---
OA_place: repository
_id: '22687'
abstract:
- lang: eng
  text: "Understanding enzyme function requires characterizing not only static structure
    but also dynamics and ligand interactions. NMR spectroscopy provides this insight
    at atomic resolution, yet for large proteins the difficulty of resonance assignment
    has largely confined such studies to systems below ∼50 kDa, or to observing only
    methyl groups. Here we present an integrated magic-angle spinning (MAS) and solution
    NMR study of the 134 kDa tetrameric malate dehydrogenase from Ignicoccus islandicus
    (IiMDH), an enzyme of particular interest as an evolutionary intermediate between
    allosteric lactate\r\ndehydrogenases and non-allosteric malate dehydrogenases.
    By combining high-dimensional (up to 4D) MAS NMR experiments on sedimented protein
    with solution NMR, we achieved 92% backbone heavy- atom assignment and 91% assignment
    of all Ile-δ1, Leu-δ1/-δ2, Val-γ1/-γ2, Met-ε and Thr-γ methyl groups. Building
    on these assignments, we use various probes of backbone and sidechain dynamics:
    elevated MAS NMR 15N rotating-frame relaxation (R1ρ) points to microsecond motions
    in functionally critical regions, including the catalytic loop and the mobile
    surface loop. Complementary methyl-axis order parameters from solution NMR identified
    additional flexible sites in the hydrophobic core. Chemical shift perturbation
    experiments upon addition of the substrate analogue oxamate, monitored via backbone
    1H-15N TROSY, revealed both active-site contacts and responses in helices α2F
    and α3G, regions implicated in allosteric signal transmission. The integrated
    approach demonstrated here exploits the distinct strengths of MAS and solution
    NMR, and provides a comprehensive view of structure, dynamics, and substrate interactions
    in a large oligomeric enzyme that would not be accessible by either technique
    alone."
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: 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 and the Lab Support Facilities. We thank Petra
  Rovó, Megha Mohan and Margarita Valhondo Falcón for excellent support of the NMR
  facility.
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
- first_name: Federico
  full_name: Napoli, Federico
  id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
  last_name: Napoli
  orcid: 0000-0002-9043-136X
citation:
  ama: 'Schanda P, Napoli F. Data and scripts for: “Integrated solid/solution NMR
    assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme.” 2026.
    doi:<a href="https://doi.org/10.15479/AT-ISTA-22687">10.15479/AT-ISTA-22687</a>'
  apa: 'Schanda, P., &#38; Napoli, F. (2026). Data and scripts for: “Integrated solid/solution
    NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme.”
    Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-22687">https://doi.org/10.15479/AT-ISTA-22687</a>'
  chicago: 'Schanda, Paul, and Federico Napoli. “Data and Scripts for: ‘Integrated
    Solid/Solution NMR Assignment Allows Mapping Dynamics and Ligand Binding in a
    134 KDa Enzyme.’” Institute of Science and Technology Austria, 2026. <a href="https://doi.org/10.15479/AT-ISTA-22687">https://doi.org/10.15479/AT-ISTA-22687</a>.'
  ieee: 'P. Schanda and F. Napoli, “Data and scripts for: ‘Integrated solid/solution
    NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme.’”
    Institute of Science and Technology Austria, 2026.'
  ista: 'Schanda P, Napoli F. 2026. Data and scripts for: ‘Integrated solid/solution
    NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme’,
    Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT-ISTA-22687">10.15479/AT-ISTA-22687</a>.'
  mla: 'Schanda, Paul, and Federico Napoli. <i>Data and Scripts for: “Integrated Solid/Solution
    NMR Assignment Allows Mapping Dynamics and Ligand Binding in a 134 KDa Enzyme.”</i>
    Institute of Science and Technology Austria, 2026, doi:<a href="https://doi.org/10.15479/AT-ISTA-22687">10.15479/AT-ISTA-22687</a>.'
  short: P. Schanda, F. Napoli, (2026).
