Table 3. Cumulative Activation and Reaction Free Energies in the GB Pathway of the Nucleotidyl-Transfer Reaction in the Water, Polβ, and Polλ Systemsa.
| TS1 | IS1 | TS2 | IS2 | TS3 | PS | |
|---|---|---|---|---|---|---|
| system | kcal mol–1 | |||||
| water | 12.6 | 10.8 | 33.9 | 33.8 | 32.9 | –2.5 |
| Polβ1 | 10.2 | 5.2 | 23.1 | 23.8 | 24.1 | –13.7 |
| 22.3 | 19.7 | 19.5 | –13.7 | |||
| Polβ2 | 9.7 | 4.4 | 21.7 | 22.2 | 22.5 | –14.0 |
| 20.9 | 18.1 | 18.2 | –13.3 | |||
| Polβ3 | 8.5 | 3.2 | 25.2 | 28.0 | 27.4 | –11.8 |
| 23.3 | 23.1 | 22.4 | –8.9 | |||
| Polβ4 | 11.2 | 6.2 | 23.8 | 23.3 | 23.2 | –12.2 |
| 26.5 | 23.2 | 23.4 | –9.7 | |||
| Polλ1 | 12.4 | 6.8 | 23.2 | 23.7 | 23.5 | –14.5 |
| 23.7 | 21.1 | 20.6 | –12.0 | |||
| Polλ2 | 13.4 | 6.0 | 22.3 | 23.0 | 22.5 | –15.1 |
| 22.5 | 21.1 | 20.8 | –12.9 | |||
| Polλ3 | 11.5 | 5.9 | 20.9 | 21.0 | 19.8 | –17.3 |
| 22.0 | 19.3 | 18.1 | –14.5 | |||
| Polλ4 | 12.4 | 6.8 | 21.6 | 21.4 | 22.0 | –15.1 |
| 21.9 | 18.7 | 17.5 | –16.6 | |||
a
TS1, transition state 1; IS1, intermediate state 1; TS2, transition state 2; IS2, intermediate state 2a or 2b (see Table 2); TS3, transition state 3; PS, product state. Upper rows for the enzyme systems: IS1 → IS2a → PS; lower rows for the enzyme systems: IS1 → IS2b → PS. Numbers in bold denote the lowest rate-determining activation free energies among the GB (this table) and SB pathways (Table 4).