Table 1.
Amino acid substitutions in the mutant DGD enzymes.
| Residue | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||||||
| 12 | 23 | 28 | 60 | 69 | 85 | 96 | 203 | 221 | 306 | 329 | 387 | 402 | |
| DGD WT | N | T | I | C | G | R | N | N | L | S | R | M | G |
| RIc1a,b | F | ||||||||||||
| RIc2 | S | ||||||||||||
| RIIc1 | S | P | F | ||||||||||
| RIIIc1 | F | ||||||||||||
| RIIIc2 | S | S | F | ||||||||||
| RIIIc3 | P | F | |||||||||||
| RIIIc4 | S | P | F | R | S | ||||||||
| RIIIc5 | I | P | F | ||||||||||
| RIIIc6 | D | P | F | ||||||||||
| RIIIc7 | F | ||||||||||||
| RIIIc8 | H | S | P | F | |||||||||
| RIIIc9 | S | S | F | ||||||||||
| RIIIc10 | S | P | F | H | |||||||||
| RIIIc11 | P | F | |||||||||||
| RIIIc12 | S | S | F | ||||||||||
| RIIIc13 | D | S | S | P | F | ||||||||
| RIIIc14 | H | S | S | F | |||||||||
| RIIIc15 | V | S | S | F | |||||||||
| RIVc1 | S | F | |||||||||||
| RIVc2 | F | ||||||||||||
| RIVc3 | H | S | S | P | F | ||||||||
| RIVc4 | F | ||||||||||||
| RIVc5 | H | S | F | ||||||||||
| RIVc6 | D | H | F | ||||||||||
| RIVc7 | I | S | F | ||||||||||
| RIVc8 | F | ||||||||||||
| RIVc9 c | D | H | S | S | F | ||||||||
| RIVc10 | D | H | S | S | F | ||||||||
| RIVc11 | F | ||||||||||||
| RIVc12 | D | H | S | S | F | ||||||||
| RIVc13 | S | F | |||||||||||
| RIVc14 | D | H | S | S | F | ||||||||
| RIVc15 | D | H | S | S | F | ||||||||
| FoldX ΔΔG d | |||||||||||||
| X-ray Cryst Structg | 1.2 | 1.2 | 0.52 | 0.40 | 0.03 | 0.63 | −0.56 | 0.70 | 3.53 | −4.7 | 0.52 | −0.07 | 1.8 |
| MD_Sim_An WTf | 1.2 | 0.38 | 0.90 | 0.73 | −1.0 | 0.26 | 0.23 | 0.78 | 1.21 | −0.70 | 1.5 | 1.9 | 4.5 |
| MD_Sim_An RIVc15e | −0.07 | −0.86 | 0.62 | −1.3 | 2.5 | ||||||||
| rvET score (scale = 1–88)h | |||||||||||||
| 52 | 51 | 38 | 39 | 65 | 42 | 61 | 47 | 21 | 11 | 28 | 48 | 31 | |
a
The mutant names represent the evolution round and clone from which the mutants were isolated. For example, RIc1 refers to the first clone isolated in evolution round I.
b
The single S306F mutant occurs seven times and is italicized and underlined.
c
The 12D/R85H/N96S/N203S/S306F mutant occurs five times and is shown in bold.
d
ΔΔG(Mut-WT) in kcal/mol calculated by FoldX.
e
Values calculated for mutation reversion with the simulated annealing model of the RIVc15 mutant as the template.
f
Values calculated with theWT simulated annealing model as the template.
g
Values calculated with theWT crystal structure as the template.
h
Real value evolutionary trace score calculated as described in Ref. [36]