Table 2.
Calculated pKa values of all adenine and cytosine residues in lead-dependent ribozyme obtained from NLPB calculations44 and CPHMDMSλD simulations indicate that both models produce consistent results and reasonable pKa shifts given structural considerations.
| Residue | Structure | NLPB | CPHMDMSλD | Abs Difference (NLPB vs CPHMDMSλD) | pKa shift (wrt to ref pKa) | ||
|---|---|---|---|---|---|---|---|
| pKa | stdev | pKa | stdev | ||||
| C2 | wc | 2.1 ± | 1.5 | 4.4 ± | 0.2 | 2.3 | + |
| A4 | wc | < 3.0 | 0.6 ± | 0.1 | − | ||
| C5 | wc | 3.0 ± | 2.0 | 3.5 ± | 0.4 | 0.5 | − |
| C6 | A+C | 2.8 ± | 2.4 | 3.0 ± | 0.3 | 0.2 | − |
| A8 | 4.9 ± | 0.8 | 3.7 ± | 0.3 | 1.2 | 0 | |
| C10 | wc | 1.4 ± | 1.5 | 1.1 ± | 0.3 | 0.3 | − |
| C11 | wc | 3.7 ± | 1.5 | 1.3 ± | 0.9 | 2.4 | − |
| A12 | wc | < 3.0 | 0.7 ± | 0.3 | − | ||
| C14 | wc | 4.6 ± | 1.0 | 3.2 ± | 0.3 | 1.4 | − |
| A16 | 3.4 ± | 1.1 | 2.6 ± | 0.1 | 0.8 | − | |
| A17 | 2.4 ± | 1.3 | 0.9 ± | 0.5 | 1.5 | − | |
| A18 | 3.6 ± | 0.9 | 3.8 ± | 0.1 | 0.2 | 0 | |
| A25 | A+C | 7.3 ± | 1.8 | 4.8 ± | 0.5 | 2.5 | + |
| C28 | wc | 3.1 ± | 0.7 | 3.7 ± | 0.1 | 0.5 | − |
| C30 | wc | 5.0 ± | 2.0 | 4.8 ± | 0.3 | 0.2 | + |
|
| |||||||
| Average Unsigned Values | 1.5 | 0.3 | 1.1 | ||||