Conformational Analysis of Glutathione in Aqueous Solution with Molecular Dynamics
Bibliographic record
Abstract
Molecular dynamics simulations over 20 ns with the Gromacs all-atom force field, coupled with cluster analyses of the trajectories, have been applied to the sixteen charge states of glutathione (GSH) in order to examine the distribution conformations in aqueous solution as a function of pH. The simulations show that GSH is very flexible and does not adopt a strongly preferred conformation at any pH. Comparison with limited conformational data deduced from NMR analyses shows little agreement. Contrary to the NMR results which found essentially equal populations of the three rotameric forms, the simulations reveal lower populations for gauche rotameric forms of the Cys and Glu side chains. In most species, the lowest populations were found for the sterically hindered gauche−gauche orientation about the C α −C β bond in both residues, except when electrostatic attraction between oppositely charged ends, unshielded by intervening water, was found to dominate. In the majority of the enzyme-bound GSH structures extracted from the Brookhaven Protein Data Bank, the bound GSH has a conformation that is either the same or similar to that free in solution. In some cases, as in the case of solid-state GSH and the oxidized form, GSSG, crystal packing and intermolecular H-bonding interactions force the GSH skeleton into a conformation that is not seen in solution. The distribution of the separation of the Cys S atom from the Glu α C−H bond was monitored over the course of the 20 ns simulations to deduce conditions under which H atom transfer may occur from the Glu α C−H bond to a thiyl radical of the Cys moiety of GSH, as has been observed experimentally.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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".