Tilted, Extended, and Lying in Wait: The Membrane-Bound Topology of Residues Lys-381−Ser-405 of the Colicin E1 Channel Domain
Bibliographic record
Abstract
The membrane-bound closed state (zero potential) of the helix 3 segment (Lys-381-Ser-405) of the colicin E1 channel domain was investigated by site-directed fluorescence labeling using a bimane probe tethered to a single cysteine residue of each mutant protein. A number of fluorescence properties of the tethered bimane probe were measured for the soluble channel mutant proteins as well as for the membrane-bound proteins. A new method called helical periodicity surface analysis was employed to fit the fluorescence data to a harmonic wave function using four different statistical methods. The fit of the various data sets to a harmonic wave function indicated that the periodicity of helix 3 in the membrane-bound state is typical for an amphipathic alpha helix (3.7-4.0 residues per turn and an angular frequency between 90 and 97 degrees). Notably, upon membrane binding, helix 3 elongates from 15 residues (soluble structure) to 20 residues by a three- and two-residue extension at the N- and C-termini of the helix, respectively. Dual quencher analysis also revealed that helix 3 is appressed to the surface of the membrane with its N-terminus more deeply buried within the interfacial region of the bilayer than its C-terminus. Finally, contrary to a previous report, our data show that helices 3 and 4 remain separate and independent helices upon membrane association in the absence of a membrane potential.
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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 | 0.000 |
| 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) | 0.001 | 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".