How short is too short for amyloid fibrils?: Molecular dynamics of oligomers of infectious prion core structures
Bibliographic record
Abstract
In many proteinopathies, the relative conformations of amyloid fibrils versus smaller oligomers remain unclear. Most tissue-derived isolates of infectious prion protein (PrP) prions are predominantly fibrillar. A few studies have asserted that prion amyloid fibrils efficiently disassemble into dimeric to tetrameric "elemental bricks" under certain detergent or chaotropic conditions, but our companion paper provides strong evidence to the contrary. Given our difficulties in isolating detectable amounts of small oligomeric (2-4-mer) prions, we performed molecular dynamics simulations to test the abilities of small fragments (dimers to 25-mers) of cryo-EM-based infectious prion fibril core structures to retain their conformational integrity. We show that dimers of the aRML prion structure lost most of their original secondary and tertiary structure within <<1 μs, while trimers maintained some intermolecular β-sheets. Further increases in fragment size helped preserve major structural motifs and the integrity of the templating surfaces responsible for self-propagation. In simulations of octamers and/or 25-mers, even at elevated temperatures, no fragmentation was observed for aRML, 22L, or 263K prion strains, although the terminal chains were substantially destabilized. Together, our results provide evidence that oligomeric fragments of prion fibril cores as small as tetramers retain substantial structural integrity. Our findings suggest that, as exemplified by PrP fibrils, short cores as small as tetramers may be stable enough to account for bioactive oligomeric species detected in brain extracts from patients with amyloidoses. However, the lack of observed spontaneous core fragmentation suggests that prion oligomers might be rare in vivo and/or produced by non-autonomous physiological cleavage processes.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".