Table I.
Characteristics of the 1m4w protein designs
| AA position | WT | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | v48 | w20 | w20v48 | SS-type | Region |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 20 | W | W | W | W | W | W | R | R | R | R | R | W | W | Strand | Finger |
| 46 | N | R | R | R | R | R | L | L | L | F | L | L | L | ||
| 48 | V | F | F | F | V | K | L | W | F | I | V | L | V | ||
| 72 | N | Y | Y | Y | Y | Y | N | N | N | N | N | N | N | Loop | |
| 74 | Y | W | F | I | L | L | R | R | R | R | R | R | R | Strand | |
| 87 | E | S | S | S | S | S | S | S | S | S | S | S | S | Palm | |
| 89 | Y | Y | Y | Y | Y | Y | H | H | H | H | H | H | H | ||
| 120 | W | T | T | T | T | T | W | W | W | W | W | W | W | Thumb | |
| 121 | R | H | H | H | H | H | R | R | R | R | R | R | R | ||
| 124 | A | V | V | V | V | V | A | A | A | A | A | A | A | ||
| 133 | F | H | H | H | H | H | Y | Y | Y | Y | Y | Y | Y | ||
| 135 | Q | S | S | S | S | S | Q | Q | Q | Q | Q | Q | Q | ||
| 176 | E | I | I | I | I | I | E | E | E | E | E | E | E | Finger | |
| # Mutations | 0 | 11 | 11 | 11 | 10 | 11 | 7 | 7 | 7 | 7 | 6 | 6 | 5 | ||
| Ligand | — | lac | lac | lac | lac | lac | ala | ala | ala | ala | ala | ala | ala | ||
| Ebind (r.e.u) | — | 19.9 | 19.9 | 19.9 | 20.2 | 19.8 | 17.6 | 17.4 | 17.2 | 17.1 | 12.9 | 13.3 | 15.4 | ||
| Affinity* (kcal/mol) | — | −7.4 | −7.4 | −7.4 | −7.6 | −7.4 | −6.2 | −6.0 | −5.9 | −5.9 | −3.5 | −3.8 | −4.9 | ||
| PDB ID | 1M4W | 3MF6 | 3MF9 | 3MFC | 3MFA |
Amino acid identities at given sequence positions for wild-type 1m4w plus 12 designed mutants. Designation of each 1m4w_‘X’ protein at top. Gray type denotes mutated amino acids. Secondary structure and protein region of mutations shown at far right. Number of mutations from wild-type, ligand target (d-ala-d-ala or d-ala-d-lac), computed RosettaLigand energy of binding in Rosetta energy units (r.e.u), RosettaLigand predicted affinity (in kcal/mol from the method of Meiler and Baker, 2006) and PDB IDs for the deposited structures are at the bottom.