Functional diversity and structural disorder in the human ubiquitination pathway

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Cellular Regulation

Background:

• The ubiquitin-proteasome system (UPS) is vital for cellular regulation and protein quality control (PQC).
• Ubiquitin ligases (E3s) are key components of the UPS, mediating substrate ubiquitination.
• E3 enzymes exhibit a hierarchical structure with E1 and E2 enzymes.

Purpose of the Study:

• To investigate the physical features of human E3 ligases, focusing on structural disorder.
• To correlate structural disorder with E3 ligase function and interaction capabilities.
• To elucidate the role of disorder in E3-mediated ubiquitin transfer.

Main Methods:

• Compilation and analysis of 563 human E3 sequences from KEGG BRITE and literature.
• Application of multiple intrinsic disorder predictors (e.g., IUPred).
• Utilized normal modes and molecular dynamics simulations (e.g., human CBL).
• Analysis of protein-protein interaction data (STRING) and structural data (PDB).

Main Results:

• Human E3 ligases exhibit a significant degree of structural disorder (20.03%), increasing with complexity.
• Single-subunit E3s (ssE3s) show higher disorder (22.98%) in substrate-binding regions compared to multi-component E3s.
• Disordered linkers, exemplified by human CBL, facilitate long-range conformational changes for efficient ubiquitin transfer.
• E3s with more interaction partners (hubs) display elevated disorder (22.90%).
• Induced folding of disordered E3 regions upon partner binding was observed in 7 out of 21 interactions.

Conclusions:

• Structural disorder plays a fundamental role in E3 ligase function, impacting substrate/adaptor binding.
• Disorder facilitates ubiquitin transfer mechanisms through long-range conformational transitions.
• The degree of disorder in E3s is linked to their functional complexity and interaction networks.