Folding of Unnatural Oligomers: Hollow Helices

State University Of New York At Buffalo, Buffalo NY

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Abstract

The proposed research involves the design of a novel class of oligomers that automatically fold into helices with large (10 Angstrom units to 30 Angstrom units) tubular cavities. Such hollow helices are suggested as potential prototypes of functional models for pore-forming protein and peptide toxins. The oligomers consist of benzene rings linked by amide groups. The backbone of an oligomer is curved due to the incorporation of intramolecular hydrogen bonds that rigidify the amide linkages. As a result, a backbone that is long enough will fold back on itself, leading to a left- or right-handed helical conformation. The helix formed is further stabilized by stacking of the aromatic rings of neighboring spiral turns. Such a backbone- based helical programming will lead to helices whose folded conformation is resilient toward structural variation of the side groups that determine the outside surface properties. The interior of a helix is featured by the amide-O atoms, which makes the tubular cavities rather hydrophilic. The internal diameters of the helices are adjustable by combining meta- and para- disubstituted benzene rings or by using larger aromatic rings such as derivatives of naphthalene and anthracene. Preliminary results from ab initio calculations, 1H-NMR and X-ray crytsallography have clearly established the feasibility of the proposed research. These helices, as nanotubes, can be used as artificial pore-forming agents that can be easily functionalized. Molecular gatekeepers based on these nanotubes can be designed by including biochemical, chemical, and physical switches into the structures. The design of pore-forming drugs, drug carriers and sensitive membrane-bound sensors can be envisioned.