---
_id: '12757'
abstract:
- lang: eng
text: My group and myself have studied respiratory complex I for almost 30 years,
starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics.
First breakthrough was the X-ray structure of the peripheral arm, followed by
structures of the membrane arm and finally the entire complex from Thermus thermophilus.
The developments in cryo-EM technology allowed us to solve the first complete
structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism
coupling, over large distances, the transfer of two electrons to pumping of four
protons across the membrane remained an enigma. Recently we have solved high-resolution
structures of mammalian and bacterial complex I under a range of redox conditions,
including catalytic turnover. This allowed us to propose a robust and universal
mechanism for complex I and related protein families. Redox reactions initially
drive conformational changes around the quinone cavity and a long-distance transfer
of substrate protons. These set up a stage for a series of electrostatically driven
proton transfers along the membrane arm (‘domino effect'), eventually resulting
in proton expulsion from the distal antiporter-like subunit. The mechanism radically
differs from previous suggestions, however, it naturally explains all the unusual
structural features of complex I. In this review I discuss the state of knowledge
on complex I, including the current most controversial issues.
article_processing_charge: No
article_type: review
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we
learned from the structures of respiratory complex I. The Biochemical Journal.
2023;480(5):319-333. doi:10.1042/BCJ20210285'
apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism:
What have we learned from the structures of respiratory complex I. The Biochemical
Journal. Portland Press. https://doi.org/10.1042/BCJ20210285'
chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism:
What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.'
ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have
we learned from the structures of respiratory complex I,” The Biochemical Journal,
vol. 480, no. 5. Portland Press, pp. 319–333, 2023.'
ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What
have we learned from the structures of respiratory complex I. The Biochemical
Journal. 480(5), 319–333.'
mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What
Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.'
short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:45:12Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1042/BCJ20210285
external_id:
isi:
- '000957065700001'
pmid:
- '36920092'
has_accepted_license: '1'
intvolume: ' 480'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BCJ20210285
month: '03'
oa: 1
oa_version: Published Version
page: 319-333
pmid: 1
publication: The Biochemical Journal
publication_identifier:
eissn:
- 1470-8728
issn:
- 0264-6021
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned
from the structures of respiratory complex I'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2023'
...
---
_id: '13232'
abstract:
- lang: eng
text: The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus
has led to its rapid spread, causing over 600 million confirmed cases and more
than 6.5 million confirmed deaths. The huge demand for the rapid development and
deployment of low-cost and effective vaccines against emerging variants has renewed
interest in DNA vaccine technology. Here, we report the rapid generation and immunological
evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron
variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP).
The delivery of DNA vaccines using electroporation in a two-dose regimen induced
high-antibody titers and profound cellular responses in mice. The antibody titers
induced against the Omicron variant of the vaccine were sufficient for effective
protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein
in the vaccine construct shifted the immune response to the favorable Th1-like
type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery
by needle-free injection allowed us to achieve antibody titers comparable with
mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform
as a promising solution for robust and effective SARS-CoV-2 protection, supporting
further translational study.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article, or the decision to submit it for publication.
The authors express their gratitude to the Institute of Physiology of the National
Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.
article_number: '1014'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Maria
full_name: Stegantseva, Maria
last_name: Stegantseva
- first_name: Sergey
full_name: Golenchenko, Sergey
last_name: Golenchenko
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Dzmitry
full_name: Lutskovich, Dzmitry
last_name: Lutskovich
- first_name: Anton
full_name: Kavaleuski, Anton
id: 62304f89-eb97-11eb-a6c2-8903dd183976
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
citation:
ama: Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of
SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6).
doi:10.3390/vaccines11061014
apa: Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M.,
Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA
vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014
chicago: Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko,
Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander
Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP
Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.
ieee: D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA
vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI,
2023.
ista: Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S,
Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2
DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.
mla: Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine
Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI,
2023, doi:10.3390/vaccines11061014.
short: D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S.
Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-02T06:31:19Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/vaccines11061014
external_id:
isi:
- '001017740000001'
file:
- access_level: open_access
checksum: 8f484c0f30f8699c589b1c29a0fd7d7f
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T07:25:43Z
date_updated: 2023-07-18T07:25:43Z
file_id: '13244'
file_name: 2023_Vaccines_Dormeshkin.pdf
file_size: 2339746
relation: main_file
success: 1
file_date_updated: 2023-07-18T07:25:43Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Vaccines
publication_identifier:
eissn:
- 2076-393X
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion
protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2023'
...
