Table 2.
Clustering of sampled trp-cage conformations
| #1 | Cluster populations | Representative structure2 | ||||||
|---|---|---|---|---|---|---|---|---|
| ε = 5 [%] | ε = 20 [%] | ε = 40 [%] | ε = 80 [%] | ε=80 + crowders [%] | Cα RMSD [Å] | Radius of gyration [Å] | Bending angle [°] | |
| 1 | 0 | 13.0 (3.2) | 58.6 (7.2) | 53.9 (3.3) | 21.9 (6.2) | 2.25 | 7.25 | 45.9 |
| 2 | 63.0 (16.5) | 40.7 (13.4) | 4.2 (1.8) | 2.7 (0.9) | 16.0 (1.6) | 1.56 | 7.09 | 18.5 |
| 3 | 1.3 (1.1) | 7.6 (1.7) | 30.5 (6.0) | 32.3 (4.4) | 35.8 (4.1) | 1.1 | 7.4 | 9.5 |
| 4 | 13.9 (4.5) | 34.5 (11.4) | 2.0 (0.7) | 1.8 (0.5) | 11.0 (3.5) | 2.37 | 7.14 | 43.9 |
| 5 | 21.8 (12.7) | 3.8 (0.3) | 0.2 (0.1) | 0 | 0.4 (0.4) | 1.75 | 7.1 | 13.9 |
| 6 | 0 | 0 | 0 | 0 | 6.0 (1.8) | 6.53 | 9.54 | 118.1 |
| 7 | 0 | 0 | 0 | 0.4 (0.2) | 5.0 (0.7) | 3.26 | 7.79 | 57.9 |
| 8 | 0 | 0 | 0 | 0 | 3.2 (0.4) | 3.59 | 8.04 | 36.6 |
K-means clustering of a combined ensemble based on the mutual structural similarity, using Cα RMSD and a 3.0 Å clustering radius. 9000 structures were selected each from simulations 1 through 4 and another 9000 structures were taken from simulations 5 through 7 to yield a total of 45000 structures that were clustered together. Populations of >10% are indicated in bold face. Uncertainties given in parentheses are estimated from block analysis according to , where σ is the standard deviation and N = 3 since 3 blocks of data were used (see individual block averages in Tables S1 and S2 of supporting information).
1
Cluster number.
2
Structure nearest to the respective cluster centroid.