Conformational and Interface Variability in Multivalent SIM–SUMO Interaction

SUMO targeted ubiqutin ligases (STUbLs) like RNF4 or Arkadia/RNF111 recognize SUMO chains through multiple SUMO interacting motifs (SIMs). Typically, these are contained in disordered regions of these enzymes and also the individual SUMO domains of SUMO chains move relatively freely. It is assumed t...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2023-05, Vol.127 (17), p.3806-3815
Main Authors: Kötter, Alex, Mootz, Henning D., Heuer, Andreas
Format: Article
Language:English
Subjects:
Amino Acid Motifs
B: Biophysical and Biochemical Systems and Processes
Molecular Conformation
Small Ubiquitin-Related Modifier Proteins - chemistry
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Summary:SUMO targeted ubiqutin ligases (STUbLs) like RNF4 or Arkadia/RNF111 recognize SUMO chains through multiple SUMO interacting motifs (SIMs). Typically, these are contained in disordered regions of these enzymes and also the individual SUMO domains of SUMO chains move relatively freely. It is assumed that binding the SIM region significantly restricts the conformational freedom of SUMO chains. Here, we present the results of extensive molecular dynamics simulations on the complex formed by the SIM2–SIM3 region of RNF4 and diSUMO3. Though our simulations highlight the importance of typical SIM–SUMO interfaces also in the multivalent situation, we observe that frequently other regions of the peptide than the canonical SIMs establish this interface. This variability regarding the individual interfaces leads to a conformationally highly flexible complex. Comparison with previous experimental measurements clearly supports our findings and indicates that our observations can be extended to other multivalent SIM–SUMO complexes.
ISSN:1520-6106
1520-5207
DOI:10.1021/acs.jpcb.2c08760