---
_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
citation:
ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its
cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781
apa: Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex
I and its cyanobacterial ortholog. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12781
chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex
I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12781.
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. Structural and Mechanistic Study of Bacterial Complex
I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12781.
short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and
Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.
date_created: 2023-03-31T12:24:42Z
date_published: 2023-03-23T00:00:00Z
date_updated: 2023-08-04T08:54:51Z
day: '23'
ddc:
- '570'
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LeSa
doi: 10.15479/at:ista:12781
ec_funded: 1
file:
- access_level: closed
checksum: 5ebb6345cb4119f93460c81310265a6d
content_type: application/pdf
creator: vkravchu
date_created: 2023-04-19T14:33:41Z
date_updated: 2023-04-19T14:33:41Z
embargo: 2024-04-20
embargo_to: local
file_id: '12852'
file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf
file_size: 6071553
relation: main_file
- access_level: closed
checksum: c12055c48411d030d2afa51de2166221
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: vkravchu
date_created: 2023-04-19T14:33:52Z
date_updated: 2023-04-20T07:02:59Z
embargo: 2024-04-20
embargo_to: local
file_id: '12853'
file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx
file_size: 19468766
relation: source_file
file_date_updated: 2023-04-20T07:02:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14040'
abstract:
- lang: eng
text: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure
efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex.
The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction
center polypeptide and promotes the initial steps of PSII assembly, but its binding
site is unclear. Here we use cryo-electron microscopy to determine the structure
of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached.
Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that
ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the
premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions
with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall,
our work provides valuable insights into the early stages of PSII assembly and
the structural changes that create the binding site for the Mn4CaO5 cluster.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: P.J.N. and J.W.M. are grateful for the support of the Biotechnology
& Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J.
Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project
19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the
IST high-performance computing cluster.
article_number: '4681'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ziyu
full_name: Zhao, Ziyu
last_name: Zhao
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Jana
full_name: Knoppová, Jana
last_name: Knoppová
- first_name: Roman
full_name: Sobotka, Roman
last_name: Sobotka
- first_name: James W.
full_name: Murray, James W.
last_name: Murray
- first_name: Peter J.
full_name: Nixon, Peter J.
last_name: Nixon
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Josef
full_name: Komenda, Josef
last_name: Komenda
citation:
ama: Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies
the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6
apa: Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon,
P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6
chicago: Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray,
Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor
Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem
II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.
ieee: Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov
LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving
manganese cluster during photosystem II biogenesis. Nature Communications. 14,
4681.
mla: Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving
Manganese Cluster during Photosystem II Biogenesis.” Nature Communications,
vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.
short: Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon,
L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2023-12-13T12:06:56Z
day: '04'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-023-40388-6
external_id:
isi:
- '001042606700004'
file:
- access_level: open_access
checksum: 3b9043df3d51c300f9be95eac3ff9d0b
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:01:12Z
date_updated: 2023-08-14T07:01:12Z
file_id: '14044'
file_name: 2023_NatureComm_Zhao.pdf
file_size: 2315325
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:01:12Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese
cluster during photosystem II biogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '10182'
abstract:
- lang: eng
text: The mitochondrial oxidative phosphorylation system is central to cellular
metabolism. It comprises five enzymatic complexes and two mobile electron carriers
that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing
equivalents coming into mitochondria to the generation and subsequent dissipation
of a proton gradient across the inner mitochondrial membrane, this electron transport
chain drives the production of ATP, which is then used as a primary energy carrier
in virtually all cellular processes. Minimal perturbations of the respiratory
chain activity are linked to diseases; therefore, it is necessary to understand
how these complexes are assembled and regulated and how they function. In this
Review, we outline the latest assembly models for each individual complex, and
we also highlight the recent discoveries indicating that the formation of larger
assemblies, known as respiratory supercomplexes, originates from the association
of the intermediates of individual complexes. We then discuss how recent cryo-electron
microscopy structures have been key to answering open questions on the function
of the electron transport chain in mitochondrial respiration and how supercomplexes
and other factors, including metabolites, can regulate the activity of the single
complexes. When relevant, we discuss how these mechanisms contribute to physiology
and outline their deregulation in human diseases.
article_processing_charge: No
article_type: original
author:
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: ' 0000-0001-5618-3449'
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial
respiratory chain. Nature Reviews Molecular Cell Biology. 2022;23:141–161.
doi:10.1038/s41580-021-00415-0
apa: Vercellino, I., & Sazanov, L. A. (2022). The assembly, regulation and function
of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology.
