Surface-Lattice Model Describes Electrostatic Interactions of Ions and Polycations with Bacterial Lipopolysaccharides: Ion Valence and Polycation’s Excluded Area
Bibliographic record
Abstract
The bacterial outer membrane (OM) is compositionally distinct and contains polyanionic lipopolysaccharide (LPS) in the outer layer as a main component. It has long been known that the cation-binding ability of LPS is one of the key determinants of OM permeability. Here we present a two-dimensional lattice model of the outer LPS layer, in which the lattice is decorated with bound ions or polycations; while small ions can occupy single binding sites, polycations, modeled as (charged) rods, compete for binding sites through their area exclusion, a consequence of their multisite binding. Our results suggest that in the parameter space of biological relevance, the effect of area exclusion is well-reflected in the competitive binding of Mg(2+) and polycations onto LPS; by reducing the apparent binding affinity of polycations, it enhances Mg(2+) binding. Despite simplifications, our results are generally consistent with the common view of Mg(2+) as OM-stabilizing and polycations as OM-perturbing agents. They will be useful for understanding how cationic antimicrobials can gain entry into the cytoplasmic membrane. We also outline a few strategies for extending our model toward a more realistic modeling of OM permeability.
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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 | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.003 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
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".