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 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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".