Springer Nature. https://doi.org/10.1038/s41580-021-00415-0
chicago: Vercellino, Irene, and Leonid A Sazanov. “The Assembly, Regulation and
Function of the Mitochondrial Respiratory Chain.” Nature Reviews Molecular
Cell Biology. Springer Nature, 2022. https://doi.org/10.1038/s41580-021-00415-0.
ieee: I. Vercellino and L. A. Sazanov, “The assembly, regulation and function of
the mitochondrial respiratory chain,” Nature Reviews Molecular Cell Biology,
vol. 23. Springer Nature, pp. 141–161, 2022.
ista: Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the
mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161.
mla: Vercellino, Irene, and Leonid A. Sazanov. “The Assembly, Regulation and Function
of the Mitochondrial Respiratory Chain.” Nature Reviews Molecular Cell Biology,
vol. 23, Springer Nature, 2022, pp. 141–161, doi:10.1038/s41580-021-00415-0.
short: I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022)
141–161.
date_created: 2021-10-24T22:01:35Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-02T06:55:42Z
day: '01'
department:
- _id: LeSa
doi: 10.1038/s41580-021-00415-0
external_id:
isi:
- '000705697100001'
pmid:
- '34621061'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 141–161
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
eissn:
- 1471-0080
issn:
- 1471-0072
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The assembly, regulation and function of the mitochondrial respiratory chain
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2022'
...
---
_id: '11167'
abstract:
- lang: eng
text: Complex I is one of the major respiratory complexes, conserved from bacteria
to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane,
thus playing a central role in the oxidative energy metabolism. In this review
we discuss our current state of understanding the structure of complex I from
various species of mammals, plants, fungi, and bacteria, as well as of several
complex I-related proteins. By comparing the structural evidence from these systems
in different redox states and data from mutagenesis and molecular simulations,
we formulate the mechanisms of electron transfer and proton pumping and explain
how they are conformationally and electrostatically coupled. Finally, we discuss
the structural basis of the deactivation phenomenon in mammalian complex I.
article_number: '102350'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint
for the mechanism. Current Opinion in Structural Biology. 2022;74. doi:10.1016/j.sbi.2022.102350
apa: Kampjut, D., & Sazanov, L. A. (2022). Structure of respiratory complex
I – An emerging blueprint for the mechanism. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2022.102350
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex
I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural
Biology. Elsevier, 2022. https://doi.org/10.1016/j.sbi.2022.102350.
ieee: D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging
blueprint for the mechanism,” Current Opinion in Structural Biology, vol.
74. Elsevier, 2022.
ista: Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging
blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I
– An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology,
vol. 74, 102350, Elsevier, 2022, doi:10.1016/j.sbi.2022.102350.
short: D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).
date_created: 2022-04-15T09:32:35Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:31:06Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.sbi.2022.102350
external_id:
isi:
- '000829029500020'
pmid:
- '35316665'
file:
- access_level: open_access
checksum: 72bdde48853643a32d42b75f54965c44
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T05:56:03Z
date_updated: 2022-08-05T05:56:03Z
file_id: '11725'
file_name: 2022_CurrentOpStructBiology_Kampjut.pdf
file_size: 815607
relation: main_file
success: 1
file_date_updated: 2022-08-05T05:56:03Z
has_accepted_license: '1'
intvolume: ' 74'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Structural Biology
publication_identifier:
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of respiratory complex I – An emerging blueprint for the mechanism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 74
year: '2022'
...
