The many types of interhelical ionic interactions in coiled coils - An overview

Coiled coils represent the most frequent protein oligomerization motif in nature and are involved in many important biological processes. The prototype interhelical ionic interaction for coiled coils described in literature is an i to i + 5 ionic interaction from heptad position g to e′, but other possible ionic interactions have also been described. Here we use a statistical approach to systematically analyze all high-quality coiled-coil structures in the RCSB protein database for their interhelical ionic interactions. We provide a complete listing of all possible arrangements and analyze the frequency of their occurrence in the primary sequence together with their probability of formation in the quaternary structure of the coiled coils. We show that the classical i to i + 5 ionic interaction is indeed characteristic for parallel dimeric and trimeric coiled coils. But we also show that there are many more i to i + 2 ionic interactions in parallel tetrameric and pentameric coiled coils, and in antiparallel coiled coils the classical i to i + 5 ionic interaction is in none of the oligomerizations states the most frequently observed ionic interaction. We also demonstrate that many ionic interactions involve residues at the core positions that are usually occupied by hydrophobic residues and that such interhelical ionic interactions are a hallmark feature of dimeric coiled coils.