Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations
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Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations. / Thomasen, F. Emil; Cuneo, Matthew J.; Mittag, Tanja; Lindorff-Larsen, Kresten.
In: eLife, Vol. 12, e84147, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations
AU - Thomasen, F. Emil
AU - Cuneo, Matthew J.
AU - Mittag, Tanja
AU - Lindorff-Larsen, Kresten
N1 - Publisher Copyright: © 2023, Thomasen et al.
PY - 2023
Y1 - 2023
N2 - 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 pathogenesis. 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 (MD) 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.
AB - 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 pathogenesis. 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 (MD) 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.
KW - human
KW - isodesmic
KW - molecular biophysics
KW - molecular simulations
KW - protein structure
KW - self-assembly
KW - small-angle x-ray scattering
KW - structural biology
U2 - 10.7554/eLife.84147
DO - 10.7554/eLife.84147
M3 - Journal article
C2 - 36856266
AN - SCOPUS:85150001376
VL - 12
JO - eLife
JF - eLife
SN - 2050-084X
M1 - e84147
ER -
ID: 341258448