---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20258'
abstract:
- lang: eng
  text: The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise
    deuterated proteins holds great potential for high-resolution solution and magic-angle
    spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues
    play key roles for example at active sites of enzymes. Taking advantage of a chemically
    synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we
    demonstrate here the usefulness of proton-detected MAS NMR approaches to probe
    arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric
    enzyme malate dehydrogenase we detected a wide range of motions, from sites that
    are rigid on time scales of at least tens of milliseconds to residues undergoing
    predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements
    enabled quantitative determination of these dynamics. We observed microsecond
    dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to
    sample different β-turn conformations on this time scale. The labeling scheme
    and experiments presented here expand the toolkit for high-resolution proton-detected
    MAS NMR.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: This work was supported financially by the Austrian Science Fund
  (FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific
  Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through
  resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support
  Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent
  support of the NMR facility.
article_number: '169379'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Darja
  full_name: Rohden, Darja
  id: 81dc668a-19fa-11f0-bf31-d56534059ef3
  last_name: Rohden
- first_name: Federico
  full_name: Napoli, Federico
  id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
  last_name: Napoli
  orcid: 0000-0002-9043-136X
- first_name: Anna
  full_name: Kapitonova, Anna
  id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
  last_name: Kapitonova
- first_name: Benjamin
  full_name: Tatman, Benjamin
  id: 71cda2f3-e604-11ee-a1df-da10587eda3f
  last_name: Tatman
- first_name: Roman J.
  full_name: Lichtenecker, Roman J.
  last_name: Lichtenecker
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
citation:
  ama: Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine
    dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme.
    <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href="https://doi.org/10.1016/j.jmb.2025.169379">10.1016/j.jmb.2025.169379</a>
  apa: Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., &#38;
    Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with
    a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.jmb.2025.169379">https://doi.org/10.1016/j.jmb.2025.169379</a>
  chicago: Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman
    J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning
    NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>.
    Elsevier, 2025. <a href="https://doi.org/10.1016/j.jmb.2025.169379">https://doi.org/10.1016/j.jmb.2025.169379</a>.
  ieee: D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P.
    Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific
    isotope-labeling scheme,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23.
    Elsevier, 2025.
  ista: Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025.
    Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling
    scheme. Journal of Molecular Biology. 437(23), 169379.
  mla: Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR
    with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>,
    vol. 437, no. 23, 169379, Elsevier, 2025, doi:<a href="https://doi.org/10.1016/j.jmb.2025.169379">10.1016/j.jmb.2025.169379</a>.
  short: D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda,
    Journal of Molecular Biology 437 (2025).
corr_author: '1'
date_created: 2025-08-31T22:01:33Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-29T14:52:17Z
day: '01'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1016/j.jmb.2025.169379
external_id:
  isi:
  - '001618289100020'
file:
- access_level: open_access
  checksum: 90d50594d8ea9860ac5da41297992847
  content_type: application/pdf
  creator: dernst
  date_created: 2025-12-29T14:51:40Z
  date_updated: 2025-12-29T14:51:40Z
  file_id: '20876'
  file_name: 2025_JourMolecularBiology_Rohden.pdf
  file_size: 2270555
  relation: main_file
  success: 1
file_date_updated: 2025-12-29T14:51:40Z
has_accepted_license: '1'
intvolume: '       437'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publication: Journal of Molecular Biology
publication_identifier:
  eissn:
  - 1089-8638
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '19956'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling
  scheme
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: 437
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20538'
abstract:
- lang: eng
  text: In this study, we describe an integrated approach for methyl group assignment
    comprising precursor-based selective methyl group labeling, a novel pulse sequence
    for methyl to backbone coherence transfer and chemical shift predictions using
    UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the
    adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal
    methyl groups of leucine and valine residues to each other and to the protein
    backbone. By additional 13C,2H-labeling of residues other than valine and leucine
    residues of the protein, important chemical shift information about neighboring
    residues (following valine and leucine residues) can be achieved. Thus, different
    valine and leucine residues in a protein can be characterized as a specific chemical
    shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0
    using experimental data taken from a subset of the BMRB database revealed a correct
    assignment performance of about 90%. With applications to proteins of 60.2 kDa
    and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides
    valuable information even for very large proteins.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral
  School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B.
