Table 1.
Overall properties of various protein A domains under various conditions
| Simulation* | 〈rmsd〉3-6 ns,† Å | 〈rmsd〉Final,† Å | 〈Rg〉3-6 ns,‡ Å | Rgmax,‡ Å | Helix stability§ |
|---|---|---|---|---|---|
| Native simulations | |||||
| E(298) | 1.7 (0.3) | 1.4 (0.1) | 11.2 (0.2) | 11.7 | All stable |
| B(298) | 2.5 (0.3) | 2.5 (0.2) | 12.0 (0.2) | 12.6 | All stable |
| BZ(298) | 2.2 (0.2) | 2.3 (0.2) | 11.3 (0.2) | 12.0 | All stable |
| Denaturation simulations | |||||
| E1(498) | 10.1 (1.9) | 14.0 (0.8) | 15.0 (1.5) | 19.7 | 3 ≫ 1 > 2 |
| E2(498) | 12.1 (1.9) | 12.9 (0.8) | 15.1 (2.0) | 20.7 | 3 ≫1 > 2 |
| B1(498) | 7.7 (1.0) | 7.5 (0.6) | 12.5 (0.8) | 14.7 | 3 ≫ 2 > 1 |
| B2(498) | 7.2 (0.5) | 7.8 (0.4) | 12.1 (0.2) | 13.9 | 3 > 2 > 1 |
| Bfrag1(498) | 6.5 (0.9) | 8.2 (0.4) | 10.6 (0.5) | 12.2 | 3 > 1 > 2 |
| Bfrag2(498) | 5.5 (0.8) | 4.9 (0.5) | 11.5 (0.8) | 16.4 | 3 ≫ 1 = 2 |
*
All simulations were performed for 6 ns. Numbers in parentheses are the thermodynamic temperature.
† rmsd from the starting structure, averaged between 3 and 6 ns, for the α carbons of residues 5–52 for the E domain and 8–57 for the B domain. The final value was averaged between 5.8 and 6.0 ns. Values in parentheses are SD.
‡ Radius of gyration was based on the positions of the α carbons and averaged between 3 and 6 ns. Values in parentheses are SD.
§Qualitative assessment of helix stability based on Fig. 2.