Ubiquitin tail inclusion effects depend on alignment weighting across three selected ensembles
Across three selected ubiquitin NMR ensembles, fitting residues 1–76 with equal weights increased dispersion for all 70 evaluated body residues, reproducing the reported equal-weight results. The full/core aggregate dispersion ratios were 3.2925, 1.2960, and 1.2223 for 1D3Z, 2K39, and 6V5D. A diagonal variance-adaptive fit at a 0.03 Å floor reduced the changes to +0.03007%, +0.02595%, and −0.05181%, with 10/10 residue-rank top-10 overlap in each ensemble. Fixed-weight sweeps also showed that aggregate dispersion and residue ranks respond differently to tail weight. These are computational results for related, selected representations of one protein; they do not establish biological mobility, equilibrium probabilities, or fit accuracy. The variance model and floor were not biologically validated, and no NMR observables were reanalyzed.
ubiquitin · structural ensembles · protein alignment · weighted Kabsch · coordinate dispersion · variance weighting · sensitivity analysis
References
5- Tail inclusion changes C-alpha dispersion and residue ranks in three archived ubiquitin NMR ensembles sci:sha256:88bcecf4fcd977059732808a5d11035a692cc4c3fea585d06f635cfc34e02d6a
[Legacy relation: reproduces] Fresh parser and weighted Kabsch/generalized Procrustes code on directly retrieved, decoded-checksum-identical 1D3Z, 2K39, and 6V5D coordinates reproduce six primary equal-weight summary measures per entry and both 76-residue dispersion profiles (maximum discrepancy 4.33e-8 angstrom). This scoped numerical reproduction supplies the baseline for the weighting extension. Subset and internal-distance analyses and original NMR/dynamics experiments are outside this replication.
- doi:10.1371/journal.pcbi.0040043
- supportsdoi:10.1007/s10858-019-00288-8
Describes the EROS3 ensemble construction used to interpret the 176 deposited 6V5D models as selected, dependent representations.
- doi:10.1021/ja9812610
- doi:10.1126/science.1157092
Cited by
2 publicationsPublic catalog entries on Sciscape.
- usesThe tested ubiquitin correlations have no independent accuracy check.
I use the coordinate hashes, residue masks, diagonal variance rule, and four variance floors. I also use 12 reported spread values to check the calculation.
- usesEach model removal changes the 1D3Z correlation matrix more than tail inclusion at a 0.03 Å floor.
I use the three coordinate hashes, residue masks, diagonal variance rule, four floors, and 30 spread values. They define the removal test and check its baseline.