---
_id: '11551'
abstract:
- lang: eng
text: Imbalanced mitochondrial dNTP pools are known players in the pathogenesis
of multiple human diseases. Here we show that, even under physiological conditions,
dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues
and human cultured cells. In addition, a vast majority of mitochondrial dGTP is
tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial
respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with
deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific
function beyond stabilizing the complex I holoenzyme has been described for this
subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving
complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding
capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content,
proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction
may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability
and linking oxidative metabolism to DNA maintenance.
acknowledgement: "We thank Dr, Luke Formosa (Department of Biochemistry and Molecular
Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia)
for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc
Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology
[VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance
with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry,
Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00
to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025
to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an
NHMRC Project grant to M.R. (GNT1164459).\r\n"
article_number: '620'
article_processing_charge: No
author:
- first_name: David
full_name: Molina-Granada, David
last_name: Molina-Granada
- first_name: Emiliano
full_name: González-Vioque, Emiliano
last_name: González-Vioque
- first_name: Marris G.
full_name: Dibley, Marris G.
last_name: Dibley
- first_name: Raquel
full_name: Cabrera-Pérez, Raquel
last_name: Cabrera-Pérez
- first_name: Antoni
full_name: Vallbona-Garcia, Antoni
last_name: Vallbona-Garcia
- first_name: Javier
full_name: Torres-Torronteras, Javier
last_name: Torres-Torronteras
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Michael T.
full_name: Ryan, Michael T.
last_name: Ryan
- first_name: Yolanda
full_name: Cámara, Yolanda
last_name: Cámara
- first_name: Ramon
full_name: Martí, Ramon
last_name: Martí
citation:
ama: Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP
is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 2022;5(1). doi:10.1038/s42003-022-03568-6
apa: Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R.,
Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03568-6
chicago: Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel
Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov,
Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is
Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” Communications
Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03568-6.
ieee: D. Molina-Granada et al., “Most mitochondrial dGTP is tightly bound
to respiratory complex I through the NDUFA10 subunit,” Communications Biology,
vol. 5, no. 1. Springer Nature, 2022.
ista: Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia
A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 5(1), 620.
mla: Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to
Respiratory Complex I through the NDUFA10 Subunit.” Communications Biology,
vol. 5, no. 1, 620, Springer Nature, 2022, doi:10.1038/s42003-022-03568-6.
short: D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A.
Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R.
Martí, Communications Biology 5 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-23T00:00:00Z
date_updated: 2023-08-03T11:51:58Z
day: '23'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-022-03568-6
external_id:
isi:
- '000815098500002'
pmid:
- ' 35739187'
file:
- access_level: open_access
checksum: 965f88bbcef3fd0c3e121340555c4467
content_type: application/pdf
creator: kschuh
date_created: 2022-07-13T07:44:58Z
date_updated: 2022-07-13T07:44:58Z
file_id: '11571'
file_name: 2022_communicationsbiology_Molina-Granada.pdf
file_size: 2335369
relation: main_file
success: 1
file_date_updated: 2022-07-13T07:44:58Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- '23993642'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Most mitochondrial dGTP is tightly bound to respiratory complex I through the
NDUFA10 subunit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...
---
_id: '11648'
abstract:
- lang: eng
text: 'Progress in structural membrane biology has been significantly accelerated
by the ongoing ''Resolution Revolution'' in cryo electron microscopy (cryo-EM).
In particular, structure determination by single particle analysis has evolved
into the most powerful method for atomic model building of multisubunit membrane
protein complexes. This has created an ever increasing demand in cryo-EM machine
time, which to satisfy is in need of new and affordable cryo electron microscopes.
Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the
structure determination by single particle analysis of three different multisubunit
membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus
elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella
enterica.'
acknowledgement: "Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan
Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project
for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative
Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266
to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and
C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows
(20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from
Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer
project and also would like to thank Hideki Shigematsu for critical reading of the
manuscript. And we are indebted to the two anonymous reviewers who helped us to
improve our manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Gerle, Christoph
last_name: Gerle
- first_name: Jun-ichi
full_name: Kishikawa, Jun-ichi
last_name: Kishikawa
- first_name: Tomoko
full_name: Yamaguchi, Tomoko
last_name: Yamaguchi
- first_name: Atsuko
full_name: Nakanishi, Atsuko
last_name: Nakanishi
- first_name: Mehmet Orkun
full_name: Çoruh, Mehmet Orkun
id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef
last_name: Çoruh
orcid: 0000-0002-3219-2022
- first_name: Fumiaki
full_name: Makino, Fumiaki
last_name: Makino
- first_name: Tomoko
full_name: Miyata, Tomoko
last_name: Miyata
- first_name: Akihiro
full_name: Kawamoto, Akihiro
last_name: Kawamoto
- first_name: Ken
full_name: Yokoyama, Ken
last_name: Yokoyama
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: Genji
full_name: Kurisu, Genji
last_name: Kurisu
- first_name: Takayuki
full_name: Kato, Takayuki
last_name: Kato
citation:
ama: Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane
complexes with the CRYO ARM 200. Microscopy. 2022;71(5):249-261. doi:10.1093/jmicro/dfac037
apa: Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino,
F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the
CRYO ARM 200. Microscopy. Oxford University Press. https://doi.org/10.1093/jmicro/dfac037
chicago: Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi,
Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit
Membrane Complexes with the CRYO ARM 200.” Microscopy. Oxford University
Press, 2022. https://doi.org/10.1093/jmicro/dfac037.
