Design of Multi-Specificity in Protein Interfaces
Figure 3
Single- and Multi-Constraint Simulation Trajectories and Sequences Selected for the Multi-Specific Protein Ran
Trajectories of single-constraint (A) and multi-constraint (B) optimizations. PDB codes for all complexes with the five different binding partners are given in the legend. For reference, the score of the native amino acid sequence for each binding partner is marked on the y-axis (squares, final generation). Scores among partners are correlated for multi-constraint simulations (arrows).
(C) Optimal interface sequences taken from the endpoint of the trajectories in (A) and (B). The first row in the table contains the interface residue PDB numbering, the second row lists the native sequence (red), and the following rows list sequences predicted to be optimal in each simulation: multi-constraint (second sequence), single-constraint (third through seventh sequences). Plus signs in the table denote that the wild-type amino acid residue type was recovered as optimal. The number and percent of interface residues recovered as identical to native is shown for each simulation in the rightmost column. Grey shading denotes interface positions not within 4 Å of the shaded interaction partner (see Methods).