Table 1.
Summary of structure based predictions for thermodynamic properties and global QSFR characteristics in Trx
| Sequence range | Tm (K) | Excess Cp,max (kcal/mol K) | Rel. Cp,max (%) | Folding transition | HB No. | θRP | θnat | θTS | θunf | BH |
|---|---|---|---|---|---|---|---|---|---|---|
| 1–108 (WT) | 359 | 17.5 | 100 | Two-state | 133 | 1.05 | 1.03 | 1.77 | 2.16 | 0.67 |
| Core | 370 | 8.8 | 79 | Two-state | 92 | 0.10 | 1.57 | 1.93 | 2.35 | 1.66 |
| 22–90 | 375 | 5.7 | 51 | Two-state | 67 | 1.22 | 1.36 | 1.84 | 2.34 | 2.40 |
| 1–31 | – | No peak | – | None | 25 | Flex | – | – | – | – |
| 32–108 | 371 | 2.4 | 19 | Continuous | 77 | 0.35 | – | 1.80 | – | – |
| 1–37 | – | No peak | – | None | 34 | Flex | – | – | – | – |
| 38–108 | 363 | 2.2 | 19 | Continuous | 68 | 0.40 | – | 1.90 | – | – |
| 38–73 | – | No peak | – | None | 32 | – | – | – | – | – |
| 38–78 | – | No peak | – | None | 33 | Flex | – | – | – | – |
| 1–50 | 350 | 0.9 | 11 | Continuous | 61 | 0.5 | – | 1.67 | – | – |
| 51–108 | 361 | 1.6 | 17 | Continuous | 44 | 0.10 | – | 2.01 | – | – |
| 1–73 | 338 | 6.0 | 51 | Two-state | 92 | 1.15 | 0.99 | 1.41 | 2.02 | 1.53 |
| 74–108 | 370 | 1.6 | 28 | Two-state | 33 | 0.75 | 1.26 | 1.75 | 2.14 | 0.52 |
| 1–83 | 343 | 8.4 | 62 | Two-state | 97 | 1.20 | 1.05 | 1.56 | 2.15 | 1.50 |
For a variety of structures identified by sequence range, DCM predictions are given here for the Tm based on the maximum in the Cp curve, excess Cp,max that does not include baselines, the percent reduction of the relative scaled Cp,max compared to intact Trx, character of the folding transition, maximum number of H-bonds (HB no.) in the X-ray structure template, locations for the rigidity percolation threshold (θRP), native state (θnat), transition state (θTS) and unfolded state (θunf) in terms of global flexibility, and the normalized barrier height (BH). The core defines a structure that has the same number of residues as intact Trx, but all H-bonds (and salt-bridges) are removed that cross-link a residue that is within the range 22–90 to a residue outside this range. Intramolecular H-bonds within or outside the range 22–90 are allowed. The scaled Cp,max is defined as (Cp,max of the fragment times 108 for the number of residues in the intact Trx) all divided by (Cp,max of intact Trx times the number of residues in the fragment). The normalized barrier height is defined by (the free energy difference between the transition state and the average free energies of the native and unfolded states) all divided by RTm. When Flex is used for the value of θRP, this indicates that no peak is observed in the rigid cluster susceptibility because the structure is always flexible. The value of θTS represents the minimum in the flexibility free energy at Tm when the transition is continuous.