---
_id: '12282'
abstract:
- lang: eng
text: From a simple thought to a multicellular movement
acknowledgement: The authors want to thank Professors Carrie Bernecky, Tom Henzinger,
Martin Loose and Gaia Novarino for accepting to be interviewed, thus giving significant
contribution to the discussion that lead to this article.
article_number: '260017'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Melissa A
full_name: Stouffer, Melissa A
id: 4C9372C4-F248-11E8-B48F-1D18A9856A87
last_name: Stouffer
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
citation:
ama: Amberg N, Stouffer MA, Vercellino I. Operation STEM fatale – how an equity,
diversity and inclusion initiative has brought us to reflect on the current challenges
in cell biology and science as a whole. Journal of Cell Science. 2022;135(8).
doi:10.1242/jcs.260017
apa: Amberg, N., Stouffer, M. A., & Vercellino, I. (2022). Operation STEM fatale
– how an equity, diversity and inclusion initiative has brought us to reflect
on the current challenges in cell biology and science as a whole. Journal of
Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260017
chicago: Amberg, Nicole, Melissa A Stouffer, and Irene Vercellino. “Operation STEM
Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect
on the Current Challenges in Cell Biology and Science as a Whole.” Journal
of Cell Science. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.260017.
ieee: N. Amberg, M. A. Stouffer, and I. Vercellino, “Operation STEM fatale – how
an equity, diversity and inclusion initiative has brought us to reflect on the
current challenges in cell biology and science as a whole,” Journal of Cell
Science, vol. 135, no. 8. The Company of Biologists, 2022.
ista: Amberg N, Stouffer MA, Vercellino I. 2022. Operation STEM fatale – how an
equity, diversity and inclusion initiative has brought us to reflect on the current
challenges in cell biology and science as a whole. Journal of Cell Science. 135(8),
260017.
mla: Amberg, Nicole, et al. “Operation STEM Fatale – How an Equity, Diversity and
Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell
Biology and Science as a Whole.” Journal of Cell Science, vol. 135, no.
8, 260017, The Company of Biologists, 2022, doi:10.1242/jcs.260017.
short: N. Amberg, M.A. Stouffer, I. Vercellino, Journal of Cell Science 135 (2022).
date_created: 2023-01-16T10:03:14Z
date_published: 2022-04-19T00:00:00Z
date_updated: 2023-08-04T10:28:04Z
day: '19'
department:
- _id: SiHi
- _id: LeSa
doi: 10.1242/jcs.260017
external_id:
isi:
- '000798123600015'
pmid:
- '35438168'
intvolume: ' 135'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Operation STEM fatale – how an equity, diversity and inclusion initiative has
brought us to reflect on the current challenges in cell biology and science as a
whole
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 135
year: '2022'
...
---
_id: '10945'
abstract:
- lang: eng
text: Mica-titania pearlescent pigments (MTs) were previously coated with organic
molecules to obtain combination pigments (CPs) for achieving certain improvements
or functionalities. Anthocyanins (ACNs) are molecules that can be extracted from
natural resources and exhibit color changes via pH modifications of the enclosing
medium. The purpose of the study was to produce a new series of CPs by depositing
ACNs on MTs at different pH values, to observe the changes in color, and to associate
these changes to thermogravimetrically determined deposition efficiencies in light
of spectral differences. The extraction and deposition methods were based on aqueous
chemistry and were straightforward. The ACN deposition generally increased with
increasing pH and correlated with the consistency between the charges of the MT
surfaces and the dominant ACN species at a specific pH value. The fluorescence
of the CPs was inversely correlated with the deposition quantities invoking the
possibility of a quenching effect.
acknowledgement: "This research was partly funded by Hacettepe University (Bilimsel
Ara¸stırma Projeleri\r\nKoordinasyon Birimi), grant number FHD-2015-8094.The authors
are indebted to Ahmet Önal for his supports in acquiring the fluorescence spectra
and the decision of excitation wavelengths. The authors also acknowledge use of
the services and facilities of UNAM-National Nanotechnology Research Center at Bilkent
University and mica donation from Sabuncular Mining Co."