  This work was supported financially by the Austrian Science Fund (FWF, grant numbers
  I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific
  Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through
  resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support
  Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR
  spectrum of HsTom70.
article_number: '169465'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sonja
  full_name: Knödlstorfer, Sonja
  last_name: Knödlstorfer
- first_name: Giorgia
  full_name: Toscano, Giorgia
  id: 334a5e40-8747-11f0-b671-ba1f5154b4b4
  last_name: Toscano
- first_name: Aleksandra L.
  full_name: Ptaszek, Aleksandra L.
  last_name: Ptaszek
- first_name: Georg
  full_name: Kontaxis, Georg
  last_name: Kontaxis
- first_name: Federico
  full_name: Napoli, Federico
  id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
  last_name: Napoli
  orcid: 0000-0002-9043-136X
- first_name: Jakob
  full_name: Schneider, Jakob
  id: 64368429-eb97-11eb-a6c2-c980b1f44415
  last_name: Schneider
- first_name: Katharina
  full_name: Maier, Katharina
  last_name: Maier
- first_name: Anna
  full_name: Kapitonova, Anna
  id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
  last_name: Kapitonova
- first_name: Roman J.
  full_name: Lichtenecker, Roman J.
  last_name: Lichtenecker
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Robert
  full_name: Konrat, Robert
  last_name: Konrat
citation:
  ama: Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy
    for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with
    UCBShift 2.0. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href="https://doi.org/10.1016/j.jmb.2025.169465">10.1016/j.jmb.2025.169465</a>
  apa: Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider,
    J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment
    using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal
    of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2025.169465">https://doi.org/10.1016/j.jmb.2025.169465</a>
  chicago: Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis,
    Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC
    NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate
    Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>. Elsevier,
    2025. <a href="https://doi.org/10.1016/j.jmb.2025.169465">https://doi.org/10.1016/j.jmb.2025.169465</a>.
  ieee: S. Knödlstorfer <i>et al.</i>, “A novel HMBC-CC-HMQC NMR strategy for methyl
    assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift
    2.0,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025.
  ista: Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J,
    Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC
    NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate
    integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465.
  mla: Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment
    Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal
    of Molecular Biology</i>, vol. 437, no. 23, 169465, Elsevier, 2025, doi:<a href="https://doi.org/10.1016/j.jmb.2025.169465">10.1016/j.jmb.2025.169465</a>.
  short: S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider,
    K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of
    Molecular Biology 437 (2025).
date_created: 2025-10-26T23:01:35Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-30T10:29:20Z
day: '01'
ddc:
- '540'
department:
- _id: PaSc
- _id: GradSch
doi: 10.1016/j.jmb.2025.169465
external_id:
  pmid:
  - '41016549'
file:
- access_level: open_access
  checksum: feb92f9c79032c261165f4ca573f444a
  content_type: application/pdf
  creator: dernst
  date_created: 2025-12-30T10:29:08Z
  date_updated: 2025-12-30T10:29:08Z
  file_id: '20915'
  file_name: 2025_JourMolecularBiology_Knoedlstorfer.pdf
  file_size: 3076611
  relation: main_file
  success: 1
file_date_updated: 2025-12-30T10:29:08Z
has_accepted_license: '1'
intvolume: '       437'
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0
  grant_number: I06223
  name: Structure and mechanism of the mitochondrial MIM insertase
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publication: Journal of Molecular Biology
publication_identifier:
  eissn:
  - 1089-8638
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled
  α-ketoisovalerate integrated with UCBShift 2.0
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: 437
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19725'
abstract:
- lang: eng
  text: Protein-protein interactions (PPIs) mediate many fundamental cellular processes.
    Control of PPIs through optically or chemically responsive protein domains has
    had a profound impact on basic research and some clinical applications. Most chemogenetic
    methods induce the association, i.e., dimerization or oligomerization, of target
    proteins, whilst the few available dissociation approaches either break large
    oligomeric protein clusters or heteromeric complexes. Here, we have exploited
    the controlled dissociation of a homodimeric oxidoreductase from mycobacteria
    (MSMEG_2027) by its native cofactor, F420, which is not present in mammals, as
    a bioorthogonal monomerization switch. Using X-ray crystallography, we found that
    in the absence of F420 MSMEG_2027 forms a unique domain-swapped dimer that occludes
    the cofactor binding site. Rearrangement of the N-terminal helix upon F420 binding
    results in the dissolution of the dimer. We then showed that MSMEG_2027 can be
    fused to proteins of interest in human cells and applied it as a tool to induce
    and release MAPK/ERK signalling downstream of a chimeric fibroblast growth factor
    receptor 1 (FGFR1) tyrosine kinase. This F420-dependent chemogenetic de-homodimerization
    tool is stoichiometric and based on a single domain and thus represents a novel
    mechanism to investigate protein complexes in situ.
acknowledgement: We thank J. Kaczmarski for advice on isothermal titration calorimetry
  and helpful comments, and Alexandra Tichy, Elliot Gerrard and Rahkesh T Sabapathy
  for assistance with experiments. This study was supported by grants of the Australian
  Research Council (FT200100519 and DP200102093, to H.J.; DE190100806, DP220101901,
  FT230100203, and DP250102939 to T.P.S.D.C; DP200102093, CE200100029 and CE200100012
  to C.J.J.), the National Health and Medical Research Council (APP1187638, to H.J.).
  S.K. was supported by the graduate program MolecularDrugTargets (Austrian Science
  Fund FWF W1232). The Australian Regenerative Medicine Institute is supported by
  grants from the State Government of Victoria and the Australian Government. The
  EMBL Australia Partnership Laboratory (EMBL Australia) is supported by the National
  Collaborative Research Infrastructure Strategy (NCRIS) of the Australian Government.
