---
_id: '17042'
abstract:
- lang: eng
text: 'Bacterial cell walls are gigadalton-large cross-linked polymers with a wide
range of motional amplitudes, including rather rigid as well as highly flexible
parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information
about intact cell walls. Here we investigate sensitivity and information content
of different homonuclear 13C-13C and heteronuclear H-N, H-C and N-C correlation
experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased
signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass
sensitivity. The increased sensitivity allowed to obtain high-resolution spectra
even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H
MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints
for choosing experiments to extract atomic-level details on cell-wall samples. '
article_processing_charge: No
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Schanda P. Raw data to “MAS NMR experiments of corynebacterial cell walls:
complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” 2024.
doi:10.15479/AT:ISTA:17042'
apa: 'Schanda, P. (2024). Raw data to “MAS NMR experiments of corynebacterial cell
walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17042'
chicago: 'Schanda, Paul. “Raw Data to ‘MAS NMR Experiments of Corynebacterial Cell
Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.’”
Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17042.'
ieee: 'P. Schanda, “Raw data to ‘MAS NMR experiments of corynebacterial cell walls:
complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.’” Institute
of Science and Technology Austria, 2024.'
ista: 'Schanda P. 2024. Raw data to ‘MAS NMR experiments of corynebacterial cell
walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:17042.'
mla: 'Schanda, Paul. Raw Data to “MAS NMR Experiments of Corynebacterial Cell
Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.”
Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17042.'
short: P. Schanda, (2024).
contributor:
- contributor_type: data_collector
first_name: Alicia
last_name: Vallet
- contributor_type: data_collector
first_name: 'Isabel '
last_name: Ayala
- contributor_type: data_collector
first_name: Barbara
last_name: Perrone
- contributor_type: data_collector
first_name: Alia
last_name: Hassan
- contributor_type: data_collector
first_name: Catherine
last_name: Bougault
corr_author: '1'
date_created: 2024-05-22T12:04:54Z
date_published: 2024-05-22T00:00:00Z
date_updated: 2025-09-09T12:01:41Z
day: '22'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.15479/AT:ISTA:17042
file:
- access_level: open_access
checksum: eb55f0988342d927702353b75e07edfa
content_type: text/plain
creator: pschanda
date_created: 2024-05-22T12:05:13Z
date_updated: 2024-05-22T12:05:13Z
file_id: '17043'
file_name: Read_me.txt
file_size: 2132
relation: main_file
success: 1
- access_level: open_access
checksum: 3393592acaf5ee1e032052c236780914
content_type: application/zip
creator: pschanda
date_created: 2024-05-22T12:17:10Z
date_updated: 2024-05-22T12:17:10Z
file_id: '17044'
file_name: raw_data_CryoMAS_cyronebacteria.zip
file_size: 755704888
relation: main_file
success: 1
file_date_updated: 2024-05-22T12:17:10Z
has_accepted_license: '1'
keyword:
- nuclear magnetic resonance
- NMR
- cellwall
- structural biology
- spectroscopy
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17291'
relation: used_in_publication
status: public
status: public
title: 'Raw data to "MAS NMR experiments of corynebacterial cell walls: complementary
1H- and CPMAS CryoProbe-enhanced 13C-detected experiments"'
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
_id: '18766'
abstract:
- lang: eng
text: Poxviruses are large pleomorphic double-stranded DNA viruses that include
well known members such as variola virus, the causative agent of smallpox, Mpox
virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain
for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic
DNA viruses in general and poxviruses specifically, as many features, such as
core morphology and structural proteins, are well conserved within this family.
Despite decades of research, our understanding of the structural components and
proteins that comprise the poxvirus core in mature virions remains limited. Although
major core proteins were identified via indirect experimental evidence, the core's
complexity, with its large size, structure and number of involved proteins, has
hindered efforts to achieve high-resolution insights and to define the roles of
the individual proteins. The specific protein composition of the core's individual
layers, including the palisade layer and the inner core wall, has remained unclear.
In this study, we have merged multiple approaches, including single particle cryo
electron microscopy of purified virus cores, cryo-electron tomography and subtomogram
averaging of mature virions and molecular modeling to elucidate the structural
determinants of the VACV core. Due to the lack of experimentally derived structures,
either in situ or reconstituted in vitro, we used Alphafold to predict models
of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results
show that the VACV core is composed of several layers with varying local symmetries,
forming more intricate interactions than observed previously. This allowed us
to identify several molecular building blocks forming the viral core lattice.
In particular, we identified trimers of protein A10 as a major core structure
that forms the palisade layer of the viral core. Additionally, we revealed that
six petals of a flower shaped core pore within the core wall are composed of A10
trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that
could potentially accommodate an A3 dimer. Integrating descriptions of protein
interactions from previous studies enabled us to provide a detailed structural
model of the poxvirus core wall, and our findings indicate that the interactions
within A10 trimers are likely consistent across orthopox- and parapoxviruses.
This combined application of cryo-SPA and cryo-ET can help overcome obstacles
in studying complex virus structures in the future, including their key assembly
proteins, interactions, and the formation into a core lattice. Our work provides
important fundamental new insights into poxvirus core architecture, also considering
the recent re-emergence of poxviruses.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: "This work was funded by the Austrian Science Fund (FWF) grant P31445
and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units,
particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and
the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially
thank Alois for assisting me with the\r\ninstallation of countless new software
and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for
his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving
the process to ensure that I obtained the best possible\r\ndata from my sample."
alternative_title:
- ISTA thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
citation:
ama: Datler J. Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM. 2024. doi:10.15479/at:ista:18766
apa: Datler, J. (2024). Elucidating the structural determinants of the poxvirus
core using multi-modal cryo-EM. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18766
chicago: Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus
Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria,
2024. https://doi.org/10.15479/at:ista:18766.
ieee: J. Datler, “Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.