article_processing_charge: Yes
article_type: original
author:
- 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: Güngör
full_name: Gündüz, Güngör
last_name: Gündüz
- first_name: Üner
full_name: Çolak, Üner
last_name: Çolak
- first_name: Bora
full_name: Maviş, Bora
last_name: Maviş
citation:
ama: Çoruh MO, Gündüz G, Çolak Ü, Maviş B. pH-dependent coloring of combination
effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra.
Colorants. 2022;1(2):149-164. doi:10.3390/colorants1020010
apa: Çoruh, M. O., Gündüz, G., Çolak, Ü., & Maviş, B. (2022). pH-dependent coloring
of combination effect pigments with anthocyanins from Brassica oleracea var. capitata
F. rubra. Colorants. MDPI. https://doi.org/10.3390/colorants1020010
chicago: Çoruh, Mehmet Orkun, Güngör Gündüz, Üner Çolak, and Bora Maviş. “PH-Dependent
Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea
Var. Capitata F. Rubra.” Colorants. MDPI, 2022. https://doi.org/10.3390/colorants1020010.
ieee: M. O. Çoruh, G. Gündüz, Ü. Çolak, and B. Maviş, “pH-dependent coloring of
combination effect pigments with anthocyanins from Brassica oleracea var. capitata
F. rubra,” Colorants, vol. 1, no. 2. MDPI, pp. 149–164, 2022.
ista: Çoruh MO, Gündüz G, Çolak Ü, Maviş B. 2022. pH-dependent coloring of combination
effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra.
Colorants. 1(2), 149–164.
mla: Çoruh, Mehmet Orkun, et al. “PH-Dependent Coloring of Combination Effect Pigments
with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” Colorants,
vol. 1, no. 2, MDPI, 2022, pp. 149–64, doi:10.3390/colorants1020010.
short: M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164.
date_created: 2022-04-04T09:03:54Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2023-08-09T10:12:22Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/colorants1020010
file:
- access_level: open_access
checksum: 2c15c8d3041ebc36bc64870247081758
content_type: application/pdf
creator: dernst
date_created: 2022-04-04T10:39:24Z
date_updated: 2022-04-04T10:39:24Z
file_id: '10949'
file_name: 2022_Colorants_Coruh.pdf
file_size: 2437988
relation: main_file
success: 1
file_date_updated: 2022-04-04T10:39:24Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 149-164
publication: Colorants
publication_identifier:
issn:
- 2079-6447
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: pH-dependent coloring of combination effect pigments with anthocyanins from
Brassica oleracea var. capitata F. rubra
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2022'
...
---
_id: '11462'
abstract:
- lang: eng
text: Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic
agents and components of immunoassay systems. Synthetic antibody libraries that
could be designed and generated once and for various applications could yield
binders to virtually any targets, even for non-immunogenic or toxic ones, in a
short term. One of the most difficult tasks is to obtain antibodies with a high
affinity and specificity to polyglycosylated proteins. It requires antibody libraries
with extremely high functional diversity and the use of sophisticated selection
techniques. Here we report a development of a novel sandwich immunoassay involving
a combination of the synthetic library-derived VHH-Fc fusion protein as a capture
antibody and the immune single-chain fragment variable (scFv) as a tracer for
the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus).
We succeeded in the generation of a number of specific scFv antibodies against
PAG from the mouse immune library. Subsequent selection using the immobilized
scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse
synthetic library without any overlapping with the capture antibody binding site.
The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was
established. This is the first successful example of the combination of synthetic
and immune antibody libraries in a single sandwich immunoassay. Thus, our approach
could be used for the express isolation of antibody pairs and the development
of sandwich immunoassays for challenging antigens.
acknowledgement: This study was financially supported by the State Committee on Science
and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute
of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.
