Structure predictions of MuRF1-UBE2 complexes identify amino acid residues governing interaction selectivity for each...

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• The E3 ubiquitin ligase MuRF1 (TRIM63) is crucial in skeletal muscle atrophy, targeting contractile proteins.
• MuRF1 interacts with four distinct E2 enzymes (UBE2E1, UBE2J1, UBE2J2, UBE2L3) in vitro, suggesting specialized roles.
• Understanding the molecular basis of these interactions is key to modulating MuRF1 activity.

Purpose of the Study:

• To investigate the molecular interfaces between MuRF1 and its E2 enzyme partners.
• To elucidate the structural basis for selective E2 enzyme recruitment by MuRF1.
• To identify potential therapeutic targets for muscle atrophy based on MuRF1-E2 interactions.

Main Methods:

• Computational modeling using AlphaFold2 and AlphaFold3 to predict complex interfaces.
• Surface plasmon resonance (SPR) experiments to assess differential sensitivity and binding affinities.
• Affinity measurements using point-mutant E2 enzymes and truncated MuRF1.
• Fluorescence-based assays to detect interaction-induced changes.

Main Results:

• AlphaFold predictions revealed unique interface residues for each MuRF1-E2 complex.
• SPR experiments confirmed distinct interface differences and binding characteristics.
• Affinity measurements validated specific interaction points and identified unique interactions for MuRF1-UBE2E1.
• MuRF1-UBE2E1 interaction may involve domains outside the canonical RING domain.

Conclusions:

• MuRF1 exhibits selective E2 enzyme recruitment through distinct interfaces.
• The MuRF1-UBE2E1 interaction has unique features, potentially involving non-RING domains.
• Deciphering these selective interactions offers a pathway for developing targeted therapies against muscle atrophy.