example the ferryl (F) to oxidized (O) reaction was faster with the yeast (0.4 ms) than with the bovine oxidase (similar to 1 ms) and a larger fraction Cu-A was oxidized with the yeast than with the bovine oxidase in the peroxy (P-R) to F reaction. Furthermore, upon replacement of Glu243, located at the end of the so-called D proton pathway, by Asp the P-R -> F and F -> O reactions were slowed by factors of similar to 3 and similar to 10, respectively, and electron transfer from Cu-A to heme a during the P-R -> F reaction was not observed. These data indicate that during reduction of dioxygen protons are transferred through the D pathway, via Glu243, to the catalytic site in the yeast mitochondrial oxidase. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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| 9. |
- Uzdavinys, Povilas, 1985-
(författare)
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Establishing the molecular mechanism of sodium/proton exchangers
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Sodium/proton exchangers are ubiquitous secondary active transporters that can be found in all kingdoms of life. These proteins facilitate the transport of protons in exchange for sodium ions to help regulate internal pH, sodium levels, and cell volume. Na+/H+ exchangers belong to the SLC9 family and are involved in many physiological processes including cell proliferation, cell migration and vesicle trafficking. Dysfunction of these proteins has been linked to physiological disorders, such as hypertension, heart failure, epilepsy and diabetes.The goal of my thesis is to establish the molecular basis of ion exchange in Na+/H+ exchangers. By establishing how they bind and catalyse the movement of ions across the membrane, we hope we can better understand their role in human physiology.In my thesis, I will first present an overview of Na+/H+ exchangers and their molecular mechanism of ion translocation as was currently understood by structural and functional studies when I started my PhD studies. I will outline our important contributions to this field, which were to (i) obtain the first atomic structures of the same Na+/H+ exchanger (NapA) in two major alternating conformations, (ii) show how a transmembrane embedded lysine residue is essential for carrying out electrogenic transport, and (iii) isolate and recorde the first kinetic data of a mammalian Na+/H+ exchanger (NHA2) in an isolated liposome reconstitution system.
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| 10. |
- von Ballmoos, Christoph, et al.
(författare)
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Proton transfer in ba(3) cytochrome c oxidase from Thermus thermophilus
- 2012
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1817:4, s. 650-657
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Forskningsöversikt (refereegranskat)abstract
- The respiratory heme-copper oxidases catalyze reduction of O-2 to H2O, linking this process to transmembrane proton pumping. These oxidases have been classified according to the architecture, location and number of proton pathways. Most structural and functional studies to date have been performed on the A-class oxidases, which includes those that are found in the inner mitochondrial membrane and bacteria such as Rhodobacter sphaeroides and Paracoccus denitrificans (aa(3)-type oxidases in these bacteria). These oxidases pump protons with a stoichiometry of one proton per electron transferred to the,catalytic site. The bacterial A-class oxidases use two proton pathways (denoted by letters D and K, respectively), for the transfer of protons to the catalytic site, and protons that are pumped across the membrane. The B-type oxidases such as, for example, the ba(3) oxidase from Thermus thermophilus, pump protons with a lower stoichiometry of 0.5 H+/electron and use only one proton pathway for the transfer of all protons. This pathway overlaps in space with the K pathway in the A class oxidases without showing any sequence homology though. Here, we review the functional properties of the A- and the B-class ba3 oxidases with a focus on mechanisms of proton transfer and pumping. This article is part of a Special Issue entitled: Respiratory Oxidases.
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