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: Alena
full_name: Karputs, Alena
last_name: Karputs
- first_name: Anton
full_name: Kavaleuski, Anton
id: 62304f89-eb97-11eb-a6c2-8903dd183976
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Ivan
full_name: Kuzminski, Ivan
last_name: Kuzminski
- first_name: Elena
full_name: Stepanova, Elena
last_name: Stepanova
- first_name: Andrei
full_name: Gilep, Andrei
last_name: Gilep
citation:
ama: Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune
scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied
Microbiology and Biotechnology. 2022;106:5093-5103. doi:10.1007/s00253-022-12022-w
apa: Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova,
E., & Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries
for pregnancy-associated glycoproteins ELISA development. Applied Microbiology
and Biotechnology. Springer Nature. https://doi.org/10.1007/s00253-022-12022-w
chicago: Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan
Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and
Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.”
Applied Microbiology and Biotechnology. Springer Nature, 2022. https://doi.org/10.1007/s00253-022-12022-w.
ieee: D. Dormeshkin et al., “Combining of synthetic VHH and immune scFv libraries
for pregnancy-associated glycoproteins ELISA development,” Applied Microbiology
and Biotechnology, vol. 106. Springer Nature, pp. 5093–5103, 2022.
ista: Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E,
Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated
glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106,
5093–5103.
mla: Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries
for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology
and Biotechnology, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:10.1007/s00253-022-12022-w.
short: D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova,
A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.
date_created: 2022-06-26T22:01:34Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-10-10T07:15:02Z
day: '01'
department:
- _id: GradSch
- _id: LeSa
doi: 10.1007/s00253-022-12022-w
external_id:
isi:
- '000813677500001'
pmid:
- '35723693'
intvolume: ' 106'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 5093-5103
pmid: 1
publication: Applied Microbiology and Biotechnology
publication_identifier:
eissn:
- 1432-0614
issn:
- 0175-7598
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Combining of synthetic VHH and immune scFv libraries for pregnancy-associated
glycoproteins ELISA development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2022'
...
---
_id: '8993'
abstract:
- lang: eng
text: N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar)
transport of the hormone auxin in plants. For decades, it has been a pivotal tool
in elucidating the unique polar auxin transport-based processes underlying plant
growth and development. Its exact mode of action has long been sought after and
is still being debated, with prevailing mechanistic schemes describing only indirect
connections between NPA and the main transporters responsible for directional
transport, namely PIN auxin exporters. Here we present data supporting a model
in which NPA associates with PINs in a more direct manner than hitherto postulated.
We show that NPA inhibits PIN activity in a heterologous oocyte system and that
expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to
specific saturable NPA binding. We thus propose that PINs are a bona fide NPA
target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent
auxin transport and a logical parsimonious explanation for the known physiological
effects of NPA on plant growth, as well as an alternative hypothesis to interpret
past and future results. We also introduce PIN dimerization and describe an effect
of NPA on this, suggesting that NPA binding could be exploited to gain insights
into structural aspects of PINs related to their transport mechanism.
acknowledgement: "This work was supported by Austrian Science Fund Grant FWF P21533-B20
(to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European
Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra
Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa
Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing
access to mass spectrometry instruments at the Vienna BioCenter Core Facilities.
We thank PNAS reviewers for the many comments and suggestions that helped to improve
this manuscript."
article_number: e2020857118
article_processing_charge: No
article_type: original
author:
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Martina
full_name: Kolb, Martina
last_name: Kolb
- first_name: Johannes
full_name: Stadlmann, Johannes
last_name: Stadlmann
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Kristina
full_name: Lukic, Kristina
id: 2B04DB84-F248-11E8-B48F-1D18A9856A87
last_name: Lukic
orcid: 0000-0003-1581-881X
- first_name: Claus
full_name: Schwechheimer, Claus
last_name: Schwechheimer
- 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: Lukas
full_name: Mach, Lukas
last_name: Mach
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
citation:
ama: Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. PNAS. 2021;118(1). doi:10.1073/pnas.2020857118
apa: Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer,
C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118
chicago: Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina
Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich
Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.”
PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118.
ieee: L. Abas et al., “Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters,” PNAS, vol. 118, no. 1. National Academy of Sciences,
2021.
ista: Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov
LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.
mla: Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN
Auxin Transporters.” PNAS, vol. 118, no. 1, e2020857118, National Academy
of Sciences, 2021, doi:10.1073/pnas.2020857118.
short: L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer,
L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2023-08-07T13:29:23Z
day: '05'
department:
- _id: JiFr
- _id: LeSa
doi: 10.1073/pnas.2020857118
ec_funded: 1
external_id:
isi:
- '000607270100073'
pmid:
- '33443187'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2020857118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: PNAS
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2102232118
scopus_import: '1'
status: public
title: Naphthylphthalamic acid associates with and inhibits PIN auxin transporters
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9205'
abstract:
- lang: eng
text: Cryo-EM grid preparation is an important bottleneck in protein structure determination,
especially for membrane proteins, typically requiring screening of a large number
of conditions. We systematically investigated the effects of buffer components,
blotting conditions and grid types on the outcome of grid preparation of five
different membrane protein samples. Aggregation was the most common type of problem
which was addressed by changing detergents, salt concentration or reconstitution
of proteins into nanodiscs or amphipols. We show that the optimal concentration
of detergent is between 0.05 and 0.4% and that the presence of a low concentration
of detergent with a high critical micellar concentration protects the proteins
from denaturation at the air-water interface. Furthermore, we discuss the strategies
for achieving an adequate ice thickness, particle coverage and orientation distribution
on free ice and on support films. Our findings provide a clear roadmap for comprehensive
screening of conditions for cryo-EM grid preparation of membrane proteins.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank the Electron Microscopy Facilities at the Institute of Science
and Technology Austria and at the Vienna Biocenter for providing access and training
for the electron microscopes. 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 .
article_number: '102139'
article_processing_charge: No
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
- 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, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins.
iScience. 2021;24(3). doi:10.1016/j.isci.2021.102139
apa: Kampjut, D., Steiner, J., & Sazanov, L. A. (2021). Cryo-EM grid optimization
for membrane proteins. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102139
chicago: Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization
for Membrane Proteins.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102139.
ieee: D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for
membrane proteins,” iScience, vol. 24, no. 3. Elsevier, 2021.
ista: Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane
proteins. iScience. 24(3), 102139.
mla: Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience,
vol. 24, no. 3, 102139, Elsevier, 2021, doi:10.1016/j.isci.2021.102139.
short: D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).
date_created: 2021-02-28T23:01:24Z
date_published: 2021-03-19T00:00:00Z
date_updated: 2023-08-07T13:54:06Z
day: '19'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.isci.2021.102139
ec_funded: 1
external_id:
isi:
- '000631646000012'
pmid:
- '33665558'
file:
- access_level: open_access
checksum: 50585447386fe5842f07ab9b3a66e7e9
content_type: application/pdf
creator: dernst
date_created: 2021-03-03T07:38:14Z
date_updated: 2021-03-03T07:38:14Z
file_id: '9219'
file_name: 2021_iScience_Kampjut.pdf
file_size: 7431411
relation: main_file
success: 1
file_date_updated: 2021-03-03T07:38:14Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: iScience
publication_identifier:
eissn:
- '25890042'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-EM grid optimization for membrane proteins
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2021'
...
