Figure 1.
The Native (Green) and Redesigned (Cyan) Chey Protein (PDB: 3chy), Using Medusa Fixed-Backbone Redesign
The backbone structure is shown in cartoon, and the sidechains of recapitulated residues are shown in stick representation.
Figure 2.
The Sequence Entropy Computed from Simulations versus the Naturally Occurring Sequence Entropy Computed from HSSP
Three families of protein homologs were studied: HPR domain (A,D,G), ROSSMAN fold (B,E,H), and SH3 domain (C,F,I). The open circles (○) in (A–F) correspond to the functionally important residues. In (G–I), these functionally important residues are shown in stick representation. In (G,H), the SO42− ions are used to mimic the phosphate anion in crystal preparation. In (I), the poly-proline peptide are shown in yellow and the peptide-binding residues form a continuous surface, shown in mesh representation.
Figure 3.
The Sequence Identity for the Constructed Homologous Structures
Three different protein folds are studied: HPR domain (A,B), ROSSMAN fold (D,E), and SH3 domain (G,H). (A,C,E) The sequence identities of the redesigned proteins using the flexible-backbone design simulation are presented as the function of the backbone-RMSD from the reference protein. (B,D,F) The sequence identity of the core is also plotted against the overall sequence identity. The “twilight zone” of sequence identity (20%–30%) corresponds to regions between horizontal (A,C,E) or vertical (B,D,F) lines.