---
OA_place: publisher
_id: '17319'
abstract:
- lang: eng
  text: "This thesis comprises two distinct projects, each offering unique insights
    into fundamental\r\ncellular processes. While distinct in their focus, these different
    perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the
    proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP
    synthesis, effectively bridging the membrane protein\r\nstructure and function
    from the realms of plant biology and cellular bioenergetics.\r\nThe first project
    of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane
    transporters pivotal in the regulation of auxin transport and distribution in\r\nplants.
    PINs form a conserved and phylogenetically abundant group of transporters present
    in\r\nland plants and certain algae. Despite their great importance, they were
    one of the few elusive\r\nproteins essential for plant development not to be structurally
    and mechanistically\r\ncharacterised since their discovery almost 30 years ago.
    This work aimed to uncover the\r\nstructural and functional dynamics of the PIN
    protein-mediated auxin transport using an array\r\nof experimental techniques,
    including protein purification, biochemical assays and structural\r\nanalysis.
    Through an exhaustive screening process that took several years and included testing\r\ndifferent
    PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped
    a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover,
    utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits
    detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and
    6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking,
    we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural
    studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently
    published structures,\r\nour map implies major pH-dependent conformational changes
    and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe
    subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto
    cellular energy metabolism. Through an approach integrating biochemical assays
    and\r\nstructural analysis, this research aimed to unveil the molecular mechanism
    of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential
    therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP
    synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits
    both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide
    inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition
    in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for
    the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState
    2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in
    our maps;\r\nhowever, we cannot definitively determine the exact mechanism of
    yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal
    binding of the inhibitor."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kristina
  full_name: Lukic, Kristina
  id: 2B04DB84-F248-11E8-B48F-1D18A9856A87
  last_name: Lukic
  orcid: 0000-0003-1581-881X
citation:
  ama: 'Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating
    auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor
    Yaku’amide B. 2024. doi:<a href="https://doi.org/10.15479/at:ista:17319">10.15479/at:ista:17319</a>'
  apa: 'Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics :
    Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the
    novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/at:ista:17319">https://doi.org/10.15479/at:ista:17319</a>'
  chicago: 'Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics :
    Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the
    Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024.
    <a href="https://doi.org/10.15479/at:ista:17319">https://doi.org/10.15479/at:ista:17319</a>.'
  ieee: 'K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating
    auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor
    Yaku’amide B,” Institute of Science and Technology Austria, 2024.'
  ista: 'Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics :
    Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the
    novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.'
  mla: 'Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics :
    Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the
    Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria,
    2024, doi:<a href="https://doi.org/10.15479/at:ista:17319">10.15479/at:ista:17319</a>.'
  short: 'K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating
    Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor
    Yaku’amide B, Institute of Science and Technology Austria, 2024.'
corr_author: '1'
date_created: 2024-07-26T09:05:55Z
date_published: 2024-07-26T00:00:00Z
date_updated: 2026-04-07T13:20:44Z
day: '26'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: LeSa
- _id: GradSch
doi: 10.15479/at:ista:17319
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: '224'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Leonid A
  full_name: Sazanov, Leonid A
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
  last_name: Sazanov
  orcid: 0000-0002-0977-7989
title: 'Membrane proteins in plant physiology and bioenergetics : Investigating auxin
  efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku''amide
  B'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '12781'
abstract:
- lang: eng
  text: "Most energy in humans is produced in form of ATP by the mitochondrial respiratory
    chain consisting of several protein assemblies embedded into lipid membrane (complexes
    I-V). Complex I is the first and the largest enzyme of the respiratory chain which
    is essential for energy production. It couples the transfer of two electrons from
    NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial
    membrane. The coupling mechanism between electron transfer and proton translocation
    is one of the biggest enigma in bioenergetics and structural biology. Even though
    the enzyme has been studied for decades, only recent technological advances in
    cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from
    E.coli appears to be of special importance because it is a perfect model system
    with a rich mutant library, however the structure of the entire complex was unknown.
