Biophysical and Structural Characterization of a Robust Octameric β-Peptide Bundle

Abstract

Proteins composed of α-amino acids are essential components of the machinery required for life. Stanley Miller's renowned electric discharge experiment provided evidence that an environment of methane, ammonia, water, and hydrogen was sufficient to produce α-amino acids. This reaction also generated other potential protein building blocks such as the β-amino acid β-glycine (also known as β-alanine); however, the potential of these species to form complex ordered structures that support functional roles has not been widely investigated. In this report we apply a variety of biophysical techniques, including circular dichroism, differential scanning calorimetry, analytical ultracentrifugation, NMR and X-ray crystallography, to characterize the oligomerization of two 12-mer β 3 -peptides, Acid-1Y and Acid-1Y*. Like the previously reported β 3 -peptide Zwit-1F, Acid-1Y and Acid-1Y* fold spontaneously into discrete, octameric quaternary structures that we refer to as β-peptide bundles. Surprisingly, the Acid-1Y octamer is more stable than the analogous Zwit-1F octamer, in terms of both its thermodynamics and kinetics of unfolding. The structure of Acid-1Y, reported here to 2.3 Å resolution, provides intriguing hypotheses for the increase in stability. To summarize, in this work we provide additional evidence that nonnatural β-peptide oligomers can assemble into cooperatively folded structures with potential application in enzyme design, and as medical tools and nanomaterials. Furthermore, these studies suggest that nature's selection of α-amino acid precursors was not based solely on their ability to assemble into stable oligomeric structures.

β-Peptide foldamer helices with tailored diameters

“…18,31 It has been shown that β and αβ-peptidic sequences are able to form quaternary structures with self-assembling helical building blocks. [32][33][34][35] These processes are very similar to the solvophobic interaction-driven tertiary/quaternary-structure formation observed for natural proteins. We planned to investigate the folding and the possibility of higher-ordered structure formation in alternating heterochiral trans-ACPC-containing β-peptide foldamer systems.…”

“…31 Various β-and α,β-peptide sequences have recently been found to form quaternary structures through self-assembling helical building blocks. [32][33][34][35] Infinite pleated sheet aggregates have also been observed, which appeared in the form of nanostrucuted fibrils. 113,129,210,213,214 Peptidic foldamers have the ability to fold into large-diameter helices, 68,215 which can participate in stable axial (head-to-tail) interactions through backbone hydrogen-bonds and side-chain interactions.…”

Sophistication of foldamer form and function in vitro and in vivo

“…Extensive solution characterization is consistent with the formation of an octamer, and indicates that these helical bundles unfold with a protein-like thermal denaturation profile, and have kinetic and thermodynamic stabilities only slightly less than those of natural proteins [61••]. Substitution of multiple residues has generated a virtually identical structure with enhanced kinetic and thermodynamic stability [62]. This robustness has likely not been fully exploited.…”

Foldameric β‐H18/20P Mixed Helix Stabilized by Head‐to‐Tail Contacts: A Way to Higher‐Order Structures

“…It has been shown that peptidic foldamers are able to fold cooperatively into helix bundles; [20] β-and α,β-peptide sequences that were disordered at low concentrations have recently been shown to form quaternary structures through self-assembling helical building blocks. [21][22][23][24] Infinite pleated sheet aggregates were also observed, which eventually appeared in the form of nanostructured fibrils. [25][26][27][28][29] These processes are very similar to those leading to the formation of solvophobic interaction-driven tertiary/ quaternary structures observed for natural proteins.…”