ista: Datler J. 2024. Elucidating the structural determinants of the poxvirus core
using multi-modal cryo-EM. Institute of Science and Technology Austria.
mla: Datler, Julia. Elucidating the Structural Determinants of the Poxvirus Core
Using Multi-Modal Cryo-EM. Institute of Science and Technology Austria, 2024,
doi:10.15479/at:ista:18766.
short: J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using
Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2025-01-07T10:23:12Z
date_published: 2024-12-30T00:00:00Z
date_updated: 2026-04-07T12:59:44Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:18766
file:
- access_level: closed
checksum: 3e51cab327c754045c3d29c1a50cc9a9
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jstanger
date_created: 2025-01-07T12:15:11Z
date_updated: 2025-01-07T12:15:11Z
file_id: '18769'
file_name: PhD_thesis_Julia_Datler.docx
file_size: 38814932
relation: source_file
- access_level: open_access
checksum: 22fabe5b97950bf852212f6edb555173
content_type: application/pdf
creator: jstanger
date_created: 2025-01-07T12:15:14Z
date_updated: 2025-01-07T12:15:14Z
file_id: '18770'
file_name: PhD_thesis_Julia_Datler.pdf
file_size: 12044865
relation: main_file
success: 1
file_date_updated: 2025-01-07T12:15:14Z
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- cryo-SPA
- Structural Virology
- Poxvirus
- Vaccinia Virus
- Structural Biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '106'
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication_identifier:
isbn:
- 978-3-99078-049-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12334'
relation: part_of_dissertation
status: public
- id: '14979'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Elucidating the structural determinants of the poxvirus core using multi-modal
cryo-EM
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
APC_amount: 11700 EUR
OA_place: publisher
OA_type: hybrid
_id: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.
corr_author: '1'
date_created: 2024-02-12T09:59:45Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-07T12:59:44Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
isi:
- '001158144600002'
pmid:
- '38316877'
file:
- access_level: open_access
checksum: bda7bf65d81455480efaed8ca293b0db
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:27:22Z
date_updated: 2024-07-22T11:27:22Z
file_id: '17307'
file_name: 2024_NatureStrucBio_Datler.pdf
file_size: 17485494
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:27:22Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1114-1123
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/
record:
- id: '18766'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2024'
...
---
_id: '12114'
abstract:
- lang: eng
text: 'Probing the dynamics of aromatic side chains provides important insights
into the behavior of a protein because flips of aromatic rings in a protein’s
hydrophobic core report on breathing motion involving a large part of the protein.
Inherently invisible to crystallography, aromatic motions have been primarily
studied by solution NMR. The question how packing of proteins in crystals affects
ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning
NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a
protein in three different crystal packing environments to shed light onto possible
impact of packing on ring flips. The flips of the two Phe residues in ubiquitin,
both surface exposed, appear remarkably conserved in the different crystal forms,
even though the intermolecular packing is quite different: Phe4 flips on a ca.
10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to
µs motion. Our findings suggest that intramolecular influences are more important
for ring flips than intermolecular (packing) effects.'
acknowledgement: The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within
the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche)
CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research
Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the
Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI
(ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership
for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing
and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg
State University in a form of the grant 92425251 and the access to the MRR, MCT
and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact
that “tensor asymmetry” is better called “tensor biaxiality”.
article_number: '100079'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Olga O.
full_name: Lebedenko, Olga O.
last_name: Lebedenko
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Roman
full_name: Lichtenecker, Roman
last_name: Lichtenecker
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079'
apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R.,
Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently
packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural
Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079'
chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman
Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in
Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal
of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.'
ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin
protein crystals from MAS NMR and MD,” Journal of Structural Biology: X,
vol. 7. Elsevier, 2023.'
ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR,
Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals
from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.'
mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin
Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X,
vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.'
short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R.
Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).'
corr_author: '1'
date_created: 2023-01-12T11:55:38Z
date_published: 2023-01-01T00:00:00Z
date_updated: 2024-10-09T21:04:02Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.yjsbx.2022.100079
external_id:
pmid:
- '36578472'
file:
- access_level: open_access
checksum: b4b1c10a31018aafe053b7d55a470e54
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T09:36:28Z
date_updated: 2023-08-16T09:36:28Z
file_id: '14064'
file_name: 2023_JourStrucBiologyX_Gauto.pdf
file_size: 5132322
relation: main_file
success: 1
file_date_updated: 2023-08-16T09:36:28Z
has_accepted_license: '1'
intvolume: ' 7'
keyword:
- Structural Biology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of Structural Biology: X'
publication_identifier:
issn:
- 2590-1524
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS
NMR and MD
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12163'
abstract:
- lang: eng
text: Small GTPases play essential roles in the organization of eukaryotic cells.
In recent years, it has become clear that their intracellular functions result
from intricate biochemical networks of the GTPase and their regulators that dynamically
bind to a membrane surface. Due to the inherent complexities of their interactions,
however, revealing the underlying mechanisms of action is often difficult to achieve
from in vivo studies. This review summarizes in vitro reconstitution approaches
developed to obtain a better mechanistic understanding of how small GTPase activities
are regulated in space and time.
acknowledgement: The authors acknowledge support from IST Austria and helpful comments
from the anonymous reviewers that helped to improve this manuscript. We apologize
to the authors of primary literature and outstanding research not cited here due
to space restraints.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: Hanifatul R
full_name: Budiman, Hanifatul R
id: 55380f95-15b2-11ec-abd3-aff8e230696b
last_name: Budiman
- first_name: Lukasz M
full_name: Kowalski, Lukasz M
id: e3a512e2-4bbe-11eb-a68a-e3857a7844c2
last_name: Kowalski
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
citation:
ama: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro
reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777.
doi:10.1002/1873-3468.14540
apa: Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic,
I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters.
Wiley. https://doi.org/10.1002/1873-3468.14540
chicago: Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz
M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.
ieee: M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic,
“In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol.
597, no. 6. Wiley, pp. 762–777, 2023.
ista: Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In
vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.
mla: Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.”
FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.
short: M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic,
FEBS Letters 597 (2023) 762–777.
corr_author: '1'
date_created: 2023-01-12T12:09:58Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2024-10-09T21:03:42Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1002/1873-3468.14540
external_id:
isi:
- '000891573000001'
pmid:
- '36448231'
file:
- access_level: open_access
checksum: 7492244d3f9c5faa1347ef03f6e5bc84
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:31:04Z
date_updated: 2023-08-16T08:31:04Z
file_id: '14063'
file_name: 2023_FEBSLetters_Loose.pdf
file_size: 3148143
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:31:04Z
has_accepted_license: '1'
intvolume: ' 597'
isi: 1
issue: '6'
keyword:
- Cell Biology
- Genetics
- Molecular Biology
- Biochemistry
- Structural Biology
- Biophysics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 762-777
pmid: 1
publication: FEBS Letters
publication_identifier:
eissn:
- 1873-3468
issn:
- 0014-5793
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: In vitro reconstitution of small GTPase regulation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 597
year: '2023'
...
---
_id: '15149'
abstract:
- lang: eng
text: The genomic binding sites of the transcription factor (TF) and tumor suppressor
p53 are unusually diverse with regard to their chromatin features, including histone
modifications, raising the possibility that the local chromatin environment can
contextualize p53 regulation. Here, we show that epigenetic characteristics of
closed chromatin, such as DNA methylation, do not influence the binding of p53
across the genome. Instead, the ability of p53 to open chromatin and activate
its target genes is locally restricted by its cofactor Trim24. Trim24 binds to
both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing
to those p53 sites that reside in closed chromatin, whereas it is deterred from
accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell
viability upon stress and enables p53 to affect gene expression as a function
of the local chromatin state. These findings link H3K4 methylation to p53 function
and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic
sensitivity to histone modifications, but by employing chromatin-sensitive cofactors
that locally modulate TF function.
article_processing_charge: No
article_type: original
author:
- first_name: Luke
full_name: Isbel, Luke
last_name: Isbel
- first_name: Murat
full_name: Iskar, Murat
last_name: Iskar
- first_name: Sevi
full_name: Durdu, Sevi
last_name: Durdu
- first_name: Joscha
full_name: Weiss, Joscha
last_name: Weiss
- first_name: Ralph S.
full_name: Grand, Ralph S.
last_name: Grand
- first_name: Eric
full_name: Hietter-Pfeiffer, Eric
last_name: Hietter-Pfeiffer
- first_name: Zuzanna
full_name: Kozicka, Zuzanna
last_name: Kozicka
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Lukas
full_name: Burger, Lukas
last_name: Burger
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
- first_name: Dirk
full_name: Schübeler, Dirk
last_name: Schübeler
citation:
ama: Isbel L, Iskar M, Durdu S, et al. Readout of histone methylation by Trim24
locally restricts chromatin opening by p53. Nature Structural & Molecular
Biology. 2023;30(7):948-957. doi:10.1038/s41594-023-01021-8
apa: Isbel, L., Iskar, M., Durdu, S., Weiss, J., Grand, R. S., Hietter-Pfeiffer,
E., … Schübeler, D. (2023). Readout of histone methylation by Trim24 locally restricts
chromatin opening by p53. Nature Structural & Molecular Biology. Springer
Nature. https://doi.org/10.1038/s41594-023-01021-8
chicago: Isbel, Luke, Murat Iskar, Sevi Durdu, Joscha Weiss, Ralph S. Grand, Eric
Hietter-Pfeiffer, Zuzanna Kozicka, et al. “Readout of Histone Methylation by Trim24
Locally Restricts Chromatin Opening by P53.” Nature Structural & Molecular
Biology. Springer Nature, 2023. https://doi.org/10.1038/s41594-023-01021-8.
ieee: L. Isbel et al., “Readout of histone methylation by Trim24 locally
restricts chromatin opening by p53,” Nature Structural & Molecular Biology,
vol. 30, no. 7. Springer Nature, pp. 948–957, 2023.
ista: Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka
Z, Michael AK, Burger L, Thomä NH, Schübeler D. 2023. Readout of histone methylation
by Trim24 locally restricts chromatin opening by p53. Nature Structural &
Molecular Biology. 30(7), 948–957.
mla: Isbel, Luke, et al. “Readout of Histone Methylation by Trim24 Locally Restricts
Chromatin Opening by P53.” Nature Structural & Molecular Biology, vol.
30, no. 7, Springer Nature, 2023, pp. 948–57, doi:10.1038/s41594-023-01021-8.
short: L. Isbel, M. Iskar, S. Durdu, J. Weiss, R.S. Grand, E. Hietter-Pfeiffer,
Z. Kozicka, A.K. Michael, L. Burger, N.H. Thomä, D. Schübeler, Nature Structural
& Molecular Biology 30 (2023) 948–957.
date_created: 2024-03-21T07:53:24Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2024-03-25T12:37:20Z
day: '29'
doi: 10.1038/s41594-023-01021-8
extern: '1'
external_id:
pmid:
- '37386214'
intvolume: ' 30'
issue: '7'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41594-023-01021-8
month: '06'
oa: 1
oa_version: Published Version
page: 948-957
pmid: 1
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Readout of histone methylation by Trim24 locally restricts chromatin opening
by p53
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
OA_place: publisher
_id: '12491'
abstract:
- lang: eng
text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional
network consisting of proteins, polysaccharides, and water. It provides structural
scaffolding for the cells embedded within it and is essential in regulating numerous
physiological processes, including cell migration and proliferation, wound healing,
and stem cell fate. \r\nDespite extensive study, detailed structural knowledge
of ECM components in physiologically relevant conditions is still rudimentary.