  T.P.S.D.C. acknowledges the University of Adelaide for a Future Making Fellowship.
  E.R.R.M acknowledges the Grains Research and Development Corporation (9176977) for
  support through a PhD scholarship and operational funding. J.A. and E.R.R.M. were
  supported by Australian Research Training Program scholarship. MicroMon of Monash
  University provided Sanger sequencing services. Imaging was performed in the CellScreen
  SA screening center of Flinders University. C.J.J. thanks the ARC Centre of Excellence
  for Innovations in Peptide and Protein Science and the ARC Centre of Excellence
  in Synthetic Biology. We thank the staff of the MX2 beamline at the Australian Synchrotron,
  part of ANSTO, which made use of the Australian Cancer Research Foundation (ACRF)
  detector.
article_number: '169184'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: James
  full_name: Antoney, James
  last_name: Antoney
- first_name: Stephanie
  full_name: Kainrath, Stephanie
  id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
  last_name: Kainrath
  orcid: 0000-0002-6709-2195
- first_name: Joshua G.
  full_name: Dubowsky, Joshua G.
  last_name: Dubowsky
- first_name: F. Hafna
  full_name: Ahmed, F. Hafna
  last_name: Ahmed
- first_name: Suk Woo
  full_name: Kang, Suk Woo
  last_name: Kang
- first_name: Emily R.R.
  full_name: Mackie, Emily R.R.
  last_name: Mackie
- first_name: Gustavo
  full_name: Bracho Granado, Gustavo
  last_name: Bracho Granado
- first_name: Tatiana P.
  full_name: Soares Da Costa, Tatiana P.
  last_name: Soares Da Costa
- first_name: Colin J.
  full_name: Jackson, Colin J.
  last_name: Jackson
- first_name: Harald L
  full_name: Janovjak, Harald L
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
citation:
  ama: Antoney J, Kainrath S, Dubowsky JG, et al. A F420-dependent single domain chemogenetic
    tool for protein de-dimerization. <i>Journal of Molecular Biology</i>. 2025;437(17).
    doi:<a href="https://doi.org/10.1016/j.jmb.2025.169184">10.1016/j.jmb.2025.169184</a>
  apa: Antoney, J., Kainrath, S., Dubowsky, J. G., Ahmed, F. H., Kang, S. W., Mackie,
    E. R. R., … Janovjak, H. L. (2025). A F420-dependent single domain chemogenetic
    tool for protein de-dimerization. <i>Journal of Molecular Biology</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.jmb.2025.169184">https://doi.org/10.1016/j.jmb.2025.169184</a>
  chicago: Antoney, James, Stephanie Kainrath, Joshua G. Dubowsky, F. Hafna Ahmed,
    Suk Woo Kang, Emily R.R. Mackie, Gustavo Bracho Granado, Tatiana P. Soares Da
    Costa, Colin J. Jackson, and Harald L Janovjak. “A F420-Dependent Single Domain
    Chemogenetic Tool for Protein de-Dimerization.” <i>Journal of Molecular Biology</i>.
    Elsevier, 2025. <a href="https://doi.org/10.1016/j.jmb.2025.169184">https://doi.org/10.1016/j.jmb.2025.169184</a>.
  ieee: J. Antoney <i>et al.</i>, “A F420-dependent single domain chemogenetic tool
    for protein de-dimerization,” <i>Journal of Molecular Biology</i>, vol. 437, no.
    17. Elsevier, 2025.
  ista: Antoney J, Kainrath S, Dubowsky JG, Ahmed FH, Kang SW, Mackie ERR, Bracho
    Granado G, Soares Da Costa TP, Jackson CJ, Janovjak HL. 2025. A F420-dependent
    single domain chemogenetic tool for protein de-dimerization. Journal of Molecular
    Biology. 437(17), 169184.
  mla: Antoney, James, et al. “A F420-Dependent Single Domain Chemogenetic Tool for
    Protein de-Dimerization.” <i>Journal of Molecular Biology</i>, vol. 437, no. 17,
    169184, Elsevier, 2025, doi:<a href="https://doi.org/10.1016/j.jmb.2025.169184">10.1016/j.jmb.2025.169184</a>.
  short: J. Antoney, S. Kainrath, J.G. Dubowsky, F.H. Ahmed, S.W. Kang, E.R.R. Mackie,
    G. Bracho Granado, T.P. Soares Da Costa, C.J. Jackson, H.L. Janovjak, Journal
    of Molecular Biology 437 (2025).
date_created: 2025-05-25T22:16:39Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2025-12-30T08:18:25Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1016/j.jmb.2025.169184
external_id:
  isi:
  - '001494762800001'
  pmid:
  - '40324743'
file:
- access_level: open_access
  checksum: fb6e84ba7dc92faee97647fd2bc8cca8
  content_type: application/pdf
  creator: dernst
  date_created: 2025-12-30T08:18:07Z
  date_updated: 2025-12-30T08:18:07Z
  file_id: '20892'
  file_name: 2025_JourMolecularBiology_Antoney.pdf
  file_size: 1682721
  relation: main_file
  success: 1
file_date_updated: 2025-12-30T08:18:07Z
has_accepted_license: '1'
intvolume: '       437'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 255A6082-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication: Journal of Molecular Biology
publication_identifier:
  eissn:
  - 1089-8638
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A F420-dependent single domain chemogenetic tool for protein de-dimerization
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: 437
year: '2025'
...
