Fig. 2.

Design of the ubiquitin surface mutant library. (A) Ubiquitin and Ubl homology alignment. Ubiquitin, Nedd8, Hub1, and Smt3 were aligned using the Lalign multiple sequence server. Similar residues shared between all Ubls and ubiquitin are bolded. Conserved residues between only ubiquitin and Nedd8 are outlined in a green dashed box. The surface residues in ubiquitin that were mutated to alanine are shaded. The colors, and the numbers above, indicate the groupings in the 13 surface mutants. Individual sequences are annotated in SI Appendix, Fig. S4. (B) Visual representation of the ubiquitin surface mutants mapped on to the ubiquitin structure (PDB ID code 1UBQ3) in their respective color. Homologous regions between ubiquitin and Nedd8, but not Hub1 and Smt3, are shown in a dashed green line.