This is due to methodological limitations in specimen preparation protocols which
are incompatible with keeping large samples, such as the ECM, in their native
state for subsequent imaging. Conventional electron microscopy (EM) techniques
rely on fixation, dehydration, contrasting, and sectioning. This results in the
alteration of a highly hydrated environment and the potential introduction of
artifacts. Other structural biology techniques, such as nuclear magnetic resonance
(NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of
protein structures but only work on homogenous and purified samples, hence lacking
contextual information. Currently, no approach exists for the ultrastructural
and structural study of extracellular components under native conditions in a
physiological, 3D environment. \r\nIn this thesis, I have developed a workflow
that allows for the ultrastructural analysis of the ECM in near-native conditions
at molecular resolution. The developments I introduced include implementing a
novel specimen preparation workflow for cell-derived matrices (CDMs) to render
them compatible with ion-beam milling and subsequent high-resolution cryo-electron
tomography (ET). \r\nTo this end, I have established protocols to generate CDMs
grown over several weeks on EM grids that are compatible with downstream cryo-EM
sample preparation and imaging techniques. Characterization of these ECMs confirmed
that they contain essential ECM components such as collagen I, collagen VI, and
fibronectin I in high abundance and hence represent a bona fide biologically-relevant
sample. I successfully optimized vitrification of these specimens by testing various
vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution
molecular insights into the ultrastructure and organization of CDMs, I established
cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging
and complex specimens. I explored different approaches for the creation of thin
cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique,
resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution
Cryo-ET of these lamellae revealed for the first time the architecture of native
CDM in the context of matrix-secreting cells. This allowed for the in situ visualization
of fibrillar matrix proteins such as collagen, laying the foundation for future
structural and ultrastructural characterization of these proteins in their near-native
environment. \r\nIn summary, in this thesis, I present a novel workflow that combines
state-of-the-art cryo-EM specimen preparation and imaging technologies to permit
characterization of the ECM, an important tissue component in higher organisms.
This innovative and highly versatile workflow will enable addressing far-reaching
questions on ECM architecture, composition, and reciprocal ECM-cell interactions."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
citation:
ama: Zens B. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491
apa: Zens, B. (2023). Ultrastructural characterization of natively preserved
extracellular matrix by cryo-electron tomography. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:12491
chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved
Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12491.
ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography,” Institute of Science and Technology Austria,
2023.
ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. Institute of Science and Technology Austria.
mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12491.
short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria,
2023.
corr_author: '1'
date_created: 2023-02-02T14:50:20Z
date_published: 2023-02-02T00:00:00Z
date_updated: 2026-04-07T13:49:23Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:12491
file:
- access_level: open_access
checksum: 069d87f025e0799bf9e3c375664264f2
content_type: application/pdf
creator: bzens
date_created: 2023-02-07T13:07:38Z
date_updated: 2024-02-08T23:30:04Z
embargo: 2024-02-07
file_id: '12527'
file_name: PhDThesis_BettinaZens_2023_final.pdf
file_size: 23082464
relation: main_file
- access_level: closed
checksum: 8c66ed203495d6e078ed1002a866520c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: bzens
date_created: 2023-02-07T13:09:05Z
date_updated: 2024-02-08T23:30:04Z
embargo_to: open_access
file_id: '12528'
file_name: PhDThesis_BettinaZens_2023_final.docx
file_size: 106169509
relation: source_file
file_date_updated: 2024-02-08T23:30:04Z
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- FIB milling
- method development
- FIBSEM
- extracellular matrix
- ECM
- cell-derived matrices
- CDMs
- cell culture
- high pressure freezing
- HPF
- structural biology
- tomography
- collagen
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '187'
project:
- _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3
name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria"
publication_identifier:
isbn:
- 978-3-99078-027-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8586'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Ultrastructural characterization of natively preserved extracellular matrix
by cryo-electron tomography
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_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: '12262'
abstract:
- lang: eng
text: The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that
initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases
the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear
export, a strict requirement for downstream maturation. The molecular mechanism
of release remained elusive. Here, we report a series of cryo-EM structures that
captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae
Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion
segment ES27 form a joint docking platform that positions Drg1 for efficient extraction
of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the
Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction
by a hand-over-hand translocation mechanism. Our results uncover substrate recognition
and processing by Drg1 step by step and provide a comprehensive mechanistic picture
of the conserved modus operandi of AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert,
J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported
by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants
32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A.
J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1
and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann
and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM
during early phases of this\r\nproject. This research was supported by the Scientific
Service Units of IST Austria through\r\nresources provided by the Electron Microscopy
Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics),
University Graz for support with the quantification of\r\nthe SPR particle release
assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences,
Vienna for her help in early stages of the SPR experiments."
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Carolin
full_name: Sailer, Carolin
last_name: Sailer
- first_name: Vasileios
full_name: Kargas, Vasileios
last_name: Kargas
- first_name: Mathias
full_name: Loibl, Mathias
last_name: Loibl
- first_name: Magdalena
full_name: Gerhalter, Magdalena
last_name: Gerhalter
- first_name: Lisa
full_name: Kofler, Lisa
last_name: Kofler
- first_name: Alan J.
full_name: Warren, Alan J.
last_name: Warren
- first_name: Florian
full_name: Stengel, Florian
last_name: Stengel
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor
extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural
& Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser,
G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction
from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina
Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing
Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.”
Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.
ieee: M. Prattes et al., “Visualizing maturation factor extraction from the
nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular
Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer
C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D,
Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome
by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.
mla: Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the
Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular
Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser,
C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel,
D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022)
942–953.
date_created: 2023-01-16T09:59:06Z
date_published: 2022-09-12T00:00:00Z
date_updated: 2023-08-04T09:52:20Z
day: '12'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41594-022-00832-5
external_id:
isi:
- '000852942100004'
pmid:
- '36097293'
file:
- access_level: open_access
checksum: 2d5c3ec01718fefd7553052b0b8a0793
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:00:04Z
date_updated: 2023-01-30T10:00:04Z
file_id: '12447'
file_name: 2022_NatureStrucMolecBio_Prattes.pdf
file_size: 9935057
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:00:04Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '9'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 942-953
pmid: 1
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase
Drg1
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: 29
year: '2022'
...
