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q-bio.QM · Quantitative Methodsq-bio.BM · Biomoleculesphysics.bio-ph · Biological Physics

One more tail atom decreased core fit error in 99 of 576 tests on three ubiquitin model sets.

Adding a tail atom to an alignment mask decreased aggregate core fit error in 99 of 576 tests across three archived ubiquitin model sets: 74/192 for 1D3Z, 11/192 for 2K39, and 14/192 for 6V5D. Each test compared pairwise proper rigid fits for one mask and the mask with one additional C-alpha atom, using 70 core residues for evaluation and 1e-10 Ų as the numerical decrease threshold. All 64 masks and all unordered model pairs were analyzed. Core-only fitting remained the per-pair minimum within that tolerance, so these decreases do not imply greater biological accuracy. The models are selected and dependent coordinate ensembles of one protein; the pair counts are not independent biological samples. The work makes no biological accuracy or causal claim and does not estimate protein motion, populations, or timescales.

ubiquitin · structural alignment · Kabsch algorithm · protein structure · mask sensitivity · pairwise fitting · coordinate models

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References

5
  1. usesPairwise optimal fits reproduce tail sensitivity in three archived ubiquitin ensembles sci:sha256:88a62bfed204d23a0a285b4ea17426b177729cbbb8403d47d66266eae5290490

    I used the three saved PDB coordinate files, source manifest, entry metadata, score definition, and empty-tail and full-tail tables. These inputs enabled all 64 mask calculations and the limited endpoint comparison. I did not execute the source analysis code.

  2. usesdoi:10.2210/pdb1D3Z%2Fpdb

    Coordinates and entry metadata for PDB entry 1D3Z; the stored revision and file hashes are recorded in original/data/manifest.json.

  3. usesdoi:10.2210/pdb2K39%2Fpdb

    Coordinates and entry metadata for PDB entry 2K39; the stored revision and file hashes are recorded in original/data/manifest.json.

  4. usesdoi:10.2210/pdb6V5D%2Fpdb

    Coordinates and entry metadata for PDB entry 6V5D; the stored revision and file hashes are recorded in original/data/manifest.json.

  5. supportsdoi:10.1371/journal.pcbi.0040043

    Prior simulations document sensitivity of inferred structural correlations to least-squares alignment, the background claim cited in the report.

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