    In this thesis I have resolved structures of the minimal complex I version from
    E. coli in different states including reduced, inhibited, under reaction turnover
    and several others. Extensive structural analyses of these structures and comparison
    to structures from other species allowed to derive general features of conformational
    dynamics and propose a universal coupling mechanism. The mechanism is straightforward,
    robust and consistent with decades of experimental data available for complex
    I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I)
    is a part of broad complex I superfamily and was studied as well in this thesis.
    It plays an important role in cyclic electron transfer (CET), during which electrons
    are cycled within PSI through ferredoxin and plastoquinone to generate proton
    gradient without NADPH production. Here, I solved structure of NDH and revealed
    additional state, which was not observed before. The novel “resting” state allowed
    to propose the mechanism of CET regulation. Moreover, conformational dynamics
    of NDH resembles one in complex I which suggest more broad universality of the
    proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped
    to interpret decades of experimental data for complex I and contributed to fundamental
    mechanistic understanding of protein function.\r\n"
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vladyslav
  full_name: Kravchuk, Vladyslav
  id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
  last_name: Kravchuk
  orcid: 0000-0001-9523-9089
citation:
  ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its
    cyanobacterial ortholog. 2023. doi:<a href="https://doi.org/10.15479/at:ista:12781">10.15479/at:ista:12781</a>
  apa: Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex
    I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/at:ista:12781">https://doi.org/10.15479/at:ista:12781</a>
  chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex
    I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria,
    2023. <a href="https://doi.org/10.15479/at:ista:12781">https://doi.org/10.15479/at:ista:12781</a>.
  ieee: V. Kravchuk, “Structural and mechanistic study of bacterial complex I and
    its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.
  ista: Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I
    and its cyanobacterial ortholog. Institute of Science and Technology Austria.
  mla: Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex
    I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria,
    2023, doi:<a href="https://doi.org/10.15479/at:ista:12781">10.15479/at:ista:12781</a>.
  short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and
    Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-03-31T12:24:42Z
date_published: 2023-03-23T00:00:00Z
date_updated: 2026-04-07T14:10:40Z
day: '23'
ddc:
- '570'
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LeSa
doi: 10.15479/at:ista:12781
ec_funded: 1
file:
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  creator: vkravchu
  date_created: 2023-04-19T14:33:41Z
  date_updated: 2024-04-22T22:30:06Z
  embargo: 2024-04-20
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  date_created: 2023-04-19T14:33:52Z
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  relation: source_file
file_date_updated: 2024-04-22T22:30:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '127'
project:
- _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E
  grant_number: '25541'
  name: 'Structural characterization of E. coli complex I: an important mechanistic
    model'
- _id: 627abdeb-2b32-11ec-9570-ec31a97243d3
  call_identifier: H2020
  grant_number: '101020697'
  name: Structure and mechanism of respiratory chain molecular machines
publication_identifier:
  isbn:
  - 978-3-99078-029-9
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '12138'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Leonid A
  full_name: Sazanov, Leonid A
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
  last_name: Sazanov
  orcid: 0000-0002-0977-7989
title: Structural and mechanistic study of bacterial complex I and its cyanobacterial
  ortholog
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '8353'
abstract:
- lang: eng
  text: "Mrp (Multi resistance and pH adaptation) are broadly distributed secondary
    active antiporters that catalyze the transport of monovalent ions such as sodium
    and potassium outside of the cell coupled to the inward translocation of protons.
    Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG)
    encoded in a single operon, whereas other antiporters catalyzing the same reaction
    are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular
    pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline
    environments and for reduction of the intracellular concentration of toxic cations.
    Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp
    subunits have primary sequence similarity to essential redox-driven proton pumps,
    such as respiratory complex I and membrane-bound hydrogenases. This similarity
    reinforces the hypothesis that these present day redox-driven proton pumps are
    descended from the Mrp antiporter. The Mrp structure serves as a model to understand
    the yet obscure coupling mechanism between ion or electron transfer and proton
    translocation in this large group of proteins. In the thesis, I am presenting
    the purification, biochemical analysis, cryo-EM analysis and molecular structure
    of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å
    resolution. Numerous conditions were screened to purify Mrp to high homogeneity
    and to obtain an appropriate distribution of single particles on cryo-EM grids
    covered with a continuous layer of ultrathin carbon. A preferred particle orientation
    problem was solved by performing a tilted data collection. The activity assays
    showed the specific pH-dependent\r\nprofile of secondary active antiporters. The
    molecular structure shows that Mrp is a dimer of seven-subunit protomers with
    50 trans-membrane helices each. The dimer interface is built by many short and
    tilted transmembrane helices, probably causing a thinning of the bacterial membrane.
    The surface charge distribution shows an extraordinary asymmetry within each monomer,
    revealing presumable proton and sodium translocation pathways. The two largest\r\nand
    homologous Mrp subunits MrpA and MrpD probably translocate one proton each into
    the cell. The sodium ion is likely being translocated in the opposite direction
    within the small subunits along a ladder of charged and conserved residues. Based
    on the structure, we propose a mechanism were the antiport activity is accomplished
    via electrostatic interactions between the charged cations and key charged residues.
    The flexible key TM helices coordinate these\r\nelectrostatic interactions, while
    the membrane thinning between the monomers enables the translocation of sodium
    across the charged membrane. The entire family of redox-driven proton pumps is
    likely to perform their mechanism in a likewise manner."
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
acknowledgement: "I acknowledge the scientific service units of the IST Austria for
  providing resources by the Life Science Facility, the Electron Microscopy Facility
  and the high-performance computer cluster. Special thanks to the cryo-EM specialists
  Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front
  of the microscope and for supporting me to collect the data presented here. I also
  want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from
  Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian
  Academy of Sciences."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
  full_name: Steiner, Julia
  id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
  last_name: Steiner
  orcid: 0000-0003-0493-3775
citation:
  ama: Steiner J. Biochemical and structural investigation of the Mrp antiporter,
    an ancestor of complex I. 2020. doi:<a href="https://doi.org/10.15479/AT:ISTA:8353">10.15479/AT:ISTA:8353</a>
  apa: Steiner, J. (2020). <i>Biochemical and structural investigation of the Mrp
    antiporter, an ancestor of complex I</i>. Institute of Science and Technology
    Austria. <a href="https://doi.org/10.15479/AT:ISTA:8353">https://doi.org/10.15479/AT:ISTA:8353</a>
  chicago: Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter,
    an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020.
    <a href="https://doi.org/10.15479/AT:ISTA:8353">https://doi.org/10.15479/AT:ISTA:8353</a>.
  ieee: J. Steiner, “Biochemical and structural investigation of the Mrp antiporter,
    an ancestor of complex I,” Institute of Science and Technology Austria, 2020.
  ista: Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter,
    an ancestor of complex I. Institute of Science and Technology Austria.
  mla: Steiner, Julia. <i>Biochemical and Structural Investigation of the Mrp Antiporter,
    an Ancestor of Complex I</i>. Institute of Science and Technology Austria, 2020,
    doi:<a href="https://doi.org/10.15479/AT:ISTA:8353">10.15479/AT:ISTA:8353</a>.