contributor:
- contributor_type: researcher
  first_name: Federico
  id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
  last_name: Napoli
  orcid: 0000-0002-9043-136X
- contributor_type: project_leader
  first_name: Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- contributor_type: project_member
  first_name: Rajkumar
  id: a3089acd-6806-11ee-bacc-f0c7d500ad20
  last_name: Singh
- contributor_type: project_member
  first_name: Anna
  id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
  last_name: Kapitonova
- contributor_type: project_member
  first_name: Virgil
  last_name: Aitenbichler
- contributor_type: project_member
  first_name: Giorgia
  id: 334a5e40-8747-11f0-b671-ba1f5154b4b4
  last_name: Toscano
- contributor_type: data_collector
  first_name: Barbara
  last_name: Perrone
corr_author: '1'
date_created: 2026-08-12T16:12:19Z
date_published: 2026-08-20T00:00:00Z
date_updated: 2026-08-20T07:40:15Z
day: '20'
department:
- _id: PaSc
doi: 10.15479/AT-ISTA-22687
doi_confirm: '1'
file:
- access_level: open_access
  checksum: dd23db23f7e75bafad6c67381163c1e2
  content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
  creator: fnapoli
  date_created: 2026-08-18T07:13:26Z
  date_updated: 2026-08-18T07:13:26Z
  file_id: '22725'
  file_name: Pulse_parameters.xlsx
  file_size: 59096
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a7ad194d8d7f780725bc2c60c63d686d
  content_type: application/zip
  creator: fnapoli
  date_created: 2026-08-18T07:16:00Z
  date_updated: 2026-08-18T07:16:00Z
  file_id: '22726'
  file_name: Scripts_submission.zip
  file_size: 3591173
  relation: main_file
  success: 1
- access_level: open_access
  checksum: dc099c298844973512ab224464964a1a
  content_type: application/zip
  creator: fnapoli
  date_created: 2026-08-18T07:15:59Z
  date_updated: 2026-08-18T07:15:59Z
  file_id: '22727'
  file_name: FLYA_runs.zip
  file_size: 28750919
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 04bcce8eb20c90089cbd2fb5e0c50a7f
  content_type: application/zip
  creator: fnapoli
  date_created: 2026-08-18T07:33:47Z
  date_updated: 2026-08-18T07:33:47Z
  file_id: '22728'
  file_name: spectra_Bruker.zip
  file_size: 3824856998
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 91c1161ca98632ed643d2b564395da5b
  content_type: application/zip
  creator: fnapoli
  date_created: 2026-08-18T08:03:33Z
  date_updated: 2026-08-18T08:03:33Z
  file_id: '22729'
  file_name: Titration_data.zip
  file_size: 17880653
  relation: main_file
  success: 1
- access_level: open_access
  checksum: ca2cf03b82656ae2858931d4391a3158
  content_type: text/plain
  creator: arashid
  date_created: 2026-08-20T07:35:05Z
  date_updated: 2026-08-20T07:35:05Z
  file_id: '22743'
  file_name: README.txt
  file_size: 868
  relation: main_file
  success: 1
file_date_updated: 2026-08-20T07:35:05Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: None
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publisher: Institute of Science and Technology Austria
status: public
title: 'Data and scripts for: "Integrated solid/solution NMR assignment allows mapping
  dynamics and ligand binding in a 134 kDa enzyme"'
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '21327'
abstract:
- lang: eng
  text: Proteins exist as a dynamic ensemble of multiple conformations, and these
    motions are often crucial for their functions. However, current structure prediction
    methods predominantly yield a single conformation, overlooking the conformational
    heterogeneity revealed by diverse experimental modalities. Here, we present a
    framework for building experiment-grounded protein structure generative models
    that infer conformational ensembles consistent with measured experimental data.
