Saman Salike

A team used RFdiffusion3 to design ubiquitin ligases from scratch around a cysteine catalytic triad, conjugating an activated ubiquitin donor directly to a chosen lysine on a target protein. Against a 19-residue model peptide with a single lysine, 35 of 48 designs showed measurable ubiquitylation activity, and four reached near-quantitative transfer without experimental optimization. Against the homotrimeric sliding clamp PCNA, only four of 48 designs were active, and PL4 modified K164 alone; a single N148A substitution then let PL4.1 convert 90% of PCNA to ubiquitylated product in 3 hours.

A team used RFdiffusion3 to design ubiquitin ligases from scratch around a cysteine catalytic triad, conjugating an activated ubiquitin donor directly to a chosen lysine on a target protein. Against a 19-residue model peptide with a single lysine, 35 of 48 designs showed measurable ubiquitylation activity, and four reached near-quantitative transfer without experimental optimization. Against the homotrimeric sliding clamp PCNA, only four of 48 designs were active, and PL4 modified K164 alone; a single N148A substitution then let PL4.1 convert 90% of PCNA to ubiquitylated product in 3 hours.