  short: J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter,
    an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-09-09T14:27:01Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2026-04-08T07:23:36Z
day: '09'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: LeSa
doi: 10.15479/AT:ISTA:8353
file:
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language:
- iso: eng
month: '09'
oa: 1
oa_version: None
page: '191'
project:
- _id: 26169496-B435-11E9-9278-68D0E5697425
  grant_number: '24741'
  name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex
    I
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '8284'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Leonid A
  full_name: Sazanov, Leonid A
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
  last_name: Sazanov
  orcid: 0000-0002-0977-7989
title: Biochemical and structural investigation of the Mrp antiporter, an ancestor
  of complex I
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
OA_place: publisher
_id: '8340'
abstract:
- lang: eng
  text: Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative
    phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven
    proton pumping machines which establish a proton motive force across the inner
    mitochondrial membrane. This electrochemical proton gradient is used to drive
    ATP synthesis, which powers the majority of cellular processes such as protein
    synthesis, locomotion and signalling. In this thesis I investigate the structures
    and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory
    complex I and transhydrogenase. I present the first high-resolution structure
    of the full transhydrogenase from any species, and a significantly improved structure
    of complex I. Improving the resolution from 3.3 Å available previously to up to
    2.3 Å in this thesis allowed us to model bound water molecules, crucial in the
    proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different
    substrates and inhibitors bound were solved to delineate the catalytic cycle and
    understand the proton pumping mechanism. In transhydrogenase, the proton channel
    is gated by reversible detachment of the NADP(H)-binding domain which opens the
    proton channel to the opposite sites of the membrane. In complex I, the proton
    channels are gated by reversible protonation of key glutamate and lysine residues
    and breaking of the water wire connecting the proton pumps with the quinone reduction
    site. The tight coupling between the redox and the proton pumping reactions in
    transhydrogenase is achieved by controlling the NADP(H) exchange which can only
    happen when the NADP(H)-binding domain interacts with the membrane domain. In
    complex I, coupling is achieved by cycling of the whole complex between the closed
    state, in which quinone can get reduced, and the open state, in which NADH can
    induce quinol ejection from the binding pocket. On the basis of these results
    I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex
    I that are consistent with a large amount of previous work. In both enzymes, conformational
    and electrostatic mechanisms contribute to the overall catalytic process. Results
    presented here could be used for better understanding of the human pathologies
    arising from deficiencies of complex I or transhydrogenase and could be used to
    develop novel therapies.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'I acknowledge the support of IST facilities, especially the Electron
  Miscroscopy facility for providing training and resources. Special thanks also go
  to cryo-EM specialists who helped me to collect the data present here: Dr Valentin
  Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni.
  of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT,
  project number 653706, funded by the Horizon 2020 programme of the European Union.
  This project has received funding from the European Union’s Horizon 2020 research
  and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Domen
  full_name: Kampjut, Domen
  id: 37233050-F248-11E8-B48F-1D18A9856A87
  last_name: Kampjut
  orcid: 0000-0002-6018-3422
citation:
  ama: Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping
    enzymes. 2020. doi:<a href="https://doi.org/10.15479/AT:ISTA:8340">10.15479/AT:ISTA:8340</a>
  apa: Kampjut, D. (2020). <i>Molecular mechanisms of mitochondrial redox-coupled
    proton pumping enzymes</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:8340">https://doi.org/10.15479/AT:ISTA:8340</a>
  chicago: Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
    Pumping Enzymes.” Institute of Science and Technology Austria, 2020. <a href="https://doi.org/10.15479/AT:ISTA:8340">https://doi.org/10.15479/AT:ISTA:8340</a>.
  ieee: D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping
    enzymes,” Institute of Science and Technology Austria, 2020.
  ista: Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton
    pumping enzymes. Institute of Science and Technology Austria.
  mla: Kampjut, Domen. <i>Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
    Pumping Enzymes</i>. Institute of Science and Technology Austria, 2020, doi:<a
    href="https://doi.org/10.15479/AT:ISTA:8340">10.15479/AT:ISTA:8340</a>.
  short: D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping
    Enzymes, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-09-07T18:42:23Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2026-04-08T07:43:58Z
day: '09'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: LeSa
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  name: International IST Doctoral Program
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publication_status: published
publisher: Institute of Science and Technology Austria
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status: public
supervisor:
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  full_name: Sazanov, Leonid A
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
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title: Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes
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year: '2020'
...
