Topology of an Outer-Membrane Enzyme: Measuring Oxygen and Water Contacts in Solution NMR Studies of PagP
Bibliographic record
Abstract
The topology of the bacterial outer-membrane enzyme, PagP, in dodecylphosphocholine micelles was studied by solution NMR using oxygen and water contacts as probes of hydrophobicity and topology. The effects of oxygen on amide protons were measured at an oxygen partial pressure of 20 atm through the paramagnetic contribution to the relaxation rates associated with the decay of two-spin order. A significant gradation of paramagnetic rates was observed for backbone amides belonging to the transmembrane residues. These rates were observed to depend on immersion depth, local hydrophobicity, and steric effects. Variations in the paramagnetic relaxation rates due to local hydrophobicity or steric effects could be, to some extent, averaged out by considering an azimuthally averaged quantity. This averaged paramagnetic rate was found to have a distinct maximum exactly in the middle of the transmembrane domain of PagP, assuming the immersion depth axis is tilted by 25 degrees with respect to the barrel axis. Contact between the protein surface and water was assessed by measuring the amide decay rates during water saturation. The comparison of local contrast effects from both water and oxygen allows one to distinguish among steric effects, local hydrophobicity, and immersion depth. For example, the absence of contrast effects from either water or oxygen at the periplasmic end of beta-strands B and C was consistent with protection effects arising from the association with the N-terminal alpha-helix. A parameter defined by the natural logarithm of the ratio of the normalized paramagnetic relaxation rate to the normalized amide decay rate under water saturation was found to correlate with immersion depth of the corresponding backbone amide nuclei. The results suggest that the oxygen/water contrast experiments give direct information regarding membrane protein topology and surface hydrophobicities, thereby complementing existing NMR structure studies and ESR spin-labeling studies.
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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".