Principal component analysis of alpha-helix deformations in transmembrane proteins
Bibliographic record
Abstract
α-helices are deformable secondary structural components regularly observed in protein folds. The overall flexibility of an α-helix can be resolved into constituent physical deformations such as bending in two orthogonal planes and twisting along the principal axis. We used Principal Component Analysis to identify and quantify the contribution of each of these dominant deformation modes in transmembrane α-helices, extramembrane α-helices, and α-helices in soluble proteins. Using three α-helical samples from Protein Data Bank entries spanning these three cellular contexts, we determined that the relative contributions of these modes towards total deformation are independent of the α-helix's surroundings. This conclusion is supported by the observation that the identities of the top three deformation modes, the scaling behaviours of mode eigenvalues as a function of α-helix length, and the percentage contribution of individual modes on total variance were comparable across all three α-helical samples. These findings highlight that α-helical deformations are independent of cellular location and will prove to be valuable in furthering the development of flexible templates in de novo protein design.
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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".