Description
RBX1 Binder Design: Multi-Method Iterative Optimization
Target Analysis
RBX1 (PDB 2LGV, 108 aa) presents a compact RING-H2 domain (residues 40-108) stabilized by three zinc ions, with an intrinsically disordered N-terminus (1-39). Our primary binding surface targets helix alpha2 (residues 81-90) and the adjacent E2-binding groove. Key hotspot residues W87 and R91, validated by mutagenesis (Spratt et al., JBC 2012), anchor our interface design. All designs are Cys-free to avoid interference with the three structural zinc coordination sites.
Key Design Principles
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Cys-free by design: All 100 sequences contain zero cysteine residues, preventing interference with RBX1's three structural zinc coordination sites.
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Multi-method coverage: 6 design methods (Mosaic, BLOSUM62, ProTrek, ESM2-optimization, AntiBERTy, DSM Synteract) ensure diverse sequence exploration strategies.
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Boltz-2-calibrated ranking: 141 unique sequences have been evaluated by the platform across 4 submissions. Ranking is driven by experimental binding prediction metrics (iptm, ipsae) rather than monomer-only metrics.
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Decorrelated top ranks: Top 10 sequences span 7 distinct sequence families and 4 design methods, maximizing the probability that at least one candidate succeeds in experimental validation.
