Table 1. pKa Values Obtained from Titration Simulationsa.
| tripeptide
simulations69,70 |
|||
|---|---|---|---|
| pKa values |
|||
| amino acid | CHARMM36 | MARTINI | exp. |
| Asp | 3.61 ± 0.03 | 3.69 ± 0.02 | 3.65 |
| Glu | 4.26 ± 0.04 | 4.30 ± 0.03 | 4.25 |
| His macroscopic | 6.34 ± 0.08 | 6.40 ± 0.03 | 6.42 |
| His HSD | 6.56 ± 0.06 | 6.53 | |
| His HSE | 6.90 ± 0.05 | 6.94 | |
| simulation
of cardiotoxin V71,72 |
|||
|---|---|---|---|
| pKa values |
|||
| amino acid | CHARMM36 | MARTINI | exp. |
| His-4 | 5.14 ± 0.16 | 4.54 ± 0.09 | 5.5 |
| Glu-17 | 4.08 ± 0.08 | 4.36 ± 0.04 | 4 |
| Asp-42 | 4.02 ± 0.10 | 4.30 ± 0.05 | 3.2 |
| Asp-59 | 2.41 ± 0.07 | 1.45 ± 0.03 | <2 |
| r = 0.96 | r = 0.80 | ||
| MSE = 0.24 | MSE = 0.64 | ||
| RMSE = 0.49 | RMSE = 0.80 | ||
| simulation
of HEWL73 |
|||
|---|---|---|---|
| pKa values |
|||
| amino acid | CHARMM36 | MARTINI | exp. |
| Glu-7 | 2.82 ± 0.07 | 4.86 ± 0.05 | 2.6 |
| His-15 | 4.84 ± 0.05 | 5.42 ± 0.05 | 5.5 |
| Asp-18 | 3.35 ± 0.05 | 3.31 ± 0.03 | 2.8 |
| Glu-35 | 7.64 ± 0.13 | 6.36 ± 0.05 | 6.1 |
| Asp-48 | 0.99 ± 0.07 | 3.36 ± 0.05 | 1.4 |
| Asp-52 | 5.69 ± 0.12 | 7.18 ± 0.10 | 3.6 |
| Asp-66 | 1.70 ± 0.10 | 5.22 ± 0.05 | 1.2 |
| Asp-87 | 1.73 ± 0.03 | 3.47 ± 0.05 | 2.2 |
| Asp-101 | 5.43 ± 0.11 | 4.20 ± 0.06 | 4.5 |
| Asp-119 | 2.77 ± 0.05 | 3.80 ± 0.05 | 3.5 |
| r = 0.90 | r = 0.49 | ||
| MSE = 0.96 | MSE = 4.01 | ||
| RMSE = 0.98 | RMSE = 2.00 | ||
a
The reference pKa values for tripeptides are given in the last column that contain the experimental pKa values. The values for Asp and Glu are taken from ref (69), while the microscopic and macroscopic pKa values for His are taken from ref (70). Experimental pKa values for cardiotoxin V are from refs (71 and 72) and for HEWL from ref (73). For both proteins Pearson correlation (r), MSE and RMSE errors are provided.