In vivo selection of heterotypically interacting transmembrane helices: Complementary helix surfaces, rather than conserved interaction motifs, drive formation of transmembrane hetero-dimers

Abstract

Single pass transmembrane proteins make up almost half of the whole transmembrane proteome. Contacts between such bitopic transmembrane proteins are common, and oligomerization of their single transmembrane helix is involved in triggering and regulation of signal transduction across cell membranes. In several recent analyses the distribution of amino acids at helix-helix contact sides has been analyzed, and e.g. a preference of amino acids with small side chains has been identified. Here we select amino acids, amino acid pairings and amino acid motifs, which mediate strong interactions of single-span transmembrane α-helices. Our analysis illustrates an architecture of TM helix dimers that is much more complex and diverse as might be expected from previous screens selecting homo-dimerizing TM helices. However, our findings are in excellent agreement with several previous computational analyses of existing transmembrane proteins and thus indicate that our screen nicely resembled the forces having guided evolution of transmembrane bundle structures. Furthermore, the results of this study indicate that helices do not per se have a strong propensity to interact via identical or highly similar helix surfaces, rather the geometries of two interacting helix surfaces “just” have to match to tightly pack and thereby form a stable transmembrane helix dimer. Finally, while evolution of transmembrane helix-helix interactions most likely was a compromise between formation of thermodynamically stable contact surfaces and protein function, our results suggest that “stability” was a major driving force during the evolution of α-helical transmembrane proteins.