---
_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. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801.
    doi:<a href="https://doi.org/10.1016/j.jmb.2020.09.001">10.1016/j.jmb.2020.09.001</a>'
  apa: 'Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira,
    H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin
    interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.jmb.2020.09.001">https://doi.org/10.1016/j.jmb.2020.09.001</a>'
  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.”
    <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href="https://doi.org/10.1016/j.jmb.2020.09.001">https://doi.org/10.1016/j.jmb.2020.09.001</a>.'
  ieee: 'H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces:
    The switches hold the key,” <i>Journal of Molecular Biology</i>, 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.” <i>Journal of Molecular Biology</i>, vol. 432, no.
    21, Elsevier, 2020, pp. 5784–801, doi:<a href="https://doi.org/10.1016/j.jmb.2020.09.001">10.1016/j.jmb.2020.09.001</a>.'
  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'
...
---
_id: '6564'
abstract:
- lang: eng
  text: Optogenetics enables the spatio-temporally precise control of cell and animal
    behavior. Many optogenetic tools are driven by light-controlled protein–protein
    interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs).
    Applying light-controlled PPIs to new target proteins is challenging because it
    is difficult to predict which of the many available LSDs, if any, will yield robust
    light regulation. As a consequence, fusion protein libraries need to be prepared
    and tested, but methods and platforms to facilitate this process are currently
    not available. Here, we developed a genetic engineering strategy and vector library
    for the rapid generation of light-controlled PPIs. The strategy permits fusing
    a target protein to multiple LSDs efficiently and in two orientations. The public
    and expandable library contains 29 vectors with blue, green or red light-responsive
    LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate
    the versatility of the approach and the necessity for sampling LSDs by generating
    light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a
    new resource for optical regulation of a broad range of target proteins in cell
    and developmental biology.
article_processing_charge: No
article_type: original
author:
- first_name: Alexandra-Madelaine
  full_name: Tichy, Alexandra-Madelaine
  id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
  last_name: Tichy
- first_name: Elliot J.
  full_name: Gerrard, Elliot J.
  last_name: Gerrard
- first_name: Julien M.D.
  full_name: Legrand, Julien M.D.
  last_name: Legrand
- first_name: Robin M.
  full_name: Hobbs, Robin M.
  last_name: Hobbs
- first_name: Harald L
  full_name: Janovjak, Harald L
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
citation:
  ama: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy
    and vector library for the rapid generation of modular light-controlled protein–protein
    interactions. <i>Journal of Molecular Biology</i>. 2019;431(17):3046-3055. doi:<a
    href="https://doi.org/10.1016/j.jmb.2019.05.033">10.1016/j.jmb.2019.05.033</a>
  apa: Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., &#38; Janovjak,
    H. L. (2019). Engineering strategy and vector library for the rapid generation
    of modular light-controlled protein–protein interactions. <i>Journal of Molecular
    Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2019.05.033">https://doi.org/10.1016/j.jmb.2019.05.033</a>
  chicago: Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin
    M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for
    the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.”
    <i>Journal of Molecular Biology</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.jmb.2019.05.033">https://doi.org/10.1016/j.jmb.2019.05.033</a>.
  ieee: A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak,
    “Engineering strategy and vector library for the rapid generation of modular light-controlled
    protein–protein interactions,” <i>Journal of Molecular Biology</i>, vol. 431,
    no. 17. Elsevier, pp. 3046–3055, 2019.
  ista: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering
    strategy and vector library for the rapid generation of modular light-controlled
    protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.
  mla: Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library
    for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.”
    <i>Journal of Molecular Biology</i>, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55,
    doi:<a href="https://doi.org/10.1016/j.jmb.2019.05.033">10.1016/j.jmb.2019.05.033</a>.
  short: A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal
    of Molecular Biology 431 (2019) 3046–3055.
date_created: 2019-06-16T21:59:14Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2025-07-10T11:53:33Z
day: '09'
department:
- _id: HaJa
doi: 10.1016/j.jmb.2019.05.033
external_id:
  isi:
  - '000482872100002'
intvolume: '       431'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://www.biorxiv.org/content/10.1101/583369v1
month: '08'
oa: 1
oa_version: Preprint
page: 3046-3055
publication: Journal of Molecular Biology
publication_identifier:
  eissn:
  - 1089-8638
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Engineering strategy and vector library for the rapid generation of modular
  light-controlled protein–protein interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 431
year: '2019'
...
---
_id: '8462'
abstract:
- lang: eng
  text: The transition of proteins from their soluble functional state to amyloid
    fibrils and aggregates is associated with the onset of several human diseases.
