Functional Coiled-Coil-like Assembly by Knob-into-Hole Packing of Single Heptad Repeat

Abstract

Coiled-coil peptides represent the principal building blocks for structure-based design of bionanomaterials. The sequence–structure relationship and precise nanoscale ordering of the coiled-coil helices originate from the knob-into-hole (KIH) packing of side chains. The helical interface stabilized by the KIH interaction is known to have chain lengths ranging from 30 to 1000 residues. Yet the shortest peptide required for oligomerization through KIH assembly is still unknown. Here, we report that through atomic resolution a minimal seven-residue amphipathic helix forms a different type of KIH motif, termed “supramolecular KIH packing”, which confers an exceptional stability to the helical dimers. Significantly, at a low pH, the peptide self-assembles into nanofibers with coiled-coil architecture resembling the natural fibrous proteins. Furthermore, hierarchical ordering of the nanofibers affords lyotropic liquid crystals composed of a shortest natural helical sequence. Thus, this study expands the sequence space for a coiled-coil folding manifold and provides another paradigm for designer nanomaterials from minimal helical sequences.

Molecular design of stapled pentapeptides as building blocks of self-assembled coiled coil–like fibers

“…Apart from the better helicity, our simulations further suggested that the long linker in the App substituent may also permit better intermolecular aromatic stacking of the Ph groups. In contrast, the formation of aromatic packing between Phe/Hpa side chains would be incompatible to the helical conformation of backbone, consistent with previous reports (18). Together, the current findings above add a crucial layer of details to our understanding of the substitution effects on the self-assembly of ultrashort helical peptides.…”

“…The combination of self-assembly simulations and various spectroscopic characterizations also offered molecular insights into the self-assembly behavior of this peptide and its organization into fibers. The overall molecular architecture of the fibers formed by our stapled peptides was similar to those formed by other short peptides (14,18,34). The peptides stacked on top of one another in a headto-tail manner, forming helical columns that further assembled laterally.…”

“…There have been numerous efforts in designing self-assembling ultrashort peptides using helix-promoting noncoded amino acids such as -amino acids and -aminoisobutyric acid (15,16). For example, it has recently been shown that -aminoisobutyric acids could stabilize a single helical heptad that can self-assemble into dimeric fibrous structures (17,18). This helical heptad has served as a template for the design of other types of assemblies (19).…”

“…A further complication is that short peptides with noncoded amino acid substitutions, due to direct modification to their backbones, can often deviate from the canonical helical structures seen in coiled coils (20). As a result, with few exceptions (18,21), the empirical rules derived for naturally occurring coiled coils are rarely applicable to the design of self-assembling ultrashort peptides.…”

From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non‐Canonical Amino Acids

“…Furthermore, this super helical arrangement of the peptide produced supramolecular rod‐like nanofibers at low pH, followed by lyotropic liquid crystals with predictable thermotropic properties. [ 79 ]…”