---
_id: '15131'
abstract:
- lang: eng
text: RNA modifications are widespread in biology and abundant in ribosomal RNA.
However, the importance of these modifications is not well understood. We show
that methylation of a single nucleotide, in the catalytic center of the large
subunit, gates ribosome assembly. Massively parallel mutational scanning of the
essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly
with the 2′-O-methylated A-site base Gm2922. We found
that methylation of G2922 is needed for assembly and efficient nuclear export
of the large subunit. Critically, we identified single amino acid changes in Nog2
that completely bypass dependence on G2922 methylation and used cryoelectron microscopy
to directly visualize how methylation flips Gm2922 into the active site channel
of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint
in ribosome biogenesis, suggesting that such modifications can play an important
role in regulation and assembly of macromolecular machines.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: James N.
full_name: Yelland, James N.
last_name: Yelland
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Joshua J.
full_name: Black, Joshua J.
last_name: Black
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Arlen W.
full_name: Johnson, Arlen W.
last_name: Johnson
citation:
ama: Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. A single 2′-O-methylation
of ribosomal RNA gates assembly of a functional ribosome. Nature Structural
& Molecular Biology. 2022;30:91-98. doi:10.1038/s41594-022-00891-8
apa: Yelland, J. N., Bravo, J. P. K., Black, J. J., Taylor, D. W., & Johnson,
A. W. (2022). A single 2′-O-methylation of ribosomal RNA gates assembly of a functional
ribosome. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00891-8
chicago: Yelland, James N., Jack Peter Kelly Bravo, Joshua J. Black, David W. Taylor,
and Arlen W. Johnson. “A Single 2′-O-Methylation of Ribosomal RNA Gates Assembly
of a Functional Ribosome.” Nature Structural & Molecular Biology. Springer
Nature, 2022. https://doi.org/10.1038/s41594-022-00891-8.
ieee: J. N. Yelland, J. P. K. Bravo, J. J. Black, D. W. Taylor, and A. W. Johnson,
“A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome,”
Nature Structural & Molecular Biology, vol. 30. Springer Nature, pp.
91–98, 2022.
ista: Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. 2022. A single 2′-O-methylation
of ribosomal RNA gates assembly of a functional ribosome. Nature Structural &
Molecular Biology. 30, 91–98.
mla: Yelland, James N., et al. “A Single 2′-O-Methylation of Ribosomal RNA Gates
Assembly of a Functional Ribosome.” Nature Structural & Molecular Biology,
vol. 30, Springer Nature, 2022, pp. 91–98, doi:10.1038/s41594-022-00891-8.
short: J.N. Yelland, J.P.K. Bravo, J.J. Black, D.W. Taylor, A.W. Johnson, Nature
Structural & Molecular Biology 30 (2022) 91–98.
date_created: 2024-03-20T10:41:45Z
date_published: 2022-12-19T00:00:00Z
date_updated: 2024-06-04T06:27:09Z
day: '19'
doi: 10.1038/s41594-022-00891-8
extern: '1'
external_id:
pmid:
- '36536102'
intvolume: ' 30'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41594-022-00891-8
month: '12'
oa: 1
oa_version: Published Version
page: 91-98
pmid: 1
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2022'
...
---
_id: '15268'
abstract:
- lang: eng
text: Apolipoprotein A‐I (apoA‐I) has a key function in the reverse cholesterol
transport. However, aggregation of apoA‐I single point mutants can lead to hereditary
amyloid pathology. Although several studies have tackled the biophysical and structural
consequences introduced by these mutations, there is little information addressing
the relationship between the evolutionary and structural features that contribute
to the amyloid behavior of apoA‐I. We combined evolutionary studies, in silico
mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive
analysis of the conservation and pathogenic role of the aggregation‐prone regions
(APRs) present in apoA‐I. Sequence analysis demonstrated that among the four amyloidogenic
regions described for human apoA‐I, only two (APR1 and APR4) are evolutionary
conserved across different species of Sarcopterygii. Moreover, stability analysis
carried out with the FoldX engine showed that APR1 contributes to the marginal
stability of apoA‐I. Structural properties of full‐length apoA‐I models suggest
that aggregation is avoided by placing APRs into highly packed and rigid portions
of its native fold. Compared to silent variants extracted from the gnomAD database,
the thermodynamic and pathogenic impact of amyloid mutations showed evidence of
a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced
the partial unfolding of the alpha‐helix bundle with the concomitant exposure
of APR1 to the solvent, suggesting an insight into the early steps involved in
its aggregation. Our findings highlight APR1 as a relevant component for apoA‐I
structural integrity and emphasize a destabilizing effect of amyloid variants
that leads to the exposure of this region.
article_processing_charge: No
article_type: original
author:
- first_name: Romina A.
full_name: Gisonno, Romina A.
last_name: Gisonno
- first_name: Tomas
full_name: Masson, Tomas
id: 93ac43e8-8599-11eb-9b86-f6efb0a4c207
last_name: Masson
orcid: 0000-0002-2634-6283
- first_name: Nahuel A.
full_name: Ramella, Nahuel A.
last_name: Ramella
- first_name: Exequiel E.
full_name: Barrera, Exequiel E.
last_name: Barrera
- first_name: Víctor
full_name: Romanowski, Víctor
last_name: Romanowski
- first_name: M. Alejandra
full_name: Tricerri, M. Alejandra
last_name: Tricerri
citation:
ama: 'Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. Evolutionary
and structural constraints influencing apolipoprotein A‐I amyloid behavior. Proteins:
Structure, Function, and Bioinformatics. 2022;90(1):258-269. doi:10.1002/prot.26217'
apa: 'Gisonno, R. A., Masson, T., Ramella, N. A., Barrera, E. E., Romanowski, V.,
& Tricerri, M. A. (2022). Evolutionary and structural constraints influencing
apolipoprotein A‐I amyloid behavior. Proteins: Structure, Function, and Bioinformatics.
