Simulated force-induced unfolding of α-helices: dependence of stretching stability on primary sequence
Bibliographic record
Abstract
Some of the principles that determine a protein's native fold can be probed with techniques for single-molecule manipulation. Yet, understanding the effects of an external force at atomic level still requires computer simulations. Here, we employ a novel protocol for steered molecular dynamics that allows for internal energy redistribution (and possibly, re-equilibration) while the molecule is subject to a mechanical perturbation. The approach is used to study how the stretching of alpha-helices is qualitatively affected by variations in primary sequence. Despite the simplifications introduces, our results indicate a trend whereby different amino acids can increase the resistance to mechanical unfolding depending on side chain polarity and the dynamics of side-chain internal torsions. Whereas the cooperative transition from alpha-helix to 310-helix and to a rod-like conformer prevails when stretching many sequences, we also find that the onset of the unfolding can be delayed by a range of alternative pathways which include events of helical refolding or long-lived intermediates with partial helical content.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".