---
_id: '10146'
abstract:
- lang: eng
text: The enzymes of the mitochondrial electron transport chain are key players
of cell metabolism. Despite being active when isolated, in vivo they associate
into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2
(refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in
mammals, but in contrast to CICIII2 and the respirasome, to date the only known
eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and
plants13, which have different organization. Here we present the first, to our
knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly
intermediates, in different conformations. We describe the assembly of CIII2CIV
from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion
of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while
its C terminus is integrated into CIV. Our structures (which include CICIII2 and
the respirasome) also confirm that SCAF1 is exclusively required for the assembly
of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2
is asymmetric due to the presence of only one copy of subunit 9, which straddles
both monomers and prevents the attachment of a second copy of SCAF1 to CIII2,
explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we
show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex
and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer
in the electron transport chain.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino
for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan
Krios data collection, performed at the IST Austria. The data processing was performed
at the IST high-performance computing cluster. This project has received funding
from the European Union’s Horizon 2020 research and innovation program under the
Marie Skłodowska-Curie grant agreement no. 754411.
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. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z
apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the
mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer
Nature. https://doi.org/10.1038/s41586-021-03927-z
chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the
Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer
Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z.
ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian
mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no.
7880. Springer Nature, pp. 364–367, 2021.
ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial
supercomplex CIII2CIV. Nature. 598(7880), 364–367.
mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian
Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no.
7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.
short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.
date_created: 2021-10-17T22:01:17Z
date_published: 2021-10-14T00:00:00Z
date_updated: 2023-08-14T08:01:21Z
day: '14'
department:
- _id: LeSa
doi: 10.1038/s41586-021-03927-z
ec_funded: 1
external_id:
isi:
- '000704581600001'
pmid:
- '34616041'
intvolume: ' 598'
isi: 1
issue: '7880'
language:
- iso: eng
month: '10'
oa_version: None
page: 364-367
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/boosting-the-cells-power-house/
scopus_import: '1'
status: public
title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 598
year: '2021'
...
---
_id: '10310'
abstract:
- lang: eng
text: A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI)
from Thermosynechococcus elongatus was reported as the first atomic model of PSI
almost 20 years ago. However, the monomeric PSI structure has not yet been reported
despite long-standing interest in its structure and extensive spectroscopic characterization
of the loss of red chlorophylls upon monomerization. Here, we describe the structure
of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the
trimer structure gave detailed insights into monomerization-induced changes in
both the central trimerization domain and the peripheral regions of the complex.
Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls
adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization
of red chlorophylls and that lipids of the surrounding membrane present a major
source of thermal energy for uphill excitation energy transfer from red chlorophylls
to P700.
acknowledgement: We are grateful for additional support and valuable scientific input
for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata,
Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias
Rögner. Parts of this research were funded by the German Research Council (DFG)
within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the
Platform Project for Supporting Drug Discovery and Life Science Research [Basis
for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from
AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and
C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.),
17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research
Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic
Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED
to K.N. and G.K.
article_number: '304'
article_processing_charge: No
article_type: original
author:
- 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: Anna
full_name: Frank, Anna
last_name: Frank
- first_name: Hideaki
full_name: Tanaka, Hideaki
last_name: Tanaka
- first_name: Akihiro
full_name: Kawamoto, Akihiro
last_name: Kawamoto
- first_name: Eithar
full_name: El-Mohsnawy, Eithar
last_name: El-Mohsnawy
- first_name: Takayuki
full_name: Kato, Takayuki
last_name: Kato
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: Christoph
full_name: Gerle, Christoph
last_name: Gerle
- first_name: Marc M.
full_name: Nowaczyk, Marc M.
last_name: Nowaczyk
- first_name: Genji
full_name: Kurisu, Genji
last_name: Kurisu
citation:
ama: Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric
Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster.
Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9
apa: Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T.,
… Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I
from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications
Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9
chicago: Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar
El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk,
and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from
Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications
Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.
ieee: M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem
I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications
Biology, vol. 4, no. 1. Springer , 2021.
ista: Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle
C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem
I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications
Biology. 4(1), 304.
mla: Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem
I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications
Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.
short: M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K.
Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).
date_created: 2021-11-19T11:37:29Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2023-08-14T11:51:19Z
day: '08'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-021-01808-9
external_id:
isi:
- '000627440700001'
pmid:
- '33686186'
file:
- access_level: open_access
checksum: 8ffd39f2bba7152a2441802ff313bf0b
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-19T15:09:18Z
date_updated: 2021-11-19T15:09:18Z
file_id: '10318'
file_name: 2021_CommBio_Çoruh.pdf
file_size: 6030261
relation: main_file
success: 1
file_date_updated: 2021-11-19T15:09:18Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '1'
keyword:
- general agricultural and biological Sciences
- general biochemistry
- genetics and molecular biology
- medicine (miscellaneous)
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: 'Springer '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus
elongatus reveals red chlorophyll cluster
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: 4
year: '2021'
...
---
_id: '7788'
abstract:
- lang: eng
text: Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative
phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly
understood pediatric disorder featuring brain-specific anomalies and early death.
To study the LS pathomechanism, we here compared OXPHOS proteomes between various
Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit
levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal
muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4
induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction
in other CI subunit levels, and an increase in specific CI assembly factors. Among
the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2,
identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs)
and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ
but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex
(CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells,
NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association
to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with
mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830
(NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological
and CI in silico structural analysis, we conclude that absence of NDUFS4 induces
near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes
active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial
inner membrane lipids.
article_number: '148213'
article_processing_charge: No
article_type: original
author:
- first_name: Merel J.W.
full_name: Adjobo-Hermans, Merel J.W.
last_name: Adjobo-Hermans
- first_name: Ria
full_name: De Haas, Ria
last_name: De Haas
- first_name: Peter H.G.M.
full_name: Willems, Peter H.G.M.
last_name: Willems
- first_name: Aleksandra
full_name: Wojtala, Aleksandra
last_name: Wojtala
- first_name: Sjenet E.
full_name: Van Emst-De Vries, Sjenet E.
last_name: Van Emst-De Vries
- first_name: Jori A.
full_name: Wagenaars, Jori A.
last_name: Wagenaars
- first_name: Mariel
full_name: Van Den Brand, Mariel
last_name: Van Den Brand
- first_name: Richard J.
full_name: Rodenburg, Richard J.
last_name: Rodenburg
- first_name: Jan A.M.
full_name: Smeitink, Jan A.M.
last_name: Smeitink
- first_name: Leo G.
full_name: Nijtmans, Leo G.
last_name: Nijtmans
- 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: Mariusz R.
full_name: Wieckowski, Mariusz R.
last_name: Wieckowski
- first_name: Werner J.H.
full_name: Koopman, Werner J.H.
last_name: Koopman
citation:
ama: 'Adjobo-Hermans MJW, De Haas R, Willems PHGM, et al. NDUFS4 deletion triggers
loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role
for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 2020;1861(8).
doi:10.1016/j.bbabio.2020.148213'
apa: 'Adjobo-Hermans, M. J. W., De Haas, R., Willems, P. H. G. M., Wojtala, A.,
Van Emst-De Vries, S. E., Wagenaars, J. A., … Koopman, W. J. H. (2020). NDUFS4
deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients:
A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics.
Elsevier. https://doi.org/10.1016/j.bbabio.2020.148213'
chicago: 'Adjobo-Hermans, Merel J.W., Ria De Haas, Peter H.G.M. Willems, Aleksandra
Wojtala, Sjenet E. Van Emst-De Vries, Jori A. Wagenaars, Mariel Van Den Brand,
et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome
Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta -
Bioenergetics. Elsevier, 2020. https://doi.org/10.1016/j.bbabio.2020.148213.'
ieee: 'M. J. W. Adjobo-Hermans et al., “NDUFS4 deletion triggers loss of
NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for
NDUFAF2,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no.
