Here Be Coiled-Coil Dragons: Computational Search for New Hendecad Coiled Coils

Repetition is a powerful mechanism to generate innovation in proteomes, which ultimately enables the adaptation of biological organisms to their environment. No other protein motif exemplifies this better than the coiled coil motif, which owing to its relatively short repeat size, high level of degeneracy and periodically reocurring interactions that could potentially extendindefinitely, can be found in virtually every proteome. This wealth of natural examples as well as their uniquely parameterizable structure have allowed for the development of robust prediction and design protocols for coiled coils, granting them the consideration of the best understood protein fold. The vast majority of coiled coils in nature consist of heptad (7) repeats, but other repeat types such as hendecads (11) or pentadecads (15) are also compatible with coiled-coil structure. Typically, these non-canonical coiled-coil repeats, of which the most common is the hendecad, are found in low-copy number interspersed between heptads, where they introduce local changes in the packing of the side-chains as well as distortions in the protein backbone. In contrast, there are very few examples of coiled-coil sequences composed mainly or entirely of non-heptad repeats. This motivated us to search for new hendecads, in order to expand our coiled-coil prediction and design protocols even further. Here, we present a search strategy based on tandem repeat detection which we have employed to obtain a reliable set of hendecad coiled coils. These new hendecad families illustrate the immense versatility of coiled coils, in the form of phage Tail Measure Proteins, membrane-bound bacterial proteins, fungal kinesins, and the largest known hendecad coiled coil which evolved from a cell-division protein broadly conserved in Gram-positive bacteria