Table 1.
Calculated and experimental pKa values of three proteins
| Residue | Experimenta |
GBa |
All-atom CpHMD |
||
|---|---|---|---|---|---|
| Time (ns)b | 0–1 | 0–5 | 5–10 | 0–10 | |
| HP36 | |||||
| Asp44 | 3.10 (0.01) | 3.2 (0.1) | 2.0 | 3.0 | 2.6 (0.5) |
| Glu45 | 3.95 (0.01) | 3.5 (0.1) | 4.3 | 4.5 | 4.4 (0.1) |
| Asp46 | 3.45 (0.12) | 3.5 (0.1) | 2.4 | 3.7 | 3.1 (0.6) |
| Glu72 | 4.37 (0.03) | 3.5 (0.1) | 4.4 | 4.4 | 4.4 (0.0) |
| BBL | |||||
| Asp129 | 3.88 (0.02) | 3.2 (0.0) | 2.2 | 3.2 | 2.7 (0.5) |
| Glu141 | 4.46 (0.04) | 4.3 (0.0) | 4.0 | 4.4 | 4.2 (0.2) |
| His142 | 6.47 (0.04) | 7.1 (0.0) | 5.9 | 5.8 | 5.8 (0.0) |
| Asp145 | 3.65 (0.04) | 2.8 (0.2) | 3.0 | 3.1 | 3.1 (0.0) |
| Glu161 | 3.72 (0.05) | 3.6 (0.3) | 4.2 | 3.9 | 4.0 (0.2) |
| Asp162 | 3.18 (0.04) | 3.4 (0.3) | 2.9 | 3.5 | 3.2 (0.3) |
| Glu164 | 4.50 (0.03) | 4.5 (0.1) | 5.7 | 4.6 | 5.2 (0.6) |
| His166 | 5.39 (0.02) | 5.4 (0.1) | 4.4 | 4.4 | 4.4 (0.0) |
| HEWL | |||||
| Glu7 | 2.6 (0.2) | 2.6 (0.1) | 3.6 | 3.4 | 3.5 (0.1) |
| His15 | 5.5 (0.2) | 5.3 (0.5) | 5.1 | 5.1 | 5.1 (0.0) |
| Asp18 | 2.8 (0.3) | 2.9 (0.0) | 2.5 | 3.3 | 2.9 (0.4) |
| Glu35 | 6.1 (0.4) | 4.4 (0.2) | 8.5 | 8.7 | 8.6 (0.1) |
| Asp48 | 1.4 (0.2) | 2.8 (0.2) | −0.1 | 1.1 | 0.6 (0.6) |
| Asp52 | 3.6 (0.3) | 4.6 (0.0) | 5.4 | 5.6 | 5.5 (0.1) |
| Asp66 | 1.2 (0.2) | 1.2 (0.4) | −0.6 | 0.8 | 0.3 (0.7) |
| Asp87 | 2.2 (0.1) | 2.0 (0.1) | 0.8 | 2.1 | 1.5 (0.7) |
| Asp101 | 4.5 (0.1) | 3.3 (0.3) | 6.1 | 5.7 | 5.9 (0.2) |
| Asp119 | 3.5 (0.3) | 2.5 (0.1) | 3.0 | 3.3 | 3.2 (0.1) |
| Maximum absolute deviation | 1.8 | 2.4 | 2.6 | 2.5 | |
| Average absolute deviation (RMS deviation) | 0.5 (0.7) | 1.0 (1.2) | 0.6 (0.9) | 0.7 (0.9) | |
| Linear fit R2 (slope) | 0.7 (0.8) | 0.8 (1.4) | 0.7 (1.1) | 0.8 (1.2) | |
a
Taken from Wallace and Shen (12). The pKa's of BBL were recalculated.
b
Sampling time per pH replica.