Modular Design of Self-Assembling Peptide-Based Nanotubes

Abstract

An ability to design peptide-based nanotubes (PNTs) rationally with defined and mutable internal channels would advance understanding of peptide self-assembly, and present new biomaterials for nanotechnology and medicine. PNTs have been made from Fmoc dipeptides, cyclic peptides, and lock-washer helical bundles. Here we show that blunt-ended α-helical barrelsi.e., pre-assembled bundles of α-helices with central channels-can be used as building blocks for PNTs. This approach is general and systematic, and uses a set of de novo helical bundles as standards. One of these bundles, a hexameric α-helical barrel, assembles into highly ordered PNTs, for which we have determined a structure by combining cryo-transmission electron microscopy, Xray fiber diffraction and model building. The structure reveals that the overall symmetry of the peptide module plays a critical role in ripening and ordering of the supramolecular assembly. PNTs based on pentameric, hexameric and heptameric α-helical barrels sequester hydrophobic dye within their lumens.

Controlling the Assembly of Coiled–Coil Peptide Nanotubes

“…In these cases, the inner diameter can be tailored via the ring size of the peptide 2. The modular approach that we present to assemble PNTs from αHBs allows similar control mechanisms 7a. We have shown that the inner diameter varies with the oligomer state of the αHB, allowing PNTs with channels of 5–7 Å to be achieved.…”

“…Our designs carry certain advantages, principally modularity and generality. Therefore, the control mechanisms that we describe should be readily transferrable to other αHB building blocks of varying pore size 7a,7c. The inner lumens of these barrels are also mutable,7b, 10 which should facilitate further the design of functional PNTs.…”

“…To promote end‐to‐end self‐assembly, these are permuted to expose hydrophobic patches at the N ‐termini, and leave overall and complementary negative and positive charges at the C ‐ and N ‐termini, respectively, Figure 1 7a. As mentioned, these redesigns associated both longitudinally and laterally to give broadened assemblies compared to the widths of the building blocks (Figure 2 a,b).…”

“…In hydrophobic environments, DPH fluoresces, Figure 4 c, but this is quenched in water. DPH binds strongly to thickened CC‐Hex‐T PNTs (Figure 4 d) 7a. Although DPH bound to both of the single‐PNT redesigns, Figure 4 c, the saturation binding curve for CC‐Hex‐T+ showed reduced binding affinity compared to CC‐Hex‐T, Figure 4 d. We propose that this is best explained by CC‐Hex‐T+ PNTs being less stable than CC‐Hex‐T, as any stabilization from lateral association of fibrils will be lost in the CC‐Hex‐T+ PNTs.…”

Structural and Functional Modeling of Artificial Bioactive Proteins

“…The overall goal of the paper is to investigate whether the use of standard bioinformatics algorithms is applicable for efficient and accurate structure-function modeling of the synthetic proteins subsets Hecht_α and Hecht_β. The applicability of the presented methodology will be discussed considering de novo protein subsets recently reported by Woolfson and co-workers [4,5,[23][24][25] and Baker and co-workers [1,26].…”