Table 1.
Relative free energies and internuclear distances at various states of RNA self-cleavage catalysis in hammerhead ribozymesa
| React. | TS1 | Int. | TS2 | Prod. | |
|---|---|---|---|---|---|
| Nu-P | 3.50(04) | 1.76(05) | 1.66(03) | 1.67(03) | 1.68(03) |
| P-Lea | 1.65(03) | 2.11(05) | 4.51(04) | 4.24(48) | 3.63(23) |
| gA-H | 0.96(00) | 0.96(00) | 0.96(00) | 1.78(04) | 3.75(04) |
| H-Lea | 2.57(51) | 4.07(47) | 4.13(73) | 1.04(03) | 1.00(03) |
| Mg2+-Lea | 3.99(18) | 3.61(17) | 2.02(05) | 2.83(86) | 4.48(05) |
| Mg2+-gA | 4.56(18) | 4.03(18) | 4.33(06) | 3.38(86) | 2.03(05) |
| ΔG | 0.0(4) | 24.4(6) | -6.7(3) | 13.7(7) | -13.6(9) |
a
Free energies (ΔG) are in kcal/mol, which were extracted from 1D PMF profiles along the minimum free-energy path through the 2D profiles. Average distances (X-Y) are in Å. Standard deviations are listed in parentheses divided by the decimal precision of the average values. The abbreviations “React”, “TS”, “Int”, and “Prod” signify reactant, transition, intermediate, and product states, respectively, and for the distance metrics, “Nu”, “Lea”, “gA” and “H” refer to the O2′ nucleophile, O5′ leaving group, general acid residues G8:O2′ and H2′, respectively.