ieee: C. Gerle et al., “Structures of multisubunit membrane complexes with
the CRYO ARM 200,” Microscopy, vol. 71, no. 5. Oxford University Press,
pp. 249–261, 2022.
ista: Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata
T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit
membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.
mla: Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with
the CRYO ARM 200.” Microscopy, vol. 71, no. 5, Oxford University Press,
2022, pp. 249–61, doi:10.1093/jmicro/dfac037.
short: C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino,
T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy
71 (2022) 249–261.
date_created: 2022-07-25T10:04:58Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T12:13:37Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1093/jmicro/dfac037
external_id:
isi:
- '000837950900001'
pmid:
- '35861182'
file:
- access_level: open_access
checksum: 23b51c163636bf9313f7f0818312e67e
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T08:34:48Z
date_updated: 2023-02-03T08:34:48Z
file_id: '12498'
file_name: 2022_Microscopy_Gerle.pdf
file_size: 7812696
relation: main_file
success: 1
file_date_updated: 2023-02-03T08:34:48Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '5'
keyword:
- Radiology
- Nuclear Medicine and imaging
- Instrumentation
- Structural Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 249-261
pmid: 1
publication: Microscopy
publication_identifier:
eissn:
- 2050-5701
issn:
- 2050-5698
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structures of multisubunit membrane complexes with the CRYO ARM 200
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 71
year: '2022'
...
---
_id: '12138'
abstract:
- lang: eng
text: 'Complex I is the first enzyme in the respiratory chain, which is responsible
for energy production in mitochondria and bacteria1. Complex I couples the transfer
of two electrons from NADH to quinone and the translocation of four protons across
the membrane2, but the coupling mechanism remains contentious. Here we present
cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different
redox states, including catalytic turnover. EcCI exists mostly in the open state,
in which the quinone cavity is exposed to the cytosol, allowing access for water
molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI
can convert to the closed state only during turnover, showing that closed and
open states are genuine turnover intermediates. The open-to-closed transition
results in the tightly engulfed quinone cavity being connected to the central
axis of the membrane arm, a source of substrate protons. Consistently, the proportion
of the closed state increases with increasing pH. We propose a detailed but straightforward
and robust mechanism comprising a ‘domino effect’ series of proton transfers and
electrostatic interactions: the forward wave (‘dominoes stacking’) primes the
pump, and the reverse wave (‘dominoes falling’) results in the ejection of all
pumped protons from the distal subunit NuoL. This mechanism explains why protons
exit exclusively from the NuoL subunit and is supported by our mutagenesis data.
We contend that this is a universal coupling mechanism of complex I and related
enzymes.'
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by the Electron Microscopy Facility (EMF),
the Life Science Facility (LSF) and the IST high-performance computing cluster.
We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance
with collecting cryo-EM data and A. Charnagalov for the assistance with protein
purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of
Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are
funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also
supported by the Medical Research Council (UK).
article_processing_charge: No
article_type: original
author:
- first_name: Vladyslav
full_name: Kravchuk, Vladyslav
id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
last_name: Kravchuk
- first_name: Olga
full_name: Petrova, Olga
id: 5D8C9660-5D49-11EA-8188-567B3DDC885E
last_name: Petrova
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Anna
full_name: Wojciechowska-Bason, Anna
last_name: Wojciechowska-Bason
- first_name: Zara
full_name: Breese, Zara
last_name: Breese
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov
LA. A universal coupling mechanism of respiratory complex I. Nature. 2022;609(7928):808-814.
doi:10.1038/s41586-022-05199-7
apa: Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z.,
& Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex
I. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05199-7
chicago: Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason,
Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory
Complex I.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05199-7.
ieee: V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and
L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” Nature,
vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.
ista: Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov
LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928),
808–814.
mla: Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory
Complex I.” Nature, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14,
doi:10.1038/s41586-022-05199-7.
short: V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A.
