Table 1.
Rg for Each System As Determined from a Guinier Analysis of the Experimental Data, Analysis of the cMD and aMD Trajectories, and from the Bayesian Ensemble Fitting Protocola
| system | experiment (Å) | cMD (Å) | aMD (Å) | ensemble (Å) |
|---|---|---|---|---|
| K6 | 22.9 ± 0.1 | 19.0 ± 0.1 | 19.3 ± 0.2 | 21.8 ± 0.1 |
| K11 | 21.4 ± 0.1 | 20.5 ± 0.1 | 19.5 ± 0.1 | 21.7 ± 0.6 |
| K29 | 23.3 ± 0.3 | 24.6 ± 0.1 | 20.3 ± 0.2 | 24.9 ± 1.5 |
| K48 | 22.3 ± 0.1 | 23.6 ± 0.3 | 21.3 ± 0.3 | 22.4 ± 0.3 |
| nK48 | 23.7 ± 0.1 | 22.4 ± 1.0 | 23.4 ± 0.2 | 24.1 ± 0.6 |
| K63 | 28.0 ± 0.1 | 25.0 ± 0.2 | 22.5 ± 0.2 | 28.3 ± 0.3 |
| nK63 | 27.0 ± 0.2 | 25.6 ± 0.3 | 21.1 ± 0.5 | 28.6 ± 1.1 |
a
The Rg of a ubiquitin trimer appears to be directly related to the geometry of the linkage. Furthermore, ensemble reweighting produces better agreement with experimental values than the raw MD trajectories. nK48 and nK63 denote trimers with the native isopeptide linkage.