Table 2.
pKa valuesa for protein 2LZT (Lysozyme) calculated for different values of DI.
| Residues | (pKo)b | pKac | DI=20.0a | DI=16.0a | DI=12.0a | DI=8.0a | DI=4.0a |
|---|---|---|---|---|---|---|---|
| NEND | 7.5 | 7.9 | 7.4 | 7.4 | 7.5 | 7.3 | 7.1 |
| GLU7 | 4.4 | 2.8 | 3.8 | 3.5 | 3.6 | 3.5 | 3.6 |
| HIS15 | 6.6 | 5.4 – 5.6d | 6.7 | 6.8 | 7.1 | 7.3 | 8.5 |
| ASP18 | 4.0 | 2.7 | 2.9 | 2.8 | 2.4 | 2.6 | 2.2 |
| TYR20 | 9.6 | 10.3 | 9.5 | 9.5 | 9.9 | 10.1 | > 14e |
| TYR23 | 9.6 | 9.8 | 9.2 | 9.1 | 8.9 | 8.7 | > 14e |
| GLU35 | 4.4 | 6.2 | 4.7 | 4.9 | 4.7 | 4.1 | 4.7 |
| ASP48 | 4.0 | 1.6 | 3.7 | 3.4 | 3.5 | 3.7 | 4.6 |
| ASP52 | 4.0 | 3.7 | 3.5 | 3.4 | 3.3 | 3.1 | 2.9 |
| TYR53 | 9.6 | 12.1 | 11.0 | 11.4 | 11.1 | 13.3 | >14e |
| ASP66 | 4.0 | 0.9 | 2.2 | 1.7 | 2.1 | 3.1 | 6.2 |
| ASP87 | 4.0 | 2.1 | 3.2 | 2.7 | 2.9 | 2.9 | 2.6 |
| ASP101 | 4.0 | 4.1 | 3.8 | 3.5 | 3.3 | 3.3 | 3.5 |
| ASP119 | 4.0 | 3.2 | 3.1 | 2.8 | 2.8 | 2.7 | 2.4 |
| CEND | 3.8 | 2.8 | 2.9 | 2.7 | 2.6 | 2.2 | 1.4 |
| < Δ > f | 0.8 | 0.7 | 0.8 | 1.1 | - | ||
| Δmax g | 2.1 | 1.8 | 1.9 | 2.2 | - |
Average pKa calculated for equilibrium MD trajectory of 10 ns with different DI of protein internal dielectric constant;
experimental pKovalues in 0.15 M NaCl at T = 300 K (Demchuk, Wade, 1996);
experimental values of pKa for residues in 0.15 M NaCl at T= 300 K (Song, Mao, Gunner, 2009; Kilambi, Gray, 2012);
range of variation of the observed pKa values from two different sources (Song, Mao, Gunner, 2009; Kilambi, Gray, 2012);
for the purpose of computing Δ (see below, item f) a pKa = 14.01, was adopted.
<Δ> is the average absolute difference, in pKa units, between the computed pKa (at each DI) and the observed pKa value (column 3);
Δmax is the maximum difference in pKa unit.