    The key idea is to treat stateof-the-art protein structure predictors (e.g., AlphaFold3)
    as sequence-conditioned structural priors, and cast ensemble modeling as posterior
    inference of protein structures given experimental measurements. Through extensive
    real-data experiments, we demonstrate the generality of our method to incorporate
    a variety of experimental measurements. In particular, our framework uncovers
    previously unmodeled conformational heterogeneity from crystallographic densities,
    and generates high-accuracy NMR ensembles orders of magnitude faster than the
    status quo. Notably, we demonstrate that our ensembles outperform AlphaFold3 (Abramson
    et al., 2024) and sometimes better fit experimental data than publicly deposited
    structures to the Protein Data Bank (PDB, Burley et al. (2017)). We believe that
    this approach will unlock building predictive models that fully embrace experimentally
    observed conformational diversity.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'This work was supported by the Israeli Science Foundation (ISF)
  grant number 1834/24. We acknowledge support from the Austrian Science Fund (FWF,
  grant numbers I5812-B and I6223) and the financial support of the Helmsley Fellowships
  Program for Sustainability and Health. This research uses resources of the Institute
  of Science and Technology Austria’s scientific computing cluster. '
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Sai A
  full_name: Maddipatla, Sai A
  id: e957f5e5-91c9-11f0-a95f-e090f66ecb4d
  last_name: Maddipatla
- first_name: Nadav E
  full_name: Sellam, Nadav E
  id: ef280fe0-91c9-11f0-a95f-8dea3f5bc513
  last_name: Sellam
- first_name: Meital I
  full_name: Bojan, Meital I
  id: 11d88cf5-91ca-11f0-a95f-edf9f08f47b7
  last_name: Bojan
- first_name: Sanketh
  full_name: Vedula, Sanketh
  id: 94f2fe44-70fa-11f0-b76b-92922c09452b
  last_name: Vedula
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Ailie
  full_name: Marx, Ailie
  last_name: Marx
- first_name: Alexander
  full_name: Bronstein, Alexander
  id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
  last_name: Bronstein
  orcid: 0000-0001-9699-8730
citation:
  ama: 'Maddipatla SA, Sellam NE, Bojan MI, et al. Inverse problems with experiment-guided
    AlphaFold. In: <i>Proceedings of the 42nd International Conference on Machine
    Learning</i>. Vol 267. ML Research Press; 2025:42366-42393.'
  apa: 'Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Vedula, S., Schanda, P., Marx,
    A., &#38; Bronstein, A. M. (2025). Inverse problems with experiment-guided AlphaFold.
    In <i>Proceedings of the 42nd International Conference on Machine Learning</i>
    (Vol. 267, pp. 42366–42393). Vancouver, Canada: ML Research Press.'
  chicago: Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Sanketh Vedula, Paul
    Schanda, Ailie Marx, and Alex M. Bronstein. “Inverse Problems with Experiment-Guided
    AlphaFold.” In <i>Proceedings of the 42nd International Conference on Machine
    Learning</i>, 267:42366–93. ML Research Press, 2025.
  ieee: S. A. Maddipatla <i>et al.</i>, “Inverse problems with experiment-guided AlphaFold,”
    in <i>Proceedings of the 42nd International Conference on Machine Learning</i>,
    Vancouver, Canada, 2025, vol. 267, pp. 42366–42393.
  ista: 'Maddipatla SA, Sellam NE, Bojan MI, Vedula S, Schanda P, Marx A, Bronstein
    AM. 2025. Inverse problems with experiment-guided AlphaFold. Proceedings of the
    42nd International Conference on Machine Learning. ICML: International Conference
    on Machine Learning, PMLR, vol. 267, 42366–42393.'
  mla: Maddipatla, Sai A., et al. “Inverse Problems with Experiment-Guided AlphaFold.”
    <i>Proceedings of the 42nd International Conference on Machine Learning</i>, vol.
    267, ML Research Press, 2025, pp. 42366–93.
  short: S.A. Maddipatla, N.E. Sellam, M.I. Bojan, S. Vedula, P. Schanda, A. Marx,
    A.M. Bronstein, in:, Proceedings of the 42nd International Conference on Machine
    Learning, ML Research Press, 2025, pp. 42366–42393.
conference:
  end_date: 2025-07-19
  location: Vancouver, Canada
  name: 'ICML: International Conference on Machine Learning'
  start_date: 2025-07-13
corr_author: '1'
date_created: 2026-02-18T12:11:17Z
date_published: 2025-07-30T00:00:00Z
date_updated: 2026-02-19T08:56:43Z
day: '30'
ddc:
- '000'
- '540'
department:
- _id: PaSc
- _id: AlBr
- _id: GradSch
external_id:
  arxiv:
  - '2502.09372'
file:
- access_level: open_access
  checksum: f33230a6d59b7978d4cd72795e4e9059
  content_type: application/pdf
  creator: dernst
  date_created: 2026-02-19T08:56:10Z
  date_updated: 2026-02-19T08:56:10Z
  file_id: '21338'
  file_name: 2025_ICML_Maddipatla.pdf
  file_size: 1924177
  relation: main_file
  success: 1
file_date_updated: 2026-02-19T08:56:10Z
has_accepted_license: '1'
intvolume: '       267'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 42366 - 42393
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
- _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0
  grant_number: I06223
  name: Structure and mechanism of the mitochondrial MIM insertase
publication: Proceedings of the 42nd International Conference on Machine Learning
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: Inverse problems with experiment-guided AlphaFold
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 267
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19555'
abstract:
- lang: eng
  text: The charged arginine side chain is unique in determining many innate properties
    of proteins, contributing to stability and interaction surfaces, and directing
    allosteric regulation and enzymatic catalysis. NMR experiments can be used to
    reveal these processes at the molecular level, but it often requires selective
    insertion of carbon-13, nitrogen-15, and deuterium at defined atomic positions.
