Abstract
The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I–K–E–I–A–x–Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.
Highlights
IntroductionNatural coiled-coil (CC) peptides form dimers, trimers and tetramers with consolidated hydrophobic cores.[1,2] Control over oligomeric state is achieved by different combinations of mainly isoleucine (Ile, I) and leucine (Leu, L) residues in the core.[3,4] Larger oligomers are rare in nature.[5,6] Interestingly, some of these larger structures are a-helical barrels (aHBs) with accessible central channels making them appealing scaffolds for functional design, e.g. binding, catalysis, delivery, and transport.[7,8,9,10,11,12,13] Variants of a natural dimer and de novo tetramer serendipitously form heptameric and hexameric aHBs, respectively.[14,15] To automate the design of aHBs, we have developed computational-design tools to deliver 5-, 6- or 7-helix aHBs.[16] These oligomers can be rationalized retrospectively to advance further sequence-to-structure relationships for CC design
The mostfavoured states were those observed experimentally,[16] the exception being CC-Type2-(AgIaId)[4], which predicted as a hexamer as observed in solution, but crystallized as an octamer.[18]
Because of the apparent structural duality with Gly@g, we examined the oligomeric states of all peptides in solution by analytical ultracentrifugation (AUC; Table 1, Fig. S10–S13†)
Summary
Natural coiled-coil (CC) peptides form dimers, trimers and tetramers with consolidated hydrophobic cores.[1,2] Control over oligomeric state is achieved by different combinations of mainly isoleucine (Ile, I) and leucine (Leu, L) residues in the core.[3,4] Larger oligomers are rare in nature.[5,6] Interestingly, some of these larger structures are a-helical barrels (aHBs) with accessible central channels making them appealing scaffolds for functional design, e.g. binding, catalysis, delivery, and transport.[7,8,9,10,11,12,13] Variants of a natural dimer and de novo tetramer serendipitously form heptameric and hexameric aHBs, respectively.[14,15] To automate the design of aHBs, we have developed computational-design tools to deliver 5-, 6- or 7-helix aHBs.[16] These oligomers can be rationalized retrospectively to advance further sequence-to-structure relationships for CC design
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