    Protein aggregation often requires some structural reshaping and the subsequent
    formation of intermolecular contacts. Therefore, the study of the conformation
    of excited protein states and their ability to form oligomers is of primary importance
    for understanding the molecular basis of amyloid fibril formation. Here, we investigated
    the oligomerization processes that occur along the folding of the amyloidogenic
    human protein β2-microglobulin. The combination of real-time two-dimensional NMR
    data with real-time small-angle X-ray scattering measurements allowed us to derive
    thermodynamic and kinetic information on protein oligomerization of different
    conformational states populated along the folding pathways. In particular, we
    could demonstrate that a long-lived folding intermediate (I-state) has a higher
    propensity to oligomerize compared to the native state. Our data agree well with
    a simple five-state kinetic model that involves only monomeric and dimeric species.
    The dimers have an elongated shape with the dimerization interface located at
    the apical side of β2-microglobulin close to Pro32, the residue that has a trans
    conformation in the I-state and a cis conformation in the native (N) state. Our
    experimental data suggest that partial unfolding in the apical half of the protein
    close to Pro32 leads to an excited state conformation with enhanced propensity
    for oligomerization. This excited state becomes more populated in the transient
    I-state due to the destabilization of the native conformation by the trans-Pro32
    configuration.
article_processing_charge: No
article_type: original
author:
- first_name: E.
  full_name: Rennella, E.
  last_name: Rennella
- first_name: T.
  full_name: Cutuil, T.
  last_name: Cutuil
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: I.
  full_name: Ayala, I.
  last_name: Ayala
- first_name: F.
  full_name: Gabel, F.
  last_name: Gabel
- first_name: V.
  full_name: Forge, V.
  last_name: Forge
- first_name: A.
  full_name: Corazza, A.
  last_name: Corazza
- first_name: G.
  full_name: Esposito, G.
  last_name: Esposito
- first_name: B.
  full_name: Brutscher, B.
  last_name: Brutscher
citation:
  ama: 'Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding
    pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal
    of Molecular Biology</i>. 2013;425(15):2722-2736. doi:<a href="https://doi.org/10.1016/j.jmb.2013.04.028">10.1016/j.jmb.2013.04.028</a>'
  apa: 'Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., …
    Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin:
    Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.jmb.2013.04.028">https://doi.org/10.1016/j.jmb.2013.04.028</a>'
  chicago: 'Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A.
    Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways
    of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular
    Biology</i>. Elsevier, 2013. <a href="https://doi.org/10.1016/j.jmb.2013.04.028">https://doi.org/10.1016/j.jmb.2013.04.028</a>.'
  ieee: 'E. Rennella <i>et al.</i>, “Oligomeric states along the folding pathways
    of β2-microglobulin: Kinetics, thermodynamics, and structure,” <i>Journal of Molecular
    Biology</i>, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.'
  ista: 'Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito
    G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin:
    Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15),
    2722–2736.'
  mla: 'Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin:
    Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>,
    vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:<a href="https://doi.org/10.1016/j.jmb.2013.04.028">10.1016/j.jmb.2013.04.028</a>.'
  short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza,
    G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.
date_created: 2020-09-18T10:09:12Z
date_published: 2013-08-09T00:00:00Z
date_updated: 2022-08-25T14:56:24Z
day: '09'
doi: 10.1016/j.jmb.2013.04.028
extern: '1'
intvolume: '       425'
issue: '15'
keyword:
- Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2722-2736
publication: Journal of Molecular Biology
publication_identifier:
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Oligomeric states along the folding pathways of β2-microglobulin: Kinetics,
  thermodynamics, and structure'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 425
year: '2013'
...
---
_id: '8471'
abstract:
- lang: eng
  text: Despite the importance of protein fibrils in the context of conformational
    diseases, information on their structure is still sparse. Hydrogen/deuterium exchange
    measurements of backbone amide protons allow the identification hydrogen-bonding
    patterns and reveal pertinent information on the amyloid β-sheet architecture.
    However, they provide only little information on the identity of residues exposed
    to solvent or buried inside the fibril core. NMR spectroscopy is a potent method
    for identifying solvent-accessible residues in proteins via observation of polarization
    transfer between chemically exchanging side-chain protons and water protons. We
    show here that the combined use of highly deuterated samples and fast magic-angle
    spinning greatly attenuates unwanted spin diffusion and allows identification
    of polarization exchange with the solvent in a site-specific manner. We apply
    this measurement protocol to HET-s(218–289) prion fibrils under different conditions
    (including physiological pH, where protofibrils assemble together into thicker
    fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded
    by water, thus excluding the existence of extended dry interfibril contacts. We
    also show that exchangeable side-chain protons inside the hydrophobic core of
    HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments
    proposed in this study can provide insight into the detailed structural features
    of amyloid fibrils in general.
article_processing_charge: No
article_type: original
author:
- first_name: Hélène
  full_name: Van Melckebeke, Hélène
  last_name: Van Melckebeke
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Julia
  full_name: Gath, Julia
  last_name: Gath
- first_name: Christian
  full_name: Wasmer, Christian
  last_name: Wasmer
- first_name: René
  full_name: Verel, René
  last_name: Verel
- first_name: Adam
  full_name: Lange, Adam
  last_name: Lange
- first_name: Beat H.
  full_name: Meier, Beat H.
  last_name: Meier
- first_name: Anja
  full_name: Böckmann, Anja
  last_name: Böckmann
citation:
  ama: Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in
    HET-s(218–289) amyloid fibrils by solid-state NMR. <i>Journal of Molecular Biology</i>.
