Free Energy Barrier Estimation for the Dissociation of Charged Protein Complexes in the Gas Phase
Bibliographic record
Abstract
Free energies are calculated for the protonated cytochrome c' dimer ion in the gas phase as a function of the center of mass distance between the monomers. A number of different charge partitionings are examined as well as the behavior of the neutral complex. It is found that monomer unfolding competes with complex dissociation and that the relative importance of these two factors depends upon the charge partitioning in the complex. Symmetric charge partitionings preferentially suppress the dissociation barrier relative to unfolding, and complexes tend to dissociate promptly with little structural changes occurring in the monomers. Alternatively, asymmetric charge partitionings preferentially lower the barrier for monomer unfolding relative to the dissociation barrier. In this case, the monomer with the higher charge unfolds before the complex dissociates. For the homodimer considered here, this pathway has a large free energy barrier. The results can be rationalized using schematic two-dimensional free energy surfaces. Additionally, for large multimeric complexes, it is argued that the unfolding and subsequent charging of a single monomer is a favorable process, cooperatively lowering both the unfolding and dissociation barriers at the same time.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".