Table II.
Binding Sequence Selection Results for PGA and CA Under Different Design Types
| Scaffold | No. TS rotamer | Design typea | Primary residuesb | Energy | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PGA | 25 | WT | A142 M | A146 F | B24 F | B31 Y | B56 V | B57 F | B67 S | B154 W | B177 I | −238.29 |
| (*,*,*) | + | − | − | F | F | − | K | D | R | −278.98 | ||
| (0,0,*) | + | − | − | F | F | − | V | F | F | −273.01 | ||
| (0,0,1) | + | − | − | H | F | − | V | F | F | −272.93 | ||
| (0,0,2) | F | − | − | F | L | − | Q | Q | − | −267.76 | ||
| (0,0,*)c | + | − | − | F | F | − | V | F | − | −270.59 | ||
| CA | 3455 | WT | A149 Y | B24 L | B33 Y | B50 Q | B57 R | B58 F | B68 N | B69 T | B177 F | −307.22 |
| (*,*,*)d | R | N | R | E | − | W | Q | − | E | −329.16 | ||
| (1,0,*) | F | I | F | − | − | − | Q | V | − | −325.85 | ||
| (1,0,3) | F | L | F | − | − | − | Q | − | − | −325.52 | ||
| (1,0,4) | − | I | F | − | − | − | Q | − | − | −323.77 | ||
| (1,0,5) | − | I | F | − | − | H | Q | − | − | −319.22 | ||
The design type is represented by the specified number of positively charged residues, negatively charged residues, and polar residues shown in the parenthesis. The asterisk implies that no restriction is forced on the designated residue type.
The primary residues are those that contact with TS directly and vary type and conformation simultaneously.
This sequence is found by Monte Carlo optimization based on the sequence obtained under design type (0,0,*).
The MILP solution has encountered convergence difficulties, and the sequence was arrived at 8% gap.
+: The type of designed residue is the same as that of WT, but the conformation is different.
−: The type and conformation of designed residue are the same as those of WT.