8. Elsevier, 2020.'
ista: 'Adjobo-Hermans MJW, De Haas R, Willems PHGM, Wojtala A, Van Emst-De Vries
SE, Wagenaars JA, Van Den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov
LA, Wieckowski MR, Koopman WJH. 2020. NDUFS4 deletion triggers loss of NDUFA12
in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2.
Biochimica et Biophysica Acta - Bioenergetics. 1861(8), 148213.'
mla: 'Adjobo-Hermans, Merel J. W., et al. “NDUFS4 Deletion Triggers Loss of NDUFA12
in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.”
Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8, 148213,
Elsevier, 2020, doi:10.1016/j.bbabio.2020.148213.'
short: M.J.W. Adjobo-Hermans, R. De Haas, P.H.G.M. Willems, A. Wojtala, S.E. Van
Emst-De Vries, J.A. Wagenaars, M. Van Den Brand, R.J. Rodenburg, J.A.M. Smeitink,
L.G. Nijtmans, L.A. Sazanov, M.R. Wieckowski, W.J.H. Koopman, Biochimica et Biophysica
Acta - Bioenergetics 1861 (2020).
date_created: 2020-05-03T22:00:47Z
date_published: 2020-08-01T00:00:00Z
date_updated: 2023-08-21T06:19:18Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.bbabio.2020.148213
external_id:
isi:
- '000540842000012'
pmid:
- '32335026'
file:
- access_level: open_access
checksum: a9b152381307cf45fe266a8dc5640388
content_type: application/pdf
creator: dernst
date_created: 2020-05-04T12:25:19Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7798'
file_name: 2020_BBA_Adjobo_Hermans.pdf
file_size: 3826792
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 1861'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_identifier:
eissn:
- '18792650'
issn:
- '00052728'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome
patients: A stabilizing role for NDUFAF2'
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: 1861
year: '2020'
...
---
_id: '8040'
abstract:
- lang: eng
text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes
energy from catabolic processes to synthesize ATP. Complex I, the first and the
largest protein complex of the chain, harvests electrons from NADH to reduce quinone,
while pumping protons across the mitochondrial membrane. Detailed knowledge of
the working principle of such coupled charge-transfer processes remains, however,
fragmentary due to bottlenecks in understanding redox-driven conformational transitions
and their interplay with the hydrated proton pathways. Complex I from Thermus
thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons
from NADH. Here, employing the latest crystal structure of T. thermophilus complex
I, we have used microsecond-scale molecular dynamics simulations to study the
chemo-mechanical coupling between redox changes of the iron–sulfur clusters and
conformational transitions across complex I. First, we identify the redox switches
within complex I, which allosterically couple the dynamics of the quinone binding
pocket to the site of NADH reduction. Second, our free-energy calculations reveal
that the affinity of the quinone, specifically menaquinone, for the binding-site
is higher than that of its reduced, menaquinol form—a design essential for menaquinol
release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser
than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup
of the former furnishes stronger binding interactions with the pocket, favoring
menaquinone for charge transport in T. thermophilus. Our computations are consistent
with experimentally validated mutations and hierarchize the key residues into
three functional classes, identifying new mutation targets. Third, long-range
hydrogen-bond networks connecting the quinone-binding site to the transmembrane
subunits are found to be responsible for proton pumping. Put together, the simulations
reveal the molecular design principles linking redox reactions to quinone turnover
to proton translocation in complex I.
article_processing_charge: No
article_type: original
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun Kit
full_name: Chan, Chun Kit
last_name: Chan
- first_name: Francois
full_name: Dehez, Francois
last_name: Dehez
- first_name: Mrinal
full_name: Shekhar, Mrinal
last_name: Shekhar
- first_name: M. R.
full_name: Gunner, M. R.
last_name: Gunner
- 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: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Abhishek
full_name: Singharoy, Abhishek
last_name: Singharoy
citation:
ama: Gupta C, Khaniya U, Chan CK, et al. Charge transfer and chemo-mechanical coupling
in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230.
doi:10.1021/jacs.9b13450
apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R.,
… Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory
complex I. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.9b13450
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar,
M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge
Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of
the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.
ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in
respiratory complex I,” Journal of the American Chemical Society, vol.
142, no. 20. American Chemical Society, pp. 9220–9230, 2020.
ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory
complex I. Journal of the American Chemical Society. 142(20), 9220–9230.
mla: Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory
Complex I.” Journal of the American Chemical Society, vol. 142, no. 20,
American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450.
short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A.
Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142
(2020) 9220–9230.
date_created: 2020-06-29T07:59:35Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-22T07:49:38Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450
external_id:
isi:
- '000537415600020'
pmid:
- '32347721'
intvolume: ' 142'
isi: 1
issue: '20'
language:
- iso: eng
month: '05'
oa_version: None
page: 9220-9230
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- '15205126'
issn:
- '00027863'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '9326'
relation: research_data
status: public
- id: '9713'
relation: research_data
status: public
- id: '9878'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Charge transfer and chemo-mechanical coupling in respiratory complex I
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 142
year: '2020'
...
---
_id: '9326'
abstract:
- lang: eng
text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes
energy from catabolic processes to synthesize ATP. Complex I, the first and the
largest protein complex of the chain, harvests electrons from NADH to reduce quinone,
while pumping protons across the mitochondrial membrane. Detailed knowledge of
the working principle of such coupled charge-transfer processes remains, however,
fragmentary due to bottlenecks in understanding redox-driven conformational transitions
and their interplay with the hydrated proton pathways. Complex I from Thermus
thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons
from NADH. Here, employing the latest crystal structure of T. thermophilus complex
I, we have used microsecond-scale molecular dynamics simulations to study the
chemo-mechanical coupling between redox changes of the iron–sulfur clusters and
conformational transitions across complex I. First, we identify the redox switches
within complex I, which allosterically couple the dynamics of the quinone binding
pocket to the site of NADH reduction. Second, our free-energy calculations reveal
that the affinity of the quinone, specifically menaquinone, for the binding-site
is higher than that of its reduced, menaquinol forma design essential for menaquinol
release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser
than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup
of the former furnishes stronger binding interactions with the pocket, favoring
menaquinone for charge transport in T. thermophilus. Our computations are consistent
with experimentally validated mutations and hierarchize the key residues into
three functional classes, identifying new mutation targets. Third, long-range
hydrogen-bond networks connecting the quinone-binding site to the transmembrane
subunits are found to be responsible for proton pumping. Put together, the simulations
reveal the molecular design principles linking redox reactions to quinone turnover
to proton translocation in complex I.
article_processing_charge: No
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun
full_name: Chan, Chun
last_name: Chan
- first_name: Francois
full_name: Dehez, Francois
last_name: Dehez
- first_name: Mrinal
full_name: Shekhar, Mrinal
last_name: Shekhar
- first_name: M. R.
full_name: Gunner, M. R.
last_name: Gunner
- 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: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Abhishek
full_name: Singharoy, Abhishek
last_name: Singharoy
citation:
ama: Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling
in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002
apa: Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., …
Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory
complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar,
M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge
Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical
Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.
ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in
respiratory complex I.” American Chemical Society, 2020.
ista: Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory
complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.
mla: Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in
Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.
short: C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov,
C. Chipot, A. Singharoy, (2020).
date_created: 2021-04-14T12:05:20Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2023-08-22T07:49:37Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450.s002
main_file_link:
- open_access: '1'
month: '05'
oa: 1
oa_version: Published Version
publisher: American Chemical Society
related_material:
record:
- id: '8040'
relation: used_in_publication
status: public
status: public
title: Charge transfer and chemo-mechanical coupling in respiratory complex I
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...