Protein denaturation <i>in vacuo</i>: Mechanism for centrifugal unfolding of neutral lysozyme
Bibliographic record
Abstract
Experiments on anhydrous proteins diffusing in a low-pressure gas reveal transitions that share common features with the unfolding and refolding processes observed in solution. These phenomena force us to re-evaluate the specific role played by solvent on large-scale protein rearrangements. Computer simulations, in combination with tools for molecular shape analysis, provide insights into in vacuo processes. In this work, we deal with one particular aspect of this problem: the conditions and the mechanism for spontaneous unfolding in a globally neutral protein. When coupling the protein to a simulated thermal bath, the flow of energy between rotational modes and internal modes can produce a centrifugal effect leading to unfolding. Using hen lysozyme as a system, we study the reproducibility of the unfolding transition and its dependence on the bath relaxation constant. In addition, we monitor the evolution of large-scale molecular shape features (e.g., chain entanglements) that take place during unfolding. Our results show that a change in bath relaxation constant affects the time scale of the transition and the population of intermediates, without changing the basic unfolding mechanism. We also discuss possible cycles of unfolding–refolding transitions, and their implications for our understanding of the denatured state.
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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 | 0.000 |
| 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 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".