Dimerization of transmembrane helices studied using de novo designed hydrophobic peptides
Bibliographic record
Abstract
The hydrophobic environment of the membrane interior is thought to impose restrictions on the secondary structure of proteins at the protein-lipid interface, i.e., the majority of the known structures of membrane-spanning regions are [1]. Within membrane domains, these transmembrane (TM) segments associate through specific, sequence-dependent non-covalent interactions. However, due in part to the paucity of highresolution structures of membrane proteins, little is known about what role the residues at the interface of these TM segments have on mediating such interactions. To address this issue, we are synthesizing a series of de novo designed model hydrophobic peptides with the sequence When these peptides fold into a canonical -helix (3.6 residues/turn), the residues reside on one face of the helix, where they are expected to participate in dimer formation via interchain noncovalent interactions. This situation has been previously demonstrated using nearest neighbor analysis of the interfacial residues of several crystallized membrane proteins, including the photosynthetic reaction centers, bacteriorhodopsin and cytochrome C oxidase [2].
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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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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".