Navigating the structural landscape ofde novoα–helical bundles

Abstract

The association of amphipathic a helices in water leads to a-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the a-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less-well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high-resolution X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of a-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.

The de novo design of α-helical peptides for supramolecular self-assembly

“…These are α-helical barrels as they have contiguous central channels and are able to bind and discriminate between small molecules [29]. Recently, a thoroughly characterised antiparallel homotetramer with D2 symmetry has been added to the toolkit [30].…”

Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins

“…Of note, the design of the single-chain three-helix bundle was one of the earliest efforts in the de novo protein design [ 8 ]. The design of helical bundles or mutiple-chaine coiled-coils is nowadays one of the largest fields in the protein design study, allowing diverse α-helix arrangements [ 9 ]. It is now clear what residue-residue non-local interactions can cause tight packing between α-helices [ 10 ] and result in various helix-bundle arrangements [ 11 ], which originates from analysis and design of coiled-coil structures [ 12 – 14 ].…”