Specificity in transmembrane helix–helix interactions can define a hierarchy of stability for sequence variants

The folding, stability, and oligomerization of helical membrane proteins depend in part on a precise set of packing interactions between transmembrane helices. To understand the energetic principles of these helix–helix interactions, we have used alanine-scanning mutagenesis and sedimentation equilibrium analytical ultracentrifugation to quantitatively examine the sequence dependence of the glycophorin A transmembrane helix dimerization. In all cases, we found that mutations to alanine at interface positions cost free energy of association. In contrast, mutations to alanine away from the dimer interface showed free energies of association that are insignificantly different from wild-type or are slightly stabilizing. Our study further revealed that the energy of association is not evenly distributed across the interface, but that there are several “hot spots” for interaction including both glycines participating in a GxxxG motif. Inspection of the NMR structure indicates that simple principles of protein–protein interactions can explain the changes in energy that are observed. A comparison of the dimer stability between different hydrophobic environments suggested that the hierarchy of stability for sequence variants is conserved. Together, these findings imply that the protein–protein interaction portion of the overall association energy may be separable from the contributions arising from protein–lipid and lipid–lipid energy terms. This idea is a conceptual simplification of the membrane protein folding problem and has implications for prediction and design.