    2011;405(3):765-772. doi:<a href="https://doi.org/10.1016/j.jmb.2010.11.004">10.1016/j.jmb.2010.11.004</a>
  apa: Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A.,
    … Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils
    by solid-state NMR. <i>Journal of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2010.11.004">https://doi.org/10.1016/j.jmb.2010.11.004</a>
  chicago: Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René
    Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility
    in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” <i>Journal of Molecular
    Biology</i>. Elsevier, 2011. <a href="https://doi.org/10.1016/j.jmb.2010.11.004">https://doi.org/10.1016/j.jmb.2010.11.004</a>.
  ieee: H. Van Melckebeke <i>et al.</i>, “Probing water accessibility in HET-s(218–289)
    amyloid fibrils by solid-state NMR,” <i>Journal of Molecular Biology</i>, vol.
    405, no. 3. Elsevier, pp. 765–772, 2011.
  ista: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH,
    Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils
    by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772.
  mla: Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289)
    Amyloid Fibrils by Solid-State NMR.” <i>Journal of Molecular Biology</i>, vol.
    405, no. 3, Elsevier, 2011, pp. 765–72, doi:<a href="https://doi.org/10.1016/j.jmb.2010.11.004">10.1016/j.jmb.2010.11.004</a>.
  short: H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H.
    Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772.
date_created: 2020-09-18T10:11:03Z
date_published: 2011-01-21T00:00:00Z
date_updated: 2021-01-12T08:19:30Z
day: '21'
doi: 10.1016/j.jmb.2010.11.004
extern: '1'
intvolume: '       405'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 765-772
publication: Journal of Molecular Biology
publication_identifier:
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state
  NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 405
year: '2011'
...
---
_id: '8480'
abstract:
- lang: eng
  text: The KIX domain of the transcription co-activator CBP is a three-helix bundle
    protein that folds via rapid accumulation of an intermediate state, followed by
    a slower folding phase. Recent NMR relaxation dispersion studies revealed the
    presence of a low-populated (excited) state of KIX that exists in equilibrium
    with the natively folded form under non-denaturing conditions, and likely represents
    the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium
    exchange measurements using rapid NMR data acquisition techniques with backbone
    15N and 13C relaxation dispersion experiments to further investigate the equilibrium
    folding of the KIX domain. Residual structure within the folding intermediate
    is detected by both methods, and their combination enables reliable quantification
    of the amount of persistent residual structure. Three well-defined folding subunits
    are found, which display variable stability and correspond closely to the individual
    helices in the native state. While two of the three helices (α2 and α3) are partially
    formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C),
    the third helix is disordered. The observed helical content within the excited
    state exceeds the helical propensities predicted for the corresponding peptide
    regions, suggesting that the two helices are weakly mutually stabilized, while
    methyl 13C relaxation dispersion data indicate that a defined packing arrangement
    is unlikely. Temperature-dependent experiments reveal that the largest enthalpy
    and entropy changes along the folding reaction occur during the final transition
    from the intermediate to the native state. Our experimental data are consistent
    with a folding mechanism where helices α2 and α3 form rapidly, although to different
    extents, while helix α1 consolidates only as folding proceeds to complete the
    native state-structure.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Bernhard
  full_name: Brutscher, Bernhard
  last_name: Brutscher
- first_name: Robert
  full_name: Konrat, Robert
  last_name: Konrat
- first_name: Martin
  full_name: Tollinger, Martin
  last_name: Tollinger
citation:
  ama: 'Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain:
    Characterization of the equilibrium analog of a folding intermediate using 15N/13C
    relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal
    of Molecular Biology</i>. 2008;380(4):726-741. doi:<a href="https://doi.org/10.1016/j.jmb.2008.05.040">10.1016/j.jmb.2008.05.040</a>'
  apa: 'Schanda, P., Brutscher, B., Konrat, R., &#38; Tollinger, M. (2008). Folding
    of the KIX domain: Characterization of the equilibrium analog of a folding intermediate
    using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy.
    <i>Journal of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2008.05.040">https://doi.org/10.1016/j.jmb.2008.05.040</a>'
  chicago: 'Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger.
