Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations
- University of Copenhagen, Denmark
- St. Jude Children's Research Hospital, United States
Abstract
Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP's multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP's substrate binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.
Data availability
Code and data is available at https://github.com/KULL-Centre/_2022_Thomasen_SPOP. Simulation data is available at https://doi.org/10.17894/ucph.ef999f72-b5e8-45c4-835f-3e49619a0f91. Plasmids are available from Addgene (plasmid IDs 194115 and 194116).
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Supporting data for Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulationsERDA, doi.org/10.17894/ucph.ef999f72-b5e8-45c4-835f-3e49619a0f91.
Article and author information
Author details
Kresten Lindorff-Larsen
Funding
Lundbeckfonden (R155-2015-2666)
- Kresten Lindorff-Larsen
Novo Nordisk Fonden (NNF18OC0033950)
- Kresten Lindorff-Larsen
National Institutes of Health (R01GM112846)
- Tanja Mittag
American Lebanese Syrian Associated Charities
- Tanja Mittag
Novo Nordisk Fonden (NNF18OC0032608)
- Kresten Lindorff-Larsen
National Institutes of Health (P30GM133893)
- Tanja Mittag
DOE Office of Biological and Environmental Research (KP1605010)
- Tanja Mittag
National Institutes of Health (OD012331)
- Tanja Mittag
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2023, Thomasen et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations
eLife 12:e84147.
https://doi.org/10.7554/eLife.84147
