Table 5.
NMR Structure Ensemble Statistics
| A. Structure Generation Summary
| ||
|---|---|---|
| HP5W4 | HP7 | |
| Distance Constraints | ||
| total | 137 | 82 |
| intraresidue | 15 | 5 |
| sequential | 48 | 31 |
| i/i+n (n = 2–4) | 18 | 16 |
| i/i+n (n ≥ 5) | 56 | 30 |
|
| ||
| Ensemble Statistics1 (with standard deviation) | ||
| accepted/random starts | 27 / 50 | 43 / 50 |
| ELJ (kcal/mole) | −93.75±4.55 | −62.53±2.82 |
| ENOE (kcal/mole) | 1.15±0.37 | 0.43±0.12 |
| Bond RMSD Å | 0.002±0.000 | 0.002±0.000 |
| Angles RMSD (deg) | 0.415±0.005 | 0.460±0.004 |
| Improper RMSD (deg) | 0.153±0.012 | 0.130±0.014 |
| B. Ensemble RMSD2 Values (Å)
| |||
|---|---|---|---|
| trpzip43 | HP5W4 | HP7 | |
| Backbone4 | 0.36±0.08 | 0.32±0.12 | 0.19±0.06 |
| All heavy atoms4 | 0.97±0.13 | 0.72±0.20 | 0.81±0.29 |
| Turn backbone5 | 0.20±0.07 | 0.08±0.03 | 0.09±0.05 |
| Turn heavy atoms5 | 1.21±0.256 | 0.14±0.06 | 0.18±0.08 |
| Indole rings7 | 0.43±0.18 | 0.36±0.12 | 0.12±0.06 |
| C. RMSD Comparison of HP5W4 and HP7 Ensembles (Å) | |
|---|---|
| 4–13 Backbone | 0.46±0.08 |
| 4–13 Heavy | 1.00±0.22 |
| 7–10 Backbone | 0.21±0.06 |
| 7–10 Heavy | 0.33±0.07 |
| Indole Rings 5,12 | 0.24±0.06 |
1
Calculated with CNS prior to final minimization using the AMBER forcefield.
2
Calculated (pair-wise, over the complete ensembles) using MolMol23; the mean and standard deviation are given for both intra- and inter-ensemble comparisons.
3
Calculated using PDB# 1LE3.
4
Residues 3–14 for trpzip4 and HP5W4, 4–13 for HP7
5
Residues 7–10 are the 4 turn residues: PATG for HP5W4/HP7 and DATK for trpzip4.
6
The large difference in RMSD for trpzip4 versus the two new constructs may reflect the amount of disorder possible in the sidechains of the DATK turn sequence as opposed to PATG.
7
This measure includes only the 9 heavy atoms of the indole rings.