Metastability of protein native folds with respect to global variations in primary sequence
Bibliographic record
Abstract
Abstract In the absence of water, a range of rapid large‐scale conformational rearrangements is accessible in principle to a protein. Despite this, experiments and computer simulations suggest that native states need not be totally unstable once a protein is dehydrated. Here, we explore further the possibility that native folds act as conformational attractors in vacuo, despite variations on their primary structure. To this end, we carry molecular dynamics simulations on “protein chimeras,” where a protein sequence is threaded onto the backbone corresponding to the native state of a different protein with the same chain length. The simulations mimic the conditions of unrestricted rotation and translation found in gas‐phase or in vacuo experiments. We find that the chimeras show a range of motions commensurable to that of the original native state. In no case do we observe a complete change in folding features during early relaxation; in most cases, the original fold is actually metastable. The results suggest that the initial dynamical behavior of a protein may be dictated by the large‐scale backbone folding features, and not by details of the primary structure. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 220–225, 2002
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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 | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".