Sazanov, Nature 609 (2022) 808–814.
date_created: 2023-01-12T12:04:33Z
date_published: 2022-09-22T00:00:00Z
date_updated: 2023-08-04T08:54:52Z
day: '22'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-022-05199-7
ec_funded: 1
external_id:
isi:
- '000854788200001'
pmid:
- '36104567'
file:
- access_level: open_access
checksum: d42a93e24f59e883ef0b5429832391d0
content_type: application/pdf
creator: lsazanov
date_created: 2023-05-30T17:05:31Z
date_updated: 2023-05-30T17:05:31Z
file_id: '13104'
file_name: EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf
file_size: 1425655
relation: main_file
success: 1
- access_level: open_access
checksum: 5422bc0a73b3daadafa262c7ea6deae3
content_type: application/pdf
creator: lsazanov
date_created: 2023-05-30T17:07:05Z
date_updated: 2023-05-30T17:07:05Z
file_id: '13105'
file_name: EcCxI_manuscript_rev3_SI_All_opt_upd.pdf
file_size: 9842513
relation: main_file
success: 1
file_date_updated: 2023-05-30T17:07:05Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '7928'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 808-814
pmid: 1
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: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-022-05457-8
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/proton-dominos-kick-off-life/
record:
- id: '12781'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A universal coupling mechanism of respiratory complex I
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 609
year: '2022'
...
---
_id: '12252'
abstract:
- lang: eng
text: The COVID−19 pandemic not only resulted in a global crisis, but also accelerated
vaccine development and antibody discovery. Herein we report a synthetic humanized
VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2
variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based
randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle
amplification resulted in more than 1011 diverse phage display
library in a manageable for a single person number of electroporation reactions.
We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants
of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic
humanized antibody library. In order to explore the most robust and fast method
for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling
and avidity engineering by multivalent trimeric VHH fusion protein construction.
As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in
nM and pM range respectively. Importantly, these affinities are weakly influenced
by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5.
The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and
9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron
BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2
neutralization binders with the therapeutic potential for present and future SARS-CoV-2
variants.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article or the decision to submit it for publication.
article_number: '965446'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Anton
full_name: Kavaleuski, Anton
id: 4968f7ad-eb97-11eb-a6c2-8ed382e8912c
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Alexandr
full_name: Migas, Alexandr
last_name: Migas
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
- first_name: Sergei
full_name: Semyonov, Sergei
last_name: Semyonov
citation:
ama: Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant
SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers
in Immunology. 2022;13. doi:10.3389/fimmu.2022.965446
apa: Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas,
A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology.
Frontiers Media. https://doi.org/10.3389/fimmu.2022.965446
chicago: Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai
Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of
an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody
Library.” Frontiers in Immunology. Frontiers Media, 2022. https://doi.org/10.3389/fimmu.2022.965446.
ieee: D. Dormeshkin et al., “Isolation of an escape-resistant SARS-CoV-2
neutralizing nanobody from a novel synthetic nanobody library,” Frontiers in
Immunology, vol. 13. Frontiers Media, 2022.
ista: Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko
A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13,
965446.
mla: Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing
Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology,
vol. 13, 965446, Frontiers Media, 2022, doi:10.3389/fimmu.2022.965446.
short: D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas,
A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).
date_created: 2023-01-16T09:56:57Z
date_published: 2022-09-16T00:00:00Z
date_updated: 2023-08-04T09:49:24Z
day: '16'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3389/fimmu.2022.965446
external_id:
isi:
- '000862479100001'
file:
- access_level: open_access
checksum: f8f5d8110710033d0532e7e08bf9dad4
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:22:26Z
date_updated: 2023-01-30T09:22:26Z
file_id: '12443'
file_name: 2022_FrontiersImmunology_Dormeshkin.pdf
file_size: 5695892
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:22:26Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- Immunology
- Immunology and Allergy
- COVID-19
- SARS-CoV-2
- synthetic library
- RBD
- neutralization nanobody
- VHH
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel
synthetic nanobody library
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...