    We introduce a method to endow arginine residues with defined isotope patterns,
    combining synthetic organic chemistry and cell-based protein overexpression. The
    resulting proteins feature NMR active spin systems with optimized relaxation pathways
    leading to simplified NMR spectra with a sensitive response to changes in the
    chemical environment of the nuclei observed.
acknowledged_ssus:
- _id: NMR
acknowledgement: We thank Lea Marie Becker for assistance with python scripts used
  to analyze the labeling efficiency, and Undina Guillerm, Rajkumar Singh, and Anna
  Kapitonova for help with protein production. This work was supported by the Austrian
  Science Fund (FWF; project number I5812-B) through a French-Austrian bi-national
  research project. We thank the Scientific Service Units (SSU) of Institute of Science
  and Technology Austria (ISTA) through resources provided by the NMR Facility, as
  well as the NMR center and MS center of the University of Vienna.
article_number: e202500408
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Darja
  full_name: Rohden, Darja
  id: 81dc668a-19fa-11f0-bf31-d56534059ef3
  last_name: Rohden
- first_name: Giorgia
  full_name: Toscano, Giorgia
  last_name: Toscano
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Roman J.
  full_name: Lichtenecker, Roman J.
  last_name: Lichtenecker
citation:
  ama: Rohden D, Toscano G, Schanda P, Lichtenecker RJ. Synthesis of selectively 13C/2H/15N-
    labeled arginine to probe protein conformation and interaction by NMR spectroscopy.
    <i>Chemistry - A European Journal</i>. 2025;31(24). doi:<a href="https://doi.org/10.1002/chem.202500408">10.1002/chem.202500408</a>
  apa: Rohden, D., Toscano, G., Schanda, P., &#38; Lichtenecker, R. J. (2025). Synthesis
    of selectively 13C/2H/15N- labeled arginine to probe protein conformation and
    interaction by NMR spectroscopy. <i>Chemistry - A European Journal</i>. Wiley.
    <a href="https://doi.org/10.1002/chem.202500408">https://doi.org/10.1002/chem.202500408</a>
  chicago: Rohden, Darja, Giorgia Toscano, Paul Schanda, and Roman J. Lichtenecker.
    “Synthesis of Selectively 13C/2H/15N- Labeled Arginine to Probe Protein Conformation
    and Interaction by NMR Spectroscopy.” <i>Chemistry - A European Journal</i>. Wiley,
    2025. <a href="https://doi.org/10.1002/chem.202500408">https://doi.org/10.1002/chem.202500408</a>.
  ieee: D. Rohden, G. Toscano, P. Schanda, and R. J. Lichtenecker, “Synthesis of selectively
    13C/2H/15N- labeled arginine to probe protein conformation and interaction by
    NMR spectroscopy,” <i>Chemistry - A European Journal</i>, vol. 31, no. 24. Wiley,
    2025.
  ista: Rohden D, Toscano G, Schanda P, Lichtenecker RJ. 2025. Synthesis of selectively
    13C/2H/15N- labeled arginine to probe protein conformation and interaction by
    NMR spectroscopy. Chemistry - A European Journal. 31(24), e202500408.
  mla: Rohden, Darja, et al. “Synthesis of Selectively 13C/2H/15N- Labeled Arginine
    to Probe Protein Conformation and Interaction by NMR Spectroscopy.” <i>Chemistry
    - A European Journal</i>, vol. 31, no. 24, e202500408, Wiley, 2025, doi:<a href="https://doi.org/10.1002/chem.202500408">10.1002/chem.202500408</a>.
