Quantification of helix–helix binding affinities in micelles and lipid bilayers

A theoretical approach for estimating association free energies of α‐helices in nonpolar media has been developed. The parameters of energy functions have been derived from ΔΔG values of mutants in water‐soluble proteins and partitioning of organic solutes between water and nonpolar solvents. The proposed approach was verified successfully against three sets of published data: (1) dissociation constants of α‐helical oligomers formed by 27 hydrophobic peptides; (2) stabilities of 22 bacteriorhodopsin mutants, and (3) protein‐ligand binding affinities in aqueous solution. It has been found that coalescence of helices is driven exclusively by van der Waals interactions and H‐bonds, whereas the principal destabilizing contributions are represented by side‐chain conformational entropy and transfer energy of atoms from a detergent or lipid to the protein interior. Electrostatic interactions of α‐helices were relatively weak but important for reproducing the experimental data. Immobilization free energy, which originates from restricting rotational and translational rigid‐body movements of molecules during their association, was found to be less than 1 kcal/mole. The energetics of amino acid substitutions in bacteriorhodopsin was complicated by specific binding of lipid and water molecules to cavities created in certain mutants.