Wiley. https://doi.org/10.1002/prot.26217'
chicago: 'Gisonno, Romina A., Tomas Masson, Nahuel A. Ramella, Exequiel E. Barrera,
Víctor Romanowski, and M. Alejandra Tricerri. “Evolutionary and Structural Constraints
Influencing Apolipoprotein A‐I Amyloid Behavior.” Proteins: Structure, Function,
and Bioinformatics. Wiley, 2022. https://doi.org/10.1002/prot.26217.'
ieee: 'R. A. Gisonno, T. Masson, N. A. Ramella, E. E. Barrera, V. Romanowski, and
M. A. Tricerri, “Evolutionary and structural constraints influencing apolipoprotein
A‐I amyloid behavior,” Proteins: Structure, Function, and Bioinformatics,
vol. 90, no. 1. Wiley, pp. 258–269, 2022.'
ista: 'Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA.
2022. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid
behavior. Proteins: Structure, Function, and Bioinformatics. 90(1), 258–269.'
mla: 'Gisonno, Romina A., et al. “Evolutionary and Structural Constraints Influencing
Apolipoprotein A‐I Amyloid Behavior.” Proteins: Structure, Function, and Bioinformatics,
vol. 90, no. 1, Wiley, 2022, pp. 258–69, doi:10.1002/prot.26217.'
short: 'R.A. Gisonno, T. Masson, N.A. Ramella, E.E. Barrera, V. Romanowski, M.A.
Tricerri, Proteins: Structure, Function, and Bioinformatics 90 (2022) 258–269.'
corr_author: '1'
date_created: 2024-04-03T07:49:53Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2024-10-09T21:08:44Z
day: '01'
department:
- _id: MaJö
doi: 10.1002/prot.26217
external_id:
pmid:
- '34414600'
intvolume: ' 90'
issue: '1'
keyword:
- Molecular Biology
- Biochemistry
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.09.18.304337
month: '01'
oa: 1
oa_version: Preprint
page: 258-269
pmid: 1
publication: 'Proteins: Structure, Function, and Bioinformatics'
publication_identifier:
eissn:
- 1097-0134
issn:
- 0887-3585
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid
behavior
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2022'
...
---
_id: '11155'
abstract:
- lang: eng
text: The potential of energy filtering and direct electron detection for cryo-electron
microscopy (cryo-EM) has been well documented. Here, we assess the performance
of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram
averaging (STA), an increasingly popular structural determination method for complex
3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs)
on two contemporary cryo-EM systems equipped with different energy filters and
direct electron detectors (DED), specifically a Krios G4, equipped with a cold
field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter,
and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG),
a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based
STA on equally sized datasets acquired on the respective systems. The resulting
EIAV CA hexamer reconstructions show that both systems perform comparably in the
4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition,
by employing a recently introduced multiparticle refinement approach, we obtained
a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the
potential of the new generation of energy filters and DEDs for STA, and the effects
of using different processing pipelines on their STA outcomes.
acknowledged_ssus:
- _id: LifeSc
- _id: ScienComp
- _id: EM-Fac
acknowledgement: This work was funded by the Austrian Science Fund (FWF) grant P31445
to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards
R01AI147890 to R.A.D. This research was also supported by the Scientific Service
Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We
thank Dustin Morado for providing the software SubTOM for data processing. We also
thank William Wan for critical reading of the manuscript and valuable feedback.
article_number: '107852'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Wim J.H.
full_name: Hagen, Wim J.H.
last_name: Hagen
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- first_name: Lingbo
full_name: Yu, Lingbo
last_name: Yu
- first_name: Abhay
full_name: Kotecha, Abhay
last_name: Kotecha
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution
cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal
of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852
apa: Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F.
K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities
of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852
chicago: Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha,
and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging
Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier,
2022. https://doi.org/10.1016/j.jsb.2022.107852.
ieee: M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring
high-resolution cryo-ET and subtomogram averaging capabilities of contemporary
DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022.
ista: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution
cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of
Structural Biology. 214(2), 107852.
mla: Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging
Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol.
214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852.
short: M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of
Structural Biology 214 (2022).
corr_author: '1'
date_created: 2022-04-15T07:10:26Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-04-15T08:24:50Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2022.107852
external_id:
isi:
- '000790733600001'
pmid:
- '35351542'
file:
- access_level: open_access
checksum: 0b1eb53447aae8e95ae4c12d193b0b00
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T11:07:58Z
date_updated: 2022-08-02T11:07:58Z
file_id: '11722'
file_name: 2022_JourStructuralBiology_Obr.pdf
file_size: 7080863
relation: main_file
success: 1
file_date_updated: 2022-08-02T11:07:58Z
has_accepted_license: '1'
intvolume: ' 214'
isi: 1
issue: '2'
keyword:
- Structural Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exploring high-resolution cryo-ET and subtomogram averaging capabilities of
contemporary DEDs
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: 214
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).
corr_author: '1'
date_created: 2022-04-15T09:32:35Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2024-10-09T21:02:00Z
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: '10290'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized filamentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: 'This research was supported by the Scientific Service Units (SSUs)
of IST Austria through resources provided by Scientific Computing (SciComp), the
Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data
acquisition. The authors acknowledge support from IST Austria and from the Austrian
Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.'
article_number: '107808'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal
of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier
, 2021. https://doi.org/10.1016/j.jsb.2021.107808.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data.
