Toward an Improved Understanding of the Dissociation Mechanism of Gas Phase Protein Complexes
Bibliographic record
Abstract
Understanding the dissociation mechanism of multimeric protein complex ions is important for deciphering gas phase dissociation experiments. The dissociation of cytochrome c' dimer ions in the gas phase was investigated in the present study by constrained molecular dynamics simulations. The center of mass (COM) distance between two monomers was selected as the constrained coordinate. The number of intermolecular hydrogen bonds, smallest distance of intermolecular residuals, value of dipole moments, root-mean-square deviations, and potential energy components of the force field as a function of COM distance were examined for different charge partitionings of the +10 total charge state. These data were rationalized with free energy profiles to produce a qualitative description of the dissociation process. When charges are symmetrically distributed between the monomers in the dimer, dissociation occurs at a well-defined distance with only small structural changes in the monomers. There is an elastic type of stretching that initially resists the separation of the monomers but after dissociation the monomers recoil slightly from this and relax. For asymmetrically distributed charges, the dissociation event is not nearly as well-defined because the more highly charged monomer unfolds before dissociation occurs. It is found in almost all cases, a charged N-terminus tethers this unfolding monomer to its dimer partner by binding in a nonspecific manner. This helps encourage monomer unfolding in the dissociation pathway. It is also shown that while the intermolecular Coulomb repulsion between the monomers is not the largest contribution to the overall potential energy, it dominates the potential energy difference between different charge states.
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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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.003 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| 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".