    “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding
    Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange
    NMR Spectroscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href="https://doi.org/10.1016/j.jmb.2008.05.040">https://doi.org/10.1016/j.jmb.2008.05.040</a>.'
  ieee: 'P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX
    domain: Characterization of the equilibrium analog of a folding intermediate using
    15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,”
    <i>Journal of Molecular Biology</i>, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.'
  ista: 'Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain:
    Characterization of the equilibrium analog of a folding intermediate using 15N/13C
    relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal
    of Molecular Biology. 380(4), 726–741.'
  mla: 'Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the
    Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion
    and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>,
    vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:<a href="https://doi.org/10.1016/j.jmb.2008.05.040">10.1016/j.jmb.2008.05.040</a>.'
  short: P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology
    380 (2008) 726–741.
date_created: 2020-09-18T10:12:29Z
date_published: 2008-07-18T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '18'
doi: 10.1016/j.jmb.2008.05.040
extern: '1'
intvolume: '       380'
issue: '4'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 726-741
publication: Journal of Molecular Biology
publication_identifier:
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Folding of the KIX domain: Characterization of the equilibrium analog of a
  folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange
  NMR spectroscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '8481'
abstract:
- lang: eng
  text: 'The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans
    CH34 within the complex cop cluster of genes, for which 21 genes have been identified.
    The expression of the corresponding periplasmic CopK protein is strongly upregulated
    in the presence of copper, leading to a high periplasmic accumulation. The structure
    and metal-binding properties of CopK were investigated by NMR and mass spectrometry.
    The protein is dimeric in the apo state with a dissociation constant in the range
    of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed
    that CopK has two high-affinity Cu(I)-binding sites per monomer with different
    Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific.
    The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets
    in perpendicular orientation with an unstructured C-terminal tail. The dimer interface
    is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion
    induces a major structural modification involving dissociation of the dimeric
    apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm
    the conservation of the N-terminal β-sheet, while the last strand of the C-terminal
    sheet appears in slow conformational exchange. We hypothesize that the partial
    disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange
    data acquired on the apo-protein are consistent with a lower thermodynamic stability
    of the C-terminal sheet. CopK contains seven methionine residues, five of which
    appear highly conserved. Chemical shift data suggest implication of two or three
    methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second
    Cu(I) ion further increases protein plasticity. Comparison of the structural and
    metal-binding properties of CopK with other periplasmic copper-binding proteins
    reveals two conserved features within these functionally related proteins: the
    all-β fold and the methionine-rich Cu(I)-binding site.'
article_processing_charge: No
article_type: original
author:
- first_name: Beate
  full_name: Bersch, Beate
  last_name: Bersch
- first_name: Adrien
  full_name: Favier, Adrien
  last_name: Favier
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Sébastien
  full_name: van Aelst, Sébastien
  last_name: van Aelst
- first_name: Tatiana
  full_name: Vallaeys, Tatiana
  last_name: Vallaeys
- first_name: Jacques
  full_name: Covès, Jacques
  last_name: Covès
- first_name: Max
  full_name: Mergeay, Max
  last_name: Mergeay
- first_name: Ruddy
  full_name: Wattiez, Ruddy
  last_name: Wattiez
citation:
  ama: Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding
    properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans
    CH34 during copper challenge. <i>Journal of Molecular Biology</i>. 2008;380(2):386-403.
    doi:<a href="https://doi.org/10.1016/j.jmb.2008.05.017">10.1016/j.jmb.2008.05.017</a>
  apa: Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J.,
    … Wattiez, R. (2008). Molecular structure and metal-binding properties of the
    periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper
    challenge. <i>Journal of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.jmb.2008.05.017">https://doi.org/10.1016/j.jmb.2008.05.017</a>
  chicago: Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana
    Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure
    and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus
    Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>.
    Elsevier, 2008. <a href="https://doi.org/10.1016/j.jmb.2008.05.017">https://doi.org/10.1016/j.jmb.2008.05.017</a>.
  ieee: B. Bersch <i>et al.</i>, “Molecular structure and metal-binding properties
    of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during
    copper challenge,” <i>Journal of Molecular Biology</i>, vol. 380, no. 2. Elsevier,
    pp. 386–403, 2008.
  ista: Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M,
    Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic
    CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge.
    Journal of Molecular Biology. 380(2), 386–403.
  mla: Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of
    the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during
    Copper Challenge.” <i>Journal of Molecular Biology</i>, vol. 380, no. 2, Elsevier,
    2008, pp. 386–403, doi:<a href="https://doi.org/10.1016/j.jmb.2008.05.017">10.1016/j.jmb.2008.05.017</a>.
  short: B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M.
    Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.
date_created: 2020-09-18T10:12:37Z
date_published: 2008-07-04T00:00:00Z
date_updated: 2021-01-12T08:19:34Z
day: '04'
doi: 10.1016/j.jmb.2008.05.017
extern: '1'
intvolume: '       380'
issue: '2'
keyword:
- Molecular Biology
language:
- iso: eng
month: '07'
oa_version: None
page: 386-403
publication: Journal of Molecular Biology
publication_identifier:
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Molecular structure and metal-binding properties of the periplasmic CopK protein
  expressed in Cupriavidus metallidurans CH34 during copper challenge
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2008'
...
