Energetics of Lipid Binding in a Hydrophobic Protein Cavity
Bibliographic record
Abstract
Hydrophobic bonding is central to many biochemical processes, such as protein folding and association. However, a complete description of the forces underlying hydrophobic interactions is lacking. The goal of this study was to evaluate the intrinsic energetic contributions of -CH(3), >CH(2), and -HC═CH- groups to protein-lipid binding. To this end, Arrhenius parameters were measured for dissociation of gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and a series of saturated, unsaturated, and branched fatty acids (FA). In the gas phase, the (Lg + FA)(7-) ions adopt one of two noninterconverting structures, which we refer to as the fast and slow dissociating components. The dissociation activation energies measured for the fast components of the (Lg + FA)(7-) ions were found to correlate linearly with the association free energies measured in aqueous solution, suggesting that the specific protein-lipid interactions are preserved in the gas phase. The average contributions that the -CH(3), >CH(2), and -HC═CH- groups make to the dissociation activation energies measured for the fast components of the (Lg + FA)(7-) ions were compared with enthalpies for the transfer of hydrocarbons from the gas phase to organic solvents. For >CH(2) groups, the interior of the cavity was found to most closely resemble the relatively polar solvents acetone and N,N-dimethylformamide, which have dielectric constants (ε) of 21 and 39, respectively. For -CH(3) groups, the solvent environment most closely resembles 1-butanol (ε = 17), although the energetic contribution is dependent on the location of the methyl group in the FA. In contrast, the solvation of -HC═CH- groups is similar to that afforded by the nonpolar solvent cyclohexane (ε = 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) | 0.000 | 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".