Table 2.
Calculated and experimental pKa’s of four proteins HP36, BBL, HEWL and SNase
| Residue | Expt | Hybrid | GRF | PME | Resdue | Expt | Hybrid | GRF | PME |
|---|---|---|---|---|---|---|---|---|---|
| HP36 | SNase | ||||||||
| Asp44 | 3.1 | 2.7 (0.1) | 3.5 (0.5) | 2.6 (0.0) | Glu10 | 2.8 | 3.1(0.1) | 3.9 (0.5) | 3.2 (0.0) |
| Glu45 | 4.0 | 3.4 (0.3) | 4.8 (0.1) | 3.9 (0.0) | Asp19* | 2.2 | 2.3 (0.1) | 5.8 (0.1) | 3.3 (0.6) |
| Asp46 | 3.5 | 3.0 (0.1) | 4.2 (0.6) | 3.9 (0.0) | Asp21 | 6.5 | 3.5 (0.3) | 5.3 (0.5) | 6.0 (0.3) |
| Glu72 | 4.4 | 3.5 (0.2) | 4.7 (0.0) | 4.6 (0.0) | Asp40* | 3.9 | 3.1 (0.2) | 3.9 (0.3) | 2.9 (0.0) |
| max | 0.90 | 0.80 | 0.50 | Glu43 | 4.3 | 3.8 (0.1) | 5.6 (0.3) | 4.1 (0.1) | |
| avg | 0.60 | 0.55 | 0.30 | Glu52* | 3.9 | 3.9 (0.0) | 5.9 (0.0) | 4.7 (0.2) | |
| BBL | Glu57 | 3.5 | 3.7 (0.2) | 4.8 (0.0) | 4.1 (0.3) | ||||
| Asp129 | 3.9 | 3.1 (0.0) | 3.7 (0.5) | 3.7 (0.2) | Glu67 | 3.8 | 3.7 (0.1) | 4.5 (0.2) | 4.0 (0.2) |
| Glu141 | 4.5 | 4.0 (0.0) | 4.7 (0.2) | 4.3 (0.0) | Glu73 | 3.3 | 3.5 (0.1) | 4.9 (0.0) | 3.6 (0.1) |
| His142* | 6.5 | 6.9 (0.1) | 5.5 (0.0) | 5.4 (0.0) | Glu75* | 3.3 | 3.5 (0.3) | 4.4 (0.2) | 2.7 (0.4) |
| Asp145 | 3.7 | 2.8 (0.2) | 3.6 (0.0) | 3.4 (0.1) | Asp77 | <2.2 | <0 | <−1 | <−1 |
| Glu161 | 3.7 | 3.9 (0.3) | 4.2 (0.2) | 4.0 (0.0) | Asp83 | <2.2 | 2.5 (0.1) | −0.2 | 0.0 |
| Asp162 | 3.2 | 3.8 (0.3) | 4.0 (0.3) | 2.7 (0.1) | Asp95 | 2.2 | 2.7 (0.6) | 4.0 (0.3) | 3.0 (0.0) |
| Glu164 | 4.5 | 3.9 (0.1) | 4.9 (0.6) | 4.3 (0.2) | Glu101* | 3.8 | 3.6 (0.1) | 6.3 (0.3) | 4.7 (0.2) |
| His166* | 5.4 | 5.8 (0.1) | 4.1 (0.0) | 4.1 (0.2) | Glu122 | 3.9 | 3.6 (0.0) | 5.1 (0.4) | 4.4 (0.0) |
| max | 0.90 | 1.3 | 1.3 | Glu129* | 3.8 | 3.7 (0.1) | 6.6 (0.2) | 5.5 (0.0) | |
| avg | 0.55 | 0.56 | 0.51 | Glu135* | 3.8 | 3.4 (0.2) | 4.1 (0.5) | 2.9 (0.0) | |
| HEWL | max | 3.0 | 3.6 | 1.7 | |||||
| Glu7 | 2.6 | 2.7 (0.0) | 3.7 (0.1) | 3.2 (0.0) | avg | 0.46 | 1.5 | 0.70 | |
| His15* | 5.5 | 6.6 (0.1) | 4.8 (0.0) | 4.0 (0.0) | |||||
| Asp18 | 2.8 | 3.1 (0.1) | 3.8 (0.4) | 2.9 (0.1) | |||||
| Glu35* | 6.1 | 7.2 (0.2) | 9.0 (0.1) | 7.1 (0.4) | |||||
| Asp48 | 1.4 | 1.6 (0.5) | 1.6 (0.6) | 0.9 (0.3) | |||||
| Asp52* | 3.6 | 2.9 (0.1) | 6.1 (0.1) | 5.6 (0.1) | |||||
| Asp66 | 1.2 | 1.5 (0.6) | 1.3 (0.7) | 1.1 (0.0) | |||||
| Asp87 | 2.2 | 1.5 (0.4) | 2.6 (0.7) | 2.3 (0.2) | |||||
| Asp101 | 4.5 | 3.0 (0.1) | 6.2 (0.2) | 5.2 (0.0) | All | ||||
| Asp119 | 3.5 | 2.9 (0.0) | 3.8 (0.2) | 3.5 (0.0) | max | 3.0 | 3.6 | 2.0 | |
| max | 1.5 | 2.9 | 2.0 | avg | 0.59 | 1.1 | 0.61 | ||
| avg | 0.66 | 1.1 | 0.66 | rmsd | 0.76 | 1.4 | 0.77 | ||
Experimental pKa values were determined by NMR titration for HP36,61 BBL,62,63 HEWL64 and SNase.65 pKa’s were determined by following 13C chemical shifts except for those of the two histidine in BBL, which were determined by following the sidechain proton chemical shifts.62 The accuracy of pKa’s derived from 13C and sidechain protons is believed to be about 0.5 and 0.1–0.2 pH units.64 The hybrid-solvent data was taken from Ref.,8 where pKa’s were calculated based on the last 0.75 ns of the 1-ns (per replica) simulations. The pKa’s of Asp and Glu residues of BBL were not reported in Ref.8 The GRF data was taken from Ref.25 except for the simulation of SNase which was performed in this work using the same protocol as in Ref.25 The pKa’s of GRF- and PME-CpHMD were calculated from the second half of the 10-ns (per replica) simulations. An estimate of statistical uncertainty was calculated as half of the difference between the first and second half of the simulations. Residues denoted with an asterisk have absolute pKa errors above 0.6 pH units and are discussed in the main text.