D_n-symmetrical tertiary templates for the design of tubular proteins

Antiparallel helical bundles are found in a wide range of proteins. Often, four-helical bundles form tube-like structures, with binding sites for substrates or cofactors near their centers. For example, a transmembrane four-helical bundle in cytochrome bc₁ binds a pair of porphyrins in an elongated central cavity running down the center of the structure. Anti-parallel helical barrels with larger diameters are found in the crystal structures of TolC and DSD, which form antiparallel 12-helical and six-helical bundles, respectively. The backbone geometries of the helical bundles of cytochrome bc₁, TolC, and DSD are well described using a simple D_n-symmetrical model with only eight adjustable parameters. This parameterization provides an excellent starting point for construction of minimal models of these proteins as well as the de novo design of proteins with novel functions.