  short: D. Rohden, G. Toscano, P. Schanda, R.J. Lichtenecker, Chemistry - A European
    Journal 31 (2025).
corr_author: '1'
date_created: 2025-04-13T22:01:19Z
date_published: 2025-04-25T00:00:00Z
date_updated: 2025-09-30T11:35:05Z
day: '25'
ddc:
- '540'
department:
- _id: PaSc
doi: 10.1002/chem.202500408
external_id:
  isi:
  - '001479486400019'
  pmid:
  - '40080421'
file:
- access_level: open_access
  checksum: e3788628644b5aac666cf079b05f8fa7
  content_type: application/pdf
  creator: dernst
  date_created: 2025-08-05T12:59:24Z
  date_updated: 2025-08-05T12:59:24Z
  file_id: '20136'
  file_name: 2025_ChemistryEur_Rohden.pdf
  file_size: 2840681
  relation: main_file
  success: 1
file_date_updated: 2025-08-05T12:59:24Z
has_accepted_license: '1'
intvolume: '        31'
isi: 1
issue: '24'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publication: Chemistry - A European Journal
publication_identifier:
  eissn:
  - 1521-3765
  issn:
  - 0947-6539
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synthesis of selectively 13C/2H/15N- labeled arginine to probe protein conformation
  and interaction by NMR spectroscopy
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: '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: 2026-08-13T14:19:02Z
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: '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: 2026-08-13T14:19:01Z
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'
...
---
_id: '19956'
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 arginine MAS NMR approaches to probe arginine
    dynamics. In experiments on 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
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. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific
    Isotope-Labeling Scheme. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19956">10.15479/AT-ISTA-19956</a>
  apa: Schanda, P. (2025). Arginine Dynamics Probed by Magic-Angle Spinning NMR with
    a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/AT-ISTA-19956">https://doi.org/10.15479/AT-ISTA-19956</a>
  chicago: Schanda, Paul. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with
    a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria,
    2025. <a href="https://doi.org/10.15479/AT-ISTA-19956">https://doi.org/10.15479/AT-ISTA-19956</a>.
  ieee: P. Schanda, “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific
    Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025.
  ista: Schanda P. 2025. Arginine Dynamics Probed by Magic-Angle Spinning NMR with
    a Specific Isotope-Labeling Scheme, Institute of Science and Technology Austria,
    <a href="https://doi.org/10.15479/AT-ISTA-19956">10.15479/AT-ISTA-19956</a>.
  mla: Schanda, Paul. <i>Arginine Dynamics Probed by Magic-Angle Spinning NMR with
    a Specific Isotope-Labeling Scheme</i>. Institute of Science and Technology Austria,
    2025, doi:<a href="https://doi.org/10.15479/AT-ISTA-19956">10.15479/AT-ISTA-19956</a>.
  short: P. Schanda, (2025).
contributor:
- contributor_type: researcher
  first_name: Darja
  last_name: Rohden
- contributor_type: researcher
  first_name: Federico
  last_name: Napoli
- contributor_type: researcher
  first_name: Ben
  last_name: Tatman
- contributor_type: researcher
  first_name: Paul
  last_name: Schanda
corr_author: '1'
date_created: 2025-07-03T04:21:37Z
date_published: 2025-07-03T00:00:00Z
date_updated: 2026-08-13T14:19:01Z
day: '03'
ddc:
- '572'
department:
- _id: PaSc
doi: 10.15479/AT-ISTA-19956
file:
- access_level: open_access
  checksum: a2ef61aa9fb5313c7d426913eb0482c0
  content_type: application/octet-stream
  creator: pschanda
  date_created: 2025-07-03T10:30:14Z
  date_updated: 2025-07-03T10:30:14Z
  file_id: '19960'
  file_name: README
  file_size: 1160
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 8fb77b96d0fcc95c9903005652207a8c
  content_type: application/zip
  creator: pschanda
  date_created: 2025-07-03T10:30:55Z
  date_updated: 2025-07-03T10:30:55Z
  file_id: '19961'
  file_name: data_Arg_MASNMR_Rohden.zip
  file_size: 128597184
  relation: main_file
  success: 1
- access_level: open_access
  checksum: a60cc16d20b089c4bef94040a99cfba5
  content_type: application/x-xz
  creator: pschanda
  date_created: 2025-08-14T07:06:58Z
  date_updated: 2025-08-14T07:06:58Z
  file_id: '20172'
  file_name: 20240903_ubi_DN_Argd1C13_2D_spectra.tar.xz
  file_size: 4766564
  relation: main_file
  success: 1
file_date_updated: 2025-08-14T07:06:58Z
has_accepted_license: '1'
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '20258'
    relation: used_in_publication
    status: public
status: public
title: Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling
  Scheme
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18910'
abstract:
- lang: eng
  text: Proteins often undergo large-scale conformational transitions, in which secondary
    and tertiary structure elements (loops, helices, and domains) change their structures
    or their positions with respect to each other. Simple considerations suggest that
    such dynamics should be relatively fast, but the functional cycles of many proteins
    are often relatively slow. Sophisticated experimental methods are starting to
    tackle this dichotomy and shed light on the contribution of large-scale conformational
    dynamics to protein function. In this review, we focus on the contribution of
    single-molecule Förster resonance energy transfer and nuclear magnetic resonance
    (NMR) spectroscopies to the study of conformational dynamics. We briefly describe
    the state of the art in each of these techniques and then point out their similarities
    and differences, as well as the relative strengths and weaknesses of each. Several
    case studies, in which the connection between fast conformational dynamics and
    slower function has been demonstrated, are then introduced and discussed. These
    examples include both enzymes and large protein machines, some of which have been
    studied by both NMR and fluorescence spectroscopies.
acknowledgement: G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial
  Chair. He has been partially funded by the European Research Council under the European
  Union's Horizon 2020 research and innovation program (grant 742637, SMALLOSTERY),
  by National Science Foundation–US-Israel Binational Science Foundation grant 2021700,
  and by an Israel Science Foundation Breakthrough grant (1924/22). P.S. acknowledges
  funding from the Austrian Science Fund (project “AlloSpace,” I05812) and intramural
  funding from the Institute of Science and Technology Austria.
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: Gilad
  full_name: Haran, Gilad
  last_name: Haran
citation:
  ama: Schanda P, Haran G. NMR and single-molecule FRET insights into fast protein
    motions and their relation to function. <i>Annual Review of Biophysics</i>. 2024;53:247-273.
    doi:<a href="https://doi.org/10.1146/annurev-biophys-070323-022428">10.1146/annurev-biophys-070323-022428</a>
  apa: Schanda, P., &#38; Haran, G. (2024). NMR and single-molecule FRET insights
    into fast protein motions and their relation to function. <i>Annual Review of
    Biophysics</i>. Annual Reviews. <a href="https://doi.org/10.1146/annurev-biophys-070323-022428">https://doi.org/10.1146/annurev-biophys-070323-022428</a>
  chicago: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights
    into Fast Protein Motions and Their Relation to Function.” <i>Annual Review of
    Biophysics</i>. Annual Reviews, 2024. <a href="https://doi.org/10.1146/annurev-biophys-070323-022428">https://doi.org/10.1146/annurev-biophys-070323-022428</a>.
  ieee: P. Schanda and G. Haran, “NMR and single-molecule FRET insights into fast
    protein motions and their relation to function,” <i>Annual Review of Biophysics</i>,
    vol. 53. Annual Reviews, pp. 247–273, 2024.
  ista: Schanda P, Haran G. 2024. NMR and single-molecule FRET insights into fast
    protein motions and their relation to function. Annual Review of Biophysics. 53,
    247–273.
  mla: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into
    Fast Protein Motions and Their Relation to Function.” <i>Annual Review of Biophysics</i>,
    vol. 53, Annual Reviews, 2024, pp. 247–73, doi:<a href="https://doi.org/10.1146/annurev-biophys-070323-022428">10.1146/annurev-biophys-070323-022428</a>.
  short: P. Schanda, G. Haran, Annual Review of Biophysics 53 (2024) 247–273.
corr_author: '1'
date_created: 2025-01-27T13:40:34Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-09T12:06:24Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1146/annurev-biophys-070323-022428
external_id:
  isi:
  - '001278237500012'
  pmid:
  - '38346243'
file:
- access_level: open_access
  checksum: c90861542ae3f9147939030d5bafed3c
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-27T13:44:59Z
  date_updated: 2025-01-27T13:44:59Z
  file_id: '18911'
  file_name: 2024_AnnualReviews_Schanda.pdf
  file_size: 3025589
  relation: main_file
  success: 1
file_date_updated: 2025-01-27T13:44:59Z
has_accepted_license: '1'
intvolume: '        53'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 247-273
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publication: Annual Review of Biophysics
publication_identifier:
  eissn:
  - 1936-1238
  issn:
  - 1936-122X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: NMR and single-molecule FRET insights into fast protein motions and their relation
  to function
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: 53
year: '2024'
...