---
_id: '1957'
abstract:
- lang: eng
  text: NADH:ubiquinone oxidoreductase (complex I) is the first and largest enzyme
    of the mitochondrial respiratory chain. The low-resolution structure of the complex
    is known from electron microscopy studies. The general shape of the complex is
    in the form of an L, with one arm in the membrane and the other peripheral. We
    have purified complex I from beef heart mitochondria and reconstituted the enzyme
    into lipid bilayers. Under different conditions, several two-dimensional crystal
    forms were obtained. Crystals belonging to space groups p2221 and c12 (unit cell
    488 Å x 79 Å) were obtained at 22°C and contained only the membrane fragment of
    complex I similar to hydrophobic subcomplex Iβ but lacking the ND5 subunit. A
    crystal form with larger unit cell (534 Å x 81 Å, space group c12) produced at
    4°C contained both the peripheral and membrane arms of the enzyme, except that
    ND5 was missing. Projection maps from frozen hydrated samples were calculated
    for all crystal forms. By comparing two different c12 crystal forms, extra electron
    density in the projection map of large crystal form was assigned to the peripheral
    arm of the enzyme. One of the features of the map is a deep, channel-like, cleft
    next to peripheral arm. Comparison with available structures of the intact enzyme
    indicates that large hydrophobic subunit ND5 is situated at the distal end of
    the membrane domain. Possible locations of sub-unit ND4 and of other subunits
    in the membrane domain are proposed. Implications of our findings for the mechanism
    of proton pumping by complex I are discussed. (C) 2000 Academic Press.
acknowledgement: We thank Drs I. M. Fearnley and S. Y. Peak-Chew for performing peptide
  mass mapping. We also thank Drs R. Henderson and G. F. X. Schertler for advice on
  image processing and for valuable discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A
  full_name: Sazanov, Leonid A
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
  last_name: Sazanov
  orcid: 0000-0002-0977-7989
- first_name: John
  full_name: Walker, John
  last_name: Walker
citation:
  ama: Sazanov LA, Walker J. Cryo-electron crystallography of two sub-complexes of
    bovine complex I reveals the relationship between the membrane and peripheral
    arms. <i>Journal of Molecular Biology</i>. 2000;302(2):455-464. doi:<a href="https://doi.org/10.1006/jmbi.2000.4079">10.1006/jmbi.2000.4079</a>
  apa: Sazanov, L. A., &#38; Walker, J. (2000). Cryo-electron crystallography of two
    sub-complexes of bovine complex I reveals the relationship between the membrane
    and peripheral arms. <i>Journal of Molecular Biology</i>. Elsevier. <a href="https://doi.org/10.1006/jmbi.2000.4079">https://doi.org/10.1006/jmbi.2000.4079</a>
  chicago: Sazanov, Leonid A, and John Walker. “Cryo-Electron Crystallography of Two
    Sub-Complexes of Bovine Complex I Reveals the Relationship between the Membrane
    and Peripheral Arms.” <i>Journal of Molecular Biology</i>. Elsevier, 2000. <a
    href="https://doi.org/10.1006/jmbi.2000.4079">https://doi.org/10.1006/jmbi.2000.4079</a>.
  ieee: L. A. Sazanov and J. Walker, “Cryo-electron crystallography of two sub-complexes
    of bovine complex I reveals the relationship between the membrane and peripheral
    arms,” <i>Journal of Molecular Biology</i>, vol. 302, no. 2. Elsevier, pp. 455–464,
    2000.
  ista: Sazanov LA, Walker J. 2000. Cryo-electron crystallography of two sub-complexes
    of bovine complex I reveals the relationship between the membrane and peripheral
    arms. Journal of Molecular Biology. 302(2), 455–464.
  mla: Sazanov, Leonid A., and John Walker. “Cryo-Electron Crystallography of Two
    Sub-Complexes of Bovine Complex I Reveals the Relationship between the Membrane
    and Peripheral Arms.” <i>Journal of Molecular Biology</i>, vol. 302, no. 2, Elsevier,
    2000, pp. 455–64, doi:<a href="https://doi.org/10.1006/jmbi.2000.4079">10.1006/jmbi.2000.4079</a>.
  short: L.A. Sazanov, J. Walker, Journal of Molecular Biology 302 (2000) 455–464.
date_created: 2018-12-11T11:54:55Z
date_published: 2000-09-15T00:00:00Z
date_updated: 2023-05-04T13:23:03Z
day: '15'
doi: 10.1006/jmbi.2000.4079
extern: '1'
external_id:
  pmid:
  - '10970745'
intvolume: '       302'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 455 - 464
pmid: 1
publication: Journal of Molecular Biology
publication_identifier:
  issn:
  - 0022-2836
publication_status: published
publisher: Elsevier
publist_id: '5126'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-electron crystallography of two sub-complexes of bovine complex I reveals
  the relationship between the membrane and peripheral arms
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 302
year: '2000'
...