Journal of Structural Biology. 213(4), 107808.
mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology,
vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural
Biology 213 (2021).
corr_author: '1'
date_created: 2021-11-15T12:21:42Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2025-04-15T08:25:41Z
day: '03'
ddc:
- '572'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2021.107808
external_id:
isi:
- '000720259500002'
file:
- access_level: open_access
checksum: 6b209e4d44775d4e02b50f78982c15fa
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T13:11:27Z
date_updated: 2021-11-15T13:11:27Z
file_id: '10291'
file_name: 2021_JournalStructBiol_Dimchev.pdf
file_size: 16818304
relation: main_file
success: 1
file_date_updated: 2021-11-15T13:11:27Z
has_accepted_license: '1'
intvolume: ' 213'
isi: 1
issue: '4'
keyword:
- Structural Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
related_material:
record:
- id: '14502'
relation: software
status: public
scopus_import: '1'
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
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: 213
year: '2021'
...
---
_id: '15036'
abstract:
- lang: eng
text: The assembly of a septin filament requires that homologous monomers must distinguish
between one another in establishing appropriate interfaces with their neighbors.
To understand this phenomenon at the molecular level, we present the first four
crystal structures of heterodimeric septin complexes. We describe in detail the
two distinct types of G-interface present within the octameric particles, which
must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and
between SEPT7 and SEPT3, and their description permits an understanding of the
structural basis for the selectivity necessary for correct filament assembly.
By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's
postulate, which predicts the exchangeability of septins from within a subgroup.
Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent
conformational change, have been repurposed in septins to play a fundamental role
in molecular recognition. Specifically, it is switch I which holds the key to
discriminating between the two different G-interfaces. Moreover, residues which
are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing
that the correct interfaces are formed.
article_processing_charge: No
article_type: original
author:
- first_name: Higor Vinícius Dias
full_name: Rosa, Higor Vinícius Dias
last_name: Rosa
- first_name: Diego Antonio
full_name: Leonardo, Diego Antonio
last_name: Leonardo
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: José
full_name: Brandão-Neto, José
last_name: Brandão-Neto
- first_name: Humberto
full_name: D'Muniz Pereira, Humberto
last_name: D'Muniz Pereira
- first_name: Ana Paula Ulian
full_name: Araújo, Ana Paula Ulian
last_name: Araújo
- first_name: Richard Charles
full_name: Garratt, Richard Charles
last_name: Garratt
citation:
ama: 'Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin
interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801.
doi:10.1016/j.jmb.2020.09.001'
apa: 'Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira,
H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin
interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2020.09.001'
chicago: 'Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José
Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles
Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.”
Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.'
ieee: 'H. V. D. Rosa et al., “Molecular recognition at septin interfaces:
The switches hold the key,” Journal of Molecular Biology, vol. 432, no.
21. Elsevier, pp. 5784–5801, 2020.'
ista: 'Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo
APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches
hold the key. Journal of Molecular Biology. 432(21), 5784–5801.'
mla: 'Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces:
The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no.
21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.'
short: H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira,
A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.
date_created: 2024-02-28T08:50:34Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2024-02-28T12:37:54Z
day: '02'
department:
- _id: MaLo
doi: 10.1016/j.jmb.2020.09.001
external_id:
pmid:
- '32910969'
intvolume: ' 432'
issue: '21'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jmb.2020.09.001
month: '10'
oa: 1
oa_version: Published Version
page: 5784-5801
pmid: 1
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Molecular recognition at septin interfaces: The switches hold the key'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 432
year: '2020'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '8402'
abstract:
- lang: eng
text: "Background: The mitochondrial pyruvate carrier (MPC) plays a central role
in energy metabolism by transporting pyruvate across the inner mitochondrial membrane.
Its heterodimeric composition and homology to SWEET and semiSWEET transporters
set the MPC apart from the canonical mitochondrial carrier family (named MCF or
SLC25). The import of the canonical carriers is mediated by the carrier translocase
of the inner membrane (TIM22) pathway and is dependent on their structure, which
features an even number of transmembrane segments and both termini in the intermembrane
space. The import pathway of MPC proteins has not been elucidated. The odd number
of transmembrane segments and positioning of the N-terminus in the matrix argues
against an import via the TIM22 carrier pathway but favors an import via the flexible
presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways
of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible
presequence pathway, yeast MPC proteins with an odd number of transmembrane segments
and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor
Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones
MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic
motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions:
The carrier pathway can import paired and non-paired transmembrane helices and
translocate N-termini to either side of the mitochondrial inner membrane, revealing
an unexpected versatility of the mitochondrial import pathway for non-cleavable
inner membrane proteins."
article_number: '2'
article_processing_charge: No
article_type: original
author:
- first_name: Heike
full_name: Rampelt, Heike
last_name: Rampelt
- first_name: Iva
full_name: Sucec, Iva
last_name: Sucec
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Patrick
full_name: Horten, Patrick
last_name: Horten
- first_name: Inge
full_name: Perschil, Inge
last_name: Perschil
- first_name: Jean-Claude
full_name: Martinou, Jean-Claude
last_name: Martinou
- first_name: Martin
full_name: van der Laan, Martin
last_name: van der Laan
- first_name: Nils
full_name: Wiedemann, Nils
last_name: Wiedemann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Nikolaus
full_name: Pfanner, Nikolaus
last_name: Pfanner
citation:
ama: Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports
non-canonical substrates with an odd number of transmembrane segments. BMC
Biology. 2020;18. doi:10.1186/s12915-019-0733-6
apa: Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C.,
… Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical
substrates with an odd number of transmembrane segments. BMC Biology. Springer
Nature. https://doi.org/10.1186/s12915-019-0733-6
chicago: Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil,
Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus
Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates
with an Odd Number of Transmembrane Segments.” BMC Biology. Springer Nature,
2020. https://doi.org/10.1186/s12915-019-0733-6.
ieee: H. Rampelt et al., “The mitochondrial carrier pathway transports non-canonical
substrates with an odd number of transmembrane segments,” BMC Biology,
vol. 18. Springer Nature, 2020.
ista: Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der
Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway
transports non-canonical substrates with an odd number of transmembrane segments.