---
APC_amount: 1530 EUR
OA_place: publisher
OA_type: gold
_id: '15401'
abstract:
- lang: eng
  text: Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has
    become a main technique in NMR-based structural biology. In standard deuteration
    protocols that rely on D2O-based culture media, non-exchangeable amide sites remain
    deuterated, making these sites unobservable. Here we demonstrate that proteins
    produced with a H2O-based culture medium doped with deuterated cell lysate allow
    scientists to overcome this “reprotonation bottleneck” while retaining a high
    level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence
    lifetimes of several proteins prepared with this labeling pattern over a range
    of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under
    commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling
    approach are comparable to those of perdeuterated proteins and better than those
    of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range,
    many previously unobserved amides become visible. We report how to prepare the
    deuterated cell lysate for our approach from fractions of perdeuterated cultures
    which are usually discarded, and we show that such media can be used identically
    to commercial media. The residual protonation of Hα sites allows for well-resolved
    Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment
    of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate
    deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents
    a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments.
acknowledged_ssus:
- _id: NMR
acknowledgement: "We thank Dominique Madern (IBS Grenoble) for providing the plasmid
  for MalDH and feedback on the article, Alicia Vallet for excellent support at the
  Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria
  NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of
  Max Perutz Labs for the mass spectrometry analysis using the instruments of the
  Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu
  (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition
  of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University
  Dortmund) for sharing a paper draft describing a similar study. This work was supported
  by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis
  (Lyon) and the reviewers for constructive input.\r\nThis research has been supported
  by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms
  of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the
  Grenoble Partnership for 40 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). IBS acknowledges integration
  into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien
  Arnaud was funded by GRAL."
article_processing_charge: Yes
article_type: original
author:
- first_name: Federico
  full_name: Napoli, Federico
  id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
  last_name: Napoli
  orcid: 0000-0002-9043-136X
- first_name: Jia-Ying
  full_name: Guan, Jia-Ying
  last_name: Guan
- first_name: Charles-Adrien
  full_name: Arnaud, Charles-Adrien
  last_name: Arnaud
- first_name: Pavel
  full_name: Macek, Pavel
  last_name: Macek
- first_name: Hugo
  full_name: Fraga, Hugo
  last_name: Fraga
- first_name: Cécile
  full_name: Breyton, Cécile
  last_name: Breyton
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
citation:
  ama: 'Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by
    cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without
    the reprotonation bottleneck. <i>Magnetic Resonance</i>. 2024;5(1):33-49. doi:<a
    href="https://doi.org/10.5194/mr-5-33-2024">10.5194/mr-5-33-2024</a>'
  apa: 'Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C.,
    &#38; Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution
    amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck.
    <i>Magnetic Resonance</i>. Copernicus Publications. <a href="https://doi.org/10.5194/mr-5-33-2024">https://doi.org/10.5194/mr-5-33-2024</a>'
  chicago: 'Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo
    Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell
    Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the
    Reprotonation Bottleneck.” <i>Magnetic Resonance</i>. Copernicus Publications,
    2024. <a href="https://doi.org/10.5194/mr-5-33-2024">https://doi.org/10.5194/mr-5-33-2024</a>.'
  ieee: 'F. Napoli <i>et al.</i>, “Deuteration of proteins boosted by cell lysates:
    High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation
    bottleneck,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications,
    pp. 33–49, 2024.'
  ista: 'Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024.
    Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha
    magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic
    Resonance. 5(1), 33–49.'
  mla: 'Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates:
    High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation
    Bottleneck.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications,
    2024, pp. 33–49, doi:<a href="https://doi.org/10.5194/mr-5-33-2024">10.5194/mr-5-33-2024</a>.'
  short: F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda,
    Magnetic Resonance 5 (2024) 33–49.
corr_author: '1'
date_created: 2024-05-16T15:02:43Z
date_published: 2024-04-19T00:00:00Z
date_updated: 2025-07-17T08:12:23Z
day: '19'
ddc:
- '530'
department:
- _id: PaSc
doi: 10.5194/mr-5-33-2024
external_id:
  pmid:
  - '40384771'
file:
- access_level: open_access
  checksum: 80ea50114e428461ca9530d3bd5d89e4
  content_type: application/pdf
  creator: dernst
  date_created: 2024-05-22T07:01:15Z
  date_updated: 2024-05-22T07:01:15Z
  file_id: '15413'
  file_name: 2024_MagneticResonance_Napoli.pdf
  file_size: 6657865
  relation: main_file
  success: 1
file_date_updated: 2024-05-22T07:01:15Z
has_accepted_license: '1'
intvolume: '         5'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 33-49
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
  call_identifier: FWF
  name: FWF Open Access Fund
publication: Magnetic Resonance
publication_identifier:
  issn:
  - 2699-0016
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deuteration of proteins boosted by cell lysates: High-resolution amide and
  Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck'
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: 5
year: '2024'
...
---
_id: '14036'
abstract:
- lang: eng
  text: Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing
    itself as a powerful method for the characterization of protein dynamics at the
    atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore
    microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling,
    and pulse sequence design has paved the way for quantitative analyses of even
    rare structural fluctuations. In addition to isotropic chemical-shift fluctuations
    exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has
    a wider arsenal of observables, allowing to see motions even if the exchanging
    states do not differ in their chemical shifts. We demonstrate the potential of
    the technique for probing motions in challenging large enzymes, membrane proteins,
    and protein assemblies.
acknowledgement: We thank Petra Rovó for critical reading of this manuscript. We acknowledge
  the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding
  by the Institute of Science and Technology Austria.
article_number: '102660'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
  full_name: Napoli, Federico
  id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
  last_name: Napoli
  orcid: 0000-0002-9043-136X
- 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: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
citation:
  ama: Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning
    relaxation dispersion NMR. <i>Current Opinion in Structural Biology</i>. 2023;82(10).
    doi:<a href="https://doi.org/10.1016/j.sbi.2023.102660">10.1016/j.sbi.2023.102660</a>
  apa: Napoli, F., Becker, L. M., &#38; Schanda, P. (2023). Protein dynamics detected
    by magic-angle spinning relaxation dispersion NMR. <i>Current Opinion in Structural
    Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.sbi.2023.102660">https://doi.org/10.1016/j.sbi.2023.102660</a>
  chicago: Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics
    Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” <i>Current Opinion
    in Structural Biology</i>. Elsevier, 2023. <a href="https://doi.org/10.1016/j.sbi.2023.102660">https://doi.org/10.1016/j.sbi.2023.102660</a>.
  ieee: F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle
    spinning relaxation dispersion NMR,” <i>Current Opinion in Structural Biology</i>,
    vol. 82, no. 10. Elsevier, 2023.
  ista: Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle
    spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10),
    102660.
  mla: Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning
    Relaxation Dispersion NMR.” <i>Current Opinion in Structural Biology</i>, vol.
    82, no. 10, 102660, Elsevier, 2023, doi:<a href="https://doi.org/10.1016/j.sbi.2023.102660">10.1016/j.sbi.2023.102660</a>.
  short: F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology
    82 (2023).
corr_author: '1'
date_created: 2023-08-13T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-14T09:10:17Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.sbi.2023.102660
external_id:
  isi:
  - '001053616200001'
  pmid:
  - '37536064'
file:
- access_level: open_access
  checksum: c850f7ac8a4234319755b672c1df69ae
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-30T12:36:39Z
  date_updated: 2024-01-30T12:36:39Z
  file_id: '14907'
  file_name: 2023_CurrentOpinionStrucBio_Napoli.pdf
  file_size: 1231998
  relation: main_file
  success: 1
file_date_updated: 2024-01-30T12:36:39Z
intvolume: '        82'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
  grant_number: I05812
  name: AlloSpace. The emergence and mechanisms of allostery
publication: Current Opinion in Structural Biology
publication_identifier:
  eissn:
  - 1879-033X
  issn:
  - 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protein dynamics detected by magic-angle spinning relaxation dispersion NMR
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: 82
year: '2023'
...
