Calculated binding free energy differences between the AF7 and E8 TCR
| . | . | MMPBSA protocol 1 . | MMPBSA protocol 2 . | ||
|---|---|---|---|---|---|
| TCR | MR1 Complex | ΔG (kcal mol−1) | ΔΔG(5-OP-RU-K43A) (kcal mol−1) | ΔG (kcal mol−1) | ΔΔG(5-OP-RU-K43A) (kcal mol−1) |
| AF-7 | Wt-5-OP-RU | −8.6 ± 3.2 | −19.6a | −28.9 ± 1.1 | −8.7a |
| Empty (K43A) | 11.1 ± 5.3 | −20.2 ± 3.3 | |||
| E8 | Wt-5-OP-RU | −0.8 ± 4.1 | 2.8 | −24 ± 1.6 | −0.9a |
| Empty (K43A) | −3.6 ± 3.8 | −23.1 ± 1.9 | |||
| . | . | MMPBSA protocol 1 . | MMPBSA protocol 2 . | ||
|---|---|---|---|---|---|
| TCR | MR1 Complex | ΔG (kcal mol−1) | ΔΔG(5-OP-RU-K43A) (kcal mol−1) | ΔG (kcal mol−1) | ΔΔG(5-OP-RU-K43A) (kcal mol−1) |
| AF-7 | Wt-5-OP-RU | −8.6 ± 3.2 | −19.6a | −28.9 ± 1.1 | −8.7a |
| Empty (K43A) | 11.1 ± 5.3 | −20.2 ± 3.3 | |||
| E8 | Wt-5-OP-RU | −0.8 ± 4.1 | 2.8 | −24 ± 1.6 | −0.9a |
| Empty (K43A) | −3.6 ± 3.8 | −23.1 ± 1.9 | |||
A negative ΔΔG means the 5-OP-RU bound form is more favorable than the MR1-K43A form. Errors are presented as the SD from the five replicas. MMPBSA Protocols 1 and 2 differ by the choice of internal protein dielectric constant setting. For Protocol 1, the internal dielectric constant is set to 1, for Protocol 2, the internal dielectric constant is set to 4.