Articles | Volume 2, issue 1
https://doi.org/10.5194/mr-2-187-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Special issue:
https://doi.org/10.5194/mr-2-187-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
21 Apr 2021
Research article |
| 21 Apr 2021
| 21 Apr 2021
Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy
Ulric B. le Paige
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
ShengQi Xiang
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
current address: MOE Key Lab for Membrane-less Organelles &
Cellular Dynamics, School of Life Sciences, University of Science and
Technology of China, 96 Jinzhai Road, Hefei, 230026, Anhui, China
Marco M. R. M. Hendrix
Laboratory of Self-Organizing Soft Matter, Department of Chemical
Engineering and Chemistry & Institute for Complex Molecular Systems,
Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the
Netherlands
Yi Zhang
Department of Pharmacology, University of Colorado School of
Medicine, Aurora, CO 80045, USA
Gert E. Folkers
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
Markus Weingarth
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
Alexandre M. J. J. Bonvin
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
Tatiana G. Kutateladze
Department of Pharmacology, University of Colorado School of
Medicine, Aurora, CO 80045, USA
Ilja K. Voets
Laboratory of Self-Organizing Soft Matter, Department of Chemical
Engineering and Chemistry & Institute for Complex Molecular Systems,
Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the
Netherlands
Marc Baldus
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
Hugo van Ingen
CORRESPONDING AUTHOR
Utrecht NMR Group, Bijvoet Centre for Biomolecular Research,
Utrecht University, 3584 CH, Utrecht, the Netherlands
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Cited
14 citations as recorded by crossref.
- Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release D. Rizzo et al. https://doi.org/10.1021/acs.analchem.1c01850
- Structural and dynamic studies of chromatin by solid-state NMR spectroscopy C. Jaroniec https://doi.org/10.1016/j.sbi.2024.102921
- Probing Biomolecular Interactions with Paramagnetic Nuclear Magnetic Resonance Spectroscopy H. Busch et al. https://doi.org/10.1002/cbic.202400903
- Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates L. Cerofolini et al. https://doi.org/10.1002/ange.202303202
- Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR X. Shi et al. https://doi.org/10.1038/s42003-023-05050-3
- Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates L. Cerofolini et al. https://doi.org/10.1002/anie.202303202
- Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology B. Ackermann & G. Debelouchina https://doi.org/10.3389/fmolb.2021.741581
- Recent Advances in Investigating Functional Dynamics of Chromatin X. Shi et al. https://doi.org/10.3389/fgene.2022.870640
- Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR J. Zehnder et al. https://doi.org/10.1016/j.jmr.2021.107075
- Unveiling structural and dynamical features of chromatin using NMR spectroscopy X. Shi https://doi.org/10.1016/j.mrl.2024.200153
- Histone H3 core domain in chromatin with different DNA linker lengths studied by 1H-Detected solid-state NMR spectroscopy S. Smrt et al. https://doi.org/10.3389/fmolb.2022.1106588
- Studying large biomolecules as sedimented solutes with solid-state NMR F. Shi et al. https://doi.org/10.52601/bpr.2024.240014
- Epitope Mapping and Binding Assessment by Solid-State NMR Provide a Way for the Development of Biologics under the Quality by Design Paradigm D. Rizzo et al. https://doi.org/10.1021/jacs.2c03232
- Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy P. Wu et al. https://doi.org/10.1021/jacs.3c11836
14 citations as recorded by crossref.
- Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release D. Rizzo et al. https://doi.org/10.1021/acs.analchem.1c01850
- Structural and dynamic studies of chromatin by solid-state NMR spectroscopy C. Jaroniec https://doi.org/10.1016/j.sbi.2024.102921
- Probing Biomolecular Interactions with Paramagnetic Nuclear Magnetic Resonance Spectroscopy H. Busch et al. https://doi.org/10.1002/cbic.202400903
- Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates L. Cerofolini et al. https://doi.org/10.1002/ange.202303202
- Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR X. Shi et al. https://doi.org/10.1038/s42003-023-05050-3
- Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates L. Cerofolini et al. https://doi.org/10.1002/anie.202303202
- Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology B. Ackermann & G. Debelouchina https://doi.org/10.3389/fmolb.2021.741581
- Recent Advances in Investigating Functional Dynamics of Chromatin X. Shi et al. https://doi.org/10.3389/fgene.2022.870640
- Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR J. Zehnder et al. https://doi.org/10.1016/j.jmr.2021.107075
- Unveiling structural and dynamical features of chromatin using NMR spectroscopy X. Shi https://doi.org/10.1016/j.mrl.2024.200153
- Histone H3 core domain in chromatin with different DNA linker lengths studied by 1H-Detected solid-state NMR spectroscopy S. Smrt et al. https://doi.org/10.3389/fmolb.2022.1106588
- Studying large biomolecules as sedimented solutes with solid-state NMR F. Shi et al. https://doi.org/10.52601/bpr.2024.240014
- Epitope Mapping and Binding Assessment by Solid-State NMR Provide a Way for the Development of Biologics under the Quality by Design Paradigm D. Rizzo et al. https://doi.org/10.1021/jacs.2c03232
- Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy P. Wu et al. https://doi.org/10.1021/jacs.3c11836
Saved (final revised paper)
Latest update: 05 Jun 2026
Short summary
NMR studies can be of great help in understanding the molecular mechanisms of nucleosome functions. For solid-state NMR, nucleosomes need to be tightly packed together. We show that centrifugation of nucleosomes results in formation of gels with very high packing ratios yet without pronounced order in the packing and without formation of specific or stable inter-nucleosome contacts. This makes the approach suitable also for the study of proteins that bind weakly to the nucleosome.
NMR studies can be of great help in understanding the molecular mechanisms of nucleosome...
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