BMC Biology. 18, 2.
mla: Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical
Substrates with an Odd Number of Transmembrane Segments.” BMC Biology,
vol. 18, 2, Springer Nature, 2020, doi:10.1186/s12915-019-0733-6.
short: H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou,
M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).
date_created: 2020-09-17T10:26:53Z
date_published: 2020-01-06T00:00:00Z
date_updated: 2024-10-15T13:23:11Z
day: '06'
doi: 10.1186/s12915-019-0733-6
extern: '1'
external_id:
pmid:
- '31907035'
intvolume: ' 18'
keyword:
- Biotechnology
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Developmental Biology
- Cell Biology
- Physiology
- Ecology
- Evolution
- Behavior and Systematics
- Structural Biology
- General Agricultural and Biological Sciences
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12915-019-0733-6
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Biology
publication_identifier:
issn:
- 1741-7007
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The mitochondrial carrier pathway transports non-canonical substrates with
an odd number of transmembrane segments
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 18
year: '2020'
...
---
_id: '10355'
abstract:
- lang: eng
text: The molecular machinery of life is largely created via self-organisation of
individual molecules into functional assemblies. Minimal coarse-grained models,
in which a whole macromolecule is represented by a small number of particles,
can be of great value in identifying the main driving forces behind self-organisation
in cell biology. Such models can incorporate data from both molecular and continuum
scales, and their results can be directly compared to experiments. Here we review
the state of the art of models for studying the formation and biological function
of macromolecular assemblies in living organisms. We outline the key ingredients
of each model and their main findings. We illustrate the contribution of this
class of simulations to identifying the physical mechanisms behind life and diseases,
and discuss their future developments.
acknowledgement: We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy
of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the
Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically
reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Anne E
full_name: Hafner, Anne E
last_name: Hafner
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular
self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52.
doi:10.1016/j.sbi.2019.05.018
apa: Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained
models for molecular self-organisation in biology. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018
chicago: Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained
Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural
Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018.
ieee: A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for
molecular self-organisation in biology,” Current Opinion in Structural Biology,
vol. 58. Elsevier, pp. 43–52, 2019.
ista: Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular
self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.
mla: Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation
in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier,
2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018.
short: A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology
58 (2019) 43–52.
date_created: 2021-11-26T11:33:21Z
date_published: 2019-06-18T00:00:00Z
date_updated: 2021-11-26T11:54:25Z
day: '18'
doi: 10.1016/j.sbi.2019.05.018
extern: '1'
external_id:
pmid:
- '31226513'
intvolume: ' 58'
keyword:
- molecular biology
- structural biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.09349
month: '06'
oa: 1
oa_version: Preprint
page: 43-52
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: Minimal coarse-grained models for molecular self-organisation in biology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2019'
...
---
_id: '8409'
abstract:
- lang: eng
text: The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer
that maintains the integrity of the bacterial cell. Due to its multi-gigadalton
size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex.
Solid-state NMR is an important technique to gain insight into its structure,
dynamics and interactions. Here, we explore the possibilities to study the PG
with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly
resolved spectra can be obtained, and show strategies to obtain site-specific
resonance assignments and distance information. We also explore the use of proton-proton
correlation experiments, thus opening the way for NMR studies of intact cell walls
without the need for isotope labeling.
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Bougault, Catherine
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial
peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal
of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009
apa: Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019).
Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at
100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009
chicago: Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre,
and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected
NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology.
Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.
ieee: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying
intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz
MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier,
pp. 66–72, 2019.
ista: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact
bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency.
Journal of Structural Biology. 206(1), 66–72.
mla: Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected
NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology,
vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009.
short: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of
Structural Biology 206 (2019) 66–72.
date_created: 2020-09-17T10:29:10Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:05Z
day: '01'
doi: 10.1016/j.jsb.2018.07.009
extern: '1'
external_id:
pmid:
- '30031884'
intvolume: ' 206'
issue: '1'
keyword:
- Structural Biology
language:
- iso: eng
month: '04'
oa_version: Submitted Version
page: 66-72
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy
at 100 kHz MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 206
year: '2019'
...
---
_id: '8438'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. Dynamics and
interactions of AAC3 in DPC are not functionally relevant. Nature Structural
& Molecular Biology. 2018;25(9):745-747. doi:10.1038/s41594-018-0127-4
apa: Kurauskas, V., Hessel, A., Dehez, F., Chipot, C., Bersch, B., & Schanda,
P. (2018). Dynamics and interactions of AAC3 in DPC are not functionally relevant.
Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-018-0127-4
chicago: Kurauskas, Vilius, Audrey Hessel, François Dehez, Christophe Chipot, Beate
Bersch, and Paul Schanda. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally
Relevant.” Nature Structural & Molecular Biology. Springer Nature,
2018. https://doi.org/10.1038/s41594-018-0127-4.
ieee: V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, and P. Schanda, “Dynamics
and interactions of AAC3 in DPC are not functionally relevant,” Nature Structural
& Molecular Biology, vol. 25, no. 9. Springer Nature, pp. 745–747, 2018.
ista: Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. 2018. Dynamics
and interactions of AAC3 in DPC are not functionally relevant. Nature Structural
& Molecular Biology. 25(9), 745–747.
mla: Kurauskas, Vilius, et al. “Dynamics and Interactions of AAC3 in DPC Are Not
Functionally Relevant.” Nature Structural & Molecular Biology, vol.
25, no. 9, Springer Nature, 2018, pp. 745–47, doi:10.1038/s41594-018-0127-4.
short: V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, P. Schanda, Nature
Structural & Molecular Biology 25 (2018) 745–747.
date_created: 2020-09-18T10:04:59Z
date_published: 2018-09-03T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '03'
doi: 10.1038/s41594-018-0127-4
extern: '1'
intvolume: ' 25'
issue: '9'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '09'
oa_version: None
page: 745-747
publication: Nature Structural & Molecular Biology
publication_identifier:
issn:
- 1545-9993
- 1545-9985
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Dynamics and interactions of AAC3 in DPC are not functionally relevant
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2018'
...