Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter GltPh
Bibliographic record
Abstract
We have studied Li(+)/Na(+)/K(+) selectivity of the bacterial aspartate transporter Glt(Ph) using all-atom molecular dynamics (MD) and free energy simulations (FES) to evaluate the role of different factors that control ion preferences of the binding sites identified in the crystallographic structure. The role of the bound ions in stabilizing the hairpin loop (HP2) by acting as an extracellular gate is discussed. Free energy simulations with classical and polarizable force-fields were used to characterize the role of the protein matrix, the site composition and the induced polarization in the stabilization of native and non-native cations, such as Li(+) and K(+), in the ion-binding sites of the transporter. The role of different factors that control the selectivity of the binding sites was highlighted with a number of reduced models using a scheme recently developed by Yu et al. (Proc. Natl. Acad. Sci. U. S. A., 2010, 107, 20329-20334 and J. Phys. Chem. B, 2009, 113, 8725).
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 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 | 0.001 |
| 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".